Publications

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Currently 1092 publications with reference to de.NBI Cloud are listed.

Recently added publication

Multi-label classification for multi-drug resistance prediction of Escherichia coli
Y. Ren - T. Chakraborty, S. Doijad, L. Falgenhauer, et al. - Elsevier BV, 2022

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Deciphering the Key Players of the Bacterial Microbiota Associated with Aerial Crown Gall Tumors on Rhododendron: Insights into the Gallobiome
N. Kuzmanović - J. Nesme, J. Wolf, M. Neumann-Schaal, et al. - Phytobiomes Journal, 2024

Pathogens of the oak processionary moth Thaumetopoea processionea: Developing a user-friendly bioassay system and metagenome analyses for microorganisms
L. Schäfer - J. Jehle, R. Kleespies, J. Wennmann, et al. - Journal of Invertebrate Pathology, 2024

Characterization of a highly thermostable recombinant xylanase from Anoxybacillus ayderensis
Z. Akpinar - H. Karaoglu, - Protein Expression and Purification, 2024 usegalaxy.eu

Phenomics and genomic features of Enterococcus avium IRMC1622a isolated from a clinical sample of hospitalized patient
R. AlJindan - N. Mahmoud, D. AlEraky, N. Almandil, et al. - Journal of Infection and Public Health, 2024 usegalaxy.eu

A reproducible workflow for assembling the mitochondrial genome of <i>Acheta domesticus</i> (Orthoptera: Gryllidae)
S. Homchan - W. Kutanan, Y. Gupta, - Ecology and Evolution, 2024 usegalaxy.eu

Insights on the comparative affinity of ribonucleic acids with plant-based beta carboline alkaloid, harmine: Spectroscopic, calorimetric and computational evaluation
P. Sarkar - P. Gopi, P. Pandya, S. Paria, et al. - Heliyon, 2024 usegalaxy.eu

Meiotic maturation failure in primary ovarian insufficiency: insights from a bovine model
S. Pietroforte - P. Dey, E. Ibáñez, A. Luciano, et al. - Journal of Assisted Reproduction and Genetics, 2024 usegalaxy.eu

Communicating Mass Spectrometry Quality Information in mzQC with Python, R, and Java
C. Bielow - N. Hoffmann, D. Jimenez-Morales, T. Van Den Bossche, et al. - Journal of the American Society for Mass Spectrometry, 2024

Genome sequence and RNA-seq analysis reveal genetic basis of flower coloration in the giant water lily<i>Victoria cruziana</i>
M. Nowak - B. Harder, S. Meckoni, R. Friedhoff, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

Nodulating Aeschynomene indica without Nod Factor Synthesis Genes: In Silico Analysis of Evolutionary Relationship
M. Zhao - J. Dong, Z. Zhang, E. Wang, et al. - Agronomy, 2024 usegalaxy.eu

The genomic and phylogenetic analysis of <i>Marseillevirus cajuinensis</i> raises questions about the evolution of Marseilleviridae lineages and their taxonomical organization
B. de Azevedo - V. Queiroz, I. de Aquino, T. Machado, et al. - Journal of Virology, 2024 usegalaxy.eu

Complete genome sequence of the <i>Microbacterium enclense</i> bacteriophage phiMiGM15
E. Camacho-Beltrán - J. Morales-Aguilar, M. López-Meyer, G. Rincón-Enríquez, et al. - Microbiology Resource Announcements, 2024 usegalaxy.eu

Examining Transcriptomic Alterations in Rat Models of Intracerebral Hemorrhage and Severe Intracerebral Hemorrhage
S. Thangameeran - S. Tsai, H. Liew, C. Pang, et al. - Biomolecules, 2024 usegalaxy.eu

Activation of the aryl hydrocarbon receptor improves allergen-specific immunotherapy of murine allergic airway inflammation: a novel adjuvant option?
S. Heine - F. Alessandrini, J. Grosch, C. Graß, et al. - Frontiers in Immunology, 2024 usegalaxy.eu

Partial hepatectomy accelerates colorectal metastasis by priming an inflammatory premetastatic niche in the liver
J. Luenstedt - F. Hoping, R. Feuerstein, B. Mauerer, et al. - Frontiers in Immunology, 2024 usegalaxy.eu

Genetic influence on vascular smooth muscle cell apoptosis
D. McVey - C. Andreadi, P. Gong, P. Stanczyk, et al. - Cell Death &amp; Disease, 2024 usegalaxy.eu

De novo transcriptomes of cave and surface isopod crustaceans: insights from 11 species across three suborders
L. Jovović - J. Bedek, F. Malard, H. Bilandžija, et al. - Scientific Data, 2024 usegalaxy.eu

Nuclear position and local acetyl-CoA production regulate chromatin state
P. Willnow - A. Teleman, - Nature, 2024 usegalaxy.eu

Personalized bacteriophage therapy outcomes for 100 consecutive cases: a multicentre, multinational, retrospective observational study
J. Pirnay - S. Djebara, G. Steurs, J. Griselain, et al. - Nature Microbiology, 2024 usegalaxy.eu

Whole genome sequencing reveals complex resistome features of Klebsiella pneumoniae isolated from patients at major hospitals in Trinidad, West Indies
A. Pustam - J. Jayaraman, A. Ramsubhag, - Journal of Global Antimicrobial Resistance, 2024 usegalaxy.eu

SmCYP71D373 of Salvia miltiorrhiza catalyzes the methyl oxidation reaction of tanshinone IIA-19 position
X. Qiu - Y. Zhang, Y. Luo, Y. Zhang, et al. - Industrial Crops and Products, 2024 usegalaxy.eu

Carbapenem and colistin-resistant hypervirulent Klebsiella pneumoniae: An emerging threat transcending the egyptian food chain
R. Sabala - A. Fukuda, C. Nakajima, Y. Suzuki, et al. - Journal of Infection and Public Health, 2024 usegalaxy.eu

Detection of KPC-216, a Novel KPC-3 Variant, in a Clinical Isolate of Klebsiella pneumoniae ST101 Co-Resistant to Ceftazidime-Avibactam and Cefiderocol
M. Giufrè - G. Errico, M. Del Grosso, M. Pagnotta, et al. - Antibiotics, 2024 usegalaxy.eu

Robust Graph Pruning for Efficient Segmentation and Cluster Splitting of Cell Nuclei Using Deformable Shape Models
L. Kostrykin - K. Rohr, - IEEE, 2024 usegalaxy.eu

Mini-Multilocus Sequence Typing Scheme for the Global Population of Neisseria gonorrhoeae
I. Kandinov - B. Shaskolskiy, D. Kravtsov, M. Filippova, et al. - International Journal of Molecular Sciences, 2024 usegalaxy.eu

Elucidating the impact of Y chromosome microdeletions and altered gene expression on male fertility in assisted reproduction
N. Pazoki - M. Salehi, S. Angaji, M. Abdollahpour-Alitappeh, et al. - Human Molecular Genetics, 2024 usegalaxy.eu

Genomic characterization of carbapenem and colistin-resistant Klebsiella pneumoniae isolates from humans and dogs
R. Pachanon - N. Khine, N. Phumthanakorn, T. Wongsurawat, et al. - Frontiers in Veterinary Science, 2024 usegalaxy.eu

Massively parallel CRISPR-assisted homologous recombination enables saturation editing of full-length endogenous genes in yeast
L. Deng - Y. Zhou, Z. Cai, J. Zhu, et al. - Science Advances, 2024 usegalaxy.eu

Divergence within the Taxon ‘Candidatus Phytoplasma asteris’ Confirmed by Comparative Genome Analysis of Carrot Strains
R. Toth - A. Ilic, B. Huettel, B. Duduk, et al. - Microorganisms, 2024 usegalaxy.eu

Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons
L. Dossmann - M. Emperle, M. Dukatz, A. de Mendoza, et al. - Communications Biology, 2024 usegalaxy.eu

Downregulation of HNF4A enables transcriptomic reprogramming during the hepatic acute-phase response
C. Ehle - A. Iyer-Bierhoff, Y. Wu, S. Xing, et al. - Communications Biology, 2024 usegalaxy.eu

Epigenomic and transcriptomic persistence of heat stress memory in strawberry (Fragaria vesca)
M. López - B. Denoyes, E. Bucher, - BMC Plant Biology, 2024 usegalaxy.eu

A practical guide to bioimaging research data management in core facilities
C. Schmidt - T. Boissonnet, J. Dohle, K. Bernhardt, et al. - Journal of Microscopy, 2024 usegalaxy.eu

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
N. Soleau - S. Ganet, S. Werlen, L. Collignon, et al. - International Journal of Molecular Sciences, 2024 usegalaxy.eu

Cluster efficient pangenome graph construction with nf-core/pangenome
S. Heumos - M. Heuer, F. Hanssen, L. Heumos, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

Catecholamine treatment induces reversible heart injury and cardiomyocyte gene expression
C. Bode - S. Preissl, L. Hein, A. Lother, et al. - Intensive Care Medicine Experimental, 2024 usegalaxy.eu

Reduction of APOE accounts for neurobehavioral deficits in fetal alcohol spectrum disorders
H. Hwang - S. Yamashita, Y. Matsumoto, M. Ito, et al. - Molecular Psychiatry, 2024 usegalaxy.eu

Genomic analysis of a spontaneous unifoliate mutant reveals gene candidates associated with compound leaf development in Vigna unguiculata [L] Walp
O. Edet - B. Ubi, T. Ishii, - Scientific Reports, 2024 usegalaxy.eu

Assessment and Partial Characterization of Candidate Genes in Dihydrochalcone and Arbutin Biosynthesis in an Apple–Pear Hybrid by <i>De Novo</i> Transcriptome Assembly
S. Miranda - M. Koop, A. Angeli, J. Lagrèze, et al. - Journal of Agricultural and Food Chemistry, 2024 usegalaxy.eu

Tolperisone hydrochloride improves motor functions in Parkinson’s disease via MMP-9 inhibition and by downregulating p38 MAPK and ERK1/2 signaling cascade
B. Zaman - I. Mostafa, T. Hassan, S. Ahmed, et al. - Biomedicine &amp; Pharmacotherapy, 2024 usegalaxy.eu

Metagenomic Study of Bacteria Diversity and Functional Profile in Bulk and Rhizosphere Soils of Fusarium-Wilt Infected Plantain (Musa paradisiaca)
N. C.C. - E. B.A., O. E.C., - Journal of Advances in Microbiology, 2024 usegalaxy.eu

Evaluation of novel pyridoxal isonicotinoyl hydrazone (<scp>PIH</scp>) derivatives as potential <scp>anti‐tuberculosis</scp> agents: An in silico investigation
M. Hossain - S. Al Abbad, Z. Alsunaidi, S. Rahman, et al. - International Journal of Quantum Chemistry, 2024 usegalaxy.eu

Physicochemical properties and biological efficacy of 30 DYRK2 Inhibitors for the treatment of prostate cancer
S. Joshi - R. Srivastava, - Vietnam Journal of Chemistry, 2024 usegalaxy.eu

The Damietta Server: a comprehensive protein design toolkit
I. Grin - K. Maksymenko, T. Wörtwein, M. ElGamacy, et al. - Nucleic Acids Research, 2024

DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data
J. Galvis - J. Guyon, B. Dartigues, H. Hecht, et al. - Bioinformatics, 2024 usegalaxy.eu

Expanding the Scope of Adenoviral Vectors by Utilizing Novel Tools for Recombination and Vector Rescue
J. Fischer - A. Fedotova, C. Bühler, L. Darriba, et al. - Viruses, 2024 usegalaxy.eu

Modification of Seurat v4 for the Development of a Phase Assignment Tool Able to Distinguish between G2 and Mitotic Cells
S. Watson - H. Porter, I. Sudbery, R. Thompson, et al. - International Journal of Molecular Sciences, 2024 usegalaxy.eu

The Celiac‐Disease Superantigen Oligomerizes and Increases Permeability in an Enterocyte Cell Model
M. Herrera - M. Amundarain, P. Dörfler, V. Dodero, et al. - Angewandte Chemie International Edition, 2024

A Transcriptomic Hourglass In Brown Algae
J. Lotharukpong - M. Zheng, R. Luthringer, H. Drost, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

A Minimal Metadata Schema and Its Tool to Improve the Searchableness of Research Data in Bioinformatics
O. Brandt - H. Gauza, J. Kaltenbach, M. Müller, et al. - Journal of Library Metadata, 2024

Building Domain-Specific Machine Learning Workflows: A Conceptual Framework for the State of the Practice
B. Oakes - M. Famelis, H. Sahraoui, - ACM Transactions on Software Engineering and Methodology, 2024 usegalaxy.eu

In silico exploration of phenolics as modulators of penicillin binding protein (PBP) 2× of Streptococcus pneumoniae
J. Aribisala - N. S’thebe, S. Sabiu, - Scientific Reports, 2024 usegalaxy.eu

Genomic Epidemiology of C2/H30Rx and C1-M27 Subclades of Escherichia coli ST131 Isolates from Clinical Blood Samples in Hungary
K. Tóth - I. Damjanova, L. Laczkó, L. Buzgó, et al. - Antibiotics, 2024 usegalaxy.eu

StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes
V. Bonthala - B. Stich, - Plant Cell Reports, 2024

Pannonibacter anstelovis sp. nov. Isolated from Two Cases of Bloodstream Infections in Paediatric Patients
S. Castellana - V. De Laurentiis, A. Bianco, L. Del Sambro, et al. - Microorganisms, 2024 usegalaxy.eu

Deep Regression for Biological Age Estimation in Multiple Organs: Investigations on 40,000 Subjects of the UK Biobank
V. Ecker - M. Früh, B. Yang, S. Gatidis, et al. - IEEE, 2024

Advancing pathogen surveillance by nanopore sequencing and genotype characterization of Acheta domesticus densovirus in mass-reared house crickets
F. Lim - J. González-Cabrera, J. Keilwagen, R. Kleespies, et al. - Scientific Reports, 2024

Complete genome sequence of <i>Pseudomonas aeruginosa</i> phage Knedl
E. Maffei - C. Manner, U. Jenal, A. Harms, et al. - Microbiology Resource Announcements, 2024 usegalaxy.eu

Complete genome sequence of <i>Pseudomonas aeruginosa</i> phage Knedl
E. Maffei - C. Manner, U. Jenal, A. Harms, et al. - Microbiology Resource Announcements, 2024 usegalaxy.eu

Complete genome sequence of <i>Escherichia coli</i> MP1
K. Pick - P. Stothard, T. Raivio, - Microbiology Resource Announcements, 2024 usegalaxy.eu

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
F. Silva - R. Domínguez-Santos, A. Latorre, C. García-Ferris, et al. - International Journal of Molecular Sciences, 2024 usegalaxy.eu

Enhancing the image analysis community in Galaxy
L. Kostrykin - T. Woller, M. Kalaš, B. Özdemir, et al. - Center for Open Science, 2024 usegalaxy.eu

Long-read datasets of Kayu Bawang (Azadirachta excelsa (Jack) Jacobs) from 3 different identified seed stands in Bengkulu (Sumatra), Indonesia and its phylogenetic relationships
E. Depari - N. Wijayanto, L. Karlinasari, M. Rafi, et al. - F1000Research, 2024 usegalaxy.eu

The Intellectual Disability Risk Gene<i>Kdm5b</i>Regulates Long-Term Memory Consolidation in the Hippocampus
L. Pérez-Sisqués - S. Bhatt, R. Matuleviciute, T. Gileadi, et al. - The Journal of Neuroscience, 2024 usegalaxy.eu

RepEnTools: an automated repeat enrichment analysis package for ChIP-seq data reveals hUHRF1 Tandem-Tudor domain enrichment in young repeats
M. Choudalakis - P. Bashtrykov, A. Jeltsch, - Mobile DNA, 2024 usegalaxy.eu

Dataset from RNAseq analysis of differential gene expression among developmental stages of two non-marine ostracodes
M. Vences - S. Anslan, J. Sabino-Pinto, M. Bonilla-Flores, et al. - Data in Brief, 2024

ZFP982 confers mouse embryonic stem cell characteristics by regulating expression of Nanog, Zfp42, and Dppa3
F. Dehghanian - P. Bovio, F. Gather, S. Probst, et al. - Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, 2024 usegalaxy.eu

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
T. Häkkänen - R. Rimhanen-Finne, J. Antikainen, E. Ruotsalainen, et al. - International Journal for Parasitology, 2024 usegalaxy.eu

The BAS chromatin remodeler determines brassinosteroid-induced transcriptional activation and plant growth in Arabidopsis
T. Zhu - C. Wei, Y. Yu, Z. Zhang, et al. - Developmental Cell, 2024 usegalaxy.eu

Rescue of Mycobacterium bovis DNA Obtained from Cultured Samples during Official Surveillance of Animal TB: Key Steps for Robust Whole Genome Sequence Data Generation
D. Pinto - G. Themudo, A. Pereira, A. Botelho, et al. - International Journal of Molecular Sciences, 2024 usegalaxy.eu

Antimicrobial Activity of Bacillus amyloliquefaciens BS4 against Gram-Negative Pathogenic Bacteria
A. Palacios-Rodriguez - A. Espinoza-Culupú, Y. Durán, T. Sánchez-Rojas, et al. - Antibiotics, 2024 usegalaxy.eu

First detection of a cefiderocol-resistant and extensively drug-resistant Acinetobacter baumannii clinical isolate in Bulgaria
T. Strateva - S. Peykov, - Acta Microbiologica et Immunologica Hungarica, 2024 usegalaxy.eu

Quantum chemistry based prediction of electron ionization mass spectra for environmental chemicals
H. Hecht - W. Rojas, Z. Ahmad, A. Křenek, et al. - American Chemical Society (ACS), 2024 usegalaxy.eu

DNA sequence data, multispecies coalescent and morphometrics shed new light on the systematics of Iberian islamiinae springsnails (Caenogastropoda: Hydrobiidae)
D. Delicado - J. Miller, F. García-Guerrero, B. Arconada, et al. - Journal of Molluscan Studies, 2024

SpatialData: an open and universal data framework for spatial omics
L. Marconato - G. Palla, K. Yamauchi, I. Virshup, et al. - Nature Methods, 2024

An <scp>RRM</scp> domain protein <scp>SOE</scp> suppresses transgene silencing in rice
R. Zhao - W. Wu, Y. Huang, X. Li, et al. - New Phytologist, 2024 usegalaxy.eu

Whole genome discovery of regulatory genes responsible for the response of chicken to heat stress
S. Hosseinzadeh - K. Hasanpur, - Scientific Reports, 2024 usegalaxy.eu

Private and well drinking water are reservoirs for antimicrobial resistant bacteria
M. Alawi - C. Smyth, D. Drissner, A. Zimmerer, et al. - npj Antimicrobials and Resistance, 2024 usegalaxy.eu

Complete Mitochondrial Genomes of Nedyopus patrioticus: New Insights into the Color Polymorphism of Millipedes
G. Zhang - T. Xu, Y. Chen, W. Xu, et al. - Current Issues in Molecular Biology, 2024 usegalaxy.eu

Comparative genomics of four lactic acid bacteria identified with Vitek MS (MALDI-TOF) and whole-genome sequencing
Ö. Kahraman-Ilıkkan - - Molecular Genetics and Genomics, 2024 usegalaxy.eu

The altered TBI fecal microbiome is stable and functionally distinct
R. Pyles - A. Miller, R. Urban, M. Sheffield-Moore, et al. - Frontiers in Molecular Neuroscience, 2024 usegalaxy.eu

Pangeo environment in Galaxy Earth System supported by Fair-Ease
T. Carval - M. Jossé, J. Detoc, - Copernicus GmbH, 2024 usegalaxy.eu

Atlas of cardiac endothelial cell enhancer elements linking the mineralocorticoid receptor to pathological gene expression
L. Deng - L. Pollmeier, R. Bednarz, C. Cao, et al. - Science Advances, 2024 usegalaxy.eu

Human Metagenome Analysis with COVID-19 Infectious Disease
K. Jain - R. Yadav, - Current Trends in Biotechnology and Pharmacy, 2024 usegalaxy.eu

Characterization of the major autolysin (AtlC) of Staphylococcus carnosus
M. Merz - C. Schiffer, A. Klingl, M. Ehrmann, et al. - BMC Microbiology, 2024 usegalaxy.eu

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
C. Wurzbacher - T. Haufschild, J. Hammer, M. van Teeseling, et al. - Scientific Reports, 2024 usegalaxy.eu

CD38–RyR2 axis–mediated signaling impedes CD8 <sup>+</sup> T cell response to anti-PD1 therapy in cancer
A. Kar - P. Ghosh, A. Gautam, S. Chowdhury, et al. - Proceedings of the National Academy of Sciences, 2024

The contribution of BvgR, RisA, and RisS to global gene regulation, intracellular cyclic-di-GMP levels, motility, and biofilm formation in Bordetella bronchiseptica
T. Nicholson - U. Waack, D. Fleming, Q. Chen, et al. - Frontiers in Microbiology, 2024 usegalaxy.eu

Decoding chromatin states by proteomic profiling of nucleosome readers
S. Lukauskas - A. Tvardovskiy, N. Nguyen, M. Stadler, et al. - Nature, 2024

Genomic and functional analysis of the mucinolytic species Clostridium celatum, Clostridium tertium, and Paraclostridium bifermentans
F. Candeliere - E. Musmeci, L. Sola, A. Amaretti, et al. - Frontiers in Microbiology, 2024 usegalaxy.eu

A synthetic biology approach to assemble and reboot clinically relevant <i>Pseudomonas aeruginosa</i> tailed phages
T. Ipoutcha - R. Racharaks, S. Huttelmaier, C. Wilson, et al. - Microbiology Spectrum, 2024 usegalaxy.eu

Targeted RNAseq Revealed the Gene Expression Signature of Ferroptosis-Related Processes Associated with Disease Severity in Patients with Multiple Sclerosis
L. Stojkovic - I. Jovanovic, E. Dincic, A. Djordjevic, et al. - International Journal of Molecular Sciences, 2024 usegalaxy.eu

Identification of genetic determinants of bedaquiline resistance in <i>Mycobacterium tuberculosis</i> in Ural region, Russia
T. Umpeleva - E. Chetverikova, D. Belyaev, N. Eremeeva, et al. - Microbiology Spectrum, 2024 usegalaxy.eu

The genome of the blind bee louse fly reveals deep convergences with its social host and illuminates Drosophila origins
H. Bastide - H. Legout, N. Dogbo, D. Ogereau, et al. - Current Biology, 2024 usegalaxy.eu

PCID2 dysregulates transcription and viral RNA processing to promote HIV-1 latency
R. Crespo - E. Ne, J. Reinders, J. Meier, et al. - iScience, 2024 usegalaxy.eu

Nonpreferential but Detrimental Accumulation of Macrophages With Clonal Hematopoiesis-Driver Mutations in Cardiovascular Tissues—Brief Report
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The cost of adaptability: resource availability constrains functional stability under pulsed disturbances
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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
Z. Zafar - M. Wood, S. Fatima, M. Bhatti, et al. - Journal of Biomolecular Structure and Dynamics, 2024 usegalaxy.eu

Identification and functional characterisation of a locus for target site integration in Fusarium graminearum
M. Darino - M. Urban, N. Kaur, A. Machado Wood, et al. - Fungal Biology and Biotechnology, 2024 usegalaxy.eu

Enhanced weathering in the US Corn Belt delivers carbon removal with agronomic benefits
D. Beerling - D. Epihov, I. Kantola, M. Masters, et al. - Proceedings of the National Academy of Sciences, 2024 usegalaxy.eu

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
K. Donátová - M. Mladá, K. Lopušná, F. Baran, et al. - International Journal of Molecular Sciences, 2024 usegalaxy.eu

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
G. Zhang - M. Gao, Y. Chen, Y. Wang, et al. - Genes, 2024 usegalaxy.eu

Biophysical and structural characterization of tetramethrin serum protein complex and its toxicological implications
P. Singh - P. Gopi, M. Rani, S. Singh, et al. - Journal of Molecular Recognition, 2024 usegalaxy.eu

Small RNAs from mitochondrial genome recombination sites are incorporated into T. gondii mitoribosomes
S. Tetzlaff - A. Hillebrand, N. Drakoulis, Z. Gluhic, et al. - eLife, 2024 usegalaxy.eu

Genome sequence of the ornamental plant<i>Digitalis purpurea</i>reveals the molecular basis of flower color and morphology variation
J. Horz - K. Wolff, R. Friedhoff, B. Pucker, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

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
N. Rahman - C. O'Cathail, A. Zyoud, A. Sokolov, et al. - Microbial Genomics, 2024 usegalaxy.eu

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
D. Liesner - G. Cossard, M. Zheng, O. Godfroy, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2024

Molecular Phylogenetics and Light Microscopy Reveal “True” and “False” Calacarines and Novel Genital Structures in Gall Mites (Acariformes, Eriophyoidea)
P. Chetverikov - C. Craemer, V. Gankevich, N. Le, et al. - Forests, 2024 usegalaxy.eu

Genome‐wide analysis of PvMADS in common bean and functional characterization of PvMADS31 in <i>Arabidopsis thaliana</i> as a player in abiotic stress responses
K. Mostafa - B. Yerlikaya, M. Abdulla, A. Aydin, et al. - The Plant Genome, 2024 usegalaxy.eu

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

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

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

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

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

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

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

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

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

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

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

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

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

Rat1 promotes premature transcription termination at R-loops
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Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy
D. Larivière - L. Abueg, N. Brajuka, C. Gallardo-Alba, et al. - Nature Biotechnology, 2024 usegalaxy.eu

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

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

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

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

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

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

Integrated analysis of RNA-seq datasets reveals novel targets and regulators of COVID-19 severity
T. Oliveira - J. Freitas, V. de Medeiros, T. Xavier, et al. - Life Science Alliance, 2024 usegalaxy.eu

Genetic variability of New Caledonian <i>Boeckella</i> De Guerne &amp; Richard, 1889 (Copepoda: Calanoida), with the description of a new species
C. Royaux - N. Charpin, N. Rabet, - Journal of Crustacean Biology, 2024 usegalaxy.eu

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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
S. Mathura - F. Sutton, V. Bowrin, - PLOS ONE, 2023 usegalaxy.eu

Automated MRI Lung Segmentation and 3D Morphologic Features for Quantification of Neonatal Lung Disease
B. Mairhörmann - A. Castelblanco, F. Häfner, V. Koliogiannis, et al. - Radiology: Artificial Intelligence, 2023

RNA interaction format: a general data format for RNA interactions
R. Schäfer - D. Rabsch, G. Scholz, P. Stadler, et al. - Bioinformatics, 2023

SIGNed explanations: Unveiling relevant features by reducing bias
N. Gumpfer - J. Prim, T. Keller, B. Seeger, et al. - Information Fusion, 2023

Genotypic Evolution of <i>Klebsiella pneumoniae</i> Sequence Type 512 during Ceftazidime/Avibactam, Meropenem/Vaborbactam, and Cefiderocol Treatment, Italy
G. Arcari - F. Cecilia, A. Oliva, R. Polani, et al. - Emerging Infectious Diseases, 2023 usegalaxy.eu

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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Multiple transcription factors mediate acclimation of Chlamydomonas to light stress
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A comprehension on structure guided alignment dependent 3D-QSAR modelling, and molecular dynamics simulation on 2,4-thiazolidinediones as aldose reductase inhibitors for the management of diabetic complications
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Proteometabolomics of initial and recurrent glioblastoma highlights an increased immune cell signature with altered lipid metabolism
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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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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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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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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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Changes in rice rhizosphere and bulk soil bacterial communities in the Doñana wetlands at different growth stages
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Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics
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Genotypic and phenotypic insights into virulence factors of nosocomial Stenotrophomonas maltophilia isolates collected in Bulgaria (2011–2022)
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Colorectal Cancer Archaeome: A Metagenomic Exploration, Tunisia
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The de novo transcriptome assembly of Agave angustifolia Haw, mining for carbohydrates and cellulose synthesis genes profiling, and molecular markers development
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Fifth mass extinction event triggered the diversification of the largest family of freshwater gastropods (Caenogastropoda: Truncatelloidea: Hydrobiidae)
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<i>Cuscuta campestris</i> fine-tunes gene expression during haustoriogenesis as an adaptation to different hosts
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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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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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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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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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Eomes restricts Brachyury functions at the onset of mouse gastrulation
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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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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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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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Recently evolved combination of unique sulfatase and amidase genes enables bacterial degradation of the wastewater micropollutant acesulfame worldwide
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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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Ploidy in Vibrio natriegens: Very Dynamic and Rapidly Changing Copy Numbers of Both Chromosomes
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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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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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Enhanced 5mC-Methylation-Site Recognition in DNA Sequences using Token Classification and a Domain-specific Loss Function
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Ribosome profiling reveals the fine-tuned response of<i>Escherichia coli</i>to mild and severe acid stress
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Proline and Silver Nitrate Promotes Multiple Shoot Induction from Mature Embryo and Shoot Tip Explants of Sorghum
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Laktik Asit Bakterilerinde Tetrasiklin Direncinin Fenotipik ve Tüm Genom Dizilerinde in silico Genotipik Olarak Araştırılması
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Comparative genome features and secondary metabolite biosynthetic potential of Kutzneria chonburiensis and other species of the genus Kutzneria
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A Roadmap for the Human Gut Cell Atlas
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CpG DNA methylation changes during epididymal sperm maturation in bulls
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SARS-CoV-2 spike protein diversity at an intra-host level, among SARS-CoV-2 infected individuals in South Africa, 2020 to 2022
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Species Delineation and Comparative Genomics within the<i>Campylobacter ureolyticus</i>Complex
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Genome-Based Retrospective Analysis of a Providencia stuartii Outbreak in Rome, Italy: Broad Spectrum IncC Plasmids Spread the NDM Carbapenemase within the Hospital
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β-Cell–Specific <i>E2f1</i> Deficiency Impairs Glucose Homeostasis, β-Cell Identity, and Insulin Secretion
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Comparative genomics of Brucella abortus and Brucella melitensis unravels the gene sharing, virulence factors and SNP diversity among the standard, vaccine and field strains
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<i>De Novo</i> Whole-Genome Sequencing of Two Pathogenic Pasteurella multocida Type D:6 Strains Isolated from Pigs
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Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA
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Genomic and transcriptomic analysis of camptothecin producing novel fungal endophyte -<i>Alternaria burnsii</i>NCIM 1409
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Single‐heartbeat cardiac cine imaging via jointly regularized nonrigid motion‐corrected reconstruction
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APOE expression and secretion are modulated by mitochondrial dysfunction
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Mapping cells through time and space with moscot
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MpoxRadar: a worldwide MPXV genomic surveillance dashboard
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Neonatal immune challenge poses a sex-specific risk for epigenetic microglial reprogramming and behavioral impairment
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Discovery and biosynthetic assessment of 'Streptomyces ortus' sp. nov. isolated from a deep-sea sponge
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Genetic architecture of brain age and its causal relations with brain and mental disorders
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A draft human pangenome reference
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Biosynthetic Potential of Hypogymnia Holobionts: Insights into Secondary Metabolite Pathways
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Phased grapevine genome sequence of an Rpv12 carrier for biotechnological exploration of resistance to Plasmopara viticola
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Emergence of Azithromycin-Resistant Neisseria gonorrhoeae Isolates Belonging to the NG-MAST Genogroup 12302 in Russia
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Mechanism-based and computational modeling of hydrogen sulfide biogenesis inhibition: interfacial inhibition
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Comparative Genomic Analysis and Species Delimitation: A Case for Two Species in the Zoonotic Cestode Dipylidium caninum
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Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in Prokaryotic metagenome-assembled genome recovery
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Automatic annotation of the bHLH gene family in plants
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ODNA: identification of organellar DNA by machine learning
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Free-breathing Arterial Spin Labeling MRI for the Detection of Pulmonary Embolism
A. Othman - C. Liang, Y. Komma, M. Munz, et al. - Radiology, 2023

Free-breathing Arterial Spin Labeling MRI for the Detection of Pulmonary Embolism
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Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
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Botryosphaeriaceae gene machinery: Correlation between diversity and virulence
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Direct Xylella fastidiosa whole genome sequencing from various plant species using targeted enrichment
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Rise and fall of SARS-CoV-2 variants in Rotterdam: Comparison of wastewater and clinical surveillance
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Foremost report of the whole genome of Spirabiliibacterium mucosae from India and comparative genomics of the novel genus Spirabiliibacterium
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Increasing complexity of opsin expression across stomatopod development
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How does particulate matter affect plant transcriptome and microbiome?
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DIET-like mutualism of Geobacter and methanogens at specific electrode potential boosts production of both methane and hydrogen from propionate
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Bioprospecting phytochemicals of Rosmarinus officinalis L. for targeting SARS-CoV-2 main protease (Mpro): a computational study
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Morphology and taxonomic assessment of eight genetic clades of Mercuria Boeters, 1971 (Caenogastropoda, Hydrobiidae), with the description of five new species
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Mapping lineage-traced cells across time points with moslin
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A physiologically based pharmacokinetic model for CYP2E1 phenotyping via chlorzoxazone
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Aircraft surveys for air eDNA: probing biodiversity in the sky
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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
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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
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Agrobacterium cucumeris sp. nov. isolated from crazy roots on cucumber (Cucumis sativus)
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Mapping Normative Trajectories of Cognitive Function and Its Relation to Psychopathology Symptoms and Genetic Risk in Youth
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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
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DNA ultra-sensitive quantification, a technology for studying HIV unintegrated linear DNA
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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
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Comparative genomic analysis of Colistin resistant Escherichia coli isolated from pigs, a human and wastewater on colistin withdrawn pig farm
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External <scp>DNA</scp> contamination and efficiency of bleach decontamination for arthropod diet analysis
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An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype
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Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra
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New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
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Recovery of 197 eukaryotic bins reveals major challenges for eukaryote genome reconstruction from terrestrial metagenomes
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Candidate miRNAs from Oryza sativa for Silencing the Rice Tungro Viruses
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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
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Sex-biased gene expression in nutrient-sensing pathways
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Sex-biased gene expression in nutrient-sensing pathways
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Return of the Tbx5; lineage-tracing reveals ventricular cardiomyocyte-like precursors in the injured adult mammalian heart
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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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Comparative phylogenomic insights of KCS and ELO gene families in Brassica species indicate their role in seed development and stress responsiveness
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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.
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Analysis of biofilm formation in nosocomial Stenotrophomonas maltophilia isolates collected in Bulgaria: An 11-year study (2011–2022)
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Evaluating Tuning Strategies for Sequence Generation with Protein Language Models
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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
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Proteomics analysis reveals three potential cacao target that interacts with Moniliophthora perniciosa NEP during witches broom disease
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Zinc controls operator affinity of human transcription factor YY1 by mediating dimerization via its N-terminal region
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A comprehensive review of bioinformatics tools for chromatin loop calling
L. Liu - K. Han, H. Sun, L. Han, et al. - Briefings in Bioinformatics, 2023 usegalaxy.eu

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

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

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

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

Draft Genome Sequence of an Isolate of Genotype VII Newcastle Disease Virus Isolated from an Outbreak in Fighting Cock in Peru
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S-Locus Genotyping in Japanese Plum by High Throughput Sequencing Using a Synthetic S-Loci Reference Sequence
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Whole genome sequence analysis of the first reported isolate of Salmonella Agona carrying blaCTX-M-55 gene in Brazil
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Tailored Multiplex Real-Time RT-PCR with Species-Specific Internal Positive Controls for Detecting SARS-CoV-2 in Canine and Feline Clinical Samples
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Ceftazidime–avibactam resistance in Klebsiella pneumoniae sequence type 37: a decade of persistence and concealed evolution
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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
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Intrasexual cuticular hydrocarbon dimorphism in a wasp sheds light on hydrocarbon biosynthesis genes in Hymenoptera
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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
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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
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Sensitive clustering of protein sequences at tree-of-life scale using DIAMOND DeepClust
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A Physcomitrella <scp>PIN</scp> protein acts in spermatogenesis and sporophyte retention
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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
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The Full Genome Sequences of Pseudomonas sp. Strain MM221 and <i>Pseudoarthrobacter</i> sp. Strain MM222, Isolated from a Meadow in Bielefeld, Germany
M. Eisenhut - M. Hawrylo, K. Trevlopoulou, H. Fingerhut, et al. - Microbiology Resource Announcements, 2023

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

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
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Melibiose–X-Gal–MacConkey Agar for Presumptive Differentiation of Escherichia albertii from E. coli and Salmonella from Poultry Meat
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nf-root: a best-practice pipeline for deep learning-based analysis of apoplastic pH in microscopy images of developmental zones in plant root tissue
J. Wanner - L. Cuellar, L. Rausch, K. Berendzen, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2023

Apiaceae FNS I originated from F3H through tandem gene duplication
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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
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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>
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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
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Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work
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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

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

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

Transcriptional Profiling Identifies Prognostic Gene Signatures for Conjunctival Extranodal Marginal Zone Lymphoma
J. Wolf - T. Reinhard, R. Hajdu, G. Schlunck, et al. - Biomolecules, 2023 usegalaxy.eu

MuLan-Methyl - Multiple Transformer-based Language Models for Accurate DNA Methylation Prediction
W. Zeng - A. Gautam, D. Huson, - bioRxiv - Cold Spring Harbor Laboratory, 2023

Multimodal epigenetic changes and altered NEUROD1 chromatin binding in the mouse hippocampus underlie FOXG1 syndrome
I. Akol - A. Izzo, F. Gather, S. Strack, et al. - Proceedings of the National Academy of Sciences, 2023 usegalaxy.eu

Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa
A. Soorni - M. Karimi, B. Al Sharif, K. Habibi, et al. - BMC Plant Biology, 2023 usegalaxy.eu

Physics-Driven Deep Learning for Computational Magnetic Resonance Imaging: Combining physics and machine learning for improved medical imaging
K. Hammernik - T. Kustner, B. Yaman, Z. Huang, et al. - IEEE Signal Processing Magazine, 2023

CRISPRi screening identifies CASP8AP2 as an essential viability factor in lung cancer controlling tumor cell death via the AP-1 pathway
K. Myacheva - A. Walsh, M. Riester, G. Pelos, et al. - Cancer Letters, 2023 usegalaxy.eu

RPS6 transcriptional modulation in neural tissues of Nauphoeta cinerea during streptozotocin-associated sugar metabolism impairment.
O. Olagoke - A. Segatto, B. Afolabi, D. Ardisson-Araujo, et al. - Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, 2023 usegalaxy.eu

The regulation of glutathione s-transferases by gibberellic acid application in salt treated maize leaves
B. Seckin Dinler - H. Cetinkaya, Z. Secgin, - Physiology and Molecular Biology of Plants, 2023 usegalaxy.eu

Triose phosphate export from chloroplasts and cellular sugar content regulate anthocyanin biosynthesis during high light acclimation
M. Zirngibl - G. Araguirang, A. Kitashova, K. Jahnke, et al. - Plant Communications, 2023 usegalaxy.eu

Cell Segmentation of in situ Transcriptomics Data Using Signed Graph Partitioning
A. Andersson - A. Behanova, C. Wählby, F. Malmberg, et al. - Springer Nature Switzerland, 2023

Revealing the small proteome of<i>Haloferax volcanii</i>by combining ribosome profiling and small-protein optimized mass spectrometry
L. Hadjeras - J. Bartel, L. Maier, S. Maaß, et al. - microLife, 2023

Unraveling the small proteome of the plant symbiont<i>Sinorhizobium meliloti</i>by ribosome profiling and proteogenomics
L. Hadjeras - B. Heiniger, S. Maaß, R. Scheuer, et al. - microLife, 2023

Characterization of mercury species and microbial communities in sediments and suspended particulate matter from historically contaminated river systems
J. Wiederhold - L. Gfeller, N. Marquardt, A. Alten, et al. - European Association of Geochemistry, 2023

DIAMOND +  MEGAN Microbiome Analysis
A. Gautam - W. Zeng, D. Huson, - Springer US, 2023

Mimicking Tumor Cell Heterogeneity of Colorectal Cancer in a Patient-derived Organoid-Fibroblast Model
V. Atanasova - C. de Jesus Cardona, V. Hejret, A. Tiefenbacher, et al. - Cellular and Molecular Gastroenterology and Hepatology, 2023

Unraveling the small proteome of the plant symbiont<i>Sinorhizobium meliloti</i>by ribosome profiling and proteogenomics
L. Hadjeras - B. Heiniger, S. Maaß, R. Scheuer, et al. - microLife, 2023

A bibliometric analysis and visualization of spatially resolved transcriptomics
D. Huang . - Y. Gou, X. Wang, Q. Li, et al. - Blood&amp;Genomics, 2023

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

Structural modelling of human complement FHR1 and two of its synthetic derivatives provides insight into their in-vivo functions
N. Ruiz-Molina - J. Parsons, E. Decker, R. Reski, et al. - Computational and Structural Biotechnology Journal, 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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Hybrid Genome Assembly of Short and Long Reads in Galaxy
T. Ohta - Y. Shiwa, - Springer US, 2023 usegalaxy.eu

Detection of domestic cat hepadnavirus by next-generation sequencing and epidemiological survey in Japan
H. SAKAMOTO - G. ITO, Y. GOTO-KOSHINO, M. SAKAMOTO, et al. - Journal of Veterinary Medical Science, 2023 usegalaxy.eu

Genomic Epidemiological Analysis of Antimicrobial-Resistant Bacteria with Nanopore Sequencing
M. Suzuki - Y. Hashimoto, A. Hirabayashi, K. Yahara, et al. - Springer US, 2023 usegalaxy.eu

Analysis of RNA Sequences and Modifications Using NASE
S. Wein - - Springer US, 2023 usegalaxy.eu

Exploring Scutellaria baicalensis bioactives as EGFR tyrosine kinase inhibitors: Cheminformatics and molecular docking studies
A. Yusuf - A. Adegboyega, A. Yakubu, G. Johnson, et al. - Informatics in Medicine Unlocked, 2023 usegalaxy.eu

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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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
A. Kumar - G. Cuccuru, B. Grüning, R. Backofen, et al. - GigaScience, 2022 usegalaxy.eu

Genomic epidemiology of SARS- CoV-2 Omicron variants in the Republic of Korea
D. Lee - J. Kim, A. Park, D. Kim, et al. - Scientific Reports, 2022 usegalaxy.eu

Guiding the choice of informatics software and tools for lipidomics research applications
Z. Ni - M. Wölk, G. Jukes, K. Mendivelso Espinosa, et al. - Nature Methods, 2022

The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain
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Better Together
S. Gatidis - T. Kart, M. Fischer, S. Winzeck, et al. - Investigative Radiology, 2022

Better Together
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Genomic analysis and biological characterization of a novel Schitoviridae phage infecting Vibrio alginolyticus
S. Tajuddin - A. Khan, L. Chong, C. Wong, et al. - Applied Microbiology and Biotechnology, 2022 usegalaxy.eu

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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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
R. Morard - C. Hassenrück, M. Greco, A. Fernandez-Guerra, et al. - Nature Communications, 2022

Frequent spontaneous structural rearrangements promote rapid genome diversification in a Brassica napus F1 generation
M. Orantes-Bonilla - M. Makhoul, H. Lee, H. Chawla, et al. - Frontiers in Plant Science, 2022

MarineMetagenomeDB: a public repository for curated and standardized metadata for marine metagenomes
M. Nata’ala - A. Avila Santos, J. Coelho Kasmanas, A. Bartholomäus, et al. - Environmental Microbiome, 2022

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
T. Zhang - C. Künne, D. Ding, S. Günther, et al. - Nature Communications, 2022 usegalaxy.eu

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

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
H. Mack - L. Buck, S. Skalet, J. Kremer, et al. - Cells, 2022

Automated imaging-based abdominal organ segmentation and quality control in 20,000 participants of the UK Biobank and German National Cohort Studies
T. Kart - M. Fischer, S. Winzeck, B. Glocker, et al. - Scientific Reports, 2022

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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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
A. Ardisasmita - I. Schene, I. Joore, G. Kok, et al. - Communications Biology, 2022 usegalaxy.eu

Disturbed trophoblast transition links preeclampsia progression from placenta to the maternal syndrome
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The first transcriptomic analyses of fruits and cladodes for comparison between three species of Opuntia
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Epigenetic nature of <i>Arabidopsis thaliana</i> telomeres
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
S. Mehta - V. Carvalho, A. Rajczewski, O. Pible, et al. - Viruses, 2022 usegalaxy.eu

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
S. Gatidis - T. Hepp, M. Früh, C. La Fougère, et al. - Scientific Data, 2022

Self-supervised learning for automated anatomical tracking in medical image data with minimal human labeling effort
M. Frueh - T. Kuestner, M. Nachbar, D. Thorwarth, et al. - Computer Methods and Programs in Biomedicine, 2022

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
M. Orantes-Bonilla - H. Wang, H. Lee, A. Golicz, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

On the way to plant data commons – a genotyping use case
M. Feser - P. König, A. Fiebig, D. Arend, et al. - Journal of Integrative Bioinformatics, 2022

Detecting DNA of novel fungal pathogens using ResNets and a curated fungi-hosts data collection
J. Bartoszewicz - F. Nasri, M. Nowicka, B. Renard, et al. - Bioinformatics, 2022

CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection
A. Mitrofanov - M. Ziemann, O. Alkhnbashi, W. Hess, et al. - Bioinformatics, 2022 usegalaxy.eu

Identification of SARS-CoV-2 Variants of Concern Using Amplicon Next-Generation Sequencing
A. Nasereddin - H. Golan Berman, D. Wolf, E. Oiknine-Djian, et al. - Microbiology Spectrum, 2022 usegalaxy.eu

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>
B. Frommer - S. Müllner, D. Holtgräwe, P. Viehöver, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

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

Recurrent founder-event speciation across the Mediterranean likely shaped the species diversity and geographic distribution of the freshwater snail genus Mercuria Boeters, 1971 (Caenogastropoda: Hydrobiidae)
J. Miller - D. Delicado, F. García-Guerrero, M. Ramos, et al. - Molecular Phylogenetics and Evolution, 2022

An outbreak sustained by ST15 Klebsiella pneumoniae carrying 16S rRNA methyltransferases and blaNDM: evaluation of the global dissemination of these resistance determinants
F. Sacco - G. Raponi, A. Oliva, G. Bibbolino, et al. - International Journal of Antimicrobial Agents, 2022 usegalaxy.eu

Microbiome of the freshwater sponge <i>Ephydatia muelleri</i> shares compositional and functional similarities with those of marine sponges
S. Sugden - J. Holert, E. Cardenas, W. Mohn, et al. - The ISME Journal, 2022

Genetic and genomic diversity in the sorghum gene bank collection of Uganda
S. Chakrabarty - R. Mufumbo, S. Windpassinger, D. Jordan, et al. - BMC Plant Biology, 2022

Potential of enriched and stabilized anaerobic lignocellulolytic fungi coexisting with bacteria and methanogens for enhanced methane production from rice straw
N. Thongbunrod - P. Chaiprasert, - Biomass Conversion and Biorefinery, 2022 usegalaxy.eu

Concurrent molecular characterization of sand flies and Leishmania parasites by amplicon-based next-generation sequencing
A. Nasereddin - S. Ereqat, A. Al-Jawabreh, M. Taradeh, et al. - Parasites &amp; Vectors, 2022 usegalaxy.eu

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
W. Liao - M. Asri, J. Ebler, D. Doerr, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

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

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

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

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

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

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

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

Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors
S. Feng - C. Rastogi, R. Loker, W. Glassford, et al. - Nature Communications, 2022 usegalaxy.eu

Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy
M. Liu - A. Hernandez-Morales, J. Clark, T. Le, et al. - Nature Communications, 2022 usegalaxy.eu

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)
N. Kuzmanović - E. Biondi, J. Overmann, J. Puławska, et al. - BMC Genomics, 2022

MuDoGeR: Multi-Domain Genome Recovery from metagenomes made easy
U. Nunes da Rocha - J. Kasmanas, R. Kallies, J. Saraiva, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

Histone Deacetylase 6 Inhibitor JS28 Prevents Pathological Gene Expression in Cardiac Myocytes
V. Ngo - B. Fleischmann, M. Jung, L. Hein, et al. - Journal of the American Heart Association, 2022 usegalaxy.eu

BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis
W. Ouyang - F. Beuttenmueller, E. Gómez-de-Mariscal, C. Pape, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

Structural analysis of microbiomes from salt caverns used for underground gas storage
L. Schwab - D. Popp, G. Nowack, P. Bombach, et al. - International Journal of Hydrogen Energy, 2022

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

AB12PHYLO: An Integrated Pipeline for Maximum Likelihood Phylogenetic Inference from ABI Trace Data
L. Kaindl - C. Small, R. Stam, - PhytoFrontiers™, 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.
H. Mafakheri - S. Taghavi, K. Khezerpour, N. Kuzmanović, et al. - Phytopathology®, 2022

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
S. Ereqat - S. Cauchi, K. Eweidat, M. Elqadi, et al. - Biomedical Reports, 2022 usegalaxy.eu

A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data
M. Neumann - X. Xu, C. Smaczniak, J. Schumacher, et al. - Nature Communications, 2022

Construction and characterization of a de novo draft genome of garden cress (Lepidium sativum L.)
A. Patat - F. Sen, B. Erdogdu, A. Uncu, et al. - Functional &amp; Integrative Genomics, 2022 usegalaxy.eu

Absence of increased genomic variants in the cyanobacterium Chroococcidiopsis exposed to Mars-like conditions outside the space station
A. Napoli - D. Micheletti, M. Pindo, S. Larger, et al. - Scientific Reports, 2022 usegalaxy.eu

Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria
M. Mungan - T. Harbig, N. Perez, S. Edenhart, et al. - Nucleic Acids Research, 2022

Transcriptomic changes induced by applications of a commercial extract of Ascophyllum nodosum on tomato plants
O. Ali - A. Ramsubhag, S. Daniram Benn Jr. Ramnarine, J. Jayaraman, et al. - Scientific Reports, 2022 usegalaxy.eu

Ezh2 competes with p53 to license lncRNA Neat1 transcription for inflammasome activation
J. Yuan - Q. Zhu, X. Zhang, Z. Wen, et al. - Cell Death &amp; Differentiation, 2022 usegalaxy.eu

ODGI: understanding pangenome graphs
A. Guarracino - S. Heumos, S. Nahnsen, P. Prins, et al. - Bioinformatics, 2022

Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity
K. Fröhlich - E. Brombacher, M. Fahrner, D. Vogele, et al. - Nature Communications, 2022 usegalaxy.eu

Interactive analysis of biosurfactants in fruit-waste fermentation samples using BioSurfDB and MEGAN
G. Silva - A. Gautam, I. Duarte, T. Delforno, et al. - Scientific Reports, 2022

Genetic Divergence of Lineage-Specific Tandemly Duplicated Gene Clusters in Four Diploid Potato Genotypes
V. Bonthala - B. Stich, - Frontiers in Plant Science, 2022

Identification of SARS‐CoV‐2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021
K. Subramoney - N. Mtileni, A. Bharuthram, A. Davis, et al. - Journal of Medical Virology, 2022 usegalaxy.eu

MaxQuant and MSstats in Galaxy Enable Reproducible Cloud-Based Analysis of Quantitative Proteomics Experiments for Everyone
N. Pinter - D. Glätzer, M. Fahrner, K. Fröhlich, et al. - Journal of Proteome Research, 2022 usegalaxy.eu

The potential of bacterial key species as a tool for monitoring peatland quality
F. Saragih - . Nelvia, N. Pratiwi, D. Zul, et al. - IOP Conference Series: Earth and Environmental Science, 2022 usegalaxy.eu

Bacterial key species candidates for biomonitoring peatland burnt in the Giam Siak Kecil-Bukit Batu biosphere reserve, Riau
P. Zebua - . Nelvia, N. Pratiwi, D. Zul, et al. - IOP Conference Series: Earth and Environmental Science, 2022 usegalaxy.eu

Agrobacterium vaccinii sp. nov. isolated from galls on blueberry plants (Vaccinium corymbosum)
J. Puławska - N. Kuzmanović, P. Trzciński, - Systematic and Applied Microbiology, 2022

Genomic Analysis of Endophytic Bacillus-Related Strains Isolated from the Medicinal Plant Origanum vulgare L. Revealed the Presence of Metabolic Pathways Involved in the Biosynthesis of Bioactive Compounds
G. Semenzato - T. Alonso-Vásquez, S. Del Duca, A. Vassallo, et al. - Microorganisms, 2022 usegalaxy.eu

Age-related brain deviations and aggression
N. Holz - D. Floris, A. Llera, P. Aggensteiner, et al. - Psychological Medicine, 2022

Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water
J. Farrell - L. Whitmore, N. Mashkour, D. Rollinson Ramia, et al. - Molecular Ecology Resources, 2022 usegalaxy.eu

A quantitative framework to infer the effect of traits, diversity and environment on dispersal and extinction rates from fossils
T. Hauffe - M. Pires, T. Quental, T. Wilke, et al. - Methods in Ecology and Evolution, 2022

Genotyping of Circulating Free DNA Enables Monitoring of Tumor Dynamics in Synovial Sarcomas
A. Eisenhardt - Z. Brugger, U. Lausch, J. Kiefer, et al. - Cancers, 2022 usegalaxy.eu

Variant Analysis and Strategic Clustering to Sub-Lineage of Double Mutant Strain B.1.617 of SARS-CoV-2
V. Mevada - R. Patel, P. Dudhagara, H. Gandhi, et al. - COVID, 2022 usegalaxy.eu

Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease
S. Bray - T. Dudgeon, R. Skyner, R. Backofen, et al. - Journal of Cheminformatics, 2022 usegalaxy.eu

Goslin 2.0 Implements the Recent Lipid Shorthand Nomenclature for MS-Derived Lipid Structures
D. Kopczynski - N. Hoffmann, B. Peng, G. Liebisch, et al. - Analytical Chemistry, 2022

Identification and annotation of peptide allergens in Prunus dulcis
A. Singh - A. Upadhyay, - Research Square - Research Square Platform LLC, 2022 usegalaxy.eu

Ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of phosphorylated and cross-linked peptides
T. Altenburg - S. Giese, S. Wang, T. Muth, et al. - Nature Machine Intelligence, 2022

NFATc1 signaling drives chronic ER stress responses to promote NAFLD progression
M. Latif - G. Schmidt, S. Mercan, R. Rahman, et al. - Gut, 2022 usegalaxy.eu

Critical Assessment of Metagenome Interpretation: the second round of challenges
F. Meyer - A. Fritz, Z. Deng, D. Koslicki, et al. - Nature Methods, 2022

Evaluation of machine learning strategies for imaging confirmed prostate cancer recurrence prediction on electronic health records
J. Beinecke - P. Anders, T. Schurrat, D. Heider, et al. - Computers in Biology and Medicine, 2022

Enabling technologies towards personalization of scaffolds for large bone defect regeneration
P. Poh - T. Lingner, S. Kalkhof, S. Märdian, et al. - Current Opinion in Biotechnology, 2022

Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes
J. Ebler - P. Ebert, W. Clarke, T. Rausch, et al. - Nature Genetics, 2022

Comparative transcriptome analysis of human and murine choroidal neovascularization identifies fibroblast growth factor inducible-14 as phylogenetically conserved mediator of neovascular age-related macular degeneration
J. Wolf - A. Schlecht, D. Rosmus, S. Boneva, et al. - Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 2022 usegalaxy.eu

Unifying the known and unknown microbial coding sequence space
C. Vanni - M. Schechter, S. Acinas, A. Barberán, et al. - eLife, 2022

Sex differences in the early life stages of the salmon louse Lepeophtheirus salmonis (Copepoda: Caligidae)
A. Borchel - A. Komisarczuk, F. Nilsen, - PLOS ONE, 2022 usegalaxy.eu

Machine learning-assisted identification of bioindicators predicts medium-chain carboxylate production performance of an anaerobic mixed culture
B. Liu - H. Sträuber, J. Saraiva, H. Harms, et al. - Microbiome, 2022

Taxonomy of Rhizobiaceae revisited: proposal of a new framework for genus delimitation
N. Kuzmanović - C. Fagorzi, A. Mengoni, F. Lassalle, et al. - International Journal of Systematic and Evolutionary Microbiology, 2022

Multi-Modality Microscopy Image Style Augmentation for Nuclei Segmentation
Y. Liu - S. Wagner, T. Peng, - Journal of Imaging, 2022

Deciphering the Molecular Signature of Human Hyalocytes in Relation to Other Innate Immune Cell Populations
J. Wolf - S. Boneva, D. Rosmus, H. Agostini, et al. - Investigative Opthalmology &amp; Visual Science, 2022 usegalaxy.eu

Mimicking tumor cell heterogeneity of colorectal cancer in a patient-derived organoid-fibroblast model
V. Atanasova - C. de Jesus Cardona, V. Hejret, A. Tiefenbacher, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2022

Genome and proteome analyses show the gaseous alkane degrader <i>Desulfosarcina</i> sp. strain <scp>BuS5</scp> as an extreme metabolic specialist
S. Chen - J. Ji, D. Popp, U. Jaekel, et al. - Environmental Microbiology, 2022

Transcriptomic Stress Response in Streptococcus mutans following Treatment with a Sublethal Concentration of Chlorhexidine Digluconate
D. Muehler - X. Mao, S. Czemmel, J. Geißert, et al. - Microorganisms, 2022

Micro-RNA-Regulated SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) Gene Expression and Cytokinin Accumulation Distinguish Early-Developing Male and Female Inflorescences in Oil Palm (Elaeis guineensis)
J. Tregear - F. Richaud, M. Collin, J. Esbelin, et al. - Plants, 2022 usegalaxy.eu

Pathogenicity of Shiga toxin-producing Escherichia coli (STEC) from wildlife: Should we care?
D. Dias - S. Costa, C. Fonseca, R. Baraúna, et al. - Science of The Total Environment, 2022 usegalaxy.eu

In vitro and in silico analysis of Brilliant Black degradation by Actinobacteria and a Paraburkholderia sp.
S. Kumaran - A. Ngo, F. Schultes, V. Saravanan, et al. - Genomics, 2022 usegalaxy.eu

Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N6-carboxymethyllysine
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The Human Eye Transcriptome Atlas: A searchable comparative transcriptome database for healthy and diseased human eye tissue
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SSAM-lite: A Light-Weight Web App for Rapid Analysis of Spatially Resolved Transcriptomics Data
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Olfactomedin-4 improves cutaneous wound healing by promoting skin cell proliferation and migration through POU5F1/OCT4 and ESR1 signalling cascades
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Environmental filtering drives assembly of diatom communities over evolutionary time‐scales
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Shell features and anatomy of the springsnail genus <i>Radomaniola</i> (Caenogastropoda: Hydrobiidae) show a different pace and mode of evolution over five million years
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Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis
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Whole-Genome Sequence of Pseudomonas sp. Strain MM211, Isolated from Soil in Langenfeld, Germany
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Onset of Late Cretaceous diversification in Europe’s freshwater gastropod fauna links to global climatic and biotic events
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Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives
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Pluripotency factors determine gene expression repertoire at zygotic genome activation
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Unsupervised encoding selection through ensemble pruning for biomedical classification
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STENCIL: A web templating engine for visualizing and sharing life science datasets
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Identification Of Taxa and Functional Pathway Information Of Mycobacterium tuberculosis Microbiome And High Throughput Simulation Studies With Mycobacteriophage
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Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines
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Phage Genome Diversity in a Biogas-Producing Microbiome Analyzed by Illumina and Nanopore GridION Sequencing
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Targeted DamID in <i>C. elegans</i> reveals a direct role for LIN-22 and NHR-25 in antagonizing the epidermal stem cell fate
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Drivers of diversification in freshwater gastropods vary over deep time
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The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities
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Impact of high platelet turnover on the platelet transcriptome: Results from platelet RNA-sequencing in patients with sepsis
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sPLINK: a hybrid federated tool as a robust alternative to meta-analysis in genome-wide association studies
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Ultraviolet vision in larval <i>Neogonodactylus oerstedii</i>
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Ultraviolet vision in larval <i>Neogonodactylus oerstedii</i>
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TcTI, a Kunitz-type trypsin inhibitor from cocoa associated with defense against pathogens
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What’s left in the tank? Identification of non-ascribed aquarium’s coral collections with DNA barcodes as part of an integrated diagnostic approach
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SARS-CoV-2 Reverse Zoonoses to Pumas and Lions, South Africa
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<i>Saccharomyces boulardii</i> CNCM I‐745 supplementation modifies the fecal resistome during <i>Helicobacter pylori</i> eradication therapy
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Interplay between Klebsiella pneumoniae producing KPC-31 and KPC-3 under treatment with high dosage meropenem: a case report
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Regulation of fatty acid desaturase- and immunity gene-expression by mbk-1/DYRK1A in Caenorhabditis elegans
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LAMP Assay for Distinguishing <i>Fusarium oxysporum</i> and <i>Fusarium commune</i> in Lotus (<i>Nelumbo nucifera</i>) Rhizomes
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Expanding the Galaxy’s reference data
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Multi-label classification for multi-drug resistance prediction of Escherichia coli
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Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework
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A Tetragenococcus halophilus human gut isolate
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Oxa-376 and Oxa-530 variants of β-lactamase: computational study uncovers potential therapeutic targets of<i>Acinetobacter baumannii</i>
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Recapitulating Cholangiopathy-Associated Necroptotic Cell Death In Vitro Using Human Cholangiocyte Organoids
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Canonical Workflows to Make Data FAIR
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Plankton-infecting relatives of herpesviruses clarify the evolutionary trajectory of giant viruses
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Taxonomic transfer of two species of hydrobiid snails from western Anatolia (Caenogastropoda, Truncatelloidea) to two new genera, based on molecular and morphological evidence
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CoxBase: an Online Platform for Epidemiological Surveillance, Visualization, Analysis, and Typing of Coxiella burnetii Genomic Sequences
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Diel Protein Regulation of Marine Picoplanktonic Communities Assessed by Metaproteomics
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PLaBAse: A comprehensive web resource for analyzing the plant growth-promoting potential of plant-associated bacteria
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COVID-19++: A Citation-Aware Covid-19 Dataset for the Analysis of Research Dynamics
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An ecological perspective on microbial genes of unknown function in soil
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Transcriptomic Profiling and Microsatellite Identification in Cobia (Rachycentron canadum), Using High-Throughput RNA Sequencing
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Plant circadian clock control of <i>Medicago truncatula</i> nodulation via regulation of nodule cysteine-rich peptides
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LAPNet: Non-Rigid Registration Derived in k-Space for Magnetic Resonance Imaging
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Conservation and divergence in gene regulation between mouse and human immune cells deserves equal emphasis
S. Gilbertson - A. Weinmann, - Trends in Immunology, 2021 usegalaxy.eu

Current Trends and Future Directions of Large Scale Image and Video Annotation: Observations From Four Years of BIIGLE 2.0
M. Zurowietz - T. Nattkemper, - Frontiers in Marine Science, 2021

Using AnnoTree to get more assignments, faster, in DIAMOND+MEGAN microbiome analysis
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Expression Atlas update: gene and protein expression in multiple species
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Dissection of Quantitative Blackleg Resistance Reveals Novel Variants of Resistance Gene Rlm9 in Elite Brassica napus
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New Putative Long Non-Coding RNAs (lncRNA) Revealed by Pan-Transcriptome of the Emerging Human Pathogenic Fungus Talaromyces Marneffei
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Interactive Analysis of Biosurfactants in Fruit-Waste Fermentation Samples using BioSurfDB and MEGAN
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Peakhood: individual site context extraction for CLIP-seq peak regions
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The transcriptome of Balamuthia mandrillaris trophozoites for structure-guided drug design
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Variimorphobacter saccharofermentans gen. nov., sp. nov., a new member of the family Lachnospiraceae, isolated from a maize-fed biogas fermenter
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The chitinolytic activity of the Curtobacterium sp. isolated from field-grown soybean and analysis of its genome sequence
I. Dimkić - V. Bhardwaj, V. Carpentieri-Pipolo, N. Kuzmanović, et al. - PLOS ONE, 2021

Viral suppressor of <scp>RNA</scp> silencing in vascular plants also interferes with the development of the bryophyte <scp><i>Physcomitrella patens</i></scp>
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Constitutively enhanced genome integrity maintenance and direct stress mitigation characterize transcriptome of extreme stress‐adapted <i>Arabidopsis halleri</i>
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Somatostatin 3 loss of function impairs the innate immune response to intestinal inflammation
J. Ma - J. Chen, B. Louro, R. Martins, et al. - Aquaculture and Fisheries, 2021 usegalaxy.eu

ARTS-DB: a database for antibiotic resistant targets
M. Mungan - K. Blin, N. Ziemert, - Nucleic Acids Research, 2021

Fibropapillomatosis and Chelonid Alphaherpesvirus 5 Infection in Kemp’s Ridley Sea Turtles (Lepidochelys kempii)
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From celiac disease to coccidia infection and vice‐versa: The polyQ peptide CXCR3‐interaction axis
M. Lauxmann - D. Vazquez, H. Schilbert, P. Neubauer, et al. - BioEssays, 2021

Histone H4 lysine 16 acetylation controls central carbon metabolism and diet-induced obesity in mice
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Automatic identification and annotation of MYB gene family members in plants
B. Pucker - - bioRxiv - Cold Spring Harbor Laboratory, 2021

Weakly supervised segmentation of tumor lesions in PET-CT hybrid imaging
M. Früh - M. Fischer, A. Schilling, S. Gatidis, et al. - Journal of Medical Imaging, 2021

Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer
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TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes
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Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning
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eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
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Beta-lactam resistance development during the treatment processes of municipal wastewater treatment plants
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Ready-to-use public infrastructure for global SARS-CoV-2 monitoring
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OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes
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Screening of<i>Azadirachta indica</i>phytoconstituents as GSK-3β inhibitor and its implication in neuroblastoma: molecular docking, molecular dynamics, MM-PBSA binding energy, and in-vitro study
S. Chandel - R. Singh, A. Gautam, V. Ravichandiran, et al. - Journal of Biomolecular Structure and Dynamics, 2021

Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid
K. Peters - S. Herman, P. Khoonsari, J. Burman, et al. - Scientific Reports, 2021 usegalaxy.eu

Genomic impact of stress-induced transposable element mobility in Arabidopsis
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Nascent Transcript Sequencing for the Mapping of Promoters in Arabidopsis thaliana Mitochondria
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Multiple Occurrences of a 168-Nucleotide Deletion in SARS-CoV-2 ORF8, Unnoticed by Standard Amplicon Sequencing and Variant Calling Pipelines
D. Brandt - M. Simunovic, T. Busche, M. Haak, et al. - Viruses, 2021

Evolutionary Trajectories toward Ceftazidime-Avibactam Resistance in Klebsiella pneumoniae Clinical Isolates
A. Carattoli - G. Arcari, G. Bibbolino, F. Sacco, et al. - Antimicrobial Agents and Chemotherapy, 2021 usegalaxy.eu

FIBCD1 is a Conserved Receptor for Chondroitin Sulphate Proteoglycans of the Brain Extracellular Matrix and a Candidate Gene for a Complex Neurodevelopmental Disorder
C. Fell - A. Hagelkruys, A. Cicvaric, M. Horrer, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species
S. Hering - M. Jansson, M. Buhl, - International Journal of Systematic and Evolutionary Microbiology, 2021 usegalaxy.eu

The temperature-regulated DEAD-box RNA helicase CrhR interactome: autoregulation and photosynthesis-related transcripts
A. Migur - F. Heyl, J. Fuss, A. Srikumar, et al. - Journal of Experimental Botany, 2021 usegalaxy.eu

Occurrence of Colibacillosis in Broilers and Its Relationship With Avian Pathogenic Escherichia coli (APEC) Population Structure and Molecular Characteristics
I. Apostolakos - A. Laconi, L. Mughini-Gras, Ö. Yapicier, et al. - Frontiers in Veterinary Science, 2021 usegalaxy.eu

First complete mitochondrial genome of <i>Rhodinia</i> species (Lepidoptera: Saturniidae): genome description and phylogenetic implication
D. Chen - R. Zhang, X. Jin, J. Yang, et al. - Bulletin of Entomological Research, 2021 usegalaxy.eu

Bakta: Rapid &amp; standardized annotation of bacterial genomes via alignment-free sequence identification
O. Schwengers - L. Jelonek, M. Dieckmann, S. Beyvers, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021

Gene expression profiling of epidermal cell types in <i>C. elegans</i> using Targeted DamID
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Uncertainty estimation and explainability in deep learning-based age estimation of the human brain: Results from the German National Cohort MRI study
T. Hepp - D. Blum, K. Armanious, B. Schölkopf, et al. - Computerized Medical Imaging and Graphics, 2021

Limited access to antigen drives generation of early B cell memory while restraining the plasmablast response
V. Glaros - R. Rauschmeier, A. Artemov, A. Reinhardt, et al. - Immunity, 2021 usegalaxy.eu

Genome-wide identification of the BURP domain-containing genes in Phaseolus vulgaris
M. Kavas - K. Yıldırım, Z. Seçgin, M. Abdulla, et al. - Physiology and Molecular Biology of Plants, 2021 usegalaxy.eu

RNA-bound PGC-1α controls gene expression in liquid-like nuclear condensates
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Helios represses megakaryocyte priming in hematopoietic stem and progenitor cells
G. Cova - C. Taroni, M. Deau, Q. Cai, et al. - Journal of Experimental Medicine, 2021 usegalaxy.eu

Single‐cell omics: Overview, analysis, and application in biomedical science
C. Stein - R. Weiskirchen, F. Damm, P. Strzelecka, et al. - Journal of Cellular Biochemistry, 2021 usegalaxy.eu

Molecular and Structural Parallels between Gluten Pathogenic Peptides and Bacterial-Derived Proteins by Bioinformatics Analysis
D. Vazquez - H. Schilbert, V. Dodero, - International Journal of Molecular Sciences, 2021

Pre-activated antiviral innate immunity in the upper airways controls early SARS-CoV-2 infection in children
J. Loske - J. Röhmel, S. Lukassen, S. Stricker, et al. - Nature Biotechnology, 2021

Multidrug-Resistant Klebsiella pneumoniae Clones from Wild Chimpanzees and Termites in Senegal
S. Baron - O. Mediannikov, R. Abdallah, E. Kuete Yimagou, et al. - Antimicrobial Agents and Chemotherapy, 2021 usegalaxy.eu

Genome accessibility dynamics in response to phosphate limitation is controlled by the PHR1 family of transcription factors in<i>Arabidopsis</i>
A. Barragán-Rosillo - C. Peralta-Alvarez, J. Ojeda-Rivera, R. Arzate-Mejía, et al. - Proceedings of the National Academy of Sciences, 2021 usegalaxy.eu

Draft Genome Sequence of the Mucin Degrader Clostridium tertium WC0709
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Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: A case study of an urothelial cancer cohort analyzed in the Galaxy framework
M. Föll - V. Volkmann, K. Enderle-Ammour, K. Wilhelm, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

Polypharmacology of some medicinal plant metabolites against SARS-CoV-2 and host targets: Molecular dynamics evaluation of NSP9 RNA binding protein
S. Bandyopadhyay - O. Abiodun, B. Ogboo, A. Kola-Mustapha, et al. - Journal of Biomolecular Structure and Dynamics, 2021 usegalaxy.eu

A Genome-Wide CRISPR/Cas9 Screen Reveals the Requirement of Host Sphingomyelin Synthase 1 for Infection with Pseudorabies Virus Mutant gD–Pass
J. Hölper - F. Grey, J. Baillie, T. Regan, et al. - Viruses, 2021 usegalaxy.eu

Genomics and transcriptomics of epizoic Seisonidea (Rotifera, syn. Syndermata) reveal strain formation and gradual gene loss with growing ties to the host
K. Mauer - H. Schmidt, M. Dittrich, A. Fröbius, et al. - BMC Genomics, 2021 usegalaxy.eu

A high-quality draft genome for Melaleuca alternifolia (tea tree): a new platform for evolutionary genomics of myrtaceous terpene-rich species
J. Voelker - M. Shepherd, R. Mauleon, - Gigabyte, 2021 usegalaxy.eu

The Changes in the p53 Protein across the Animal Kingdom Point to Its Involvement in Longevity
M. Bartas - V. Brázda, A. Volná, J. Červeň, et al. - International Journal of Molecular Sciences, 2021 usegalaxy.eu

Classification of three corynebacterial strains isolated from a small paddock in North Rhine-Westphalia: proposal of Corynebacterium kalinowskii sp. nov., Corynebacterium comes sp. nov. and Corynebacterium occultum sp. nov.
L. Schaffert - M. Ruwe, J. Milse, K. Hanuschka, et al. - International Journal of Systematic and Evolutionary Microbiology, 2021

Drivers of phytoplankton community structure change with ecosystem ontogeny during the Quaternary
A. Cvetkoska - E. Jovanovska, T. Hauffe, T. Donders, et al. - Quaternary Science Reviews, 2021

A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation
Y. Dorone - S. Boeynaems, E. Flores, B. Jin, et al. - Cell, 2021 usegalaxy.eu

Eplerenone Improves Pulmonary Vascular Remodeling and Hypertension by Inhibition of the Mineralocorticoid Receptor in Endothelial Cells
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De novo transcriptome assembly, functional annotation and characterization of the Atlantic bluefin tuna (Thunnus thynnus) larval stage
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A Standardized Workflow Based on the STAVIRO Unbaited Underwater Video System for Monitoring Fish and Habitat Essential Biodiversity Variables in Coastal Areas
D. Pelletier - D. Roos, M. Bouchoucha, T. Schohn, et al. - Frontiers in Marine Science, 2021 usegalaxy.eu

Functional Analysis of Non-Genetic Resistance to Platinum in Epithelial Ovarian Cancer Reveals a Role for the MBD3-NuRD Complex in Resistance Development
T. Bauer - K. Collmar, T. Kaltofen, A. Loeffler, et al. - Cancers, 2021 usegalaxy.eu

Mitochondrial genome of Geomydoecus aurei, a pocket-gopher louse
T. Spradling - A. Place, A. Campbell, J. Demastes, et al. - PLOS ONE, 2021 usegalaxy.eu

Deep learning-based real-time detection of novel pathogens during sequencing
J. Bartoszewicz - U. Genske, B. Renard, - Briefings in Bioinformatics, 2021

Identification of pathological transcription in autosomal dominant polycystic kidney disease epithelia
S. Friedrich - H. Müller, C. Riesterer, H. Schüller, et al. - Scientific Reports, 2021 usegalaxy.eu

Performance and scaling behavior of bioinformatic applications in virtualization environments to create awareness for the efficient use of compute resources
M. Hanussek - F. Bartusch, J. Krüger, - PLOS Computational Biology, 2021

Temperature and Nutrient Limitations Decrease Transfer of Conjugative IncP-1 Plasmid pKJK5 to Wild Escherichia coli Strains
R. Pallares-Vega - G. Macedo, M. Brouwer, L. Hernandez Leal, et al. - Frontiers in Microbiology, 2021 usegalaxy.eu

Collaboration Between Host and Viral Factors Shape SARS-CoV-2 Evolution
C. Bamford - L. Broadbent, E. Aranday-Cortes, M. McCabe, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021 usegalaxy.eu

The complete mitochondrial genome of the wild silkmoth <i>Antheraea yamamai</i> from Heilongjiang, China (Lepidoptera: Saturniidae)
S. Sun - J. Huang, Y. Liu, - Mitochondrial DNA Part B, 2021 usegalaxy.eu

Pharmacokinetics of caffeine: A systematic analysis of reported data for application in metabolic phenotyping and liver function testing
J. Grzegorzewski - F. Bartsch, A. Köller, M. König, et al. - bioRxiv - Cold Spring Harbor Laboratory, 2021

Transcriptomic analysis of temporal shifts in berry development between two grapevine cultivars of the Pinot family reveals potential genes controlling ripening time
J. Theine - D. Holtgräwe, K. Herzog, F. Schwander, et al. - BMC Plant Biology, 2021

Gene Homologies Identified between Trypanosoma cruzi Antigen 36 and Mammalian TRIM21 Genes Using Bioinformatics Analysis
M. Winkler - A. Pan, - Research Square - Research Square Platform LLC, 2021 usegalaxy.eu

ONT-Based Draft Genome Assembly and Annotation of <i>Alternaria atra</i>
B. Bonthala - C. Small, M. Lutz, A. Graf, et al. - Molecular Plant-Microbe Interactions®, 2021

Age-Net: An MRI-Based Iterative Framework for Brain Biological Age Estimation
K. Armanious - S. Abdulatif, W. Shi, S. Salian, et al. - IEEE Transactions on Medical Imaging, 2021

Radiosensitivity of herbaceous plants to chronic radiation exposure: Field study in the Chernobyl exclusion zone
P. Volkova - G. Duarte, E. Kazakova, E. Makarenko, et al. - Science of The Total Environment, 2021 usegalaxy.eu

Cheminformatic Characterization of Natural Antimicrobial Products for the Development of New Lead Compounds
S. Oselusi - A. Christoffels, S. Egieyeh, - Molecules, 2021 usegalaxy.eu

Time- and Stimulus-Dependent Characteristics of Innate Immune Cells in Organ-Cultured Human Corneal Tissue
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Time- and Stimulus-Dependent Characteristics of Innate Immune Cells in Organ-Cultured Human Corneal Tissue
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Genetic Analyses and Genome-Wide Association Studies on Pathogen Resistance of Bos taurus and Bos indicus Cattle Breeds in Cameroon
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