Publications

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

Recently added publication

Modeling brain sex in the limbic system as phenotype for female-prevalent mental disorders
G. Matte Bon - D. Kraft, E. Comasco, B. Derntl, 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

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

The haplotype-resolved assembly of COL40 a cassava (<i>Manihot esculenta</i>) line with broad-spectrum resistance against viruses causing Cassava brown streak disease unveils a region of highly repeated elements on chromosome 12
C. Thoben - B. Pucker, S. Winter, B. Econopouly, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

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

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

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

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

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

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

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

Unveiling Agricultural Biotechnological Prospects: The Draft Genome Sequence of Stenotrophomonas geniculata LGMB417
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Deciphering the Key Players of the Bacterial Microbiota Associated with Aerial Crown Gall Tumors on Rhododendron: Insights into the Gallobiome
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A reproducible workflow for assembling the mitochondrial genome of <i>Acheta domesticus</i> (Orthoptera: Gryllidae)
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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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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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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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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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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>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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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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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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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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Whole genome discovery of regulatory genes responsible for the response of chicken to heat stress
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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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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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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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Small RNAs from mitochondrial genome recombination sites are incorporated into T. gondii mitoribosomes
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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
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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
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Structure and energetics of serum protein complex of tea adulterant dye Bismarck brown Y using experimental and computational methods
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Multi-omics responses of barley seedlings to low and high linear energy transfer irradiation
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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
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Predictive uncertainty in deep learning–based <scp>MR</scp> image reconstruction using deep ensembles: Evaluation on the <scp>fastMRI</scp> data set
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Rat1 promotes premature transcription termination at R-loops
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Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy
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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
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Comparative Metagenomic Analysis of Bacteriophages and Prophages in Gnotobiotic Mouse Models
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Ionizing radiation responses appear incidental to desiccation responses in the bdelloid rotifer Adineta vaga
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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
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SimLivA–Modeling ischemia‐reperfusion injury in the liver: A first step towards a clinical decision support tool
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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
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Polymyxin Resistance in Salmonella: Exploring Mutations and Genetic Determinants of Non-Human Isolates
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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
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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

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

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

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

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

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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MYC overexpression and SMARCA4 loss cooperate to drive medulloblastoma formation in mice
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RNA interaction format: a general data format for RNA interactions
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Automated MRI Lung Segmentation and 3D Morphologic Features for Quantification of Neonatal Lung Disease
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SIGNed explanations: Unveiling relevant features by reducing bias
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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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The impact of salt stress on the physiology and the transcriptome of the model streptophyte green alga <i>Chara braunii</i>
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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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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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Individual-level deviations from normative brain morphology in violence, psychosis, and psychopathy
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Proteometabolomics of initial and recurrent glioblastoma highlights an increased immune cell signature with altered lipid metabolism
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Accurate prediction of quantitative traits with failed SNP calls in canola and maize
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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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Microbiome Metabolome Integration Platform (MMIP): a web-based platform for microbiome and metabolome data integration and feature identification
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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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Complete genome sequence of a human bacteremia isolate of <i>Kalamiella piersonii</i>
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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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Activator-blocker model of transcriptional regulation by pioneer-like factors
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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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Mitochondrial polymorphism m.3017C&gt;T of SHLP6 relates to heterothermy
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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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The design of functional proteins using tensorized energy calculations
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Adaptive evolution of the enigmatic Takakia now facing climate change in Tibet
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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
Ö. ILIKKAN - - Iğdır Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 2023 usegalaxy.eu

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
S. Pan - X. Zhao, L. Coelho, - Bioinformatics, 2023 usegalaxy.eu

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
M. Zilbauer - K. James, M. Kaur, S. Pott, et al. - Nature Reviews Gastroenterology &amp; Hepatology, 2023 usegalaxy.eu

CpG DNA methylation changes during epididymal sperm maturation in bulls
E. Capra - F. Turri, B. Lazzari, S. Biffani, et al. - Epigenetics &amp; Chromatin, 2023 usegalaxy.eu

SARS-CoV-2 spike protein diversity at an intra-host level, among SARS-CoV-2 infected individuals in South Africa, 2020 to 2022
K. Subramoney - N. Mtileni, A. Davis, J. Giandhari, et al. - PLOS ONE, 2023 usegalaxy.eu

Species Delineation and Comparative Genomics within the<i>Campylobacter ureolyticus</i>Complex
J. Maki - M. Howard, S. Connelly, M. Pettengill, et al. - Journal of Clinical Microbiology, 2023 usegalaxy.eu

Genome-Based Retrospective Analysis of a Providencia stuartii Outbreak in Rome, Italy: Broad Spectrum IncC Plasmids Spread the NDM Carbapenemase within the Hospital
V. Capitani - G. Arcari, A. Oliva, F. Sacco, et al. - Antibiotics, 2023 usegalaxy.eu

β-Cell–Specific <i>E2f1</i> Deficiency Impairs Glucose Homeostasis, β-Cell Identity, and Insulin Secretion
F. Oger - C. Bourouh, M. Friano, E. Courty, et al. - Diabetes, 2023 usegalaxy.eu

Comparative genomics of Brucella abortus and Brucella melitensis unravels the gene sharing, virulence factors and SNP diversity among the standard, vaccine and field strains
S. Anbazhagan - K. Himani, R. Karthikeyan, L. Prakasan, et al. - International Microbiology, 2023 usegalaxy.eu

<i>De Novo</i> Whole-Genome Sequencing of Two Pathogenic Pasteurella multocida Type D:6 Strains Isolated from Pigs
M. Livingstone - P. Jorgensen, M. McCall, J. Thomson, et al. - Microbiology Resource Announcements, 2023 usegalaxy.eu

Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA
L. Whitmore - M. McCauley, J. Farrell, M. Stammnitz, et al. - Nature Ecology &amp; Evolution, 2023 usegalaxy.eu

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
G. Cruz - K. Hammernik, T. Kuestner, C. Velasco, et al. - NMR in Biomedicine, 2023

APOE expression and secretion are modulated by mitochondrial dysfunction
M. Wynne - O. Ogunbona, A. Lane, A. Gokhale, et al. - eLife, 2023 usegalaxy.eu

MpoxRadar: a worldwide MPXV genomic surveillance dashboard
F. Nasri - K. Kongkitimanon, A. Wittig, J. Cortés, et al. - Nucleic Acids Research, 2023

Mapping cells through time and space with moscot
D. Klein - G. Palla, M. Lange, M. Klein, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

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
S. Williams - C. Back, E. Best, J. Mantell, et al. - Microbial Genomics, 2023 usegalaxy.eu

A draft human pangenome reference
W. Liao - M. Asri, J. Ebler, D. Doerr, et al. - Nature, 2023

Genetic architecture of brain age and its causal relations with brain and mental disorders
E. Leonardsen - D. Vidal-Piñeiro, J. Roe, O. Frei, et al. - Molecular Psychiatry, 2023

Biosynthetic Potential of Hypogymnia Holobionts: Insights into Secondary Metabolite Pathways
N. Ahmad - M. Ritz, A. Calchera, J. Otte, et al. - Journal of Fungi, 2023 usegalaxy.eu

Phased grapevine genome sequence of an Rpv12 carrier for biotechnological exploration of resistance to Plasmopara viticola
B. Frommer - S. Müllner, D. Holtgräwe, P. Viehöver, et al. - Frontiers in Plant Science, 2023

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

Free-breathing Arterial Spin Labeling MRI for the Detection of Pulmonary Embolism
A. Othman - C. Liang, Y. Komma, M. Munz, et al. - Radiology, 2023

ODNA: identification of organellar DNA by machine learning
R. Martin - M. Nguyen, N. Lowack, D. Heider, et al. - Bioinformatics, 2023

Free-breathing Arterial Spin Labeling MRI for the Detection of Pulmonary Embolism
A. Othman - C. Liang, Y. Komma, M. Munz, et al. - Radiology, 2023

Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
A. Bafna - G. Banks, M. Hastings, P. Nolan, et al. - Genome Research, 2023 usegalaxy.eu

Botryosphaeriaceae gene machinery: Correlation between diversity and virulence
M. Belair - J. Restrepo-Leal, C. Praz, F. Fontaine, et al. - Fungal Biology, 2023 usegalaxy.eu

Direct Xylella fastidiosa whole genome sequencing from various plant species using targeted enrichment
A. Boutigny - B. Remenant, B. Legendre, V. Beven, et al. - Journal of Microbiological Methods, 2023 usegalaxy.eu

Building on Communities to Further Software Sustainability
A. Fouilloux - J. Iaquinta, A. Gupta, H. Struthers, et al. - Computing in Science &amp; Engineering, 2023 usegalaxy.eu

Rise and fall of SARS-CoV-2 variants in Rotterdam: Comparison of wastewater and clinical surveillance
R. Izquierdo-Lara - L. Heijnen, B. Oude Munnink, C. Schapendonk, et al. - Science of The Total Environment, 2023 usegalaxy.eu

Foremost report of the whole genome of Spirabiliibacterium mucosae from India and comparative genomics of the novel genus Spirabiliibacterium
K. Karthik - S. Anbazhagan, M. Ananda Chitra, R. Ramya, et al. - Gene, 2023 usegalaxy.eu

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
Y. Yan - J. Zhang, L. Tian, X. Yan, et al. - Water Research, 2023 usegalaxy.eu

Bioprospecting phytochemicals of Rosmarinus officinalis L. for targeting SARS-CoV-2 main protease (Mpro): a computational study
U. Patel - K. Desai, R. Dabhi, J. Maru, et al. - Journal of Molecular Modeling, 2023 usegalaxy.eu

Morphology and taxonomic assessment of eight genetic clades of Mercuria Boeters, 1971 (Caenogastropoda, Hydrobiidae), with the description of five new species
J. Miller - D. Delicado, F. García-Guerrero, N. Khalloufi, et al. - European Journal of Taxonomy, 2023

Galaxy for open-source computational drug discovery solutions
A. Singh Gaur - S. Nagamani, L. Priyadarsinee, H. Mahanta, et al. - Expert Opinion on Drug Discovery, 2023 usegalaxy.eu

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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
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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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A bibliometric analysis and visualization of spatially resolved transcriptomics
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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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Revealing the small proteome of<i>Haloferax volcanii</i>by combining ribosome profiling and small-protein optimized mass spectrometry
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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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DIAMOND +  MEGAN Microbiome Analysis
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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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Cell Segmentation of in situ Transcriptomics Data Using Signed Graph Partitioning
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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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Mimicking Tumor Cell Heterogeneity of Colorectal Cancer in a Patient-derived Organoid-Fibroblast Model
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Avoiding Shortcut-Learning by Mutual Information Minimization in Deep Learning-Based Image Processing
L. Fay - E. Cobos, B. Yang, S. Gatidis, et al. - IEEE Access, 2023

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
L. Parmigiani - R. Wittler, J. Stoye, - bioRxiv - Cold Spring Harbor Laboratory, 2022

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
Y. Ren - T. Chakraborty, S. Doijad, L. Falgenhauer, et al. - Antibiotics, 2022

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
A. Afrizal - S. Jennings, T. Hitch, T. Riedel, et al. - Cell Host &amp; Microbe, 2022

Microcystin-LR aerosol induces inflammatory responses in healthy human primary airway epithelium
J. Breidenbach - B. French, T. Gordon, A. Kleinhenz, et al. - Environment International, 2022 usegalaxy.eu

Two New <i>Rhizobiales</i> Species Isolated from Root Nodules of Common Sainfoin (Onobrychis viciifolia) Show Different Plant Colonization Strategies
S. Ashrafi - N. Kuzmanović, S. Patz, U. Lohwasser, et al. - Microbiology Spectrum, 2022

Identification of Clinical Variants beyond the Exome in Inborn Errors of Metabolism
A. Soriano-Sexto - D. Gallego, F. Leal, N. Castejón-Fernández, et al. - International Journal of Molecular Sciences, 2022 usegalaxy.eu

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
M. Gallus - I. Beer, N. Ivleva, M. Ehrmann, et al. - International Journal of Systematic and Evolutionary Microbiology, 2022 usegalaxy.eu

Cross-linking of the endolysosomal system reveals potential flotillin structures and cargo
J. Singh - H. Elhabashy, P. Muthukottiappan, M. Stepath, et al. - Nature Communications, 2022

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
E. Özkurt - J. Fritscher, N. Soranzo, D. Ng, et al. - Microbiome, 2022 usegalaxy.eu

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
E. Valadez-Moctezuma - S. Samah, J. Mascorro-Gallardo, N. Marbán-Mendoza, et al. - Genetic Resources and Crop Evolution, 2022 usegalaxy.eu

Epigenetic nature of <i>Arabidopsis thaliana</i> telomeres
M. Vaquero-Sedas - M. Vega-Palas, - Plant Physiology, 2022 usegalaxy.eu

Multivalent binding kinetics resolved by fluorescence proximity sensing
C. Schulte - A. Soldà, S. Spänig, N. Adams, et al. - Communications Biology, 2022

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
T. Küstner - J. Vogel, T. Hepp, A. Forschner, et al. - Diagnostics, 2022

DeepToA: an ensemble deep-learning approach to predicting the theater of activity of a microbiome
W. Zeng - A. Gautam, D. Huson, - Bioinformatics, 2022

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
R. Meier - G. Greve, D. Zimmer, H. Bresser, et al. - Blood Cancer Journal, 2022 usegalaxy.eu

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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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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Delineating genome-wide alternative splicing landscapes and their functional significance in orchids
A. Hazra - P. Mahadani, - South African Journal of Botany, 2022

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

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
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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

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

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
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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
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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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