Publications

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Currently 1250 publications with reference to de.NBI Cloud are listed.

Recently added publication

Glut3 promotes cellular O-GlcNAcylation as a distinctive tumor-supportive feature in Treg cells
A. Sharma - G. Sharma, Z. Gao, K. Li, et al. - Springer Science and Business Media LLC, 2024

The performance of biochar waste-derived electrodes in different bio-electrochemical applications
A. Goglio - A. Carrara, H. Elboghdady, M. Cucina, et al. - Journal of Power Sources, 2025 usegalaxy.eu

Microbial diversity and oil biodegradation potential of northern Barents Sea sediments
S. Chen - F. Musat, H. Richnow, M. Krüger, et al. - Journal of Environmental Sciences, 2024

A land plant phylogenetic framework for GLABROUS INFLORESCENCE STEMS (GIS), SUPERMAN, JAGGED and allies plus their TOPLESS co-repressor
C. Roessner - S. Griep, A. Becker, - Molecular Phylogenetics and Evolution, 2024

Jumping through hoops: Structural rearrangements and accelerated mutation rates on Dendrodorididae (Mollusca: Nudibranchia) mitogenomes rumble their evolution
C. Galià-Camps - T. Schell, A. Enguídanos, C. Pegueroles, et al. - Molecular Phylogenetics and Evolution, 2024 usegalaxy.eu

Land use intensity differently affects soil microbial functional communities in arable fields
C. Gao - S. Hannula, P. van Bodegom, T. Bezemer, et al. - Applied Soil Ecology, 2024 usegalaxy.eu

Integrated genomic and functional analysis of Streptomyces sp. UP1A-1 for bacterial wilt control and solanaceae yield increase
M. Kaari - R. Manikkam, J. Joseph, S. Krishnan, et al. - Gene Reports, 2024 usegalaxy.eu

Dataset of metagenomic profiles of human gut microbiome from frozen fecal samples sequenced using Illumina and ONT chemistries
G. Kumar - P. Bhadury, - Data in Brief, 2024 usegalaxy.eu

Hemoglobin targeting potential of aminocarb pesticide: Investigation into dynamics, conformational stability, and energetics in solvent environment
S. Singh - P. Gopi, P. Sharma, M. Rani, et al. - Biochemical and Biophysical Research Communications, 2024 usegalaxy.eu

Pan-flavivirus analysis reveals sfRNA-independent, 3′ UTR-biased siRNA production from an insect-specific flavivirus
B. Besson - G. Overheul, M. Wolfinger, S. Junglen, et al. - Journal of Virology, 2024 usegalaxy.eu

Genomics and evolutionary analysis of <i>Chlorella variabilis-</i> infecting viruses demarcate criteria for defining species of giant viruses
J. Carvalho - R. Carlson, J. Ghosh, V. Queiroz, et al. - Journal of Virology, 2024 usegalaxy.eu

The multifaceted role of vitreous hyalocytes: Orchestrating inflammation, angiomodulation and erythrophagocytosis in proliferative diabetic retinopathy
S. Boneva - J. Wolf, M. Jung, G. Prinz, et al. - Journal of Neuroinflammation, 2024 usegalaxy.eu

Circularly assembled genome sequences of <i>Asticcacaulis</i> sp. strain MM231 and <i>Brevundimonas subvibrioides</i> MM232, isolated from a pond at Bielefeld University campus
B. Laker - T. Schulze, M. Reis, S. Bormann, et al. - Microbiology Resource Announcements, 2024

Complete genome sequences of <i>Chitinophaga</i> sp. strain MM2321 and <i>Microbacterium</i> sp. strain MM2322, isolated from a sand sample in Harsewinkel, Germany
M. Eisenhut - T. Schulze, F. Matten, A. Sengewald, et al. - Microbiology Resource Announcements, 2024

Genome-Wide Analysis of the Common Fig (Ficus carica L.) R2R3-MYB Genes Reveals Their Structure, Evolution, and Roles in Fruit Color Variation
K. Chatti - N. Kmeli, I. Bettaieb, J. Hamdi, et al. - Biochemical Genetics, 2024 usegalaxy.eu

Transcriptomic and de novo proteomic analyses of organotypic entorhino-hippocampal tissue cultures reveal changes in metabolic and signaling regulators in TTX-induced synaptic plasticity
M. Lenz - P. Turko, P. Kruse, A. Eichler, et al. - Molecular Brain, 2024 usegalaxy.eu

3D chromatin maps of a brown alga reveal U/V sex chromosome spatial organization
P. Liu - J. Vigneau, R. Craig, J. Barrera-Redondo, et al. - Nature Communications, 2024

<scp>StCDF1</scp>: A ‘<i>jack of all trades</i>’ clock output with a central role in regulating potato nitrate reduction activity
M. Shaikh - L. Ramírez‐Gonzales, J. Franco‐Zorrilla, E. Steiner, et al. - New Phytologist, 2024 usegalaxy.eu

The USP12/46 deubiquitinases protect integrins from ESCRT-mediated lysosomal degradation
K. Yu - G. Wang, S. Guo, F. Bassermann, et al. - EMBO Reports, 2024 usegalaxy.eu

Positive selection, genetic recombination, and intra-host evolution in novel equine coronavirus genomes and other members of the <i>Embecovirus</i> subgenus
J. Zehr - S. Kosakovsky Pond, S. Shank, H. McQueary, et al. - Microbiology Spectrum, 2024 usegalaxy.eu

Prostaglandin E2-EP2/EP4 signaling induces immunosuppression in human cancer by impairing bioenergetics and ribosome biogenesis in immune cells
S. Punyawatthananukool - R. Matsuura, T. Wongchang, N. Katsurada, et al. - Nature Communications, 2024 usegalaxy.eu

tRNA regulation and amino acid usage bias reflect a coordinated metabolic adaptation in Plasmodium falciparum
Q. Li - L. Vetter, Y. Veith, E. Christ, et al. - iScience, 2024 usegalaxy.eu

Cell death induced by Lepeophtheirus salmonis labial gland protein 3 in salmonid fish leukocytes: A mechanism for disabling host immune responses
H. Midtbø - A. Borchel, H. Morton, R. Paley, et al. - Fish &amp; Shellfish Immunology, 2024 usegalaxy.eu

BMS345541 is predicted as a repurposed drug for the treatment of TMZ-resistant Glioblastoma using target gene expression and virtual drug screening
R. Nayak - B. Mallick, - Cancer Genetics, 2024 usegalaxy.eu

Distribution and genetic diversity of Bombyx mori nucleopolyhedrovirus in mass-reared silkworms in Thailand
J. Wennmann - S. Senger, B. Ruoff, J. Jehle, et al. - Journal of Invertebrate Pathology, 2024 usegalaxy.eu

Mitogenome of a new Ramazzottius species (Tardigrada: Eutardigrada: Ramazzottiidae) discovered in rock pools along with its temperature and desiccation-related proteins repertoire
M. Vecchi - D. Stec, - Organisms Diversity &amp; Evolution, 2024 usegalaxy.eu

Changes in growth, lanthanide binding, and gene expression in <i>Pseudomonas alloputida</i> KT2440 in response to light and heavy lanthanides
L. Gorniak - S. Bucka, B. Nasr, J. Cao, et al. - mSphere, 2024

The multifaceted role of mitochondria in cardiac function: insights and approaches
S. Ravindran - C. Rau, - Cell Communication and Signaling, 2024 usegalaxy.eu

Glut3 promotes cellular O-GlcNAcylation as a distinctive tumor-supportive feature in Treg cells
A. Sharma - G. Sharma, Z. Gao, K. Li, et al. - Cellular &amp; Molecular Immunology, 2024

Suppressive cancer nonstop extension mutations increase C-terminal hydrophobicity and disrupt evolutionarily conserved amino acid patterns
A. Ghosh - M. Riester, J. Pal, K. Lainde, et al. - Nature Communications, 2024 usegalaxy.eu

Epigenetic modulation via the C-terminal tail of H2A.Z
L. Imre - P. Nánási, I. Benhamza, K. Enyedi, et al. - Nature Communications, 2024 usegalaxy.eu

SpotMAX: a generalist framework for multi-dimensional automatic spot detection and quantification
F. Padovani - I. Čavka, A. Neves, C. López, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

Imaging mass cytometry-based characterisation of fibroblast subsets and their cellular niches in systemic sclerosis
A. Rius Rigau - M. Liang, V. Devakumar, R. Neelagar, et al. - Annals of the Rheumatic Diseases, 2024

Genome-wide identification of CAMTA genes and their expression dependence on light and calcium signaling during seedling growth and development in mung bean
A. Wicaksono - T. Buaboocha, - BMC Genomics, 2024 usegalaxy.eu

In-Silico Perspectives on the Potential Therapeutic Aids of Hesperetin Derivatives for Lung Cancer
A. Asiri - - Advancements in Life Sciences, 2024 usegalaxy.eu

Oviduct epithelial spheroids during in vitro culture of bovine embryos mitigate oxidative stress, improve blastocyst quality and change the embryonic transcriptome
T. Pranomphon - Á. López-Valiñas, C. Almiñana, C. Mahé, et al. - Biological Research, 2024 usegalaxy.eu

Intra-host genomic diversity and integration landscape of human tissue-resident DNA virome
L. Pyöriä - D. Pratas, M. Toppinen, P. Simmonds, et al. - Nucleic Acids Research, 2024 usegalaxy.eu

Unravelling the complexity of bovine milk microbiome: insights into mastitis through enterotyping using full-length 16S-metabarcoding
L. Urrutia-Angulo - M. Ocejo, B. Oporto, G. Aduriz, et al. - Animal Microbiome, 2024 usegalaxy.eu

Immunoinformatics Design of a Multiepitope Vaccine (MEV) Targeting Streptococcus mutans: A Novel Computational Approach
R. Naorem - B. Pangabam, S. Bora, C. Fekete, et al. - Pathogens, 2024 usegalaxy.eu

JunB is required for CD8+ T cell responses to acute infections
S. Sarkar - N. Taira, T. Hsieh, H. Chien, et al. - International Immunology, 2024 usegalaxy.eu

Pertussis Outbreak During 2023 in Gipuzkoa, North Spain
J. Marimón - M. Montes, N. Vizuete, L. Alvarez Guerrico, et al. - Vaccines, 2024 usegalaxy.eu

Genome sequence of a European Diplocarpon coronariae strain and in silico structure of the mating-type locus
S. Richter - S. Kind, T. Oberhänsli, M. Schneider, et al. - Frontiers in Plant Science, 2024 usegalaxy.eu

Epigenetic regulation by polycomb repressive complex 1 promotes cerebral cavernous malformations
V. Pham - C. Rödel, M. Valentino, M. Malinverno, et al. - EMBO Molecular Medicine, 2024 usegalaxy.eu

Rbm3 deficiency leads to transcriptome-wide splicing alterations
S. Erkelenz - M. Grzonka, A. Papadakis, H. Schaal, et al. - RNA Biology, 2024 usegalaxy.eu

Laminin-α2 chain deficiency in skeletal muscle causes dysregulation of multiple cellular mechanisms
S. Martins - V. Ribeiro, C. Melo, C. Paulino-Cavaco, et al. - Life Science Alliance, 2024 usegalaxy.eu

Comparison of Mitochondrial Genome Expression Differences among Four Skink Species Distributed at Different Latitudes under Low-Temperature Stress
L. Zhan - J. He, L. Ding, K. Storey, et al. - International Journal of Molecular Sciences, 2024 usegalaxy.eu

Identification of Pathogenic Copy Number Variants in Mexican Patients With Inherited Retinal Dystrophies Applying an Exome Sequencing Data‐Based Read‐Depth Approach
G. Fabian‐Morales - V. Ordoñez‐Labastida, F. Garcia‐Martínez, L. Montes‐Almanza, et al. - Molecular Genetics &amp; Genomic Medicine, 2024 usegalaxy.eu

Astrocytes originated from neural stem cells drive the regenerative remodeling of pathologic CSPGs in spinal cord injury
S. Hosseini - S. Nemati, S. Karimi-Abdolrezaee, - Stem Cell Reports, 2024 usegalaxy.eu

Rs1347093 regulates microRNA-216/-217 expression and is associated with pancreatic cancer risk
H. Huang - T. Shiu, D. Chan, C. Chang, et al. - Pancreatology, 2024 usegalaxy.eu

Impact of vaccination with the Anaplasma phagocytophilum MSP4 chimeric antigen on gene expression in the rabbit host
A. Moraga-Fernández - M. de Sousa-Blanco, J. Marques, J. Queirós, et al. - Research in Veterinary Science, 2024 usegalaxy.eu

Mitogenome-Based Phylogeny with Divergence Time Estimates Revealed the Presence of Cryptic Species within Heptageniidae (Insecta, Ephemeroptera)
Z. Guo - C. Shen, H. Cheng, Y. Chen, et al. - Insects, 2024 usegalaxy.eu

<i>In vivo</i> evolution to hypermucoviscosity and ceftazidime/avibactam resistance in a liver abscess caused by <i>Klebsiella pneumoniae</i> sequence type 512
V. Capitani - G. Arcari, C. Ambrosi, D. Scribano, et al. - mSphere, 2024 usegalaxy.eu

miRNA-mediated gene silencing in Drosophila larval development involves GW182-dependent and independent mechanisms
E. Matsuura-Suzuki - K. Kiyokawa, S. Iwasaki, Y. Tomari, et al. - The EMBO Journal, 2024 usegalaxy.eu

EXCRETE workflow enables deep proteomics of the microbial extracellular environment
D. Russo - D. Oliinyk, G. Pohnert, F. Meier, et al. - Communications Biology, 2024 usegalaxy.eu

Unravelling the main genomic features of Mycoplasma equirhinis
M. Martineau - C. Ambroset, S. Lefebvre, É. Kokabi, et al. - BMC Genomics, 2024 usegalaxy.eu

Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold-standard
Y. Lin - K. Breuer, D. Weichenhan, P. Lafrenz, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

Characterization of the angiomodulatory effects of Interleukin 11 cis- and trans-signaling in the retina
P. Liang - J. Ness, J. Rapp, S. Boneva, et al. - Journal of Neuroinflammation, 2024 usegalaxy.eu

Evidence for phosphate-dependent control of symbiont cell division in the model anemone <i>Exaiptasia diaphana</i>
N. Faulstich - A. Deloach, Y. Ksor, G. Mesa, et al. - mBio, 2024 usegalaxy.eu

DORQ-seq: high-throughput quantification of femtomol tRNA pools by combination of cDNA hybridization and Deep sequencing
M. Kristen - M. Lander, L. Kilz, L. Gleue, et al. - Nucleic Acids Research, 2024 usegalaxy.eu

Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues
R. Rebollo - P. Gerenton, E. Cumunel, A. Mary, et al. - Peer Community Journal, 2024 usegalaxy.eu

Nanopore sequencing of IPNV vp2 gene in Peruvian Andean trout ( <i>Oncorhynchus mykiss</i> ) cultures
S. Tapia - J. Orellana, Y. Duran, J. Rodriguez, et al. - Microbiology Resource Announcements, 2024 usegalaxy.eu

The Diversity of Seed-Borne Fungi Associated with Soybean Grown in Southern Poland
H. Olszak-Przybyś - G. Korbecka-Glinka, - Pathogens, 2024 usegalaxy.eu

On discovery of novel hub genes for ER+ and TN breast cancer types through RNA seq data analyses and classification models
A. Saddiqa - M. Zakir, M. Sheikh, Z. Muneer, et al. - Scientific Reports, 2024 usegalaxy.eu

Dark Mystery Solved: A Captive Black Leopard from South Africa is of Asian Descent
L. Tensen - G. Camacho, - African Journal of Wildlife Research, 2024 usegalaxy.eu

Biphasic response of human iPSC-derived neural network activity following exposure to a sarin-surrogate nerve agent
C. Bogguri - V. George, B. Amiri, A. Ladd, et al. - Frontiers in Cellular Neuroscience, 2024 usegalaxy.eu

Harnessing Lignocellulolytic and Electrogenic Potential: Insights from Shewanella oneidensis MR-1 and Cellulomonas Strains on Lignocellulosic Biomass
A. Molla - V. Mishyn, N. Bernet, T. Bouchez, et al. - Journal of The Electrochemical Society, 2024 usegalaxy.eu

Mesenchymal Osr1+ cells regulate embryonic lymphatic vessel formation
P. Vallecillo-García - M. Kühnlein, M. Orgeur, N. Hansmeier, et al. - Development, 2024 usegalaxy.eu

Gene expression networks in endothelial cells from failing human hearts
L. Wirth - E. Erny, M. Krane, H. Lahm, et al. - American Journal of Physiology-Heart and Circulatory Physiology, 2024 usegalaxy.eu

Identification of effector candidates in Bipolaris sorokiniana and their expression profile analysis during pathogen-wheat interactions
M. Kamajian - A. Soorni, R. Mehrabi, - Physiological and Molecular Plant Pathology, 2024 usegalaxy.eu

In Silico Prediction of Antibacterial Activity of Quinolone Derivatives
T. Karim - M. Almatarneh, S. Rahman, A. Alodhayb, et al. - ChemistrySelect, 2024 usegalaxy.eu

PICKLE-mediated nucleosome condensing drives H3K27me3 spreading for the inheritance of Polycomb memory during differentiation
Z. Liang - T. Zhu, Y. Yu, C. Wu, et al. - Molecular Cell, 2024 usegalaxy.eu

Characteristics and phylogenetic implications of the mitochondrial genome of a rare species, Libellula melli
B. Lin - H. Chen, J. Li, J. Liao, et al. - Gene Reports, 2024 usegalaxy.eu

Genomic characterization and identification of candidate genes for putative podophyllotoxin biosynthesis pathway in <i>Penicillium herquei</i><scp>HGN12</scp>.<scp>1C</scp>
D. Nguyen - Q. Tran, L. Le, H. Nguyen, et al. - Microbial Biotechnology, 2024 usegalaxy.eu

The mobilome of Staphylococcus aureus from wild ungulates reveals epidemiological links at the animal-human interface
B. Ramos - M. Cunha, - Environmental Pollution, 2024 usegalaxy.eu

Viral hijacking of hnRNPH1 unveils a G-quadruplex-driven mechanism of stress control
P. Schult - B. Kümmerer, M. Hafner, K. Paeschke, et al. - Cell Host &amp; Microbe, 2024 usegalaxy.eu

Innate immune training restores pro-reparative myeloid functions to promote remyelination in the aged central nervous system
V. Tiwari - B. Prajapati, Y. Asare, A. Damkou, et al. - Immunity, 2024 usegalaxy.eu

Correlation of Immunomodulatory Cytokines with Tumor Volume and Cerebrospinal Fluid in Vestibular Schwannoma Patients
A. Becker - L. Scholle, C. Klause, M. Staege, et al. - Cancers, 2024 usegalaxy.eu

Reverse vaccinology approaches to design a potent multiepitope vaccine against the HIV whole genome: immunoinformatic, bioinformatics, and molecular dynamics approaches
A. Hashempour - N. Khodadad, S. Akbarinia, F. Ghasabi, et al. - BMC Infectious Diseases, 2024 usegalaxy.eu

Whole-genome sequencing and identification of antimicrobial peptide coding genes in parsley (Petroselinum crispum), an important culinary and medicinal Apiaceae species
A. Uncu - A. Patat, A. Uncu, - Functional &amp; Integrative Genomics, 2024 usegalaxy.eu

Genomic Insights into Vietnamese Extended-Spectrum β-Lactamase-9-Producing Extensively Drug-Resistant Pseudomonas aeruginosa Isolates Belonging to the High-Risk Clone ST357 Obtained from Bulgarian Intensive Care Unit Patients
T. Strateva - A. Stratev, S. Peykov, - Pathogens, 2024 usegalaxy.eu

Genetic Polymorphisms of Angiotensin-Converting Enzyme 1 (ACE1) and ACE2 Associated With Severe Acute Respiratory Syndrome COVID-19 in the Palestinian Population
L. AbuSaleh - S. Ereqat, A. Al-Jawabreh, A. Nasereddin, et al. - Cureus, 2024 usegalaxy.eu

Coordinated metabolic adaptation of <i>Arabidopsis thaliana</i> to high light
G. Balcke - K. Vahabi, J. Giese, I. Finkemeier, et al. - The Plant Journal, 2024 usegalaxy.eu

Inference of Host–Pathogen Interaction Matrices from Genome-Wide Polymorphism Data
H. Märkle - S. John, L. Metzger, . , et al. - Molecular Biology and Evolution, 2024

Research topic displacement and the lack of interdisciplinarity: lessons from the scientific response to COVID-19
E. Seidlmayer - T. Melnychuk, L. Galke, L. Kühnel, et al. - Scientometrics, 2024

Three feminizing Wolbachia strains in a single host species: comparative genomics paves the way for identifying sex reversal factors
P. Grève - B. Moumen, D. Bouchon, - Frontiers in Microbiology, 2024 usegalaxy.eu

Parallel loss of sexual reproduction in field populations of a brown alga sheds light on the mechanisms underlying the emergence of asexuality
M. Hoshino - G. Cossard, F. Haas, E. Kane, et al. - Nature Ecology &amp; Evolution, 2024

Disseminated Echovirus 11 infection in a newborn in the Province of Bolzano, Italy
I. Bianconi - L. Battisti, A. Staffler, E. Giacobazzi, et al. - Infection, 2024 usegalaxy.eu

Identification of epigenetic modifiers essential for growth and survival of <scp>AML1</scp>/<scp>ETO</scp>‐positive leukemia
J. Duque‐Afonso - P. Veratti, U. Rehman, H. Herzog, et al. - International Journal of Cancer, 2024 usegalaxy.eu

Genomic characterization of prophage elements in Clostridium clostridioforme: an understudied component of the intestinal microbiome
S. Humphrey - A. Marouli, K. Thümmler, M. Mullin, et al. - Microbiology, 2024 usegalaxy.eu

Potential Ancestral Conoidean Toxins in the Venom Cocktail of the Carnivorous Snail Raphitoma purpurea (Montagu, 1803) (Neogastropoda: Raphitomidae)
G. Chiappa - G. Fassio, M. Modica, M. Oliverio, et al. - Toxins, 2024 usegalaxy.eu

Nonlinear latent representations of high-dimensional task-fMRI data: Unveiling cognitive and behavioral insights in heterogeneous spatial maps
M. Zabihi - S. Kia, T. Wolfers, S. de Boer, et al. - PLOS ONE, 2024

Genomic Evaluation of Multidrug-Resistant Extended-Spectrum β-Lactamase (ESBL)-Producing <i>Escherichia coli</i> from Irrigation Water and Fresh Produce in South Africa: A Cross-Sectional Analysis
L. Richter - S. Duvenage, E. du Plessis, T. Msimango, et al. - Environmental Science &amp; Technology, 2024 usegalaxy.eu

Microbial carbohydrate active enzyme (CAZyme) genes and diversity from Menagesha Suba natural forest soils of Ethiopia as revealed by shotgun metagenomic sequencing
A. Sime - B. Kifle, A. Woldesemayat, M. Gemeda, et al. - BMC Microbiology, 2024 usegalaxy.eu

Attention-Aware Non-Rigid Image Registration for Accelerated MR Imaging
A. Ghoul - J. Pan, A. Lingg, J. Kübler, et al. - IEEE Transactions on Medical Imaging, 2024

Social Cognition and Functional Connectivity in Early and Chronic Schizophrenia
S. Rutherford - C. Lasagna, S. Blain, A. Marquand, et al. - Biological Psychiatry: Cognitive Neuroscience and Neuroimaging, 2024

Biofoams with untapped enzymatic potential produced from beer bagasse by indigenous fungal strains
C. Aguirre Pranzoni - J. Bonilla, Á. Carrillo, M. López-Vidal, et al. - Bioresource Technology, 2024 usegalaxy.eu

Acute Hypoxia Does Not Alter Tumor Sensitivity to FLASH Radiation Therapy
R. Leavitt - A. Almeida, V. Grilj, P. Montay-Gruel, et al. - International Journal of Radiation Oncology*Biology*Physics, 2024 usegalaxy.eu

Differences in activity and stability drive transposable element variation in tropical and temperate maize
S. Ou - A. Scheben, T. Collins, Y. Qiu, et al. - Genome Research, 2024 usegalaxy.eu

Bioelectrochemical protein production valorising NH3-rich pig manure-derived wastewater and CO2 from anaerobic digestion
G. Soggia - A. Goglio, P. Cristiani, I. Luciani, et al. - Renewable Energy, 2024 usegalaxy.eu

Trait-mediated speciation and human-driven extinctions in proboscideans revealed by unsupervised Bayesian neural networks
T. Hauffe - J. Cantalapiedra, D. Silvestro, - Science Advances, 2024

Prostaglandin D2 receptor 2 downstream signaling and modulation of type 2 innate lymphoid cells from patients with asthma
C. Gress - M. Fuchs, S. Carstensen-Aurèche, M. Müller, et al. - PLOS ONE, 2024 usegalaxy.eu

Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level
S. Godbole - H. Voß, A. Gocke, S. Schlumbohm, et al. - Nature Communications, 2024 usegalaxy.eu

An integrated metaproteomics workflow for studying host-microbe dynamics in bronchoalveolar lavage samples applied to cystic fibrosis disease
M. Kruk - S. Mehta, K. Murray, L. Higgins, et al. - mSystems, 2024 usegalaxy.eu

Trusted Research Environments: Analysis of Characteristics and Data Availability
M. Weise - A. Rauber, - International Journal of Digital Curation, 2024 usegalaxy.eu

Sulcation in children with autism spectrum disorders
S. Burckard - I. Dupong, Y. Leprince, C. Fischer, et al. - Research Square - Springer Science and Business Media LLC, 2024

Transcription Factor 23 is an Essential Determinant of Murine Term Parturition
F. Minisy - H. Shawki, T. Fujita, A. Moustafa, et al. - Molecular and Cellular Biology, 2024 usegalaxy.eu

Spotlight on Secondary Metabolites Produced by an Early-Flowering Apulian Artichoke Ecotype Sanitized from Virus Infection by Meristem-Tip-Culture and Thermotherapy
R. Spanò - P. Gena, V. Linsalata, V. Sini, et al. - Antioxidants, 2024 usegalaxy.eu

Cytochrome <scp>P450 2J2</scp> is required for the natural compound austocystin D to elicit cancer cell toxicity
Y. Kojima - S. Fujieda, L. Zhou, M. Takikawa, et al. - Cancer Science, 2024 usegalaxy.eu

A novel deep-benthic sea cucumber species of Benthodytes (Holothuroidea, Elasipodida, Psychropotidae) and its comprehensive mitochondrial genome sequencing and evolutionary analysis
Y. He - H. Zhao, Y. Wang, C. Qu, et al. - BMC Genomics, 2024 usegalaxy.eu

Plant Thermosensors
J. Casal - G. Murcia, L. Bianchimano, - Annual Review of Genetics, 2024 usegalaxy.eu

ProSwats: A Proxy-based Scientific Workflow Retrieval Approach by Bridging the Gap between Textual and Structural Semantics
Y. Gu - J. Cao, S. Qian, N. Zhu, et al. - IEEE, 2024 usegalaxy.eu

Biodiversity and potential functionality of biofilm-sediment biotope in La Muerte lagoon, Monegros Desert, Spain
M. Berlanga - P. Picart, A. Blasco, R. Benaiges-Fernandez, et al. - Frontiers in Ecology and Evolution, 2024 usegalaxy.eu

Identification and Characterization of ATOH7-Regulated Target Genes and Pathways in Human Neuroretinal Development
D. Atac - K. Maggi, S. Feil, J. Maggi, et al. - Cells, 2024 usegalaxy.eu

ezSingleCell: an integrated one-stop single-cell and spatial omics analysis platform for bench scientists
R. Sethi - K. Ang, M. Li, Y. Long, et al. - Nature Communications, 2024 usegalaxy.eu

Expression of Transposable Elements throughout the Fasciola hepatica Trematode Life Cycle
E. Skalon - N. Panyushev, O. Podgornaya, A. Smolyaninova, et al. - Non-Coding RNA, 2024 usegalaxy.eu

The effect of successive summer drought periods on bacterial diversity along a plant species richness gradient
Y. de Souza - R. Siani, C. Albracht, Y. Huang, et al. - FEMS Microbiology Ecology, 2024 usegalaxy.eu

Shotgun metagenomic insights into secondary metabolite biosynthetic gene clusters reveal taxonomic and functional profiles of microbiomes in natural farmland soil
B. Kifle - A. Sime, M. Gemeda, A. Woldesemayat, et al. - Scientific Reports, 2024 usegalaxy.eu

Complete mitochondrial genomes of Bactrocera (Bulladacus) cinnabaria and B. (Bactrocera) propinqua (Diptera: Tephritidae) and their phylogenetic relationships with other congeners
H. Yong - S. Song, K. Chua, Y. Liew, et al. - Arthropod Systematics &amp; Phylogeny, 2024 usegalaxy.eu

Genomic prediction in <i>Brassica napus</i>: evaluating the benefit of imputed whole-genome sequencing data
S. Weber - L. Roscher-Ehrig, T. Kox, A. Abbadi, et al. - Genome, 2024

Pangenome graph layout by Path-Guided Stochastic Gradient Descent
S. Heumos - A. Guarracino, J. Schmelzle, J. Li, et al. - Bioinformatics, 2024

Unveiling Agricultural Biotechnological Prospects: The Draft Genome Sequence of Stenotrophomonas geniculata LGMB417
T. Ercole - V. Kava, D. Petters-Vandresen, R. Ribeiro, et al. - Current Microbiology, 2024 usegalaxy.eu

Pathogens of the oak processionary moth Thaumetopoea processionea: Developing a user-friendly bioassay system and metagenome analyses for microorganisms
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Insights on the comparative affinity of ribonucleic acids with plant-based beta carboline alkaloid, harmine: Spectroscopic, calorimetric and computational evaluation
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Meiotic maturation failure in primary ovarian insufficiency: insights from a bovine model
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Communicating Mass Spectrometry Quality Information in mzQC with Python, R, and Java
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Overview of transcriptome changes and phenomic profile of sanitized artichoke vis‐à‐vis non‐sanitized plants
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First Indonesian report of WGS-based MTBC L3 discovery
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Iron Chelation in Soil: Scalable Biotechnology for Accelerating Carbon Dioxide Removal by Enhanced Rock Weathering
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Wall-Associated Kinase (WAK) and WAK-like Kinase Gene Family in Sugar Beet: Genome-Wide Characterization and In Silico Expression Analysis in Response to Beet Cyst Nematode (Heterodera schachtii Schmidt) Infection
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Genome sequence and RNA-seq analysis reveal genetic basis of flower coloration in the giant water lily<i>Victoria cruziana</i>
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Nodulating Aeschynomene indica without Nod Factor Synthesis Genes: In Silico Analysis of Evolutionary Relationship
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DeepNeo: Deep Learning for neointimal tissue characterization using optical coherence tomography
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The genomic and phylogenetic analysis of <i>Marseillevirus cajuinensis</i> raises questions about the evolution of Marseilleviridae lineages and their taxonomical organization
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Complete genome sequence of the <i>Microbacterium enclense</i> bacteriophage phiMiGM15
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Examining Transcriptomic Alterations in Rat Models of Intracerebral Hemorrhage and Severe Intracerebral Hemorrhage
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Activation of the aryl hydrocarbon receptor improves allergen-specific immunotherapy of murine allergic airway inflammation: a novel adjuvant option?
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From genes to toxins: Profiling Prymnesium parvum during a riverine harmful algal bloom
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Combined Use of Phenotype-Based and Genome-Informed Approaches Identified a Unique <i>Fusarium oxysporum</i> f. sp. <i>cubense</i> Isolate in Hawaii
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First Isolation of the Heteropathotype Shiga Toxin-Producing and Extra-Intestinal Pathogenic (STEC-ExPEC) E. coli O80:H2 in French Healthy Cattle: Genomic Characterization and Phylogenetic Position
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Modeling brain sex in the limbic system as phenotype for female-prevalent mental disorders
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Evaluation of novel pyridoxal isonicotinoyl hydrazone (<scp>PIH</scp>) derivatives as potential <scp>anti‐tuberculosis</scp> agents: An in silico investigation
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Physicochemical properties and biological efficacy of 30 DYRK2 Inhibitors for the treatment of prostate cancer
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Expanding the Scope of Adenoviral Vectors by Utilizing Novel Tools for Recombination and Vector Rescue
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The Celiac‐Disease Superantigen Oligomerizes and Increases Permeability in an Enterocyte Cell Model
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A Transcriptomic Hourglass In Brown Algae
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A Minimal Metadata Schema and Its Tool to Improve the Searchableness of Research Data in Bioinformatics
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Building Domain-Specific Machine Learning Workflows: A Conceptual Framework for the State of the Practice
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In silico exploration of phenolics as modulators of penicillin binding protein (PBP) 2× of Streptococcus pneumoniae
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Genomic Epidemiology of C2/H30Rx and C1-M27 Subclades of Escherichia coli ST131 Isolates from Clinical Blood Samples in Hungary
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StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes
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Pannonibacter anstelovis sp. nov. Isolated from Two Cases of Bloodstream Infections in Paediatric Patients
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Deep Regression for Biological Age Estimation in Multiple Organs: Investigations on 40,000 Subjects of the UK Biobank
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Advancing pathogen surveillance by nanopore sequencing and genotype characterization of Acheta domesticus densovirus in mass-reared house crickets
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Complete genome sequence of <i>Pseudomonas aeruginosa</i> phage Knedl
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Complete genome sequence of <i>Escherichia coli</i> MP1
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Comparative Transcriptomics of Fat Bodies between Symbiotic and Quasi-Aposymbiotic Adult Females of Blattella germanica with Emphasis on the Metabolic Integration with Its Endosymbiont Blattabacterium and Its Immune System
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Enhancing the image analysis community in Galaxy
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Long-read datasets of Kayu Bawang (Azadirachta excelsa (Jack) Jacobs) from 3 different identified seed stands in Bengkulu (Sumatra), Indonesia and its phylogenetic relationships
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The Intellectual Disability Risk Gene<i>Kdm5b</i>Regulates Long-Term Memory Consolidation in the Hippocampus
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ZFP982 confers mouse embryonic stem cell characteristics by regulating expression of Nanog, Zfp42, and Dppa3
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Molecular characteristics of Cryptosporidium spp. in human cases in five Finnish hospital districts during 2021: first findings of Cryptosporidium mortiferum (Cryptosporidium chipmunk genotype I) in Finland
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The BAS chromatin remodeler determines brassinosteroid-induced transcriptional activation and plant growth in Arabidopsis
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Rescue of Mycobacterium bovis DNA Obtained from Cultured Samples during Official Surveillance of Animal TB: Key Steps for Robust Whole Genome Sequence Data Generation
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EpiSegMix: a flexible distribution hidden Markov model with duration modeling for chromatin state discovery
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Antimicrobial Activity of Bacillus amyloliquefaciens BS4 against Gram-Negative Pathogenic Bacteria
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Menarche, pubertal timing and the brain: female-specific patterns of brain maturation beyond age-related development
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The mitochondrial genome sequence of Syagrus coronata (Mart.) Becc. (Arecaceae) is characterized by gene insertion within intergenic spaces
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First detection of a cefiderocol-resistant and extensively drug-resistant Acinetobacter baumannii clinical isolate in Bulgaria
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Quantum chemistry based prediction of electron ionization mass spectra for environmental chemicals
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DNA sequence data, multispecies coalescent and morphometrics shed new light on the systematics of Iberian islamiinae springsnails (Caenogastropoda: Hydrobiidae)
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An <scp>RRM</scp> domain protein <scp>SOE</scp> suppresses transgene silencing in rice
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Whole genome discovery of regulatory genes responsible for the response of chicken to heat stress
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Private and well drinking water are reservoirs for antimicrobial resistant bacteria
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Complete Mitochondrial Genomes of Nedyopus patrioticus: New Insights into the Color Polymorphism of Millipedes
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Comparative genomics of four lactic acid bacteria identified with Vitek MS (MALDI-TOF) and whole-genome sequencing
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The altered TBI fecal microbiome is stable and functionally distinct
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Draft genome sequences of two <i>Micromonospora</i> strains isolated from the root nodules of <i>Alnus glutinosa</i>
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Pangeo environment in Galaxy Earth System supported by Fair-Ease
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Atlas of cardiac endothelial cell enhancer elements linking the mineralocorticoid receptor to pathological gene expression
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Human Metagenome Analysis with COVID-19 Infectious Disease
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Characterization of the major autolysin (AtlC) of Staphylococcus carnosus
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Planctoellipticum variicoloris gen. nov., sp. nov., a novel member of the family Planctomycetaceae isolated from wastewater of the aeration lagoon of a sugar processing plant in Northern Germany
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The contribution of BvgR, RisA, and RisS to global gene regulation, intracellular cyclic-di-GMP levels, motility, and biofilm formation in Bordetella bronchiseptica
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Decoding chromatin states by proteomic profiling of nucleosome readers
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Genomic and functional analysis of the mucinolytic species Clostridium celatum, Clostridium tertium, and Paraclostridium bifermentans
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A synthetic biology approach to assemble and reboot clinically relevant <i>Pseudomonas aeruginosa</i> tailed phages
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Targeted RNAseq Revealed the Gene Expression Signature of Ferroptosis-Related Processes Associated with Disease Severity in Patients with Multiple Sclerosis
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Identification of genetic determinants of bedaquiline resistance in <i>Mycobacterium tuberculosis</i> in Ural region, Russia
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The genome of the blind bee louse fly reveals deep convergences with its social host and illuminates Drosophila origins
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PCID2 dysregulates transcription and viral RNA processing to promote HIV-1 latency
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Nonpreferential but Detrimental Accumulation of Macrophages With Clonal Hematopoiesis-Driver Mutations in Cardiovascular Tissues—Brief Report
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Misidentification of neural cell identity in liver-derived organoid systems
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Identification of the odorant binding proteins of Western Flower Thrips ( <i>Frankliniella occidentalis</i> ), characterization and binding analysis of <i>FoccOBP3</i> with molecular modelling, molecular dynamics simulations and a confirmatory field trial
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Identification and functional characterisation of a locus for target site integration in Fusarium graminearum
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Enhanced weathering in the US Corn Belt delivers carbon removal with agronomic benefits
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Changes in the Expression of Proteins Associated with Neurodegeneration in the Brains of Mice after Infection with Influenza A Virus with Wild Type and Truncated NS1
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Whole-genome resequencing identifies exonic single-nucleotide variations in terpenoid biosynthesis genes of the medicinal and aromatic plant common sage (Salvia officinalis L.)
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The First Complete Mitochondrial Genome of the Genus Litostrophus: Insights into the Rearrangement and Evolution of Mitochondrial Genomes in Diplopoda
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Biophysical and structural characterization of tetramethrin serum protein complex and its toxicological implications
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Genome sequence of the ornamental plant<i>Digitalis purpurea</i>reveals the molecular basis of flower color and morphology variation
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Dynamics of cardiomyocyte gene expression and reversibility of catecholamine-induced heart injury
C. Bode - S. Preissl, L. Hein, A. Lother, et al. - Research Square - Research Square Platform LLC, 2024 usegalaxy.eu

Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses
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Draft genome sequence of <i>Streptomyces poriferorum</i> RTGN2, a bacterial endophyte isolated from <i>Alnus glutinosa</i> root nodules
R. Thompson - E. Fox, M. Montero-Calasanz, - Microbiology Resource Announcements, 2024 usegalaxy.eu

Draft genome sequences of five <i>Mycobacterium</i> strains, isolated from <i>Alnus glutinosa</i> root nodules
R. Thompson - E. Fox, M. Montero-Calasanz, - Microbiology Resource Announcements, 2024 usegalaxy.eu

Effect of <scp>Anti‐S100A4</scp> Monoclonal Antibody Treatment on Experimental Skin Fibrosis and Systemic Sclerosis–Specific Transcriptional Signatures in Human Skin
T. Trinh‐Minh - A. Györfi, M. Tomcik, C. Tran‐Manh, et al. - Arthritis &amp; Rheumatology, 2024 usegalaxy.eu

Neoadjuvant chemo‐ or chemo‐radiation‐therapy of pancreatic ductal adenocarcinoma differentially shift <scp>ECM</scp> composition, complement activation, energy metabolism and ribosomal proteins of the residual tumor mass
M. Stillger - K. Kurowski, P. Bronsert, E. Brombacher, et al. - International Journal of Cancer, 2024 usegalaxy.eu

Anthropogenic contamination sources drive differences in antimicrobial-resistant <i>Escherichia coli</i> in three urban lakes
J. Wight - A. Byrne, K. Tahlan, A. Lang, et al. - Applied and Environmental Microbiology, 2024 usegalaxy.eu

Developmental pathways underlying sexual differentiation in a U/V sex chromosome system
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Molecular Phylogenetics and Light Microscopy Reveal “True” and “False” Calacarines and Novel Genital Structures in Gall Mites (Acariformes, Eriophyoidea)
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Genome‐wide analysis of PvMADS in common bean and functional characterization of PvMADS31 in <i>Arabidopsis thaliana</i> as a player in abiotic stress responses
K. Mostafa - B. Yerlikaya, M. Abdulla, A. Aydin, et al. - The Plant Genome, 2024 usegalaxy.eu

Restraining Wnt activation and intestinal tumorigenesis by a Rab35 dependent GTPase relay
S. Redhai - T. Wang, K. Boonekamp, S. Reuter, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

The Genome of Arsenophonus sp. and Its Potential Contribution in the Corn Planthopper, Peregrinus maidis
Y. Wang - A. Mikaelyan, B. Coates, M. Lorenzen, et al. - Insects, 2024 usegalaxy.eu

The seeds of Plantago lanceolata comprise a stable core microbiome along a plant richness gradient
Y. de Souza - M. Schloter, W. Weisser, Y. Huang, et al. - Environmental Microbiome, 2024 usegalaxy.eu

From Complexity to Precision—Charting Decision-Making Through Normative Modeling
P. Kumar - P. Dayan, T. Wolfers, - JAMA Psychiatry, 2024

Characterization of Verona Integron-Encoded Metallo-β-Lactamase-Type Carbapenemase-Producing <i>Escherichia coli</i> Isolates Collected over a 16-Year Period in Bolzano (Northern Italy)
I. Bianconi - M. Spath, R. Aschbacher, R. Pedron, et al. - Microbial Drug Resistance, 2024 usegalaxy.eu

Predicting the Identities of su(met-2) and met-3 in Neurospora crassa by Genome Resequencing
K. McCluskey - D. Brown, E. Bredeweg, S. Baker, et al. - Fungal Genetics Reports, 2024 usegalaxy.eu

Cocoa Apoplastome Contains Defense Proteins Against Pathogens
I. de Oliveira - I. Moura, J. Santana, K. Gramacho, et al. - Phytopathology®, 2024 usegalaxy.eu

A hybrid receptor binding protein enables phage F341 infection of Campylobacter by binding to flagella and lipooligosaccharides
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Transcriptome dataset of gall-rust infected Sengon (Falcataria falcata) seedlings using long-read PCR-cDNA sequencing
A. Nugroho - I. Siregar, D. Matra, U. Siregar, et al. - Data in Brief, 2024 usegalaxy.eu

Structure and energetics of serum protein complex of tea adulterant dye Bismarck brown Y using experimental and computational methods
M. Shankar - M. Rani, P. Gopi, A. P, et al. - Computational Biology and Chemistry, 2024 usegalaxy.eu

Multi-omics responses of barley seedlings to low and high linear energy transfer irradiation
P. Volkova - A. Prazyan, M. Podlutskii, V. Saburov, et al. - Environmental and Experimental Botany, 2024 usegalaxy.eu

Long-Read Sequencing and De Novo Genome Assembly Pipeline of Two Plasmodium falciparum Clones (Pf3D7, PfW2) Using Only the PromethION Sequencer from Oxford Nanopore Technologies without Whole-Genome Amplification
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Integrated Analysis of Transcriptome and Epigenome Reveals <i>ENSR00000272060</i> as a Potential Biomarker in Gastric Cancer
B. Bahrami - M. Wolfien, P. Nikpour, - Epigenomics, 2024 usegalaxy.eu

TcSERPIN, an inhibitor that interacts with cocoa defense proteins and has biotechnological potential against human pathogens
M. Ferreira - K. Farias, M. Zugaib, A. Alves, et al. - Frontiers in Plant Science, 2024 usegalaxy.eu

Predictive uncertainty in deep learning–based <scp>MR</scp> image reconstruction using deep ensembles: Evaluation on the <scp>fastMRI</scp> data set
T. Küstner - K. Hammernik, D. Rueckert, T. Hepp, et al. - Magnetic Resonance in Medicine, 2024

Rat1 promotes premature transcription termination at R-loops
J. Mérida-Cerro - P. Maraver-Cárdenas, A. Rondón, A. Aguilera, et al. - Nucleic Acids Research, 2024 usegalaxy.eu

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy
D. Larivière - L. Abueg, N. Brajuka, C. Gallardo-Alba, et al. - Nature Biotechnology, 2024 usegalaxy.eu

A 14-Day Double-Blind, Randomized, Controlled Crossover Intervention Study with Anti-Bacterial Benzyl Isothiocyanate from Nasturtium (Tropaeolum majus) on Human Gut Microbiome and Host Defense
S. Pfäffle - C. Herz, E. Brombacher, M. Proietti, et al. - Nutrients, 2024 usegalaxy.eu

Comparative Metagenomic Analysis of Bacteriophages and Prophages in Gnotobiotic Mouse Models
O. Ishola - S. Kublik, A. Durai Raj, C. Ohnmacht, et al. - Microorganisms, 2024 usegalaxy.eu

Ionizing radiation responses appear incidental to desiccation responses in the bdelloid rotifer Adineta vaga
V. Moris - L. Bruneau, J. Berthe, A. Heuskin, et al. - BMC Biology, 2024 usegalaxy.eu

Challenges and perspectives for naming lipids in the context of lipidomics
M. Witting - A. Malik, A. Leach, A. Bridge, et al. - Metabolomics, 2024

Growth, Enzymatic, and Transcriptomic Analysis of xyr1 Deletion Reveals a Major Regulator of Plant Biomass-Degrading Enzymes in Trichoderma harzianum
L. Wang - Y. Zhao, S. Chen, X. Wen, et al. - Biomolecules, 2024 usegalaxy.eu

SimLivA–Modeling ischemia‐reperfusion injury in the liver: A first step towards a clinical decision support tool
H. Tautenhahn - T. Ricken, U. Dahmen, L. Mandl, et al. - GAMM-Mitteilungen, 2024

Integrated analysis of RNA-seq datasets reveals novel targets and regulators of COVID-19 severity
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Genetic variability of New Caledonian <i>Boeckella</i> De Guerne &amp; Richard, 1889 (Copepoda: Calanoida), with the description of a new species
C. Royaux - N. Charpin, N. Rabet, - Journal of Crustacean Biology, 2024 usegalaxy.eu

Polymyxin Resistance in Salmonella: Exploring Mutations and Genetic Determinants of Non-Human Isolates
T. Vieira - C. Dos Santos, A. de Jesus Bertani, G. Costa, et al. - Antibiotics, 2024 usegalaxy.eu

Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids
L. Dony - A. Krontira, L. Kaspar, R. Ahmad, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

Methanobrevibacter massiliense and Pyramidobacter piscolens Co-Culture Illustrates Transkingdom Symbiosis
V. Pilliol - M. Beye, L. Terlier, J. Balmelle, et al. - Microorganisms, 2024 usegalaxy.eu

Transcriptomic characterization of the human segmental endotoxin challenge model
C. Gress - T. Litzenburger, R. Schmid, K. Xiao, et al. - Scientific Reports, 2024 usegalaxy.eu

In Vivo Silencing of Regulatory Elements Using a Single AAV-CRISPRi Vector
P. Laurette - C. Cao, D. Ramanujam, M. Schwaderer, et al. - Circulation Research, 2024 usegalaxy.eu

Mitochondrial genome of Hancornia speciosa gomes: intergenic regions containing retrotransposons and predicted genes
F. de Souza - A. Marques, C. Almeida, - Molecular Biology Reports, 2024 usegalaxy.eu

Draft genome sequence of <i>Amycolatopsis camponoti</i> RTGN1, a bacterial endophyte isolated from <i>Alnus glutinosa</i> root nodules
R. Thompson - E. Fox, M. Montero-Calasanz, - Microbiology Resource Announcements, 2024 usegalaxy.eu

Origin and evolutionary trajectories of brown algal sex chromosomes
J. Barrera-Redondo - A. Lipinska, P. Liu, E. Dinatale, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

Association of a Specific OsCULLIN3c Haplotype with Salt Stress Responses in Local Thai Rice
B. Herwibawa - C. Lekklar, S. Chadchawan, T. Buaboocha, et al. - International Journal of Molecular Sciences, 2024 usegalaxy.eu

Tracing the pathways and mechanisms involved in medicinal uses of flaxseed with computational methods and bioinformatics tools
S. Joshi - R. Srivastava, - Frontiers in Chemistry, 2024 usegalaxy.eu

Transcriptional profiling specifies the pathogen-specific human host response to infectious keratitis
T. Lapp - P. Kammrath Betancor, G. Schlunck, C. Auw-Hädrich, et al. - Frontiers in Cellular and Infection Microbiology, 2024 usegalaxy.eu

EHMT2 LOSS-OF-FUNCTION ALTERATIONS CAUSE A KLEEFSTRA-LIKE SYNDROME
B. Martinez-Delgado - E. Lopez-Martin, J. Kerkhof, B. Baladron, et al. - medRxiv - Cold Spring Harbor Laboratory, 2024 usegalaxy.eu

Antibiotic resistance, plasmids, and virulence-associated markers in human strains of Campylobacter jejuni and Campylobacter coli isolated in Italy
A. Garcia-Fernandez - A. Janowicz, F. Marotta, M. Napoleoni, et al. - Frontiers in Microbiology, 2024 usegalaxy.eu

Oncostatin M Reduces Pathological Neovascularization in the Retina Through Müller Cell Activation
J. Rapp - A. Hospach, P. Liang, M. Schwämmle, et al. - Investigative Opthalmology &amp; Visual Science, 2024 usegalaxy.eu

hnRNP A1 dysfunction alters RNA splicing and drives neurodegeneration in multiple sclerosis (MS)
H. Salapa - P. Thibault, C. Libner, Y. Ding, et al. - Nature Communications, 2024 usegalaxy.eu

Synaptopodin Regulates Denervation-Induced Plasticity at Hippocampal Mossy Fiber Synapses
P. Kruse - G. Brandes, H. Hemeling, Z. Huang, et al. - Cells, 2024 usegalaxy.eu

Genomic analysis of multidrug-resistant Delftia tsuruhatensis isolated from raw bovine milk
P. Andriyanov - D. Kashina, A. Menshikova, - Frontiers in Microbiology, 2024 usegalaxy.eu

More May Not be Better: Enhanced Spacecraft Shielding May Exacerbate Cognitive Decrements by Increasing Pion Exposures during Deep Space Exploration
M. Vozenin - Y. Alaghband, O. Drayson, F. Piaget, et al. - Radiation Research, 2024 usegalaxy.eu

American lobster (<i>Homarus americanus</i>) hepatopancreas transcriptome reveals the significance of chitin-related genes during impoundment shell disease
N. Argenta - M. Rampaul, K. Clark, - FACETS, 2024 usegalaxy.eu

Postnatal persistence of hippocampal Cajal-Retzius cells has a crucial role in the establishment of the hippocampal circuit
I. Glærum - K. Dunville, K. Moan, M. Krause, et al. - Development, 2024 usegalaxy.eu

Two male-killing <i>Wolbachia</i> from <i>Drosophila birauraia</i> that are closely related but distinct in genome structure
H. Arai - M. Watada, D. Kageyama, - Royal Society Open Science, 2024 usegalaxy.eu

Collisions of RNA polymerases behind the replication fork promote alternative RNA splicing in newly replicated chromatin
F. Bruno - C. Coronel-Guisado, C. González-Aguilera, - Molecular Cell, 2024 usegalaxy.eu

SORCS2 activity in pancreatic α-cells safeguards insulin granule formation and release from glucose-stressed β-cells
O. Kalnytska - P. Qvist, S. Kunz, T. Conrad, et al. - iScience, 2024 usegalaxy.eu

Towards Trustworthy AI in Cardiology: A Comparative Analysis of Explainable AI Methods for Electrocardiogram Interpretation
N. Gumpfer - B. Dinov, S. Sossalla, M. Guckert, et al. - Springer Nature Switzerland, 2024

Development of Similarity Measures From Graph-Structured Bibliographic Metadata: An Application to Identify Scientific Convergence
T. Melnychuk - L. Galke, E. Seidlmayer, S. Bröring, et al. - IEEE Transactions on Engineering Management, 2024

Normative modeling for clinical neuroscience
A. Marquand - S. Rutherford, T. Wolfers, - Elsevier, 2024

Deepdefense: annotation of immune systems in prokaryotes using deep learning
S. Hauns - O. Alkhnbashi, R. Backofen, - GigaScience, 2024

Biofoams with Untapped Enzymatic Potential Produced from Beer Bagasse by Indigenous Fungal Strains
C. Aguirre Pranzoni - J. Bonilla, Á. Carrillo, M. López-Vidal, et al. - Elsevier BV, 2024 usegalaxy.eu

Amplicon-Based Bisulfite Conversion-NGS DNA Methylation Analysis Protocol
C. Albrecht - P. Bashtrykov, A. Jeltsch, - Springer US, 2024 usegalaxy.eu

Bioinformatics and Computational Biology
M. Ali - A. Zahoor, Z. Niaz, M. Jabran, et al. - Springer Nature Singapore, 2024 usegalaxy.eu

Metaproteomics for Coinfections in the Upper Respiratory Tract: The Case of COVID-19
S. Bihani - A. Gupta, S. Mehta, A. Rajczewski, et al. - Springer US, 2024 usegalaxy.eu

The Unique Specialization of Olfaction in the Senegalese Sole (Solea Senegalensis). Smelling in Co2 Acidified Water Triggers Nostril Specific Immune Processes
R. Costa - P. Hubbard, M. Manchado, D. Power, et al. - Elsevier BV, 2024 usegalaxy.eu

Evolutionary Structure Conservation and Covariance Scores
F. Eggenhofer - C. Höner zu Siederdissen, - Springer US, 2024 usegalaxy.eu

Salmonella phylogenomics
C. Jia - H. Zhou, Z. Wang, Y. Liu, et al. - Elsevier, 2024 usegalaxy.eu

<tt>CheRRI</tt>—Accurate classification of the biological relevance of putative RNA–RNA interaction sites
T. Müller - S. Mautner, P. Videm, F. Eggenhofer, et al. - GigaScience, 2024 usegalaxy.eu

Fungani, a Blast-Based Program for Analyzing Average Nucleotide Identity (Ani) between Two Fungal Genomes, Enables Easy Fungal Species Delimitation
P. Silar - C. Lalanne, - Elsevier BV, 2024 usegalaxy.eu

In-silico transcriptome analysis of antibiotic-treated Mycobacterium tuberculosis identifies novel antibiotic resistance factors
S. Sundar - - Indian Journal of Tuberculosis, 2024 usegalaxy.eu

Description of eight new mitochondrial genomes for the genus Neoarius and phylogenetic considerations for the family Ariidae (Siluriformes)
L. Pimentel - I. da Silva, I. Rodrigues-Oliveira, R. Pasa, et al. - Genomics &amp; Informatics, 2023 usegalaxy.eu

Unraveling intragenomic polymorphisms in the high-quality genome of Hypoxylaceae: a comprehensive study of the rDNA cistron
M. Cedeño-Sanchez - T. Cheng, C. Lambert, M. Kolarík, et al. - Mycological Progress, 2023

Cross-Species Variability in Lobular Geometry and Cytochrome P450 Hepatic Zonation: Insights into CYP1A2, CYP2E1, CYP2D6 and CYP3A4
M. Albadry - J. Küttner, J. Grzegorzewski, O. Dirsch, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

Transcriptional Comparison of Human and Murine Retinal Neovascularization
L. Pauleikhoff - S. Boneva, M. Boeck, A. Schlecht, et al. - Investigative Opthalmology &amp; Visual Science, 2023 usegalaxy.eu

Detailing Early Shoot Growth Arrest in Kro-0 x BG-5 Hybrids of <i>Arabidopsis thaliana</i>
K. Sageman-Furnas - G. Duarte, R. Laitinen, - Plant And Cell Physiology, 2023 usegalaxy.eu

A systematic review of the Iberian springsnail subgenus <i>Alzoniella</i> (<i>Navarriella</i>) (Caenogastropoda: Hydrobiidae), with the description of a new potentially relict subfamily
F. García-Guerrero - J. Miller, D. Delicado, M. Novo, et al. - Zoological Journal of the Linnean Society, 2023

Genome-wide identification and characterization of the plant defensins (Pdfs) gene family in selected Leguminous crops and their expression profiles in response to biotic and abiotic stresses
Z. Hassan - A. Abbas, I. Shafique, - Phytopathogenomics and Disease Control, 2023 usegalaxy.eu

Ribosome profiling reveals the fine-tuned response of <i>Escherichia coli</i> to mild and severe acid stress
K. Schumacher - R. Gelhausen, W. Kion-Crosby, L. Barquist, et al. - mSystems, 2023

USP7/Maged1-mediated H2A monoubiquitination in the paraventricular thalamus: an epigenetic mechanism involved in cocaine use disorder
J. Cheron - L. Beccari, P. Hagué, R. Icick, et al. - Nature Communications, 2023 usegalaxy.eu

Pyridylpiperazine efflux pump inhibitor boosts in vivo antibiotic efficacy against K. pneumoniae
A. Vieira Da Cruz - J. Jiménez-Castellanos, C. Börnsen, L. Van Maele, et al. - EMBO Molecular Medicine, 2023 usegalaxy.eu

High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities
P. Müller - J. de la Cuesta-Zuluaga, M. Kuhn, M. Baghai Arassi, et al. - Nature Protocols, 2023

Proteinortho6: pseudo-reciprocal best alignment heuristic for graph-based detection of (co-)orthologs
P. Klemm - P. Stadler, M. Lechner, - Frontiers in Bioinformatics, 2023 usegalaxy.eu

Rapid evolution of pre-zygotic reproductive barriers in allopatric populations
A. Mahilkar - P. Nagendra, P. Venkataraman, S. Deshmukh, et al. - Microbiology Spectrum, 2023 usegalaxy.eu

Construction and analysis of pseudogene-related ceRNA network in breast cancer
H. Mohebifar - A. Sabbaghian, T. Farazmandfar, M. Golalipour, et al. - Scientific Reports, 2023 usegalaxy.eu

Resin acids play key roles in shaping microbial communities during degradation of spruce bark
A. Ristinmaa - A. Tafur Rangel, A. Idström, S. Valenzuela, et al. - Nature Communications, 2023 usegalaxy.eu

A reappraisal of transcriptional regulation by NR5A1 and beta-catenin in adrenocortical carcinoma
E. Lalli - - Frontiers in Endocrinology, 2023 usegalaxy.eu

Environmental regulation of male fertility is mediated through Arabidopsis transcription factors bHLH89, 91, and 10
J. Robson - A. Tidy, S. Thomas, Z. Wilson, et al. - Journal of Experimental Botany, 2023 usegalaxy.eu

Oncogene-induced MALT1 protease activity drives posttranscriptional gene expression in malignant lymphomas
N. Wimberger - F. Ober, G. Avar, M. Grau, et al. - Blood, 2023

Association of Reproductive Phenology with Air Temperature in Almond (Prunus dulcis [Mill.] D.A. Webb) Cultivars Under Northwestern Himalayan Conditions
K. Kumawat - S. Raina, D. Kumar, M. Verma, et al. - Applied Fruit Science, 2023 usegalaxy.eu

Genome-wide identification, characterization, and expression analysis of the sweet potato (Ipomoea batatas [L.] Lam.) ARF, Aux/IAA, GH3, and SAUR gene families
S. Mathura - F. Sutton, V. Bowrin, - BMC Plant Biology, 2023 usegalaxy.eu

A global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes
V. Bonthala - B. Stich, - Research Square - Research Square Platform LLC, 2023

Reusability Challenges of Scientific Workflows: A Case Study for Galaxy
K. Alam - B. Roy, A. Serebrenik, - IEEE, 2023 usegalaxy.eu

Tigecycline causes loss of cell viability mediated by mitochondrial OXPHOS and RAC1 in hepatocellular carcinoma cells
D. Koch - H. Yu, I. Beirith, M. Schirren, et al. - Journal of Translational Medicine, 2023 usegalaxy.eu

Glycation Interferes with the Expression of Sialyltransferases and Leads to Increased Polysialylation in Glioblastoma Cells
P. Schildhauer - P. Selke, M. Staege, A. Harder, et al. - Cells, 2023 usegalaxy.eu

Investigating the patterns of simple sequence repeats (SSRs) inferred from the whole genome of a critically endangered species Cassine koordersii kosterm
I. Husaini - D. Rinandio, I. Martiansyah, M. Magandhi, et al. - IOP Conference Series: Earth and Environmental Science, 2023 usegalaxy.eu

Whole genome sequencing in the palm of your hand: how to implement a MinION Galaxy-based workflow in a food safety laboratory for rapid Salmonella spp. serotyping, virulence, and antimicrobial resistance gene identification
A. Lamas - A. Garrido-Maestu, A. Prieto, A. Cepeda, et al. - Frontiers in Microbiology, 2023 usegalaxy.eu

Harvesting mouse suprachiasmatic nucleus by vibrating microtome for diurnal transcriptome analysis
A. Bafna - P. Lau, G. Banks, P. Nolan, et al. - STAR Protocols, 2023 usegalaxy.eu

Detection and genomic characterization of a multidrug-resistant Salmonella Newport co-harbouring blaCMY-2, qnrB19 and mcr-9 from the diarrheic faeces of a foal
P. Braga - C. dos Santos, A. Bertani, T. Vieira, et al. - Journal of Global Antimicrobial Resistance, 2023 usegalaxy.eu

PIM kinases regulate early human Th17 cell differentiation
T. Buchacher - A. Shetty, S. Koskela, J. Smolander, et al. - Cell Reports, 2023 usegalaxy.eu

Acemannan ameliorates STZ-activated diabetes by attenuating high glucose via inhibiting inflammatory cytokines and apoptosis pathway
A. Omer - H. Altayb, F. Al-Abbasi, G. Gupta, et al. - International Journal of Biological Macromolecules, 2023 usegalaxy.eu

Low prevalence of germline TP53 and PALB2 mutations in unselected cohort of breast cancer patients from Brunei Darussalam
S. Matusin - Z. Lu, M. Haji Abdul Hamid, - F1000Research, 2023 usegalaxy.eu

Mouse models of pediatric high-grade gliomas with MYCN amplification reveal intratumoral heterogeneity and lineage signatures
M. Schoof - S. Godbole, T. Albert, M. Dottermusch, et al. - Nature Communications, 2023 usegalaxy.eu

<scp>MuDoGeR</scp>: <scp>Multi‐Domain</scp> Genome recovery from metagenomes made easy
U. Rocha - J. Coelho Kasmanas, R. Kallies, J. Saraiva, et al. - Molecular Ecology Resources, 2023

Insights into Intestinal P-glycoprotein Function using Talinolol: A PBPK Modeling Approach
B. Mallol - J. Grzegorzewski, H. Tautenhahn, M. König, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

A dual role of RBM42 in modulating splicing and translation of CDKN1A/p21 during DNA damage response
B. Ben-Oz - F. Machour, M. Nicola, A. Argoetti, et al. - Nature Communications, 2023 usegalaxy.eu

Analysis of blood microbiome dysbiosis in pulmonary sarcoidosis by decision tree model
Y. Hodzhev - - Biotechnology &amp; Biotechnological Equipment, 2023 usegalaxy.eu

Comparative analysis of gene regulatory networks identifies conserved regulators in seed plants
D. Wulf - A. Bräutigam, - bioRxiv - Cold Spring Harbor Laboratory, 2023

Dual targeting of MAPK and PI3K pathways unlocks redifferentiation of Braf-mutated thyroid cancer organoids
H. Lasolle - A. Schiavo, A. Tourneur, P. Gillotay, et al. - Oncogene, 2023 usegalaxy.eu

A high-throughput structural dynamics approach for identification of potential agonists of FFAR4 for type 2 diabetes mellitus therapy
D. Jhinjharia - A. Kaushik, S. Sahi, - Journal of Biomolecular Structure and Dynamics, 2023 usegalaxy.eu

Near complete genome sequences from Southern Vietnam revealed local features of genetic diversity and intergenerational changes in SARS- CoV-2 variants in 2020–2021
A. Gladkikh - T. Cao, E. Klyuchnikova, M. Dao, et al. - BMC Infectious Diseases, 2023 usegalaxy.eu

Phage DNA Extraction, Genome Assembly, and Genome Closure
J. Boeckman - M. Liu, J. Ramsey, J. Gill, et al. - Springer US, 2023 usegalaxy.eu

Obligate biotroph downy mildew consistently induces near-identical protective microbiomes in Arabidopsis thaliana
P. Goossens - J. Spooren, K. Baremans, A. Andel, et al. - Nature Microbiology, 2023 usegalaxy.eu

Exploring the influences of geographical variation on sequence signatures in the human gut microbiome
G. Kumar - P. Bhadury, - Journal of Genetics, 2023 usegalaxy.eu

A rabies-related lyssavirus from a <i>Nycticeinops schlieffeni</i> bat with neurological signs, South Africa
N. Viljoen - A. Ismail, J. Weyer, W. Markotter, et al. - Microbiology Resource Announcements, 2023 usegalaxy.eu

Exploring the potential of fluoro‐flavonoid derivatives as <scp>anti‐lung</scp> cancer agents: <scp>DFT</scp>, molecular docking, and molecular dynamics techniques
N. Esha - S. Quayum, M. Saif, M. Almatarneh, et al. - International Journal of Quantum Chemistry, 2023 usegalaxy.eu

Fast proliferating and slowly migrating non‐small cell lung cancer cells are vulnerable to decitabine and retinoic acid combinatorial treatment
G. Pelos - M. Riester, J. Pal, K. Myacheva, et al. - International Journal of Cancer, 2023 usegalaxy.eu

Molecular Evolution of Malacostracan Short Wavelength Sensitive Opsins
S. Palecanda - E. Madrid, M. Porter, - Journal of Molecular Evolution, 2023 usegalaxy.eu

Speos: an ensemble graph representation learning framework to predict core gene candidates for complex diseases
F. Ratajczak - M. Joblin, M. Hildebrandt, M. Ringsquandl, et al. - Nature Communications, 2023

Genome-Level Investigation of WRKY Transcription Factors and Their Potential Roles in Fruit Peel Ripening and Coloration in the Common Fig (Ficus carica L.)
N. Kmeli - I. Bettaieb, J. Hamdi, R. Mlouka, et al. - Journal of Plant Growth Regulation, 2023 usegalaxy.eu

Non-antibiotic drugs break colonization resistance against pathogenic<i>Gammaproteobacteria</i>
A. Grießhammer - J. de la Cuesta-Zuluaga, T. Zahir, P. Müller, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

Safety assessment of Enterococcus lactis strains complemented with comparative genomics analysis reveals probiotic and safety characteristics of the entire species
N. Ahmed - R. Khattab, Y. Ragab, M. Hassan, et al. - BMC Genomics, 2023 usegalaxy.eu

Conserved amino acid residues and gene expression patterns associated with the substrate preferences of the competing enzymes FLS and DFR
N. Choudhary - B. Pucker, - bioRxiv - Cold Spring Harbor Laboratory, 2023

Characterization and expression analysis of SnRK2, PYL, and ABF/ AREB/ ABI5 gene families in sweet potato
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Genotypic Evolution of <i>Klebsiella pneumoniae</i> Sequence Type 512 during Ceftazidime/Avibactam, Meropenem/Vaborbactam, and Cefiderocol Treatment, Italy
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SWORTS: A Scientific Workflow Retrieval Approach by Learning Textual and Structural Semantics
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Unraveling the transcriptional network regulated by miRNAs in blast-resistant and blast-susceptible rice genotypes during Magnaporthe oryzae interaction
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Toxic effects and molecular mechanisms of estuarian crustaceans (Scylla paramamosain) exposed to five commonly used benzophenones
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Multiple transcription factors mediate acclimation of Chlamydomonas to light stress
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Genetic background of neomycin resistance in clinical <i>Escherichia coli</i> isolated from Danish pig farms
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Individual-level deviations from normative brain morphology in violence, psychosis, and psychopathy
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A comprehension on structure guided alignment dependent 3D-QSAR modelling, and molecular dynamics simulation on 2,4-thiazolidinediones as aldose reductase inhibitors for the management of diabetic complications
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Proteometabolomics of initial and recurrent glioblastoma highlights an increased immune cell signature with altered lipid metabolism
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Domain adapted brain network fusion captures variance related to pubertal brain development and mental health
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Accurate prediction of quantitative traits with failed SNP calls in canola and maize
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Harnessing the power of comparative genomics to support the distinction of sister species within <i>Phyllosticta</i> and development of highly specific detection of <i>Phyllosticta citricarpa</i> causing citrus black spot by real-time PCR
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Integrated Meta-Omics Analysis Unveils the Pathways Modulating Tumorigenesis and Proliferation in High-Grade Meningioma
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Structural Evolution of Gene Promoters Driven by Primate-Specific KRAB Zinc Finger Proteins
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Spitting in the wind?—The challenges of RNA sequencing for biomarker discovery from saliva
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Combining Fusion of Cells with CRISPR-Cas9 Editing for the Cloning of Large DNA Fragments or Complete Bacterial Genomes in Yeast
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Interaction of Mesonivirus and Negevirus with arboviruses and the RNAi response in Culex tarsalis-derived cells
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Scaling cross-tissue single-cell annotation models
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SARS-CoV-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses
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Whole-genome sequence and mass spectrometry study of the snow blight fungus Phacidium infestans (Karsten) DSM 5139 growing at freezing temperatures
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A Galaxy of informatics resources for MS-based proteomics
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An integrated transcriptomic cell atlas of human neural organoids
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LipidSpace: Simple Exploration, Reanalysis, and Quality Control of Large-Scale Lipidomics Studies
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Global and local functions of the Fused kinase ortholog CdaH in intracellular patterning in <i>Tetrahymena</i>
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Changes in rice rhizosphere and bulk soil bacterial communities in the Doñana wetlands at different growth stages
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Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics
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Genotypic and phenotypic insights into virulence factors of nosocomial Stenotrophomonas maltophilia isolates collected in Bulgaria (2011–2022)
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Colorectal Cancer Archaeome: A Metagenomic Exploration, Tunisia
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The de novo transcriptome assembly of Agave angustifolia Haw, mining for carbohydrates and cellulose synthesis genes profiling, and molecular markers development
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Fifth mass extinction event triggered the diversification of the largest family of freshwater gastropods (Caenogastropoda: Truncatelloidea: Hydrobiidae)
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<i>Cuscuta campestris</i>fine-tunes gene expression during haustoriogenesis as an adaptation to different hosts
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Identification and Pathogenicity of Fusarium Isolated from Soybean in Poland
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Parallel loss of sex in field populations of a brown alga sheds light on the mechanisms underlying the emergence of asexuality
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Genomic and Phenotypic Characterization of Mastitis-Causing Staphylococci and Probiotic Lactic Acid Bacteria Isolated from Raw Sheep’s Milk
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Natural diversity of lactococci in γ-aminobutyric acid (GABA) production and genetic and phenotypic determinants
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Distribution, inducibility, and characteristics of <i>Latilactobacillus curvatus</i> temperate phages
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German Human Genome-Phenome Archive in an International Context: Toward a Federated Infrastructure for Managing and Analyzing Genomics and Health Data
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Embedding the de.NBI Cloud in the National Research Data Infrastructure Activities
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Haplotype blocks for genomic prediction: a comparative evaluation in multiple crop datasets
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Genomic analysis and antimicrobial activity of β-lactam/β-lactamase inhibitors and other agents against KPC-producing Klebsiella pneumoniae clinical isolates from Brazilian hospitals
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Assessing antimicrobial and metal resistance genes in Escherichia coli from domestic groundwater supplies in rural Ireland
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Whole genome sequencing of Bacillus anthracis isolated from animal in the 1960s, Brazil, belonging to the South America subclade
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DNA-directed termination of RNA polymerase II transcription
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A genomic platform for surveillance and antigen discovery in Plasmodium spp. using long-read amplicon sequencing
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Eomes restricts Brachyury functions at the onset of mouse gastrulation
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Bridging the gap in African biodiversity genomics and bioinformatics
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Transcription factors operate on a limited vocabulary of binding motifs in<i>Arabidopsis thaliana</i>
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Phylogenetic placement of Ceratophyllum submersum based on a complete plastome sequence derived from nanopore long read sequencing data
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CRISPR-Cas9 Library Screening Identifies Novel Molecular Vulnerabilities in KMT2A-Rearranged Acute Lymphoblastic Leukemia
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Integrated signaling and transcriptome analysis reveals Src family kinase individualities and novel pathways controlled by their constitutive activity
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Precision Genome Engineering in <i>Streptococcus suis</i> Based on a Broad-Host-Range Vector and CRISPR-Cas9 Technology
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The non-classical major histocompatibility complex II protein SLA-DM is crucial for African swine fever virus replication
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Multiplicity of <i>bla</i> <sub>KPC</sub> Genes and pKpQIL Plasmid Plasticity in the Development of Ceftazidime-Avibactam and Meropenem Coresistance in Klebsiella pneumoniae Sequence Type 307
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Volatile Organic Compounds Emitted by the Biocontrol Agent Pythium oligandrum Contribute to Ginger Plant Growth and Disease Resistance
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<i>kcnj13</i>regulates pigment cell shapes in zebrafish and has diverged by cis-regulatory evolution between<i>Danio</i>species
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Regional, circuit and network heterogeneity of brain abnormalities in psychiatric disorders
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A systems-level mass spectrometry-based technique for accurate and sensitive quantification of the RNA cap epitranscriptome
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The mitogenomes of Leptographium aureum, Leptographium sp., and Grosmannia fruticeta: expansion by introns
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Deciphering the molecular basis of abiotic stress response in cucumber (Cucumis sativus L.) using RNA-Seq meta-analysis, systems biology, and machine learning approaches
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Identification of radiomic biomarkers in a set of four skeletal muscle groups on Dixon MRI of the NAKO MR study
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Getting personal with epigenetics: towards individual-specific epigenomic imputation with machine learning
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A translational regulator MHZ9 modulates ethylene signaling in rice
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A pathway model of glucose-stimulated insulin secretion in the pancreatic β-cell
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Pathovar-Specific PCR Method for Detection and Identification of <i>Xanthomonas translucens</i> pv. <i>undulosa</i>
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A Chromosome-Level Reference Genome for the Black-Legged Kittiwake (<i>Rissa tridactyla</i>), a Declining Circumpolar Seabird
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Adaptive evolution of the enigmatic Takakia now facing climate change in Tibet
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The design of functional proteins using tensorized energy calculations
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Isolation, biochemical characterization, and genome sequencing of two high‐quality genomes of a novel chitinolytic <i>Jeongeupia</i> species
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Insight into the nodal cells transcriptome of the streptophyte green alga <i>Chara braunii</i> S276
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Ribosome inactivating proteins in insects: HGT, gene expression, and functional implications
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Proteogenomic data and resources for pan-cancer analysis
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Trimannose-coupled antimiR-21 for macrophage-targeted inhalation treatment of acute inflammatory lung damage
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Recently evolved combination of unique sulfatase and amidase genes enables bacterial degradation of the wastewater micropollutant acesulfame worldwide
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Fine-grained topographic organization within somatosensory cortex during resting-state and emotional face-matching task and its association with ASD traits
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Combination of two rare mutations in the SARS-CoV-2 M gene in patients with severe and prolonged COVID-19
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Discovery of putative long non-coding RNAs expressed in the eyes of Astyanax mexicanus (Actinopterygii: Characidae)
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Unified fate mapping in multiview single-cell data
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BASIDIN as a New Protein Effector of the Phytopathogen Causing Witche’s Broom Disease in Cocoa
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Diversity and Evolutionary History of Ti Plasmids of “tumorigenes” Clade of <i>Rhizobium</i> spp. and Their Differentiation from Other Ti and Ri Plasmids
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Sensitive inference of alignment-safe intervals from biodiverse protein sequence clusters using EMERALD
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Metaproteomic Analysis of Nasopharyngeal Swab Samples to Identify Microbial Peptides in COVID-19 Patients
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Ploidy in Vibrio natriegens: Very Dynamic and Rapidly Changing Copy Numbers of Both Chromosomes
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CRISPR library screening to develop HEK293-derived cell lines with improved lentiviral vector titers
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Reprogramming of the transcriptome after heat stress mediates heat hormesis in Caenorhabditis elegans
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Employing Genome Mining to Unveil a Potential Contribution of Endophytic Bacteria to Antimicrobial Compounds in the Origanum vulgare L. Essential Oil
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Comparative genomics and virulome analysis reveal unique features associated with clinical strains of Klebsiella pneumoniae and Klebsiella quasipneumoniae from Trinidad, West Indies
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Genomics and Antimicrobial Susceptibility of Clinical Pseudomonas aeruginosa Isolates from Hospitals in Brazil
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Integrative meta-omics in Galaxy and beyond
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A YAP/TAZ–ARHGAP29–RhoA Signaling Axis Regulates Podocyte Protrusions and Integrin Adhesions
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WHIRLY proteins maintain seed longevity by effects on seed oxygen signalling during imbibition
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Peptide-mediated inhibition of the transcriptional regulator Elongin BC induces apoptosis in cancer cells
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The Rhodoexplorer Platform for Red Algal Genomics and Whole-Genome Assemblies for Several <i>Gracilaria</i> Species
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EODIE — Earth Observation Data Information Extractor
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Phylogenetic placement of<i>Ceratophyllum submersum</i>based on a complete plastome sequence derived from nanopore long read sequencing data
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Cheminformatics identification of phenolics as modulators of key penicillin−binding proteins of <i>Escherichia coli</i> towards interventive antibacterial therapy
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The Amyloid Precursor Protein Regulates Synaptic Transmission at Medial Perforant Path Synapses
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Heteroresistance to Colistin in Clinical Isolates of Klebsiella pneumoniae Producing OXA-48
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A biologist’s guide to planning and performing quantitative bioimaging experiments
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Fast and accurate genome-wide predictions and structural modeling of protein–protein interactions using Galaxy
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Genome-wide identification and comparative in-silico characterization of β-galactosidase (GH-35) in ascomycetes and its role in germ tube development of Aspergillus fumigatus via RNA-seq analysis
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Genome-wide Identification of the Auxin Transporter Gene Families in Sweet Potato (Ipomoea batatas) and their Expression During Tuberization
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Identification of annotation artifacts concerning the chalcone synthase (CHS)
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MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets
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The autoPET challenge: Towards fully automated lesion segmentation in oncologic PET/CT imaging
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Multi-Omics Analysis of Vicia cracca Responses to Chronic Radiation Exposure in the Chernobyl Exclusion Zone
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A 2-million-year-old microbial and viral communities from the Kap København Formation in North Greenland
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In Silico Probiogenomic Characterization of Lactobacillus delbrueckii subsp. lactis A4 Strain Isolated from an Armenian Honeybee Gut
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Su(Hw) interacts with Combgap to establish long-range chromatin contacts
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Genetic factors explaining anthocyanin pigmentation differences
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A novel variant of the Listeria monocytogenes type VII secretion system EssC component is associated with an Rhs toxin
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Enhanced 5mC-Methylation-Site Recognition in DNA Sequences using Token Classification and a Domain-specific Loss Function
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Ribosome profiling reveals the fine-tuned response of<i>Escherichia coli</i>to mild and severe acid stress
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Proline and Silver Nitrate Promotes Multiple Shoot Induction from Mature Embryo and Shoot Tip Explants of Sorghum
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Laktik Asit Bakterilerinde Tetrasiklin Direncinin Fenotipik ve Tüm Genom Dizilerinde in silico Genotipik Olarak Araştırılması
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Laktik Asit Bakterilerinde Tetrasiklin Direncinin Fenotipik ve Tüm Genom Dizilerinde in silico Genotipik Olarak Araştırılması
Ö. ILIKKAN - - Iğdır Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 2023 usegalaxy.eu

SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing
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Comparative genome features and secondary metabolite biosynthetic potential of Kutzneria chonburiensis and other species of the genus Kutzneria
M. Chanama - P. Prombutara, S. Chanama, - Scientific Reports, 2023 usegalaxy.eu

A Roadmap for the Human Gut Cell Atlas
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CpG DNA methylation changes during epididymal sperm maturation in bulls
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SARS-CoV-2 spike protein diversity at an intra-host level, among SARS-CoV-2 infected individuals in South Africa, 2020 to 2022
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Species Delineation and Comparative Genomics within the<i>Campylobacter ureolyticus</i>Complex
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Genome-Based Retrospective Analysis of a Providencia stuartii Outbreak in Rome, Italy: Broad Spectrum IncC Plasmids Spread the NDM Carbapenemase within the Hospital
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β-Cell–Specific <i>E2f1</i> Deficiency Impairs Glucose Homeostasis, β-Cell Identity, and Insulin Secretion
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Comparative genomics of Brucella abortus and Brucella melitensis unravels the gene sharing, virulence factors and SNP diversity among the standard, vaccine and field strains
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<i>De Novo</i> Whole-Genome Sequencing of Two Pathogenic Pasteurella multocida Type D:6 Strains Isolated from Pigs
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Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA
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Genomic and transcriptomic analysis of camptothecin producing novel fungal endophyte -<i>Alternaria burnsii</i>NCIM 1409
S. Natarajan - B. Pucker, S. Srivastava, - bioRxiv - Cold Spring Harbor Laboratory, 2023

Single‐heartbeat cardiac cine imaging via jointly regularized nonrigid motion‐corrected reconstruction
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APOE expression and secretion are modulated by mitochondrial dysfunction
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Mapping cells through time and space with moscot
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MpoxRadar: a worldwide MPXV genomic surveillance dashboard
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Neonatal immune challenge poses a sex-specific risk for epigenetic microglial reprogramming and behavioral impairment
M. Schwabenland - O. Mossad, A. Sievert, A. Peres, et al. - Nature Communications, 2023 usegalaxy.eu

Discovery and biosynthetic assessment of 'Streptomyces ortus' sp. nov. isolated from a deep-sea sponge
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Genetic architecture of brain age and its causal relations with brain and mental disorders
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A draft human pangenome reference
W. Liao - M. Asri, J. Ebler, D. Doerr, et al. - Nature, 2023

Biosynthetic Potential of Hypogymnia Holobionts: Insights into Secondary Metabolite Pathways
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Phased grapevine genome sequence of an Rpv12 carrier for biotechnological exploration of resistance to Plasmopara viticola
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Emergence of Azithromycin-Resistant Neisseria gonorrhoeae Isolates Belonging to the NG-MAST Genogroup 12302 in Russia
I. Kandinov - E. Dementieva, M. Filippova, A. Vinokurova, et al. - Microorganisms, 2023 usegalaxy.eu

Mechanism-based and computational modeling of hydrogen sulfide biogenesis inhibition: interfacial inhibition
L. Le Corre - D. Padovani, - Scientific Reports, 2023 usegalaxy.eu

Comparative Genomic Analysis and Species Delimitation: A Case for Two Species in the Zoonotic Cestode Dipylidium caninum
J. Jesudoss Chelladurai - A. Abraham, T. Quintana, D. Ritchie, et al. - Pathogens, 2023 usegalaxy.eu

Automatic annotation of the bHLH gene family in plants
C. Thoben - B. Pucker, - bioRxiv - Cold Spring Harbor Laboratory, 2023

Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in Prokaryotic metagenome-assembled genome recovery
U. Nunes da Rocha - J. Kasmanas, R. Toscan, D. Sanches, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

ODNA: identification of organellar DNA by machine learning
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Free-breathing Arterial Spin Labeling MRI for the Detection of Pulmonary Embolism
A. Othman - C. Liang, Y. Komma, M. Munz, et al. - Radiology, 2023

Free-breathing Arterial Spin Labeling MRI for the Detection of Pulmonary Embolism
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Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
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Botryosphaeriaceae gene machinery: Correlation between diversity and virulence
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Direct Xylella fastidiosa whole genome sequencing from various plant species using targeted enrichment
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Building on Communities to Further Software Sustainability
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Rise and fall of SARS-CoV-2 variants in Rotterdam: Comparison of wastewater and clinical surveillance
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Foremost report of the whole genome of Spirabiliibacterium mucosae from India and comparative genomics of the novel genus Spirabiliibacterium
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Increasing complexity of opsin expression across stomatopod development
S. Palecanda - M. Steck, M. Porter, - Ecology and Evolution, 2023 usegalaxy.eu

How does particulate matter affect plant transcriptome and microbiome?
C. Vergata - F. Contaldi, I. Baccelli, M. Basso, et al. - Environmental and Experimental Botany, 2023 usegalaxy.eu

DIET-like mutualism of Geobacter and methanogens at specific electrode potential boosts production of both methane and hydrogen from propionate
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Bioprospecting phytochemicals of Rosmarinus officinalis L. for targeting SARS-CoV-2 main protease (Mpro): a computational study
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Morphology and taxonomic assessment of eight genetic clades of Mercuria Boeters, 1971 (Caenogastropoda, Hydrobiidae), with the description of five new species
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Galaxy for open-source computational drug discovery solutions
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Mapping lineage-traced cells across time points with moslin
M. Lange - Z. Piran, M. Klein, B. Spanjaard, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

A physiologically based pharmacokinetic model for CYP2E1 phenotyping via chlorzoxazone
J. Küttner - J. Grzegorzewski, H. Tautenhahn, M. König, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

Aircraft surveys for air eDNA: probing biodiversity in the sky
K. Métris - J. Métris, - PeerJ, 2023 usegalaxy.eu

Epidemiological Description and Detection of Antimicrobial Resistance in Various Aquatic Sites in Marseille, France
S. El-Sawalhi - O. Revol, A. Chamieh, A. Lacoste, et al. - Microbiology Spectrum, 2023 usegalaxy.eu

Denervated mouse CA1 pyramidal neurons express homeostatic synaptic plasticity following entorhinal cortex lesion
M. Lenz - A. Eichler, P. Kruse, P. Stöhr, et al. - Frontiers in Molecular Neuroscience, 2023 usegalaxy.eu

Total escape of SARS-CoV-2 from dual monoclonal antibody therapy in an immunocompromised patient
L. Jaki - S. Weigang, L. Kern, S. Kramme, et al. - Nature Communications, 2023 usegalaxy.eu

Comparative Analysis of Bioactive Compounds in Two Globe Artichoke Ecotypes Sanitized and Non-Sanitized from Viral Infections
R. Spanò - S. Fortunato, V. Linsalata, I. D’Antuono, et al. - Plants, 2023 usegalaxy.eu

Building pangenome graphs
E. Garrison - A. Guarracino, S. Heumos, F. Villani, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

The terpene synthase genes of Melaleuca alternifolia (tea tree) and comparative gene family analysis among Myrtaceae essential oil crops
J. Voelker - R. Mauleon, M. Shepherd, - Plant Systematics and Evolution, 2023 usegalaxy.eu

Sulfate reduction and homoacetogenesis at various hypersaline conditions: Implications for H2 underground gas storage
L. Schwab - L. Prinsen, G. Nowack, D. Popp, et al. - Frontiers in Energy Research, 2023

Sulfate reduction and homoacetogenesis at various hypersaline conditions: Implications for H2 underground gas storage
L. Schwab - L. Prinsen, G. Nowack, D. Popp, et al. - Frontiers in Energy Research, 2023

Proteome alterations in human autopsy tissues in relation to time after death
É. Kocsmár - M. Schmid, M. Cosenza-Contreras, I. Kocsmár, et al. - Cellular and Molecular Life Sciences, 2023 usegalaxy.eu

The complete reference genome for grapevine (<i>Vitis vinifera</i>L.) genetics and breeding
X. Shi - S. Cao, X. Wang, S. Huang, et al. - Horticulture Research, 2023

mlf-core: a framework for deterministic machine learning
L. Heumos - P. Ehmele, L. Kuhn Cuellar, K. Menden, et al. - Bioinformatics, 2023

Agrobacterium cucumeris sp. nov. isolated from crazy roots on cucumber (Cucumis sativus)
M. Warabieda - N. Kuzmanović, P. Trzciński, J. Puławska, et al. - Systematic and Applied Microbiology, 2023

Mapping Normative Trajectories of Cognitive Function and Its Relation to Psychopathology Symptoms and Genetic Risk in Youth
R. Kjelkenes - T. Wolfers, D. Alnæs, D. van der Meer, et al. - Biological Psychiatry Global Open Science, 2023

Identification of a Czc-like operon of the periodontal pathobiont Porphyromonas gingivalis involved in metal ion efflux
A. Gains - D. Lambert, G. Stafford, - Anaerobe, 2023 usegalaxy.eu

A comparative gene expression matrix in Apoe-deficient mice identifies unique and atherosclerotic disease stage-specific gene regulation patterns in monocytes and macrophages
C. Härdtner - A. Kumar, C. Ehlert, T. Vico, et al. - Atherosclerosis, 2023 usegalaxy.eu

DNA ultra-sensitive quantification, a technology for studying HIV unintegrated linear DNA
H. Roux - S. Figueiredo, L. Sareoua, M. Salmona, et al. - Cell Reports Methods, 2023 usegalaxy.eu

Genomics of the “tumorigenes” clade of the family <i>Rhizobiaceae</i> and description of <i>Rhizobium rhododendri</i> sp. nov.
N. Kuzmanović - G. diCenzo, B. Bunk, C. Spröer, et al. - MicrobiologyOpen, 2023

Abundance, classification and genetic potential of Thaumarchaeota in metagenomes of European agricultural soils: a meta-analysis
J. Nelkner - L. Huang, T. Lin, A. Schulz, et al. - Environmental Microbiome, 2023

Abundance, classification and genetic potential of Thaumarchaeota in metagenomes of European agricultural soils: a meta-analysis
J. Nelkner - L. Huang, T. Lin, A. Schulz, et al. - Environmental Microbiome, 2023

Nucleophosmin 1 cooperates with the methyltransferase DOT1L to regulate H3K79me2 levels and DNA satellites expression at peri-nucleolar heterochromatin
a. izzo - i. akol, A. Villarreal, M. Garcia-Miralles, et al. - Research Square - Research Square Platform LLC, 2023 usegalaxy.eu

Comparative genomic analysis of Colistin resistant Escherichia coli isolated from pigs, a human and wastewater on colistin withdrawn pig farm
N. Khine - T. Wongsurawat, P. Jenjaroenpun, D. Hampson, et al. - Scientific Reports, 2023 usegalaxy.eu

Experience of Klebsiella pneumoniae genome sequencing using the short read method on the Illumina platform
A. Shaforost - A. Ziatskov, E. Voropaev, O. Osipkina, et al. - Health and Ecology Issues, 2023 usegalaxy.eu

Phenotypic and Molecular Characteristics of Carbapenem-Resistant Acinetobacter baumannii Isolates from Bulgarian Intensive Care Unit Patients
T. Strateva - I. Sirakov, T. Stoeva, A. Stratev, et al. - Microorganisms, 2023 usegalaxy.eu

External <scp>DNA</scp> contamination and efficiency of bleach decontamination for arthropod diet analysis
M. Huszarik - N. Röder, L. Eberhardt, S. Kennedy, et al. - Environmental DNA, 2023 usegalaxy.eu

An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype
A. Velt - B. Frommer, S. Blanc, D. Holtgräwe, et al. - G3: Genes, Genomes, Genetics, 2023

Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra
J. Barrera-Redondo - J. Lotharukpong, H. Drost, S. Coelho, et al. - Genome Biology, 2023

New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
N. Leonidou - A. Renz, R. Mostolizadeh, A. Dräger, et al. - PLOS Computational Biology, 2023

Recovery of 197 eukaryotic bins reveals major challenges for eukaryote genome reconstruction from terrestrial metagenomes
J. Saraiva - A. Bartholomäus, R. Toscan, P. Baldrian, et al. - Molecular Ecology Resources, 2023

Candidate miRNAs from Oryza sativa for Silencing the Rice Tungro Viruses
N. Mohamed - N. Ngah, A. Abas, N. Talip, et al. - Agriculture, 2023 usegalaxy.eu

IDP Force Fields Applied to Model PPII-Rich 33-mer Gliadin Peptides
M. Amundarain - A. Vietri, V. Dodero, M. Costabel, et al. - The Journal of Physical Chemistry B, 2023

The giant diploid faba genome unlocks variation in a global protein crop
M. Jayakodi - A. Golicz, J. Kreplak, L. Fechete, et al. - Nature, 2023

Sex-biased gene expression in nutrient-sensing pathways
S. Bennett-Keki - E. Fowler, L. Folkes, S. Moxon, et al. - Proceedings of the Royal Society B: Biological Sciences, 2023 usegalaxy.eu

Return of the Tbx5; lineage-tracing reveals ventricular cardiomyocyte-like precursors in the injured adult mammalian heart
P. Siatra - G. Vatsellas, A. Chatzianastasiou, E. Balafas, et al. - npj Regenerative Medicine, 2023 usegalaxy.eu

Identification of Radiomic Biomarkers in a Set of Four Skeletal Muscle Groups on Dixon MRI of the NAKO MR study
M. Fischer - T. Küstner, S. Pappa, T. Niendorf, et al. - Research Square - Research Square Platform LLC, 2023

Comparative phylogenomic insights of KCS and ELO gene families in Brassica species indicate their role in seed development and stress responsiveness
U. Khan - I. Rana, N. Shaheen, Q. Raza, et al. - Scientific Reports, 2023 usegalaxy.eu

Genomic, Molecular, and Phenotypic Characterization of Arthrobacter sp. OVS8, an Endophytic Bacterium Isolated from and Contributing to the Bioactive Compound Content of the Essential Oil of the Medicinal Plant Origanum vulgare L.
G. Semenzato - S. Del Duca, A. Vassallo, A. Bechini, et al. - International Journal of Molecular Sciences, 2023 usegalaxy.eu

Analysis of biofilm formation in nosocomial Stenotrophomonas maltophilia isolates collected in Bulgaria: An 11-year study (2011–2022)
T. Strateva - A. Trifonova, I. Sirakov, D. Borisova, et al. - Acta Microbiologica et Immunologica Hungarica, 2023 usegalaxy.eu

Evaluating Tuning Strategies for Sequence Generation with Protein Language Models
A. Nathansen - K. Klein, B. Renard, M. Nowicka, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

Biophysical evaluation of the oligomerization and conformational properties of the N-terminal domain of TDP-43
M. Herrera - M. Amundarain, J. Santos, - Archives of Biochemistry and Biophysics, 2023

Embryogenesis of a calanoid copepod analyzed by transcriptomics
M. Acebal - L. Dalgaard, T. Jørgensen, B. Hansen, et al. - Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 2023 usegalaxy.eu

Proteomics analysis reveals three potential cacao target that interacts with Moniliophthora perniciosa NEP during witches broom disease
M. do Carmo Santos - N. dos Santos Lopes, M. Ferreira, G. Amaral, et al. - Physiological and Molecular Plant Pathology, 2023 usegalaxy.eu

Zinc controls operator affinity of human transcription factor YY1 by mediating dimerization via its N-terminal region
M. Figiel - F. Szubert, E. Luchinat, P. Bonarek, et al. - Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2023 usegalaxy.eu

A comprehensive review of bioinformatics tools for chromatin loop calling
L. Liu - K. Han, H. Sun, L. Han, et al. - Briefings in Bioinformatics, 2023 usegalaxy.eu

Improving deep learning-based segmentation of diatoms in gigapixel-sized virtual slides by object-based tile positioning and object integrity constraint
M. Kloster - A. Burfeid-Castellanos, D. Langenkämper, T. Nattkemper, et al. - PLOS ONE, 2023

MeganServer: facilitating interactive access to metagenomic data on a server
A. Gautam - W. Zeng, D. Huson, - Bioinformatics, 2023

Co‐action of <scp>COP1</scp>, <scp>SPA</scp> and cryptochrome in light signal transduction and photomorphogenesis of the moss <i>Physcomitrium patens</i>
M. Kreiss - F. Haas, M. Hansen, S. Rensing, et al. - The Plant Journal, 2023

Pilot Study on the Action of Thymus vulgaris Essential Oil in Treating the Most Common Bacterial Contaminants and Salmonella enterica subsp. enterica Serovar Derby in Poultry Litter
M. Galgano - F. Pellegrini, G. Fracchiolla, D. Mrenoshki, et al. - Antibiotics, 2023 usegalaxy.eu

Draft Genome Sequence of an Isolate of Genotype VII Newcastle Disease Virus Isolated from an Outbreak in Fighting Cock in Peru
M. Fernández-Díaz - A. Montalván-Avalos, G. Isasi-Rivas, D. Villanueva-Pérez, et al. - Microbiology Resource Announcements, 2023 usegalaxy.eu

S-Locus Genotyping in Japanese Plum by High Throughput Sequencing Using a Synthetic S-Loci Reference Sequence
A. Hedhly - M. Guerra, J. Grimplet, J. Rodrigo, et al. - International Journal of Molecular Sciences, 2023 usegalaxy.eu

Whole genome sequence analysis of the first reported isolate of Salmonella Agona carrying blaCTX-M-55 gene in Brazil
A. de Jesus Bertani - T. Vieira, A. Reis, C. dos Santos, et al. - Scientific Reports, 2023 usegalaxy.eu

Tailored Multiplex Real-Time RT-PCR with Species-Specific Internal Positive Controls for Detecting SARS-CoV-2 in Canine and Feline Clinical Samples
G. Jeon - H. Kim, J. Kim, J. Baek, et al. - Animals, 2023 usegalaxy.eu

Ceftazidime–avibactam resistance in Klebsiella pneumoniae sequence type 37: a decade of persistence and concealed evolution
G. Arcari - R. Polani, F. Bruno, V. Capitani, et al. - Microbial Genomics, 2023 usegalaxy.eu

Metagenomic Analysis of Anaerobic Microbial Communities Degrading Short-Chain Fatty Acids as Sole Carbon Sources
D. Becker - D. Popp, F. Bonk, S. Kleinsteuber, et al. - Microorganisms, 2023

DNA-Aeon provides flexible arithmetic coding for constraint adherence and error correction in DNA storage
M. Welzel - P. Schwarz, H. Löchel, T. Kabdullayeva, et al. - Nature Communications, 2023

MpoxRadar: a worldwide Mpox genomic surveillance dashboard
F. Nasri - K. Kongkitimanon, A. Wittig, J. Cortés, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

Intrasexual cuticular hydrocarbon dimorphism in a wasp sheds light on hydrocarbon biosynthesis genes in Hymenoptera
V. Moris - L. Podsiadlowski, S. Martin, J. Oeyen, et al. - Communications Biology, 2023 usegalaxy.eu

Simvastatin therapy in different subtypes of hypercholesterolemia – a physiologically based modelling approach
F. Bartsch - J. Grzegorzewski, H. Pujol, H. Tautenhahn, et al. - medRxiv - Cold Spring Harbor Laboratory, 2023

Genome-wide deposition of 6-methyladenine in human DNA reduces the viability of HEK293 cells and directly influences gene expression
J. Broche - A. Köhler, F. Kühnel, B. Osteresch, et al. - Communications Biology, 2023 usegalaxy.eu

Biodegradable microplastic increases CO2 emission and alters microbial biomass and bacterial community composition in different soil types
A. Rauscher - N. Meyer, A. Jakobs, R. Bartnick, et al. - Applied Soil Ecology, 2023

Modeling bile duct ischemia and reoxygenation injury in human cholangiocyte organoids for screening of novel cholangio-protective agents
S. Shi - H. Roest, T. van den Bosch, M. Bijvelds, et al. - eBioMedicine, 2023 usegalaxy.eu

Targeted and explorative profiling of kallikrein proteases and global proteome biology of pancreatic ductal adenocarcinoma, chronic pancreatitis, and normal pancreas highlights disease-specific proteome remodelling
J. Werner - P. Bernhard, M. Cosenza-Contreras, N. Pinter, et al. - Neoplasia, 2023 usegalaxy.eu

Sensitive clustering of protein sequences at tree-of-life scale using DIAMOND DeepClust
B. Buchfink - H. Ashkenazy, K. Reuter, J. Kennedy, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

A Physcomitrella <scp>PIN</scp> protein acts in spermatogenesis and sporophyte retention
V. Lüth - C. Rempfer, N. van Gessel, O. Herzog, et al. - New Phytologist, 2023

The Full Genome Sequences of Pseudomonas sp. Strain MM221 and <i>Pseudoarthrobacter</i> sp. Strain MM222, Isolated from a Meadow in Bielefeld, Germany
M. Eisenhut - M. Hawrylo, K. Trevlopoulou, H. Fingerhut, et al. - Microbiology Resource Announcements, 2023

Implementing deep learning models for the classification of Echinococcus multilocularis infection in human liver tissue
M. Sulyok - J. Luibrand, J. Strohäker, P. Karacsonyi, et al. - Parasites &amp; Vectors, 2023

Complete Genome Sequences of Pseudomonas sp. Strains MM223 and MM227 and <i>Rheinheimera</i> sp. Strain MM224, Isolated from a Pond Edge in Bielefeld, Germany
B. Frommer - T. Folchert, A. Witschel, M. Reddeker, et al. - Microbiology Resource Announcements, 2023

Delayed boosting improves human antigen-specific Ig and B cell responses to the RH5.1/AS01B malaria vaccine
C. Nielsen - J. Barrett, C. Davis, J. Fallon, et al. - JCI Insight, 2023 usegalaxy.eu

Molecular Characterizations of the Coagulase-Negative Staphylococci Species Causing Urinary Tract Infection in Tanzania: A Laboratory-Based Cross-Sectional Study
S. Phillip - M. Mushi, A. Decano, J. Seni, et al. - Pathogens, 2023 usegalaxy.eu

Melibiose–X-Gal–MacConkey Agar for Presumptive Differentiation of Escherichia albertii from E. coli and Salmonella from Poultry Meat
S. Annor - K. Salazar, S. Pillai, C. Kerth, et al. - Applied Microbiology, 2023 usegalaxy.eu

nf-root: a best-practice pipeline for deep learning-based analysis of apoplastic pH in microscopy images of developmental zones in plant root tissue
J. Wanner - L. Cuellar, L. Rausch, K. Berendzen, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

Apiaceae FNS I originated from F3H through tandem gene duplication
B. Pucker - M. Iorizzo, - PLOS ONE, 2023

New insights from short and long reads sequencing to explore cytochrome b variants in Plasmopara viticola populations collected from vineyards and related to resistance to complex III inhibitors
S. Cherrad - B. Gillet, J. Dellinger, L. Bellaton, et al. - PLOS ONE, 2023 usegalaxy.eu

A deeply conserved protease, acylamino acid-releasing enzyme (AARE), acts in ageing in Physcomitrella and Arabidopsis
S. Hoernstein - B. Özdemir, N. van Gessel, A. Miniera, et al. - Communications Biology, 2023

Genome-wide characterization of Ficus carica MADS-box transcription factors with a focus on their roles during fruit development
N. Kmeli - J. Hamdi, D. Bouktila, - Horticulture, Environment, and Biotechnology, 2023 usegalaxy.eu

Endosomal vesicle fusion machinery is involved with the contractile vacuole in <i>Dictyostelium discoideum</i>
P. Manna - L. Barlow, I. Ramirez-Macias, E. Herman, et al. - Journal of Cell Science, 2023 usegalaxy.eu

Distinct SARS-CoV-2 RNA fragments activate Toll-like receptors 7 and 8 and induce cytokine release from human macrophages and microglia
T. Wallach - M. Raden, L. Hinkelmann, M. Brehm, et al. - Frontiers in Immunology, 2023

Azithromycin Susceptibility Testing and Molecular Investigation of Neisseria gonorrhoeae Isolates Collected in Russia, 2020–2021
I. Kandinov - B. Shaskolskiy, D. Kravtsov, A. Vinokurova, et al. - Antibiotics, 2023 usegalaxy.eu

Combining Flow Cytometry and Metagenomics Improves Recovery of Metagenome-Assembled Genomes in a Cell Culture from Activated Sludge
N. Abdulkadir - J. Saraiva, F. Schattenberg, R. Toscan, et al. - Microorganisms, 2023

Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work
E. Deutsch - J. Vizcaíno, A. Jones, P. Binz, et al. - Journal of Proteome Research, 2023

A parametric approach for molecular encodings using multilevel atomic neighborhoods applied to peptide classification
G. Hattab - A. Anžel, S. Spänig, N. Neumann, et al. - NAR Genomics and Bioinformatics, 2023

MSstatsShiny: A GUI for Versatile, Scalable, and Reproducible Statistical Analyses of Quantitative Proteomic Experiments
D. Kohler - M. Kaza, C. Pasi, T. Huang, et al. - Journal of Proteome Research, 2023 usegalaxy.eu

Transcription factors mediating regulation of photosynthesis
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Transcriptional Profiling Identifies Prognostic Gene Signatures for Conjunctival Extranodal Marginal Zone Lymphoma
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MuLan-Methyl - Multiple Transformer-based Language Models for Accurate DNA Methylation Prediction
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Multimodal epigenetic changes and altered NEUROD1 chromatin binding in the mouse hippocampus underlie FOXG1 syndrome
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Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa
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Physics-Driven Deep Learning for Computational Magnetic Resonance Imaging: Combining physics and machine learning for improved medical imaging
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CRISPRi screening identifies CASP8AP2 as an essential viability factor in lung cancer controlling tumor cell death via the AP-1 pathway
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RPS6 transcriptional modulation in neural tissues of Nauphoeta cinerea during streptozotocin-associated sugar metabolism impairment.
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The regulation of glutathione s-transferases by gibberellic acid application in salt treated maize leaves
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Triose phosphate export from chloroplasts and cellular sugar content regulate anthocyanin biosynthesis during high light acclimation
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Mimicking Tumor Cell Heterogeneity of Colorectal Cancer in a Patient-derived Organoid-Fibroblast Model
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Unraveling the small proteome of the plant symbiont<i>Sinorhizobium meliloti</i>by ribosome profiling and proteogenomics
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Structural modelling of human complement FHR1 and two of its synthetic derivatives provides insight into their in-vivo functions
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Cell Segmentation of in situ Transcriptomics Data Using Signed Graph Partitioning
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Unraveling the small proteome of the plant symbiont<i>Sinorhizobium meliloti</i>by ribosome profiling and proteogenomics
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DIAMOND +  MEGAN Microbiome Analysis
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Revealing the small proteome of<i>Haloferax volcanii</i>by combining ribosome profiling and small-protein optimized mass spectrometry
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Avoiding Shortcut-Learning by Mutual Information Minimization in Deep Learning-Based Image Processing
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A bibliometric analysis and visualization of spatially resolved transcriptomics
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Characterization of mercury species and microbial communities in sediments and suspended particulate matter from historically contaminated river systems
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Assessing Antimicrobial and Metal Resistance Genes in Escherichia Coli from Domestic Groundwater Supplies in Rural Ireland
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The first cavefish in the Dinaric Karst? Cave colonization made possible by phenotypic plasticity in &lt;i&gt;Telestes karsticus&lt;/i&gt;
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SWARM: A Scientific Workflow Fragments Recommendation Approach via Contrastive Learning and Semantic Matching
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Hybrid Genome Assembly of Short and Long Reads in Galaxy
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Detection of domestic cat hepadnavirus by next-generation sequencing and epidemiological survey in Japan
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Genomic Epidemiological Analysis of Antimicrobial-Resistant Bacteria with Nanopore Sequencing
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Identification of Taxa and Functional Pathway Information of Mycobacterium tuberculosis Microbiome and High Throughput Simulation Studies with Mycobacteriophage
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Morpho-functional Characterisation of Cœlomocytes in the Aquacultivated Sea Cucumber Holothuria Scabra: From Cell Diversity to Transcriptomic Immune Response
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Analysis of RNA Sequences and Modifications Using NASE
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Exploring Scutellaria baicalensis bioactives as EGFR tyrosine kinase inhibitors: Cheminformatics and molecular docking studies
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NFATc1 Is a Central Mediator of EGFR-Induced ARID1A Chromatin Dissociation During Acinar Cell Reprogramming
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Genome sequence analysis and characterization of Bacillus altitudinis B12, a polylactic acid- and keratin-degrading bacterium
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An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy
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Genomic epidemiology of SARS- CoV-2 Omicron variants in the Republic of Korea
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Guiding the choice of informatics software and tools for lipidomics research applications
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The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain
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Better Together
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Better Together
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Genomic analysis and biological characterization of a novel Schitoviridae phage infecting Vibrio alginolyticus
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Silent gene clusters encode magnetic organelle biosynthesis in a non-magnetotactic phototrophic bacterium
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Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data
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MGnify: the microbiome sequence data analysis resource in 2023
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STAT3 signaling induced by IL-6 family cytokines modulates angiogenesis
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A Practical Bioinformatics Workflow for Routine Analysis of Bacterial WGS Data
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Rapid detection and online analysis of microbial changes through flow cytometry
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Polyphasic study of phytopathogenic bacterial strains associated with deep bark canker of walnut in Serbia revealed a new species, Brenneria izbisi sp. nov
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Renewal of planktonic foraminifera diversity after the Cretaceous Paleogene mass extinction by benthic colonizers
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MarineMetagenomeDB: a public repository for curated and standardized metadata for marine metagenomes
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Frequent spontaneous structural rearrangements promote rapid genome diversification in a Brassica napus F1 generation
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Complete Genome Sequence of Metabacillus litoralis Strain NCTR108, Isolated from Commercial Tattoo Ink
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Complete Genome Sequence of Terrisporobacter glycolicus Strain WW3900, Isolated from Influent Wastewater at a Research Center with Multiple-Species Research Animal Facilities
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Revisiting pangenome openness with k-mers
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Replication collisions induced by de-repressed S-phase transcription are connected with malignant transformation of adult stem cells
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Small proteome of the nitrogen-fixing plant symbiont<i>Sinorhizobium meliloti</i>
L. Hadjeras - B. Heiniger, S. Maaß, R. Scheuer, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

Deep Transfer Learning Enables Robust Prediction of Antimicrobial Resistance for Novel Antibiotics
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Functional and Safety Characterization of Weissella paramesenteroides Strains Isolated from Dairy Products through Whole-Genome Sequencing and Comparative Genomics
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Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen<i>Campylobacter jejuni</i>
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Further Extension of Lifespan by Unc-43/CaMKII and Egl-8/PLCβ Mutations in Germline-Deficient Caenorhabditis elegans
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Automated imaging-based abdominal organ segmentation and quality control in 20,000 participants of the UK Biobank and German National Cohort Studies
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Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities
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Microcystin-LR aerosol induces inflammatory responses in healthy human primary airway epithelium
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Two New <i>Rhizobiales</i> Species Isolated from Root Nodules of Common Sainfoin (Onobrychis viciifolia) Show Different Plant Colonization Strategies
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Identification of Clinical Variants beyond the Exome in Inborn Errors of Metabolism
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Physiologically based pharmacokinetic (PBPK) modeling of the role of CYP2D6 polymorphism for metabolic phenotyping with dextromethorphan
J. Grzegorzewski - J. Brandhorst, M. König, - Frontiers in Pharmacology, 2022

Trait-trait relationships and tradeoffs vary with genome size in prokaryotes
S. Beier - J. Werner, T. Bouvier, N. Mouquet, et al. - Frontiers in Microbiology, 2022

Fructobacillus cardui sp. nov., isolated from a thistle (Carduus nutans) flower
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Cross-linking of the endolysosomal system reveals potential flotillin structures and cargo
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Semi-automated assembly of high-quality diploid human reference genomes
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LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis
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Thin‐Plate Superstructures of the Immunogenic 33‐mer Gliadin Peptide
M. Herrera - M. Amundarain, F. Nicoletti, M. Drechsler, et al. - ChemBioChem, 2022

A comprehensive transcriptomic comparison of hepatocyte model systems improves selection of models for experimental use
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Disturbed trophoblast transition links preeclampsia progression from placenta to the maternal syndrome
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The first transcriptomic analyses of fruits and cladodes for comparison between three species of Opuntia
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Epigenetic nature of <i>Arabidopsis thaliana</i> telomeres
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Multivalent binding kinetics resolved by fluorescence proximity sensing
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Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations
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Transcriptome-wide modulation by<i>Sargassum vulgare</i>and<i>Acanthophora spicifera</i>extracts results in a prime-triggered plant signalling cascade in tomato and sweet pepper
O. Ali - A. Ramsubhag, J. Jayaraman, - AoB PLANTS, 2022 usegalaxy.eu

A whole-body FDG-PET/CT Dataset with manually annotated Tumor Lesions
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Self-supervised learning for automated anatomical tracking in medical image data with minimal human labeling effort
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Simultaneous Inference of Past Demography and Selection from the Ancestral Recombination Graph under the Beta Coalescent
K. Korfmann - T. Sellinger, F. Freund, M. Fumagalli, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

Chasing Consistency: An Update of the TCP Gene Family of Malus × Domestica
M. Tabarelli - M. Malnoy, K. Janik, - Genes, 2022 usegalaxy.eu

Short-term paleogeographic reorganizations and climate events shaped diversification of North American freshwater gastropods over deep time
T. Neubauer - M. Harzhauser, J. Hartman, D. Silvestro, et al. - Scientific Reports, 2022

Transgressive and parental dominant gene expression and cytosine methylation during seed development in<i>Brassica napus</i>hybrids
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On the way to plant data commons – a genotyping use case
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Detecting DNA of novel fungal pathogens using ResNets and a curated fungi-hosts data collection
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CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection
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In silico drug repurposing against SARS-CoV-2 using an integrative transcriptomic profiling approach: Hydrocortisone and Benzhydrocodone as potential drug candidates against COVID-19
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Identification of SARS-CoV-2 Variants of Concern Using Amplicon Next-Generation Sequencing
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Development of a Hybrid-Imaging-Based Prognostic Index for Metastasized-Melanoma Patients in Whole-Body 18F-FDG PET/CT and PET/MRI Data
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DeepToA: an ensemble deep-learning approach to predicting the theater of activity of a microbiome
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Redistribution of the SWI/SNF Complex Dictates Coordinated Transcriptional Control over Epithelial–Mesenchymal Transition of Normal Breast Cells through TGF-β Signaling
S. Jdeed - M. Lengyel, I. Uray, - Cells, 2022 usegalaxy.eu

The antileukemic activity of decitabine upon PML/RARA-negative AML blasts is supported by all-trans retinoic acid: in vitro and in vivo evidence for cooperation
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Biogenesis of <i>C. elegans</i> spermatogenesis small RNAs is initiated by a zc3h12a-like ribonuclease
H. Tsai - H. Cheng, Y. Tsai, - Science Advances, 2022 usegalaxy.eu

Phased grapevine genome sequence of an<i>Rpv12</i>carrier for biotechnological exploration of resistance to<i>Plasmopara viticola</i>
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Delineating genome-wide alternative splicing landscapes and their functional significance in orchids
A. Hazra - P. Mahadani, - South African Journal of Botany, 2022

Recurrent founder-event speciation across the Mediterranean likely shaped the species diversity and geographic distribution of the freshwater snail genus Mercuria Boeters, 1971 (Caenogastropoda: Hydrobiidae)
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An outbreak sustained by ST15 Klebsiella pneumoniae carrying 16S rRNA methyltransferases and blaNDM: evaluation of the global dissemination of these resistance determinants
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Microbiome of the freshwater sponge <i>Ephydatia muelleri</i> shares compositional and functional similarities with those of marine sponges
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Genetic and genomic diversity in the sorghum gene bank collection of Uganda
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Potential of enriched and stabilized anaerobic lignocellulolytic fungi coexisting with bacteria and methanogens for enhanced methane production from rice straw
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Concurrent molecular characterization of sand flies and Leishmania parasites by amplicon-based next-generation sequencing
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Analysis of Alternative mRNA Splicing in Vemurafenib-Resistant Melanoma Cells
H. Bokharaie - W. Kolch, A. Krstic, - Biomolecules, 2022 usegalaxy.eu

Improving deep learning-based segmentation of diatoms in gigapixel-sized virtual slides by object-based tile positioning and object integrity constraint
M. Kloster - A. Burfeid-Castellanos, D. Langenkämper, T. Nattkemper, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

Long-Amplicon Single-Molecule Sequencing Reveals Novel, Trait-Associated Variants of VERNALIZATION1 Homoeologs in Hexaploid Wheat
M. Makhoul - H. Chawla, B. Wittkop, A. Stahl, et al. - Frontiers in Plant Science, 2022

A Draft Human Pangenome Reference
W. Liao - M. Asri, J. Ebler, D. Doerr, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

MetHoS: a platform for large-scale processing, storage and analysis of metabolomics data
K. Tzanakis - T. Nattkemper, K. Niehaus, S. Albaum, et al. - BMC Bioinformatics, 2022

A fully phased interspecific grapevine rootstock genome sequence representing<i>V. riparia</i>and<i>V. cinerea</i>and allele-aware annotation of the phylloxera resistance locus<i>Rdv1</i>
B. Frommer - L. Hausmann, D. Holtgräwe, P. Viehöver, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

Custos Secrets: a Service for Managing User-Provided Resource Credential Secrets for Science Gateways
I. Ranawaka - N. Goonasekara, E. Afgan, J. Basney, et al. - ACM, 2022 usegalaxy.eu

CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance
A. Wittig - F. Miranda, M. Hölzer, T. Altenburg, et al. - Bioinformatics, 2022

Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs
G. Formenti - L. Abueg, A. Brajuka, N. Brajuka, et al. - Bioinformatics, 2022 usegalaxy.eu

Characterization of regulatory transcriptional mechanisms in hepatocyte lipotoxicity
J. Pérez-Schindler - E. Vargas-Fernández, B. Karrer-Cardel, D. Ritz, et al. - Scientific Reports, 2022 usegalaxy.eu

KIPEs3: Automatic annotation of biosynthesis pathways
A. Rempel - N. Choudhary, B. Pucker, - bioRxiv - Cold Spring Harbor Laboratory, 2022

Genome-wide analysis of DUF221 domain-containing gene family in common bean and identification of its role on abiotic and phytohormone stress response
M. Kavas - K. Mostafa, Z. Seçgin, B. Yerlikaya, et al. - Genetic Resources and Crop Evolution, 2022 usegalaxy.eu

Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors
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Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy
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A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics
N. Hoffmann - G. Mayer, C. Has, D. Kopczynski, et al. - Metabolites, 2022

Genomic analysis provides novel insights into diversification and taxonomy of Allorhizobium vitis (i.e. Agrobacterium vitis)
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MuDoGeR: Multi-Domain Genome Recovery from metagenomes made easy
U. Nunes da Rocha - J. Kasmanas, R. Kallies, J. Saraiva, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

Histone Deacetylase 6 Inhibitor JS28 Prevents Pathological Gene Expression in Cardiac Myocytes
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BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis
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GRACE: a comprehensive web-based platform for integrative single-cell transcriptome analysis
H. Yu - Y. Wang, X. Zhang, Z. Wang, et al. - NAR Genomics and Bioinformatics, 2022 usegalaxy.eu

AB12PHYLO: An Integrated Pipeline for Maximum Likelihood Phylogenetic Inference from ABI Trace Data
L. Kaindl - C. Small, R. Stam, - PhytoFrontiers™, 2022

Sequence-based pangenomic core detection
T. Schulz - R. Wittler, J. Stoye, - iScience, 2022

Genomic Analyses of Rose Crown Gall-Associated Bacteria Revealed Two New <i>Agrobacterium</i> Species: <i>Agrobacterium burrii</i> sp. nov. and <i>Agrobacterium shirazense</i> sp. nov.
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Structural analysis of microbiomes from salt caverns used for underground gas storage
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P989: DYNAMIC CHANGES IN THE HISTONE H3 LYSINE 27 TRIMETHYLATION EPIGENETIC LANDSCAPE FOLLOWING RUXOLITINIB ADMINISTRATION
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Evaluation of the potential prebiotic effect of Himanthalia elongata, an Atlantic brown seaweed, in an in vitro model of the human distal colon
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Association of DNA methylation and genetic variations of the <i>APOE</i> gene with the risk of diabetic dyslipidemia
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A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data
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Construction and characterization of a de novo draft genome of garden cress (Lepidium sativum L.)
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Absence of increased genomic variants in the cyanobacterium Chroococcidiopsis exposed to Mars-like conditions outside the space station
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Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria
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Ezh2 competes with p53 to license lncRNA Neat1 transcription for inflammasome activation
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ODGI: understanding pangenome graphs
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Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity
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Genetic Divergence of Lineage-Specific Tandemly Duplicated Gene Clusters in Four Diploid Potato Genotypes
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Interactive analysis of biosurfactants in fruit-waste fermentation samples using BioSurfDB and MEGAN
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Identification of SARS‐CoV‐2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021
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MaxQuant and MSstats in Galaxy Enable Reproducible Cloud-Based Analysis of Quantitative Proteomics Experiments for Everyone
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The potential of bacterial key species as a tool for monitoring peatland quality
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Bacterial key species candidates for biomonitoring peatland burnt in the Giam Siak Kecil-Bukit Batu biosphere reserve, Riau
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Agrobacterium vaccinii sp. nov. isolated from galls on blueberry plants (Vaccinium corymbosum)
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Genomic Analysis of Endophytic Bacillus-Related Strains Isolated from the Medicinal Plant Origanum vulgare L. Revealed the Presence of Metabolic Pathways Involved in the Biosynthesis of Bioactive Compounds
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Computational identification and characterization of vascular wilt pathogen (<i>Fusarium oxysporum f. sp. lycopersici</i>) CAZymes in tomato xylem sap
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Age-related brain deviations and aggression
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Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water
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A quantitative framework to infer the effect of traits, diversity and environment on dispersal and extinction rates from fossils
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Genotyping of Circulating Free DNA Enables Monitoring of Tumor Dynamics in Synovial Sarcomas
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Variant Analysis and Strategic Clustering to Sub-Lineage of Double Mutant Strain B.1.617 of SARS-CoV-2
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Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease
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Goslin 2.0 Implements the Recent Lipid Shorthand Nomenclature for MS-Derived Lipid Structures
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Identification and annotation of peptide allergens in Prunus dulcis
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Ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of phosphorylated and cross-linked peptides
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NFATc1 signaling drives chronic ER stress responses to promote NAFLD progression
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Enabling technologies towards personalization of scaffolds for large bone defect regeneration
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Evaluation of machine learning strategies for imaging confirmed prostate cancer recurrence prediction on electronic health records
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Critical Assessment of Metagenome Interpretation: the second round of challenges
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Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes
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Comparative transcriptome analysis of human and murine choroidal neovascularization identifies fibroblast growth factor inducible-14 as phylogenetically conserved mediator of neovascular age-related macular degeneration
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Unifying the known and unknown microbial coding sequence space
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Sex differences in the early life stages of the salmon louse Lepeophtheirus salmonis (Copepoda: Caligidae)
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Machine learning-assisted identification of bioindicators predicts medium-chain carboxylate production performance of an anaerobic mixed culture
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Taxonomy of Rhizobiaceae revisited: proposal of a new framework for genus delimitation
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Multi-Modality Microscopy Image Style Augmentation for Nuclei Segmentation
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Deciphering the Molecular Signature of Human Hyalocytes in Relation to Other Innate Immune Cell Populations
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Mimicking tumor cell heterogeneity of colorectal cancer in a patient-derived organoid-fibroblast model
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Genome and proteome analyses show the gaseous alkane degrader <i>Desulfosarcina</i> sp. strain <scp>BuS5</scp> as an extreme metabolic specialist
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Transcriptomic Stress Response in Streptococcus mutans following Treatment with a Sublethal Concentration of Chlorhexidine Digluconate
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Micro-RNA-Regulated SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) Gene Expression and Cytokinin Accumulation Distinguish Early-Developing Male and Female Inflorescences in Oil Palm (Elaeis guineensis)
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Pathogenicity of Shiga toxin-producing Escherichia coli (STEC) from wildlife: Should we care?
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In vitro and in silico analysis of Brilliant Black degradation by Actinobacteria and a Paraburkholderia sp.
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Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N6-carboxymethyllysine
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The Human Eye Transcriptome Atlas: A searchable comparative transcriptome database for healthy and diseased human eye tissue
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SSAM-lite: A Light-Weight Web App for Rapid Analysis of Spatially Resolved Transcriptomics Data
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Olfactomedin-4 improves cutaneous wound healing by promoting skin cell proliferation and migration through POU5F1/OCT4 and ESR1 signalling cascades
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Environmental filtering drives assembly of diatom communities over evolutionary time‐scales
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Shell features and anatomy of the springsnail genus <i>Radomaniola</i> (Caenogastropoda: Hydrobiidae) show a different pace and mode of evolution over five million years
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Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis
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Whole-Genome Sequence of Pseudomonas sp. Strain MM211, Isolated from Soil in Langenfeld, Germany
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Onset of Late Cretaceous diversification in Europe’s freshwater gastropod fauna links to global climatic and biotic events
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Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives
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Pluripotency factors determine gene expression repertoire at zygotic genome activation
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Unsupervised encoding selection through ensemble pruning for biomedical classification
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STENCIL: A web templating engine for visualizing and sharing life science datasets
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Identification Of Taxa and Functional Pathway Information Of Mycobacterium tuberculosis Microbiome And High Throughput Simulation Studies With Mycobacteriophage
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Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines
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Phage Genome Diversity in a Biogas-Producing Microbiome Analyzed by Illumina and Nanopore GridION Sequencing
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Targeted DamID in <i>C. elegans</i> reveals a direct role for LIN-22 and NHR-25 in antagonizing the epidermal stem cell fate
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Drivers of diversification in freshwater gastropods vary over deep time
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The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities
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Impact of high platelet turnover on the platelet transcriptome: Results from platelet RNA-sequencing in patients with sepsis
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sPLINK: a hybrid federated tool as a robust alternative to meta-analysis in genome-wide association studies
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Ultraviolet vision in larval <i>Neogonodactylus oerstedii</i>
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TcTI, a Kunitz-type trypsin inhibitor from cocoa associated with defense against pathogens
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What’s left in the tank? Identification of non-ascribed aquarium’s coral collections with DNA barcodes as part of an integrated diagnostic approach
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SARS-CoV-2 Reverse Zoonoses to Pumas and Lions, South Africa
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<i>Saccharomyces boulardii</i> CNCM I‐745 supplementation modifies the fecal resistome during <i>Helicobacter pylori</i> eradication therapy
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Interplay between Klebsiella pneumoniae producing KPC-31 and KPC-3 under treatment with high dosage meropenem: a case report
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Regulation of fatty acid desaturase- and immunity gene-expression by mbk-1/DYRK1A in Caenorhabditis elegans
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LAMP Assay for Distinguishing <i>Fusarium oxysporum</i> and <i>Fusarium commune</i> in Lotus (<i>Nelumbo nucifera</i>) Rhizomes
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Expanding the Galaxy’s reference data
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Multi-label classification for multi-drug resistance prediction of Escherichia coli
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Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework
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A Tetragenococcus halophilus human gut isolate
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Oxa-376 and Oxa-530 variants of β-lactamase: computational study uncovers potential therapeutic targets of<i>Acinetobacter baumannii</i>
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Recapitulating Cholangiopathy-Associated Necroptotic Cell Death In Vitro Using Human Cholangiocyte Organoids
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Canonical Workflows to Make Data FAIR
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Plankton-infecting relatives of herpesviruses clarify the evolutionary trajectory of giant viruses
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CoxBase: an Online Platform for Epidemiological Surveillance, Visualization, Analysis, and Typing of Coxiella burnetii Genomic Sequences
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Taxonomic transfer of two species of hydrobiid snails from western Anatolia (Caenogastropoda, Truncatelloidea) to two new genera, based on molecular and morphological evidence
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Diel Protein Regulation of Marine Picoplanktonic Communities Assessed by Metaproteomics
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PLaBAse: A comprehensive web resource for analyzing the plant growth-promoting potential of plant-associated bacteria
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COVID-19++: A Citation-Aware Covid-19 Dataset for the Analysis of Research Dynamics
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An ecological perspective on microbial genes of unknown function in soil
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Transcriptomic Profiling and Microsatellite Identification in Cobia (Rachycentron canadum), Using High-Throughput RNA Sequencing
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Plant circadian clock control of <i>Medicago truncatula</i> nodulation via regulation of nodule cysteine-rich peptides
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LAPNet: Non-Rigid Registration Derived in k-Space for Magnetic Resonance Imaging
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Conservation and divergence in gene regulation between mouse and human immune cells deserves equal emphasis
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Current Trends and Future Directions of Large Scale Image and Video Annotation: Observations From Four Years of BIIGLE 2.0
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Using AnnoTree to get more assignments, faster, in DIAMOND+MEGAN microbiome analysis
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Expression Atlas update: gene and protein expression in multiple species
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Dissection of Quantitative Blackleg Resistance Reveals Novel Variants of Resistance Gene Rlm9 in Elite Brassica napus
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New Putative Long Non-Coding RNAs (lncRNA) Revealed by Pan-Transcriptome of the Emerging Human Pathogenic Fungus Talaromyces Marneffei
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Interactive Analysis of Biosurfactants in Fruit-Waste Fermentation Samples using BioSurfDB and MEGAN
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Peakhood: individual site context extraction for CLIP-seq peak regions
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The transcriptome of Balamuthia mandrillaris trophozoites for structure-guided drug design
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Variimorphobacter saccharofermentans gen. nov., sp. nov., a new member of the family Lachnospiraceae, isolated from a maize-fed biogas fermenter
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The chitinolytic activity of the Curtobacterium sp. isolated from field-grown soybean and analysis of its genome sequence
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Viral suppressor of <scp>RNA</scp> silencing in vascular plants also interferes with the development of the bryophyte <scp><i>Physcomitrella patens</i></scp>
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Constitutively enhanced genome integrity maintenance and direct stress mitigation characterize transcriptome of extreme stress‐adapted <i>Arabidopsis halleri</i>
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Somatostatin 3 loss of function impairs the innate immune response to intestinal inflammation
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ARTS-DB: a database for antibiotic resistant targets
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Fibropapillomatosis and Chelonid Alphaherpesvirus 5 Infection in Kemp’s Ridley Sea Turtles (Lepidochelys kempii)
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From celiac disease to coccidia infection and vice‐versa: The polyQ peptide CXCR3‐interaction axis
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Histone H4 lysine 16 acetylation controls central carbon metabolism and diet-induced obesity in mice
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Automatic identification and annotation of MYB gene family members in plants
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Weakly supervised segmentation of tumor lesions in PET-CT hybrid imaging
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Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer
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TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes
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Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning
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eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
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Beta-lactam resistance development during the treatment processes of municipal wastewater treatment plants
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Ready-to-use public infrastructure for global SARS-CoV-2 monitoring
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OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes
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Screening of<i>Azadirachta indica</i>phytoconstituents as GSK-3β inhibitor and its implication in neuroblastoma: molecular docking, molecular dynamics, MM-PBSA binding energy, and in-vitro study
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Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid
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Genomic impact of stress-induced transposable element mobility in Arabidopsis
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Nascent Transcript Sequencing for the Mapping of Promoters in Arabidopsis thaliana Mitochondria
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Multiple Occurrences of a 168-Nucleotide Deletion in SARS-CoV-2 ORF8, Unnoticed by Standard Amplicon Sequencing and Variant Calling Pipelines
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Evolutionary Trajectories toward Ceftazidime-Avibactam Resistance in Klebsiella pneumoniae Clinical Isolates
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FIBCD1 is a Conserved Receptor for Chondroitin Sulphate Proteoglycans of the Brain Extracellular Matrix and a Candidate Gene for a Complex Neurodevelopmental Disorder
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Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species
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The temperature-regulated DEAD-box RNA helicase CrhR interactome: autoregulation and photosynthesis-related transcripts
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Occurrence of Colibacillosis in Broilers and Its Relationship With Avian Pathogenic Escherichia coli (APEC) Population Structure and Molecular Characteristics
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First complete mitochondrial genome of <i>Rhodinia</i> species (Lepidoptera: Saturniidae): genome description and phylogenetic implication
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Bakta: Rapid &amp; standardized annotation of bacterial genomes via alignment-free sequence identification
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Gene expression profiling of epidermal cell types in <i>C. elegans</i> using Targeted DamID
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Uncertainty estimation and explainability in deep learning-based age estimation of the human brain: Results from the German National Cohort MRI study
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Limited access to antigen drives generation of early B cell memory while restraining the plasmablast response
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Genome-wide identification of the BURP domain-containing genes in Phaseolus vulgaris
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RNA-bound PGC-1α controls gene expression in liquid-like nuclear condensates
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Helios represses megakaryocyte priming in hematopoietic stem and progenitor cells
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Single‐cell omics: Overview, analysis, and application in biomedical science
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Molecular and Structural Parallels between Gluten Pathogenic Peptides and Bacterial-Derived Proteins by Bioinformatics Analysis
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Pre-activated antiviral innate immunity in the upper airways controls early SARS-CoV-2 infection in children
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Multidrug-Resistant Klebsiella pneumoniae Clones from Wild Chimpanzees and Termites in Senegal
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Genome accessibility dynamics in response to phosphate limitation is controlled by the PHR1 family of transcription factors in<i>Arabidopsis</i>
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Draft Genome Sequence of the Mucin Degrader Clostridium tertium WC0709
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Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: A case study of an urothelial cancer cohort analyzed in the Galaxy framework
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Polypharmacology of some medicinal plant metabolites against SARS-CoV-2 and host targets: Molecular dynamics evaluation of NSP9 RNA binding protein
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A Genome-Wide CRISPR/Cas9 Screen Reveals the Requirement of Host Sphingomyelin Synthase 1 for Infection with Pseudorabies Virus Mutant gD–Pass
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Genomics and transcriptomics of epizoic Seisonidea (Rotifera, syn. Syndermata) reveal strain formation and gradual gene loss with growing ties to the host
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A high-quality draft genome for Melaleuca alternifolia (tea tree): a new platform for evolutionary genomics of myrtaceous terpene-rich species
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The Changes in the p53 Protein across the Animal Kingdom Point to Its Involvement in Longevity
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Classification of three corynebacterial strains isolated from a small paddock in North Rhine-Westphalia: proposal of Corynebacterium kalinowskii sp. nov., Corynebacterium comes sp. nov. and Corynebacterium occultum sp. nov.
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Drivers of phytoplankton community structure change with ecosystem ontogeny during the Quaternary
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A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation
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Eplerenone Improves Pulmonary Vascular Remodeling and Hypertension by Inhibition of the Mineralocorticoid Receptor in Endothelial Cells
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De novo transcriptome assembly, functional annotation and characterization of the Atlantic bluefin tuna (Thunnus thynnus) larval stage
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A Standardized Workflow Based on the STAVIRO Unbaited Underwater Video System for Monitoring Fish and Habitat Essential Biodiversity Variables in Coastal Areas
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Functional Analysis of Non-Genetic Resistance to Platinum in Epithelial Ovarian Cancer Reveals a Role for the MBD3-NuRD Complex in Resistance Development
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Mitochondrial genome of Geomydoecus aurei, a pocket-gopher louse
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Deep learning-based real-time detection of novel pathogens during sequencing
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Identification of pathological transcription in autosomal dominant polycystic kidney disease epithelia
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Performance and scaling behavior of bioinformatic applications in virtualization environments to create awareness for the efficient use of compute resources
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Temperature and Nutrient Limitations Decrease Transfer of Conjugative IncP-1 Plasmid pKJK5 to Wild Escherichia coli Strains
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Collaboration Between Host and Viral Factors Shape SARS-CoV-2 Evolution
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The complete mitochondrial genome of the wild silkmoth <i>Antheraea yamamai</i> from Heilongjiang, China (Lepidoptera: Saturniidae)
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Pharmacokinetics of caffeine: A systematic analysis of reported data for application in metabolic phenotyping and liver function testing
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Transcriptomic analysis of temporal shifts in berry development between two grapevine cultivars of the Pinot family reveals potential genes controlling ripening time
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Gene Homologies Identified between Trypanosoma cruzi Antigen 36 and Mammalian TRIM21 Genes Using Bioinformatics Analysis
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ONT-Based Draft Genome Assembly and Annotation of <i>Alternaria atra</i>
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Age-Net: An MRI-Based Iterative Framework for Brain Biological Age Estimation
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Radiosensitivity of herbaceous plants to chronic radiation exposure: Field study in the Chernobyl exclusion zone
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Cheminformatic Characterization of Natural Antimicrobial Products for the Development of New Lead Compounds
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Time- and Stimulus-Dependent Characteristics of Innate Immune Cells in Organ-Cultured Human Corneal Tissue
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Genetic Analyses and Genome-Wide Association Studies on Pathogen Resistance of Bos taurus and Bos indicus Cattle Breeds in Cameroon
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Hierarchical reactivation of transcription during mitosis-to-G1 transition by Brn2 and Ascl1 in neural stem cells
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DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics
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SANS serif: alignment-free, whole-genome-based phylogenetic reconstruction
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Topological data analysis identifies emerging adaptive mutations in SARS-CoV-2
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Overexpression of human BAG3P209L in mice causes restrictive cardiomyopathy
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Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome
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Breast and prostate cancer risk: the interplay of polygenic risk, high-impact monogenic variants, and family history
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Assessing the role of polygenic background on the penetrance of monogenic forms in Parkinson’s disease
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RiboReport - Benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria
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AGNOSTOS-DB: a resource to unlock the uncharted regions of the coding sequence space
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A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive
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Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine
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A High-Density SNP Genetic Map Construction Using ddRAD-Seq and Mapping of Capsule Shattering Trait in Sesame
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Going to extremes – a metagenomic journey into the dark matter of life
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Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells
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CryptoGenotyper: A new bioinformatics tool for rapid Cryptosporidium identification
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Bromodomain-containing proteins BRD1, BRD2, and BRD13 are core subunits of SWI/SNF complexes and vital for their genomic targeting in Arabidopsis
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COVID-19 preVIEW: Semantic Search to Explore COVID-19 Research Preprints
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A Systematic Evaluation of Semispecific Peptide Search Parameter Enables Identification of Previously Undescribed N-Terminal Peptides and Conserved Proteolytic Processing in Cancer Cell Lines
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SimText: a text mining framework for interactive analysis and visualization of similarities among biomedical entities
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Tryptophan metabolism drives dynamic immunosuppressive myeloid states in IDH-mutant gliomas
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Current extinction rate in European freshwater gastropods greatly exceeds that of the late Cretaceous mass extinction
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Arganiella Giusti &amp; Pezzoli, 1980 (Caenogastropoda: Truncatelloidea: Hydrobiidae): a widespread genus or several narrow-range endemic genera?
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Direct Diagnosis of Echovirus 12 Meningitis Using Metagenomic Next Generation Sequencing
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EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure
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The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts
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A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19)
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Peptidotriazolamers Inhibit Aβ(1–42) Oligomerization and Cross a Blood‐Brain‐Barrier Model
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Genomic and proteomic profiles of biofilms on microplastics are decoupled from artificial surface properties
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Within-host evolution of SARS-CoV-2 in an immunosuppressed COVID-19 patient: a source of immune escape variants
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ZC3H4 restricts non-coding transcription in human cells
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Common virulence gene expression in adult first-time infected malaria patients and severe cases
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Draft genome of a biparental beetle species, Lethrus apterus
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Pruriception and neuronal coding in nociceptor subtypes in human and nonhuman primates
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Identification of X-chromosomal genes that drive sex differences in embryonic stem cells through a hierarchical CRISPR screening approach
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Photophore Distribution and Enzymatic Diversity Within the Photogenic Integument of the Cookie-Cutter Shark Isistius brasiliensis (Chondrichthyes: Dalatiidae)
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A large-scale comparative study on peptide encodings for biomedical classification
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Characterization of the Virome Associated With Haemagogus Mosquitoes in Trinidad, West Indies
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A functional LSD1 coregulator screen reveals a novel transcriptional regulatory cascade connecting R-loop homeostasis with epigenetic regulation
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Novel insights into the electrophysiology of murine cardiac macrophages: relevance of voltage-gated potassium channels
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Haplotype-resolved diverse human genomes and integrated analysis of structural variation
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Next-generation sequencing of DNA from resting eggs: signatures of eutrophication in a lake’s sediment
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Highly Efficient Genome Modification of Cultured Primordial Germ Cells with Lentiviral Vectors to Generate Transgenic Songbirds
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Data from crosslinking and analysis of cDNAs (CRAC) of Nab3 in yeast cells expressing a circular ncRNA decoy
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The endophytic microbiota of Citrus limon is transmitted from seed to shoot highlighting differences of bacterial and fungal community structures
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Distal and proximal cis-regulatory elements sense X-chromosomal dosage and developmental state at the<i>Xist</i>locus
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User-friendly, scalable tools and workflows for single-cell RNA-seq analysis
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Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring
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Replication of a Novel Parkinson's Locus in a European Ancestry Population
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Development of a Comprehensive Toxicity Pathway Model for 17α-Ethinylestradiol in Early Life Stage Fathead Minnows (<i>Pimephales promelas</i>)
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Molecular Physiological Characterization of a High Heat Resistant Spore Forming Bacillus subtilis Food Isolate
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Direct impact of commonly used dietary emulsifiers on human gut microbiota
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WASP: a versatile, web-accessible single cell RNA-Seq processing platform
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Single-Cell RNA Sequencing Procedures and Data Analysis
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Hidden species diversity of Corrosella Boeters, 1970 (Caenogastropoda: Truncatelloidea) in the Moroccan Atlas reveals the ancient biogeographic link between North Africa and Iberia
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Cell-intrinsic functions of the transcription factor Bhlhe40 in activated B cells and T follicular helper cells restrain the germinal center reaction and prevent lymphomagenesis
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The mitochondrial genome of Qinghuang_1, the first modern improved strain of Chinese oak silkworm,Antheraea pernyi (Lepidoptera: Saturniidae)
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Updates on metaQuantome Software for Quantitative Metaproteomics
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Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows
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MegaGO: A Fast Yet Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets
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Large scale genomic rearrangements in selected<i>Arabidopsis thaliana</i>T-DNA lines are caused by T-DNA insertion mutagenesis
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AB12PHYLO: an integrated pipeline for Maximum Likelihood phylogenetic inference from ABI trace data
L. Kaindl - C. Small, R. Stam, - bioRxiv - Cold Spring Harbor Laboratory, 2021

Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit
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Proximity to injury, but neither number of nuclei nor ploidy define pathological adaptation and plasticity in cardiomyocytes
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Resistome of a carbapenemase-producing novel ST232 Klebsiella michiganensis isolate from urban hospital effluent in South Africa
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VPRBP functions downstream of the androgen receptor and OGT to restrict p53 activation in prostate cancer
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Fast visual exploration of mass spectrometry images with interactive dynamic spectral similarity pseudocoloring
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Identification of Beneficial Microbial Consortia and Bioactive Compounds with Potential as Plant Biostimulants for a Sustainable Agriculture
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Decitabine Induces Gene Derepression on Monosomic Chromosomes: <i>In Vitro</i> and <i>In Vivo</i> Effects in Adverse-Risk Cytogenetics AML
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DenovoProfiling: a webserver for de novo generated molecule library profiling
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Microbial Communities in Flexible Biomethanation of Hydrogen Are Functionally Resilient Upon Starvation
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ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework
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Burkholderiaceae Are Key Acetate Assimilators During Complete Denitrification in Acidic Cryoturbated Peat Circles of the Arctic Tundra
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CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance
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Detecting high-scoring local alignments in pangenome graphs
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Interpretable detection of novel human viruses from genome sequencing data
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Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction
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Diabetes changes gene expression but not DNA methylation in cardiac cells
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3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis
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Using Galaxy to Perform Large‐Scale Interactive Data Analyses—An Update
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SRGAP1 Controls Small Rho GTPases To Regulate Podocyte Foot Process Maintenance
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ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data
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Taxonomic Evaluation of the Heyndrickxia (Basonym Bacillus) sporothermodurans Group (H. sporothermodurans, H. vini, H. oleronia) Based on Whole Genome Sequences
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Scarless engineering of the<i>Drosophila</i>genome near any site-specific integration site
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A novel deletion in FLOWERING LOCUS T modulates flowering time in winter oilseed rape
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Congenital heart disease risk loci identified by genome-wide association study in European patients
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Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortia
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Deep Learning‐Based Automated Abdominal Organ Segmentation in the UK Biobank and German National Cohort Magnetic Resonance Imaging Studies
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On the Application of Advanced Machine Learning Methods to Analyze Enhanced, Multimodal Data from Persons Infected with COVID-19
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The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses
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Three Novel Clostridia Isolates Produce n-Caproate and iso-Butyrate from Lactate: Comparative Genomics of Chain-Elongating Bacteria
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CDK8 Fine-Tunes IL-6 Transcriptional Activities by Limiting STAT3 Resident Time at the Gene Loci
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Fully Automated and Standardized Segmentation of Adipose Tissue Compartments via Deep Learning in 3D Whole-Body MRI of Epidemiologic Cohort Studies
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Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates
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Draft Genome Sequence of a New Delhi Metallo-β-Lactamase (NDM-1)-Producing Providencia stuartii Strain Isolated in Lima, Peru
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Chlorella vulgaris and Its Phycosphere in Wastewater: Microalgae-Bacteria Interactions During Nutrient Removal
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tRNA ADENOSINE DEAMINASE 3 is required for telomere maintenance in Arabidopsis thaliana
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Modification of the Histone Landscape with JAK Inhibition in Myeloproliferative Neoplasms
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An Evolutionary Cancer Epigenetic Approach Revealed DNA Hypermethylation of Ultra-Conserved Non-Coding Elements in Squamous Cell Carcinoma of Different Mammalian Species
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Transcriptional Profiling Uncovers Human Hyalocytes as a Unique Innate Immune Cell Population
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Proteomic Fingerprinting Discriminates Cryptic Gastropod Species
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Sediment Plasmidome of the Gulfs of Kathiawar Peninsula and Arabian Sea: Insights Gained from Metagenomics Data
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Characterizing Phage-Host Interactions in a Simplified Human Intestinal Barrier Model
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Long‐read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant
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Deep learning-based diatom taxonomy on virtual slides
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A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane
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ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation
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DNA Methylation of Steroidogenic Enzymes in Benign Adrenocortical Tumors: New Insights in Aldosterone-Producing Adenomas
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Training Infrastructure as a Service
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No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics
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Genomic Evidence for Sensorial Adaptations to a Nocturnal Predatory Lifestyle in Owls
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Modeling the Diversity of Epithelial Ovarian Cancer through Ten Novel Well Characterized Cell Lines Covering Multiple Subtypes of the Disease
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Draft Genome Sequences of Three <i>Clostridia</i> Isolates Involved in Lactate-Based Chain Elongation
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pyGenomeTracks: reproducible plots for multivariate genomic datasets 
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Lactate-based microbial chain elongation for n-caproate and iso-butyrate production: genomic and metabolic features of three novel Clostridia isolates
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Transcriptomic Characterization of Human Choroidal Neovascular Membranes Identifies Calprotectin as a Novel Biomarker for Patients with Age-Related Macular Degeneration
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A pan-cancer analysis reveals nonstop extension mutations causing SMAD4 tumour suppressor degradation
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Benchmarking challenging small variants with linked and long reads
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An Interactive Visualization for Feature Localization in Deep Neural Networks
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DNA Methyltransferase 1 (DNMT1) Function Is Implicated in the Age-Related Loss of Cortical Interneurons
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Genome‐wide cooperation of <scp>EMT</scp> transcription factor <scp>ZEB</scp> 1 with <scp>YAP</scp> and <scp>AP</scp> ‐1 in breast cancer
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Expression of the COVID‐19 receptor ACE2 in the human conjunctiva
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Lake expansion elevates equilibrium diversity via increasing colonization
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Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform
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Enhanced COVID-19 data for improved prediction of survival
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Noninvasive Discrimination of Low and High-risk Pancreatic Intraductal Papillary Mucinous Neoplasms
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Degradation of Non-coding RNAs Promotes Recycling of Termination Factors at Sites of Transcription
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Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus
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Genome-wide association study in European patients with congenital heart disease identifies risk loci for transposition of the great arteries and anomalies of the thoracic arteries and veins and expression of discovered candidate genes in the developing heart
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Genetic Architecture of Parkinson's Disease in the Indian Population: Harnessing Genetic Diversity to Address Critical Gaps in Parkinson's Disease Research
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Importance of Defluviitalea raffinosedens for Hydrolytic Biomass Degradation in Co-Culture with Hungateiclostridium thermocellum
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Methylation Profile of X-Chromosome–Related Genes in Male Breast Cancer
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Human exome and mouse embryonic expression data implicate ZFHX3, TRPS1, and CHD7 in human esophageal atresia
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Active and repressed biosynthetic gene clusters have spatially distinct chromosome states
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<scp>GLASSgo</scp> in <scp>Galaxy</scp>: high-throughput, reproducible and easy-to-integrate prediction of sRNA homologs
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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update
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The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform
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Galactic Circos: User-friendly Circos plots within the Galaxy platform
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iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites
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Dataset for de novo transcriptome assembly of the African bullfrog Pyxicephalus adspersus
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Independent attenuation correction of whole body [18F]FDG-PET using a deep learning approach with Generative Adversarial Networks
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Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera
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AHLF: ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of phosphorylated and cross-linked peptides
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Community Research Amid COVID-19 Pandemic: Genomics Analysis of SARS-CoV-2 over Public GALAXY server
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ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining
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Two new genera and three new subterranean species of Hydrobiidae (Caenogastropoda: Truncatelloidea) from Tunisia
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Phylogenetic relationships within <i>Pseudamnicola</i> Paulucci, 1878 (Caenogastropoda: Truncatelloidea) indicate two independent dispersal events from different continents to the Balearic Islands
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Contrast Optimization of Mass Spectrometry Imaging (MSI) Data Visualization by Threshold Intensity Quantization (TrIQ)
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A framework for designing miRNA-based distributed cell classifier circuits
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Connecting data, tools and people across Europe: ELIXIR’s response to the COVID-19 pandemic
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LINC00261 Is Differentially Expressed in Pancreatic Cancer Subtypes and Regulates a Pro-Epithelial Cell Identity
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A Sectioning and Database Enrichment Approach for Improved Peptide Spectrum Matching in Large, Genome-Guided Protein Sequence Databases
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A Modular Metagenomics Pipeline Allowing for the Inclusion of Prior Knowledge Using the Example of Anaerobic Digestion
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Comparative Genomics Suggests Mechanisms of Genetic Adaptation toward the Catabolism of the Phenylurea Herbicide Linuron in Variovorax
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The sex-specific role of p38 MAP kinase in CNS autoimmunity is regulated by estrogen receptor alpha
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MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome
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The Great Oxidation Event expanded the genetic repertoire of arsenic metabolism and cycling
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Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive<i>de novo</i>DNA methylation mechanisms
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Fully Automated Segmentation and Shape Analysis of the Thoracic Aorta in Non–contrast-enhanced Magnetic Resonance Images of the German National Cohort Study
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Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus
H. Lee - H. Chawla, C. Obermeier, F. Dreyer, et al. - Frontiers in Plant Science, 2020

Microbial Resource Management for Ex Situ Biomethanation of Hydrogen at Alkaline pH
W. Logroño - D. Popp, S. Kleinsteuber, H. Sträuber, et al. - Microorganisms, 2020

Evolution of Human Brain Size-Associated NOTCH2NL Genes Proceeds toward Reduced Protein Levels
G. Lodewijk - D. Fernandes, I. Vretzakis, J. Savage, et al. - Molecular Biology and Evolution, 2020 usegalaxy.eu

An epigenetic map of malaria parasite development from host to vector
K. Witmer - S. Fraschka, D. Vlachou, R. Bártfai, et al. - Scientific Reports, 2020 usegalaxy.eu

Laniakea: an open solution to provide Galaxy “on-demand” instances over heterogeneous cloud infrastructures
M. Tangaro - G. Donvito, M. Antonacci, M. Chiara, et al. - GigaScience, 2020 usegalaxy.eu

The importance of incorporating transcript information in CLIP-seq data analysis
M. Uhl - D. Tran, R. Backofen, - Research Square Platform LLC, 2020 usegalaxy.eu

Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration
T. McGowan - J. Johnson, P. Kumar, R. Sajulga, et al. - GigaScience, 2020 usegalaxy.eu

A benchmark of hemoglobin blocking during library preparation for mRNA-Sequencing of human blood samples
F. Uellendahl-Werth - M. Wolfien, A. Franke, O. Wolkenhauer, et al. - Scientific Reports, 2020 usegalaxy.eu

Draft genome sequence of Kocuria indica DP-K7, a methyl red degrading actinobacterium
S. Kumaran - A. Ngo, F. Schultes, D. Tischler, et al. - 3 Biotech, 2020 usegalaxy.eu

Design of Bacterial Strain-Specific qPCR Assays Using NGS Data and Publicly Available Resources and Its Application to Track Biocontrol Strains
I. Hernández - C. Sant, R. Martínez, C. Fernández, et al. - Frontiers in Microbiology, 2020 usegalaxy.eu

Identification of X-chromosomal genes that drive global X-dosage effects in mouse embryonic stem cells
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ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates
O. Schwengers - A. Hoek, M. Fritzenwanker, L. Falgenhauer, et al. - PLOS Computational Biology, 2020

Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics
I. Maus - M. Klocke, J. Derenkó, Y. Stolze, et al. - Environmental Microbiome, 2020

Effects of simulated dose variation on contrast-enhanced CT-based radiomic analysis for Non-Small Cell Lung Cancer
T. Hepp - A. Othman, A. Liebgott, J. Kim, et al. - European Journal of Radiology, 2020

PromA Plasmids Are Instrumental in the Dissemination of Linuron Catabolic Genes Between Different Genera
J. Werner - E. Nour, B. Bunk, C. Spröer, et al. - Frontiers in Microbiology, 2020

Identification and validation of reference genes for RT-qPCR normalization in wheat meiosis
J. Garrido - M. Aguilar, P. Prieto, - Scientific Reports, 2020 usegalaxy.eu

Global Diversification Dynamics Since the Jurassic: Low Dispersal and Habitat-Dependent Evolution Explain Hotspots of Diversity and Shell Disparity in River Snails (Viviparidae)
B. Stelbrink - R. Richter, F. Köhler, F. Riedel, et al. - Systematic Biology, 2020

Gene expression in immortalized versus primary isolated cardiac endothelial cells
L. Deng - L. Pollmeier, Q. Zhou, S. Bergemann, et al. - Scientific Reports, 2020 usegalaxy.eu

Widespread correlation of KRAB zinc finger protein binding with brain-developmental gene expression patterns
G. Farmiloe - G. Lodewijk, S. Robben, E. van Bree, et al. - Philosophical Transactions of the Royal Society B: Biological Sciences, 2020 usegalaxy.eu

Engineering of Effector Domains for Targeted DNA Methylation with Reduced Off-Target Effects
D. Hofacker - J. Broche, L. Laistner, S. Adam, et al. - International Journal of Molecular Sciences, 2020 usegalaxy.eu

Draft Genome Sequences of 12 Leuconostoc carnosum Strains Isolated from Cooked Ham Packaged in a Modified Atmosphere and from Fresh Sausages
F. Candeliere - S. Raimondi, G. Spampinato, M. Tay, et al. - Microbiology Resource Announcements, 2020 usegalaxy.eu

BOOTABLE: Bioinformatics benchmark tool suite for applications and hardware
M. Hanussek - F. Bartusch, J. Krüger, - Future Generation Computer Systems, 2020

MedGAN: Medical image translation using GANs
K. Armanious - C. Jiang, M. Fischer, T. Küstner, et al. - Computerized Medical Imaging and Graphics, 2020

Computing the Rearrangement Distance of Natural Genomes
L. Bohnenkämper - M. Braga, D. Doerr, J. Stoye, et al. - Springer International Publishing, 2020

Unsupervised Knowledge Transfer for Object Detection in Marine Environmental Monitoring and Exploration
M. Zurowietz - T. Nattkemper, - IEEE Access, 2020

GLP: A requirement in cell therapies - perspectives for the cardiovascular field
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BRIDGE: An Open Platform for Reproducible Protein-Ligand Simulations and Free Energy of Binding Calculations
T. Senapathi - C. Barnett, K. Naidoo, - BIO-PROTOCOL, 2020 usegalaxy.eu

Horizontal Gene Transfer Phylogenetics: A Random Walk Approach
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Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines
Y. Perez‐Riverol - P. Moreno, - PROTEOMICS, 2019 usegalaxy.eu

SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
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A Glyphosate Pulse to Brackish Long-Term Microcosms Has a Greater Impact on the Microbial Diversity and Abundance of Planktonic Than of Biofilm Assemblages
R. Janßen - W. Skeff, J. Werner, M. Wirth, et al. - Frontiers in Marine Science, 2019

13-gene DNA Methylation Analysis from Oral Brushing: A Promising Non Invasive Tool in the Follow-up of Oral Cancer Patients
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Accessible and reproducible mass spectrometry imaging data analysis in Galaxy
M. Föll - L. Moritz, T. Wollmann, M. Stillger, et al. - GigaScience, 2019

A Galaxy-based training resource for single-cell RNA-sequencing quality control and analyses
G. Etherington - N. Soranzo, S. Mohammed, W. Haerty, et al. - GigaScience, 2019 usegalaxy.eu

An artificial neural network and Random Forest identify glyphosate-impacted brackish communities based on 16S rRNA amplicon MiSeq read counts
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Full-coverage native RNA sequencing of HIV-1 viruses
A. Gener - J. Kimata, - bioRxiv - Cold Spring Harbor Laboratory, 2019 usegalaxy.eu

mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation
J. Werner - A. Géron, J. Kerssemakers, S. Matallana-Surget, et al. - Biology Direct, 2019

Maternally regulated gastrulation as a source of variation contributing to cavefish forebrain evolution
J. Torres-Paz - J. Leclercq, S. Rétaux, - eLife, 2019 usegalaxy.eu

Expression Atlas update: from tissues to single cells
I. Papatheodorou - P. Moreno, J. Manning, A. Fuentes, et al. - Nucleic Acids Research, 2019 usegalaxy.eu

Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics
A. Géron - J. Werner, R. Wattiez, P. Lebaron, et al. - Frontiers in Microbiology, 2019

Mutations of R882 change flanking sequence preferences of the DNA methyltransferase DNMT3A and cellular methylation patterns
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Highly Efficient Library Preparation for Ion Torrent Sequencing Using Y-Adapters
L. Forth - D. Höper, - BioTechniques, 2019 usegalaxy.eu

Characterization of Core Microbiomes and Functional Profiles of Mesophilic Anaerobic Digesters Fed With Chlorella vulgaris Green Microalgae and Maize Silage
R. Wirth - T. Böjti, G. Lakatos, G. Maróti, et al. - Frontiers in Energy Research, 2019 usegalaxy.eu

An intrinsically disordered proteins community for ELIXIR
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Interplay and Targetome of the Two Conserved Cyanobacterial sRNAs Yfr1 and Yfr2 in Prochlorococcus MED4
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Development of novel microsatellite markers for <i>Alkanna tinctoria</i> by comparative transcriptomics
M. Ahmad - D. Lazic, K. Hansel‐Hohl, C. Lexer, et al. - Applications in Plant Sciences, 2019 usegalaxy.eu

Identification and tissue-expression profiling of novel chicken c-type lectin-like domain containing proteins as potential targets for carbohydrate-based vaccine strategies
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ΔN-Tp63 Mediates Wnt/β-Catenin-Induced Inhibition of Differentiation in Basal Stem Cells of Mucociliary Epithelia
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<i>Candida auris</i> in Germany and Previous Exposure to Foreign Healthcare
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Historical faunal exchange between the Pontocaspian Basin and North America
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Draft Genome Sequence of a <i>Chitinimonas</i> Species from Hudson Valley Waterways That Expresses Violacein Pigment
B. Jude - - Microbiology Resource Announcements, 2019 usegalaxy.eu

Pheno-seq – linking visual features and gene expression in 3D cell culture systems
S. Tirier - J. Park, F. Preußer, L. Amrhein, et al. - Scientific Reports, 2019

Bhlhe40 and Bhlhe41 transcription factors regulate alveolar macrophage self‐renewal and identity
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GRUU-Net: Integrated convolutional and gated recurrent neural network for cell segmentation
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PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping
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Cyclization of RGD Peptides by Suzuki–Miyaura Cross-Coupling
I. Kemker - C. Schnepel, D. Schröder, A. Marion, et al. - Journal of Medicinal Chemistry, 2019

U2 <scp>AF</scp> <sup>65</sup> assemblies drive sequence‐specific splice site recognition
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Complex Bacterial Consortia Reprogram the Colitogenic Activity of Enterococcus faecalis in a Gnotobiotic Mouse Model of Chronic, Immune-Mediated Colitis
I. Lengfelder - I. Sava, J. Hansen, K. Kleigrewe, et al. - Frontiers in Immunology, 2019 usegalaxy.eu

A pan-cancer analysis of synonymous mutations
Y. Sharma - M. Miladi, S. Dukare, K. Boulay, et al. - Nature Communications, 2019 usegalaxy.eu

de.NBI Cloud federation through ELIXIR AAI
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Hyperparameter optimization for image analysis: application to prostate tissue images and live cell data of virus-infected cells
C. Ritter - T. Wollmann, P. Bernhard, M. Gunkel, et al. - International Journal of Computer Assisted Radiology and Surgery, 2019

Versatile interactions and bioinformatics analysis of noncoding RNAs
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Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes
J. Nelkner - C. Henke, T. Lin, W. Pätzold, et al. - Genes, 2019

RNApolis: Computational Platform for RNA Structure Analysis
M. Szachniuk - - Foundations of Computing and Decision Sciences, 2019 usegalaxy.eu

BIIGLE2Go—A scalable image annotation system for easy deployment on cruises
M. Zurowietz - D. Langenkamper, T. Nattkemper, - IEEE, 2019

A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set
B. Pucker - D. Holtgräwe, K. Stadermann, K. Frey, et al. - PLOS ONE, 2019

TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy
J. Meier-Kolthoff - M. Göker, - Nature Communications, 2019

The RNA workbench 2.0: next generation RNA data analysis
J. Fallmann - P. Videm, A. Bagnacani, B. Batut, et al. - Nucleic Acids Research, 2019 usegalaxy.eu

Reproducible Scientific Workflows for High Performance and Cloud Computing
F. Bartusch - M. Hanussek, J. Kruger, O. Kohlbacher, et al. - IEEE, 2019

BOOTABLE: Bioinformatics Benchmark Tool Suite
M. Hanussek - F. Bartusch, J. Kruger, O. Kohlbacher, et al. - IEEE, 2019

Mapping-based Genome Size Estimation
S. Natarajan - J. Gehrke, B. Pucker, - bioRxiv - Cold Spring Harbor Laboratory, 2019

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
M. Brunet X. Roucou - - Journal of Visualized Experiments, 2019 usegalaxy.eu

Influence of Urbanization on Epiphytic Bacterial Communities of the Platanus × hispanica Tree Leaves in a Biennial Study
J. Espenshade - S. Thijs, S. Gawronski, H. Bové, et al. - Frontiers in Microbiology, 2019 usegalaxy.eu

Intercellular communication is required for trap formation in the nematode-trapping fungus Duddingtonia flagrans
L. Youssar - V. Wernet, N. Hensel, X. Yu, et al. - PLOS Genetics, 2019 usegalaxy.eu

1,4-Disubstituted 1H-1,2,3-Triazole Containing Peptidotriazolamers: A New Class of Peptidomimetics With Interesting Foldamer Properties
D. Schröder - O. Kracker, T. Fröhr, J. Góra, et al. - Frontiers in Chemistry, 2019

Insight into the genome and brackish water adaptation strategies of toxic and bloom-forming Baltic Sea Dolichospermum sp. UHCC 0315
J. Teikari - R. Popin, S. Hou, M. Wahlsten, et al. - Scientific Reports, 2019 usegalaxy.eu

Multilocus phylogeny, species delimitation and biogeography of Iberian valvatiform springsnails (Caenogastropoda: Hydrobiidae), with the description of a new genus
D. Delicado - B. Arconada, A. Aguado, M. Ramos, et al. - Zoological Journal of the Linnean Society, 2019

Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)
T. Senapathi - S. Bray, C. Barnett, B. Grüning, et al. - Bioinformatics, 2019 usegalaxy.eu

CAMISIM: simulating metagenomes and microbial communities
A. Fritz - P. Hofmann, S. Majda, E. Dahms, et al. - Microbiome, 2019

Whole-Genome Sequencing of Klebsiella pneumoniae Isolates to Track Strain Progression in a Single Patient With Recurrent Urinary Tract Infection
K. Wylie - T. Wylie, P. Minx, D. Rosen, et al. - Frontiers in Cellular and Infection Microbiology, 2019 usegalaxy.eu

Malpighian tubules of caterpillars: blending RNAseq and physiology to reveal regional functional diversity and novel epithelial ion transport control mechanisms
D. Kolosov - M. O'Donnell, - Journal of Experimental Biology, 2019 usegalaxy.eu

Endothelial cell mineralocorticoid receptors oppose VEGF-induced gene expression and angiogenesis
A. Lother - L. Deng, M. Huck, D. Fürst, et al. - Journal of Endocrinology, 2019 usegalaxy.eu

RNA-sequencing in ophthalmology research: considerations for experimental design and analysis
N. Owen - M. Moosajee, - Therapeutic Advances in Ophthalmology, 2019 usegalaxy.eu

Tools for Understanding miRNA–mRNA Interactions for Reproducible RNA Analysis
A. Bagnacani - M. Wolfien, O. Wolkenhauer, - Springer New York, 2019 usegalaxy.eu

Genome-Wide Analysis of the Nucleosome Landscape in Individuals with Coffin-Siris Syndrome
A. Kalmbach - C. Schröder, L. Klein-Hitpass, K. Nordström, et al. - Cytogenetic and Genome Research, 2019 usegalaxy.eu

Proof of concept web application for understanding the energetic basis of oligonucleotide unfolding
I. Prislan - S. Sajko, N. Ulrih, L. Fürst, et al. - RSC Advances, 2019 usegalaxy.eu

Workflow Development for the Functional Characterization of ncRNAs
M. Wolfien - D. Brauer, A. Bagnacani, O. Wolkenhauer, et al. - Springer New York, 2019 usegalaxy.eu

QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics
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Proteogenomic Analysis of Epibacterium Mobile BBCC367, a Relevant Marine Bacterium Isolated From the South Pacific Ocean
S. Matallana-Surget - J. Werner, R. Wattiez, K. Lebaron, et al. - Frontiers in Microbiology, 2018

FOXG1 Regulates PRKAR2B Transcriptionally and Posttranscriptionally via miR200 in the Adult Hippocampus
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Combination treatment of acute myeloid leukemia cells with DNMT and HDAC inhibitors: predominant synergistic gene downregulation associated with gene body demethylation
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MAIA—A machine learning assisted image annotation method for environmental monitoring and exploration
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eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
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Aequatus: an open-source homology browser
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Differential Methylation of H3K79 Reveals DOT1L Target Genes and Function in the Cerebellum In Vivo
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Common ELIXIR Service for Researcher Authentication and Authorisation
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Draft genome sequence of Rhodococcus erythropolis B7g, a biosurfactant producing actinobacterium
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Ultrastructural alterations in the retinal pigment epithelium and photoreceptors of a Stargardt patient and three Stargardt mouse models: indication for the central role of RPE melanin in oxidative stress
T. Taubitz - A. Tschulakow, M. Tikhonovich, B. Illing, et al. - PeerJ, 2018

Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors
I. Maus - M. Rumming, I. Bergmann, K. Heeg, et al. - Biotechnology for Biofuels, 2018

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization
J. Wolff - V. Bhardwaj, S. Nothjunge, G. Richard, et al. - Nucleic Acids Research, 2018 usegalaxy.eu

Community-Driven Data Analysis Training for Biology
B. Batut - S. Hiltemann, A. Bagnacani, D. Baker, et al. - Cell Systems, 2018 usegalaxy.eu

ASaiM: a Galaxy-based framework to analyze microbiota data
B. Batut - K. Gravouil, C. Defois, S. Hiltemann, et al. - GigaScience, 2018 usegalaxy.eu

Biology Needs Evolutionary Software Tools: Let’s Build Them Right
A. Nekrutenko - G. Team, J. Goecks, J. Taylor, et al. - Molecular Biology and Evolution, 2018 usegalaxy.eu

Structure and Interaction Prediction in Prokaryotic RNA Biology
P. Wright* - M. Mann*, R. Backofen*, - Microbiology Spectrum, 2018 usegalaxy.eu

CMV: visualization for RNA and protein family models and their comparisons
F. Eggenhofer - I. Hofacker, R. Backofen, C. Höner zu Siederdissen, et al. - Bioinformatics, 2018 usegalaxy.eu

Targeted <i>in situ</i> metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants
Y. Stolze - A. Bremges, I. Maus, A. Pühler, et al. - Microbial Biotechnology, 2017

Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes
I. Maus - A. Bremges, Y. Stolze, S. Hahnke, et al. - Biotechnology for Biofuels, 2017

The utility and perspectives of NGS-based methods in BSL-3 and BSL-4 laboratory – sequencing and analysis strategies
T. Wołkowicz - - Briefings in Functional Genomics, 2017 usegalaxy.eu

Workflows for microscopy image analysis and cellular phenotyping
T. Wollmann - H. Erfle, R. Eils, K. Rohr, et al. - Journal of Biotechnology, 2017

Bioinformatics for NGS-based metagenomics and the application to biogas research
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The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy
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Deep residual Hough voting for mitotic cell detection in histopathology images
T. Wollmann - K. Rohr, - IEEE, 2017

BIIGLE 2.0 - Browsing and Annotating Large Marine Image Collections
D. Langenkämper - M. Zurowietz, T. Schoening, T. Nattkemper, et al. - Frontiers in Marine Science, 2017

Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants
Y. Stolze - A. Bremges, M. Rumming, C. Henke, et al. - Biotechnology for Biofuels, 2016