Publications

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Currently 647 publications with reference to de.NBI Cloud are listed.

Recently added publication

The RNA workbench 2.0: next generation RNA data analysis
J. Fallmann - P. Videm, A. Bagnacani, B. Batut, et al. - Oxford University Press (OUP), 2019 usegalaxy.eu


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

Mapping lineage-traced cells across time points with moslin
M. Lange - Z. Piran, M. Klein, B. Spanjaard, et al. - Cold Spring Harbor Laboratory, 2023

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

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

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

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

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

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

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

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

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

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

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

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

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

Evaluating Prompt Tuning for Conditional Protein Sequence Generation
A. Nathansen - K. Klein, B. Renard, M. Nowicka, et al. - Cold Spring Harbor Laboratory, 2023

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Pathovar-Specific PCR Method for Detection and Identification of Xanthomonas translucens pv. undulosa
H. Alvandi - S. Taghavi, M. Khojasteh, T. Rahimi, et al. - Plant Disease, 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

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

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. - Cold Spring Harbor Laboratory, 2023

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

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

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

Hybrid Genome Assembly of Short and Long Reads in Galaxy
T. Ohta - Y. Shiwa, - Springer US, 2023 usegalaxy.eu

Assessing Antimicrobial and Metal Resistance Genes in Escherichia Coli from Domestic Groundwater Supplies in Rural Ireland
L. Andrade - M. Ryan, L. Burke, P. Hynds, et al. - Elsevier BV, 2023 usegalaxy.eu

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

NFATc1 Is a Central Mediator of EGFR-Induced ARID1A Chromatin Dissociation During Acinar Cell Reprogramming
Z. Zhang - X. Wang, F. Hamdan, A. Likhobabina, et al. - Cellular and Molecular Gastroenterology and Hepatology, 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

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

The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain
L. Weber - Y. Jia, B. Stielow, S. Gisselbrecht, et al. - Nucleic Acids Research, 2022 usegalaxy.eu

Better Together
S. Gatidis - T. Kart, M. Fischer, S. Winzeck, et al. - Investigative Radiology, 2022

Megan Server: facilitating interactive access to metagenomic data on a server
A. Gautam - W. Zeng, D. Huson, - Cold Spring Harbor Laboratory, 2022

MGnify: the microbiome sequence data analysis resource in 2023
L. Richardson - B. Allen, G. Baldi, M. Beracochea, et al. - Nucleic Acids Research, 2022

STAT3 signaling induced by IL-6 family cytokines modulates angiogenesis
J. Rapp - M. Jung, R. Klar, J. Wolf, et al. - Journal of Cell Science, 2022 usegalaxy.eu

Rapid detection and online analysis of microbial changes through flow cytometry
J. Kupschus - S. Janssen, A. Hoek, J. Kuska, et al. - Cytometry Part A, 2022

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

Complete Genome Sequence of Metabacillus litoralis Strain NCTR108, Isolated from Commercial Tattoo Ink
S. Kim - C. Summage-West, M. Reyna, S. Kim, et al. - Microbiology Resource Announcements, 2022 usegalaxy.eu

Revisiting pangenome openness with<i>k</i>-mers
L. Parmigiani - R. Wittler, J. Stoye, - 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. - 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

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

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

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

Multi-histone ChIP-Seq Analysis with DecoDen
T. Narendra - G. Visonà, C. de Jesus Cardona, G. Schweikert, et al. - Cold Spring Harbor Laboratory, 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

Semi-automated assembly of high-quality diploid human reference genomes
E. Jarvis - G. Formenti, A. Rhie, A. Guarracino, et al. - Nature, 2022 usegalaxy.eu

Thin‐Plate Superstructures of the Immunogenic 33‐mer Gliadin Peptide
M. Herrera - M. Amundarain, F. Nicoletti, M. Drechsler, et al. - ChemBioChem, 2022

A comprehensive transcriptomic comparison of hepatocyte model systems improves selection of models for experimental use
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
O. Nonn - O. Debnath, D. Valdes, K. Sallinger, et al. - Cold Spring Harbor Laboratory, 2022

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

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

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

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

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. - 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

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. - 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

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

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

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

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. - Cold Spring Harbor Laboratory, 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

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

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. - 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

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

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

Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra
J. Barrera-Redondo - J. Lotharukpong, H. Drost, S. Coelho, et al. - Cold Spring Harbor Laboratory, 2022

KIPEs3: Automatic annotation of biosynthesis pathways
A. Rempel - N. Choudhary, B. Pucker, - 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

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

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

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

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

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. - Cold Spring Harbor Laboratory, 2022

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

Evaluation of the potential prebiotic effect of Himanthalia elongata, an Atlantic brown seaweed, in an in vitro model of the human distal colon
A. Lopez-Santamarina - A. Cardelle-Cobas, A. del Carmen Mondragon, L. Sinisterra-Loaiza, et al. - Food Research International, 2022 usegalaxy.eu

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

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

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

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
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Recovery of 447 Eukaryotic bins reveals major challenges for Eukaryote genome reconstruction from metagenomes
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Identification and annotation of peptide allergens in Prunus dulcis
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NFATc1 signaling drives chronic ER stress responses to promote NAFLD progression
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Critical Assessment of Metagenome Interpretation: the second round of challenges
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Enabling technologies towards personalization of scaffolds for large bone defect regeneration
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Evaluation of machine learning strategies for imaging confirmed prostate cancer recurrence prediction on electronic health records
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Sex differences in the early life stages of the salmon louse Lepeophtheirus salmonis (Copepoda: Caligidae)
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Unifying the known and unknown microbial coding sequence space
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Deciphering the Molecular Signature of Human Hyalocytes in Relation to Other Innate Immune Cell Populations
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Mimicking tumor cell heterogeneity of colorectal cancer in a patient-derived organoid-fibroblast model
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Taxonomy of Rhizobiaceae revisited: proposal of a new framework for genus delimitation
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In vitro and in silico analysis of Brilliant Black degradation by Actinobacteria and a Paraburkholderia sp.
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Pathogenicity of Shiga toxin-producing Escherichia coli (STEC) from wildlife: Should we care?
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Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N6-carboxymethyllysine
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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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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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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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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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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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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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Expanding the Galaxy’s reference data
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Canonical Workflows to Make Data FAIR
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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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Recapitulating Cholangiopathy-Associated Necroptotic Cell Death In Vitro Using Human Cholangiocyte Organoids
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Multi-label classification for multi-drug resistance prediction of Escherichia coli
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Plankton-infecting relatives of herpesviruses clarify the evolutionary trajectory of giant viruses
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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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Transcriptomic Profiling and Microsatellite Identification in Cobia (Rachycentron canadum), Using High-Throughput RNA Sequencing
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An ecological perspective on microbial genes of unknown function in soil
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Plant circadian clock control of <i>Medicago truncatula</i> nodulation via regulation of nodule cysteine-rich peptides
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LAPNet: Non-Rigid Registration Derived in k-Space for Magnetic Resonance Imaging
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Conservation and divergence in gene regulation between mouse and human immune cells deserves equal emphasis
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Using AnnoTree to get more assignments, faster, in DIAMOND+MEGAN microbiome analysis
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Expression Atlas update: gene and protein expression in multiple species
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Dissection of Quantitative Blackleg Resistance Reveals Novel Variants of Resistance Gene Rlm9 in Elite Brassica napus
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New Putative Long Non-Coding RNAs (lncRNA) Revealed by Pan-Transcriptome of the Emerging Human Pathogenic Fungus Talaromyces Marneffei
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Interactive Analysis of Biosurfactants in Fruit-Waste Fermentation Samples using BioSurfDB and MEGAN
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Peakhood: individual site context extraction for CLIP-seq peak regions
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The transcriptome of Balamuthia mandrillaris trophozoites for structure-guided drug design
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Variimorphobacter saccharofermentans gen. nov., sp. nov., a new member of the family Lachnospiraceae, isolated from a maize-fed biogas fermenter
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The chitinolytic activity of the Curtobacterium sp. isolated from field-grown soybean and analysis of its genome sequence
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Somatostatin 3 loss of function impairs the innate immune response to intestinal inflammation
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Fibropapillomatosis and Chelonid Alphaherpesvirus 5 Infection in Kemp’s Ridley Sea Turtles (Lepidochelys kempii)
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ARTS-DB: a database for antibiotic resistant targets
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From celiac disease to coccidia infection and vice‐versa: The polyQ peptide CXCR3‐interaction axis
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Automatic identification and annotation of MYB gene family members in plants
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Weakly supervised segmentation of tumor lesions in PET-CT hybrid imaging
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Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer
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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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Genomic impact of stress-induced transposable element mobility in Arabidopsis
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Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid
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Nascent Transcript Sequencing for the Mapping of Promoters in Arabidopsis thaliana Mitochondria
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Evolutionary Trajectories toward Ceftazidime-Avibactam Resistance in Klebsiella pneumoniae Clinical Isolates
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Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species
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The temperature-regulated DEAD-box RNA helicase CrhR interactome: autoregulation and photosynthesis-related transcripts
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Occurrence of Colibacillosis in Broilers and Its Relationship With Avian Pathogenic Escherichia coli (APEC) Population Structure and Molecular Characteristics
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First complete mitochondrial genome of <i>Rhodinia</i> species (Lepidoptera: Saturniidae): genome description and phylogenetic implication
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Bakta: Rapid &amp; standardized annotation of bacterial genomes via alignment-free sequence identification
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Gene expression profiling of epidermal cell types in <i>C. elegans</i> using Targeted DamID
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Uncertainty estimation and explainability in deep learning-based age estimation of the human brain: Results from the German National Cohort MRI study
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Genome-wide identification of the BURP domain-containing genes in Phaseolus vulgaris
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Limited access to antigen drives generation of early B cell memory while restraining the plasmablast response
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RNA-bound PGC-1α controls gene expression in liquid-like nuclear condensates
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Helios represses megakaryocyte priming in hematopoietic stem and progenitor cells
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Single‐cell omics: Overview, analysis, and application in biomedical science
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Molecular and Structural Parallels between Gluten Pathogenic Peptides and Bacterial-Derived Proteins by Bioinformatics Analysis
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Pre-activated antiviral innate immunity in the upper airways controls early SARS-CoV-2 infection in children
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Multidrug-Resistant Klebsiella pneumoniae Clones from Wild Chimpanzees and Termites in Senegal
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Genome accessibility dynamics in response to phosphate limitation is controlled by the PHR1 family of transcription factors in <i>Arabidopsis</i>
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Draft Genome Sequence of the Mucin Degrader Clostridium tertium WC0709
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Polypharmacology of some medicinal plant metabolites against SARS-CoV-2 and host targets: Molecular dynamics evaluation of NSP9 RNA binding protein
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The Changes in the p53 Protein across the Animal Kingdom Point to Its Involvement in Longevity
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Drivers of phytoplankton community structure change with ecosystem ontogeny during the Quaternary
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A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation
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A Standardized Workflow Based on the STAVIRO Unbaited Underwater Video System for Monitoring Fish and Habitat Essential Biodiversity Variables in Coastal Areas
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Mitochondrial genome of Geomydoecus aurei, a pocket-gopher louse
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Trait-trait relationships and tradeoffs vary with genome size in prokaryotes
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Identification of pathological transcription in autosomal dominant polycystic kidney disease epithelia
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Deep learning-based real-time detection of novel pathogens during sequencing
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Temperature and Nutrient Limitations Decrease Transfer of Conjugative IncP-1 Plasmid pKJK5 to Wild Escherichia coli Strains
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Collaboration Between Host and Viral Factors Shape SARS-CoV-2 Evolution
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Pharmacokinetics of caffeine: A systematic analysis of reported data for application in metabolic phenotyping and liver function testing
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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
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ONT-Based Draft Genome Assembly and Annotation of <i>Alternaria atra</i>
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Cheminformatic Characterization of Natural Antimicrobial Products for the Development of New Lead Compounds
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Time- and Stimulus-Dependent Characteristics of Innate Immune Cells in Organ-Cultured Human Corneal Tissue
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Time- and Stimulus-Dependent Characteristics of Innate Immune Cells in Organ-Cultured Human Corneal Tissue
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Hierarchical reactivation of transcription during mitosis-to-G1 transition by Brn2 and Ascl1 in neural stem cells
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DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics
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Topological data analysis identifies emerging adaptive mutations in SARS-CoV-2
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Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome
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Assessing the role of polygenic background on the penetrance of monogenic forms in Parkinson’s disease
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RiboReport - Benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria
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Breast and prostate cancer risk: the interplay of polygenic risk, high-impact monogenic variants, and family history
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A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive
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AGNOSTOS-DB: a resource to unlock the uncharted regions of the coding sequence space
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Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine
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A High-Density SNP Genetic Map Construction Using ddRAD-Seq and Mapping of Capsule Shattering Trait in Sesame
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Going to extremes – a metagenomic journey into the dark matter of life
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Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells
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CryptoGenotyper: A new bioinformatics tool for rapid Cryptosporidium identification
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COVID-19 preVIEW: Semantic Search to Explore COVID-19 Research Preprints
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SimText: a text mining framework for interactive analysis and visualization of similarities among biomedical entities
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Tryptophan metabolism drives dynamic immunosuppressive myeloid states in IDH-mutant gliomas
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Current extinction rate in European freshwater gastropods greatly exceeds that of the late Cretaceous mass extinction
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Direct Diagnosis of Echovirus 12 Meningitis Using Metagenomic Next Generation Sequencing
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EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure
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The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts
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A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19)
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Genomic and proteomic profiles of biofilms on microplastics are decoupled from artificial surface properties
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Peptidotriazolamers Inhibit Aβ(1–42) Oligomerization and Cross a Blood‐Brain‐Barrier Model
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Within-host evolution of SARS-CoV-2 in an immunosuppressed COVID-19 patient: a source of immune escape variants
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Replication of a Novel Parkinson's Locus in a European Ancestry Population
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Development of a Comprehensive Toxicity Pathway Model for 17α-Ethinylestradiol in Early Life Stage Fathead Minnows (<i>Pimephales promelas</i>)
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Molecular Physiological Characterization of a High Heat Resistant Spore Forming Bacillus subtilis Food Isolate
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Updates on metaQuantome Software for Quantitative Metaproteomics
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MegaGO: A Fast Yet Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets
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VPRBP functions downstream of the androgen receptor and OGT to restrict p53 activation in prostate cancer
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Decitabine Induces Gene Derepression on Monosomic Chromosomes: <i>In Vitro</i> and <i>In Vivo</i> Effects in Adverse-Risk Cytogenetics AML
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Microbial Communities in Flexible Biomethanation of Hydrogen Are Functionally Resilient Upon Starvation
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Detecting high-scoring local alignments in pangenome graphs
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Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction
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Interpretable detection of novel human viruses from genome sequencing data
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3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis
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Using Galaxy to Perform Large‐Scale Interactive Data Analyses—An Update
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Diabetes changes gene expression but not DNA methylation in cardiac cells
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SRGAP1 Controls Small Rho GTPases To Regulate Podocyte Foot Process Maintenance
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ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data
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Scarless engineering of the<i>Drosophila</i>genome near any site-specific integration site
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A novel deletion in FLOWERING LOCUS T modulates flowering time in winter oilseed rape
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Congenital heart disease risk loci identified by genome-wide association study in European patients
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ActivinA Induced SMAD1/5 Signaling in an iPSC Derived EC Model of Fibrodysplasia Ossificans Progressiva (FOP) Can Be Rescued by the Drug Candidate Saracatinib
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SANS serif: alignment-free, whole-genome based phylogenetic reconstruction
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Electroactive microorganisms in mouse feces
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Tool recommender system in Galaxy using deep learning
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Current status of use of high throughput nucleotide sequencing in rheumatology
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RNA-Seq Data Analysis in Galaxy
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RI-SEC-seq: Comprehensive Profiling of Nonvesicular Extracellular RNAs with Different Stabilities
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Self-Supervised Learning for Automated Anatomical Tracking in Medical Image Data with Minimal Human Labeling Effort
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MOSGA 2: Comparative genomics and validation tools
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The bone-degrading enzyme machinery: From multi-component understanding to the treatment of residues from the meat industry
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Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19
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Tuning the Biological Activity of RGD Peptides with Halotryptophans
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Population studies of the wild tomato species <i>Solanum chilense</i> reveal geographically structured major gene-mediated pathogen resistance
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Genomic analysis provides novel insights into diversification and taxonomy of <i>Allorhizobium vitis</i> (i.e. <i>Agrobacterium vitis</i>)
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Stable Protein Sialylation in Physcomitrella
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The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses
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Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK–driven lymphomagenesis
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Genome-wide investigation of the dynamic changes of epigenome modifications after global DNA methylation editing
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Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
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Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities
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Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities
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Epigenetic alterations underlie airway macrophage differentiation and phenotype during lung fibrosis
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A secreted endoribonuclease ENDU-2 from the soma protects germline immortality in<i>C. elegans</i>
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MACE RNA sequencing analysis of conjunctival squamous cell carcinoma and papilloma using formalin-fixed paraffin-embedded tumor tissue
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Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq)
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Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning
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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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CDK8 Fine-Tunes IL-6 Transcriptional Activities by Limiting STAT3 Resident Time at the Gene Loci
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Corneal tissue induces transcription of metallothioneins in monocyte-derived human macrophages
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A reciprocal regulation of spermidine and autophagy in podocytes maintains the filtration barrier
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CoxBase: an online platform for epidemiological surveillance, visualization, analysis and typing of<i>Coxiella burnetii</i>genomic sequences
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Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra
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RNA nucleation by MSL2 induces selective X chromosome compartmentalization
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Synergistic biodegradation of aromatic-aliphatic copolyester plastic by a marine microbial consortium
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Survey of metaproteomics software tools for functional microbiome analysis
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PK-DB: pharmacokinetics database for individualized and stratified computational modeling
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Fully Automated and Standardized Segmentation of Adipose Tissue Compartments via Deep Learning in 3D Whole-Body MRI of Epidemiologic Cohort Studies
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Unexpected variations in posttranscriptional gene silencing induced by differentially produced dsRNAs in tobacco cells
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Next generation sequencing study on RNA viruses of<i>Vespa velutina</i>and<i>Apis mellifera</i>sharing the same foraging area
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High prevalence of mcr-1-encoded colistin resistance in commensal Escherichia coli from broiler chicken in Bangladesh
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The environment drives microbial trait variability in aquatic habitats
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Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics
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The Polycomb group methyltransferase StE(z)2 and deposition of H3K27me3 and H3K4me3 regulate the expression of tuberization genes in potato
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The Polycomb group methyltransferase StE(z)2 and deposition of H3K27me3 and H3K4me3 regulate the expression of tuberization genes in potato
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Transcriptional characterization of conjunctival melanoma identifies the cellular tumor microenvironment and prognostic gene signatures
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Near-complete nucleotide sequence of a border disease virus genotype BDV-7 isolate from Italy
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The transcriptional response of pathogenic Leptospira to peroxide reveals new defenses against infection-related oxidative stress
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Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates
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Deep drilling reveals massive shifts in evolutionary dynamics after formation of ancient ecosystem
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Molecular analysis of GPI-anchor biosynthesis pathway genes in rat strains used for the Pig-a gene mutation assay
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A single-cell RNA-sequencing training and analysis suite using the Galaxy framework
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3′ MACE RNA-sequencing allows for transcriptome profiling in human tissue samples after long-term storage
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Nephronophthisis gene products display RNA-binding properties and are recruited to stress granules
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Draft Genome Sequence of a New Delhi Metallo-β-Lactamase (NDM-1)-Producing Providencia stuartii Strain Isolated in Lima, Peru
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Chlorella vulgaris and Its Phycosphere in Wastewater: Microalgae-Bacteria Interactions During Nutrient Removal
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tRNA ADENOSINE DEAMINASE 3 is required for telomere maintenance in Arabidopsis thaliana
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Entropic Ranks: A Methodology for Enhanced, Threshold-Free, Information-Rich Data Partition and Interpretation
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Modification of the Histone Landscape with JAK Inhibition in Myeloproliferative Neoplasms
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The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR
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Transcriptional Profiling Uncovers Human Hyalocytes as a Unique Innate Immune Cell Population
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Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial
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Proteomic Fingerprinting Discriminates Cryptic Gastropod Species
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Sediment Plasmidome of the Gulfs of Kathiawar Peninsula and Arabian Sea: Insights Gained from Metagenomics Data
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Characterizing Phage-Host Interactions in a Simplified Human Intestinal Barrier Model
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Long‐read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant
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Deep learning-based diatom taxonomy on virtual slides
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A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane
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ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation
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DNA Methylation of Steroidogenic Enzymes in Benign Adrenocortical Tumors: New Insights in Aldosterone-Producing Adenomas
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Training Infrastructure as a Service
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No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics
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Genomic Evidence for Sensorial Adaptations to a Nocturnal Predatory Lifestyle in Owls
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Microbiomes in Supragingival Biofilms and Saliva of Adolescent Patients with Induced and Naturally Occurring Gingivitis Relative to Gingival Health
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Draft Genome Sequences of Three <i>Clostridia</i> Isolates Involved in Lactate-Based Chain Elongation
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pyGenomeTracks: reproducible plots for multivariate genomic datasets 
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Prevotella vespertina sp. nov., isolated from an abscess of a hospital patient
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Ultrastructural, transcriptional, and functional differences between human reticulated and non‐reticulated platelets
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SNP dependent modulation of circulating miRNAs from the miR25/93/106 cluster in patients undergoing weight loss
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A pan-cancer analysis reveals nonstop extension mutations causing SMAD4 tumour suppressor degradation
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Benchmarking challenging small variants with linked and long reads
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An Interactive Visualization for Feature Localization in Deep Neural Networks
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DNA Methyltransferase 1 (DNMT1) Function Is Implicated in the Age-Related Loss of Cortical Interneurons
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Genome‐wide cooperation of <scp>EMT</scp> transcription factor <scp>ZEB</scp> 1 with <scp>YAP</scp> and <scp>AP</scp> ‐1 in breast cancer
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The landscape of SARS-CoV-2 RNA modifications
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Expression of the COVID‐19 receptor ACE2 in the human conjunctiva
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Lake expansion elevates equilibrium diversity via increasing colonization
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Enhanced COVID-19 data for improved prediction of survival
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Noninvasive Discrimination of Low and High-risk Pancreatic Intraductal Papillary Mucinous Neoplasms
S. Roth - P. Bose, M. Alhamdani, S. Mustafa, et al. - Annals of Surgery, 2020

Unifying the known and unknown microbial coding sequence space
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ganon: precise metagenomics classification against large and up-to-date sets of reference sequences
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Degradation of Non-coding RNAs Promotes Recycling of Termination Factors at Sites of Transcription
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Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus
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Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus
C. Buttimer - C. Lynch, H. Hendrix, H. Neve, et al. - Antibiotics, 2020 usegalaxy.eu

Methylation Profile of X-Chromosome–Related Genes in Male Breast Cancer
M. Foschini - L. Morandi, A. Sanchez, A. Santoro, et al. - Frontiers in Oncology, 2020 usegalaxy.eu

Human exome and mouse embryonic expression data implicate ZFHX3, TRPS1, and CHD7 in human esophageal atresia
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Active and repressed biosynthetic gene clusters have spatially distinct chromosome states
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<scp>GLASSgo</scp> in <scp>Galaxy</scp>: high-throughput, reproducible and easy-to-integrate prediction of sRNA homologs
R. Schäfer - S. Lott, J. Georg, B. Grüning, et al. - Bioinformatics, 2020 usegalaxy.eu

Galactic Circos: User-friendly Circos plots within the Galaxy platform
H. Rasche S. Hiltemann - - GigaScience, 2020 usegalaxy.eu

The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform
S. Bray - X. Lucas, A. Kumar, B. Grüning, et al. - Journal of Cheminformatics, 2020 usegalaxy.eu

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update
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iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites
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Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera
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Two new genera and three new subterranean species of Hydrobiidae (Caenogastropoda: Truncatelloidea) from Tunisia
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ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining
M. Mungan M. Alanjary K. Blin T. Weber M. Medema N. Ziemert - - Nucleic Acids Research, 2020

Contrast Optimization of Mass Spectrometry Imaging (MSI) Data Visualization by Threshold Intensity Quantization (TrIQ)
R. Winkler - I. Rosas-Román, - American Chemical Society (ACS), 2020 usegalaxy.eu

Connecting data, tools and people across Europe: ELIXIR’s response to the COVID-19 pandemic
N. Blomberg - K. Lauer, - European Journal of Human Genetics, 2020 usegalaxy.eu

A framework for designing miRNA-based distributed cell classifier circuits
M. Nowicka - H. Siebert, - Cold Spring Harbor Laboratory, 2020

LINC00261 Is Differentially Expressed in Pancreatic Cancer Subtypes and Regulates a Pro-Epithelial Cell Identity
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A Sectioning and Database Enrichment Approach for Improved Peptide Spectrum Matching in Large, Genome-Guided Protein Sequence Databases
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Comparative Genomics Suggests Mechanisms of Genetic Adaptation toward the Catabolism of the Phenylurea Herbicide Linuron in Variovorax
B. Öztürk J. Werner J. Meier-Kolthoff B. Bunk C. Spröer D. Springael - - Genome Biology and Evolution, 2020

The sex-specific role of p38 MAP kinase in CNS autoimmunity is regulated by estrogen receptor alpha
M. McGill - B. Sabikunnahar, Q. Fang, C. Teuscher, et al. - Journal of Neuroimmunology, 2020 usegalaxy.eu

MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome
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Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive<i>de novo</i>DNA methylation mechanisms
L. Gao - M. Emperle, Y. Guo, S. Grimm, et al. - Cold Spring Harbor Laboratory, 2020 usegalaxy.eu

The Great Oxidation Event expanded the genetic repertoire of arsenic metabolism and cycling
S. Chen - G. Sun, Y. Yan, K. Konstantinidis, et al. - Proceedings of the National Academy of Sciences, 2020

Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus
H. Lee - H. Chawla, C. Obermeier, F. Dreyer, et al. - Frontiers in Plant Science, 2020

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

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

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

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

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

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

Draft genome sequence of Kocuria indica DP-K7, a methyl red degrading actinobacterium
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Design of Bacterial Strain-Specific qPCR Assays Using NGS Data and Publicly Available Resources and Its Application to Track Biocontrol Strains
I. Hernández - C. Sant, R. Martínez, C. Fernández, et al. - Frontiers in Microbiology, 2020 usegalaxy.eu

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

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

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

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

Widespread correlation of KRAB zinc finger protein binding with brain-developmental gene expression patterns
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Gene expression in immortalized versus primary isolated cardiac endothelial cells
L. Deng - L. Pollmeier, Q. Zhou, S. Bergemann, et al. - Scientific Reports, 2020 usegalaxy.eu

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

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

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

BRIDGE: An Open Platform for Reproducible Protein-Ligand Simulations and Free Energy of Binding Calculations
T. Senapathi - C. Barnett, K. Naidoo, - BIO-PROTOCOL, 2020 usegalaxy.eu

GLP: A requirement in cell therapies - perspectives for the cardiovascular field
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Computing the Rearrangement Distance of Natural Genomes
L. Bohnenkämper - M. Braga, D. Doerr, J. Stoye, et al. - Springer International Publishing, 2020

Horizontal Gene Transfer Phylogenetics: A Random Walk Approach
G. Sevillya D. Doerr Y. Lerner J. Stoye M. Steel S. Snir - - Molecular Biology and Evolution, 2019

Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines
Y. Perez‐Riverol - P. Moreno, - PROTEOMICS, 2019 usegalaxy.eu

SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
M. Lewinski - Y. Bramkamp, T. Köster, D. Staiger, et al. - Cold Spring Harbor Laboratory, 2019

13-gene DNA Methylation Analysis from Oral Brushing: A Promising Non Invasive Tool in the Follow-up of Oral Cancer Patients
D. Gissi - A. Tarsitano, A. Gabusi, R. Rossi, et al. - Journal of Clinical Medicine, 2019 usegalaxy.eu

Accessible and reproducible mass spectrometry imaging data analysis in Galaxy
M. Föll - L. Moritz, T. Wollmann, M. Stillger, et al. - GigaScience, 2019

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

Full-coverage native RNA sequencing of HIV-1 viruses
A. Gener - J. Kimata, - Cold Spring Harbor Laboratory, 2019 usegalaxy.eu

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

Highly efficient library preparation for Ion Torrent sequencing using Y-adapters
L. Forth - D. Höper, - BioTechniques, 2019 usegalaxy.eu

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

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

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

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

Mutations of R882 change flanking sequence preferences of the DNA methyltransferase DNMT3A and cellular methylation patterns
M. Emperle - S. Adam, S. Kunert, M. Dukatz, et al. - Nucleic Acids Research, 2019 usegalaxy.eu

An intrinsically disordered proteins community for ELIXIR
N. Davey - M. Babu, M. Blackledge, A. Bridge, et al. - F1000Research, 2019 usegalaxy.eu

Interplay and Targetome of the Two Conserved Cyanobacterial sRNAs Yfr1 and Yfr2 in Prochlorococcus MED4
S. Lambrecht - Y. Kanesaki, J. Fuss, B. Huettel, et al. - Scientific Reports, 2019 usegalaxy.eu

Development of novel microsatellite markers for <i>Alkanna tinctoria</i>  by comparative transcriptomics
M. Ahmad - D. Lazic, K. Hansel‐Hohl, C. Lexer, et al. - Applications in Plant Sciences, 2019 usegalaxy.eu

ΔN-Tp63 Mediates Wnt/β-Catenin-Induced Inhibition of Differentiation in Basal Stem Cells of Mucociliary Epithelia
M. Haas - J. Gómez Vázquez, D. Sun, H. Tran, et al. - Cell Reports, 2019 usegalaxy.eu

<i>Candida auris</i> in Germany and Previous Exposure to Foreign Healthcare
A. Hamprecht - A. Barber, S. Mellinghoff, P. Thelen, et al. - Emerging Infectious Diseases, 2019 usegalaxy.eu

Historical faunal exchange between the Pontocaspian Basin and North America
J. Vandendorpe - C. Baak, B. Stelbrink, D. Delicado, et al. - Ecology and Evolution, 2019

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

Bhlhe40 and Bhlhe41 transcription factors regulate alveolar macrophage self‐renewal and identity
R. Rauschmeier - C. Gustafsson, A. Reinhardt, N. A‐Gonzalez, et al. - The EMBO Journal, 2019 usegalaxy.eu

GRUU-Net: Integrated convolutional and gated recurrent neural network for cell segmentation
T. Wollmann - M. Gunkel, I. Chung, H. Erfle, et al. - Medical Image Analysis, 2019

PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping
L. Sánchez - B. Burger, C. Horro, A. Fabregat, et al. - GigaScience, 2019 usegalaxy.eu

Cyclization of RGD Peptides by Suzuki–Miyaura Cross-Coupling
I. Kemker - C. Schnepel, D. Schröder, A. Marion, et al. - Journal of Medicinal Chemistry, 2019

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

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

de.NBI Cloud federation through ELIXIR AAI
P. Belmann - B. Fischer, J. Krüger, M. Procházka, et al. - F1000Research, 2019

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

Versatile interactions and bioinformatics analysis of noncoding RNAs
Q. Chen - X. Meng, Q. Liao, M. Chen, et al. - Briefings in Bioinformatics, 2019 usegalaxy.eu

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics
P. Kumar - P. Panigrahi, J. Johnson, W. Weber, et al. - Journal of Proteome Research, 2018 usegalaxy.eu

Proteogenomic Analysis of Epibacterium Mobile BBCC367, a Relevant Marine Bacterium Isolated From the South Pacific Ocean
S. Matallana-Surget - J. Werner, R. Wattiez, K. Lebaron, et al. - Frontiers in Microbiology, 2018

FOXG1 Regulates PRKAR2B Transcriptionally and Posttranscriptionally via miR200 in the Adult Hippocampus
S. Weise - G. Arumugam, A. Villarreal, P. Videm, et al. - Molecular Neurobiology, 2018 usegalaxy.eu

MAIA—A machine learning assisted image annotation method for environmental monitoring and exploration
M. Zurowietz - D. Langenkämper, B. Hosking, H. Ruhl, et al. - PLOS ONE, 2018

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
J. Huerta-Cepas - D. Szklarczyk, D. Heller, A. Hernández-Plaza, et al. - Nucleic Acids Research, 2018

Aequatus: an open-source homology browser
A. Thanki - N. Soranzo, J. Herrero, W. Haerty, et al. - GigaScience, 2018 usegalaxy.eu

Differential Methylation of H3K79 Reveals DOT1L Target Genes and Function in the Cerebellum In Vivo
P. Bovio - H. Franz, S. Heidrich, T. Rauleac, et al. - Molecular Neurobiology, 2018 usegalaxy.eu

Common ELIXIR Service for Researcher Authentication and Authorisation
M. Linden - M. Prochazka, I. Lappalainen, D. Bucik, et al. - F1000Research, 2018

Draft genome sequence of Rhodococcus erythropolis B7g, a biosurfactant producing actinobacterium
G. Retamal-Morales - T. Heine, J. Tischler, B. Erler, et al. - Journal of Biotechnology, 2018 usegalaxy.eu

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

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

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

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

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

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

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

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

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

Bioinformatics for NGS-based metagenomics and the application to biogas research
S. Jünemann - N. Kleinbölting, S. Jaenicke, C. Henke, et al. - Journal of Biotechnology, 2017

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy
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BIIGLE 2.0 - Browsing and Annotating Large Marine Image Collections
D. Langenkämper - M. Zurowietz, T. Schoening, T. Nattkemper, et al. - Frontiers in Marine Science, 2017