Scientific research using & citing the European Galaxy server

This is the list of scientific publications that cited the European Galaxy instance sorted by year. Please help us to support this project with your acknowledgement.


  1. Aguirre Pranzoni,C. et al. (2024) Biofoams with Untapped Enzymatic Potential Produced from Beer Bagasse by Indigenous Fungal Strains.
  2. Akpinar,Z. and Karaoglu,H. (2024) Characterization of a highly thermostable recombinant xylanase from Anoxybacillus ayderensis. Protein Expression and Purification, 219, 106478.
  3. Alawi,M. et al. (2024) Private and well drinking water are reservoirs for antimicrobial resistant bacteria. npj Antimicrobials and Resistance, 2, 1–16.
  4. AlJindan,R. et al. (2024) Phenomics and genomic features of Enterococcus avium IRMC1622a isolated from a clinical sample of hospitalized patient. Journal of Infection and Public Health.
  5. Andriyanov,P.A. et al. (2024) Genomic analysis of multidrug-resistant Delftia tsuruhatensis isolated from raw bovine milk. Frontiers in Microbiology, 14.
  6. Arai,H. et al. (2024) Two male-killing Wolbachia from Drosophila birauraia that are closely related but distinct in genome structure. Royal Society Open Science, 11, 231502.
  7. Aribisala,J.O. et al. (2024) In silico exploration of phenolics as modulators of penicillin binding protein (PBP) 2× of Streptococcus pneumoniae. Scientific Reports, 14, 8788.
  8. Arnold,N.D. (2024) Unlocking a Potent Chitin Saccharification System in a Novel Bacterium Through Omics and Bioinformatics.
  9. Bahrami,B. et al. (2024) Integrated analysis of transcriptome and epigenome reveals ENSR00000272060 as a potential biomarker in gastric cancer. Epigenomics, 16, 159–173.
  10. Bastide,H. et al. (2024) The genome of the blind bee louse fly reveals deep convergences with its social host and illuminates Drosophila origins. Current Biology.
  11. Bawin,T. et al. (2024) Cuscuta campestris fine-tunes gene expression during haustoriogenesis as an adaptation to different hosts. Plant Physiology, 194, 258–273.
  12. Beerling,D.J. et al. (2024) Enhanced weathering in the US Corn Belt delivers carbon removal with agronomic benefits. Proceedings of the National Academy of Sciences, 121, e2319436121.
  13. Berlanga,M. et al. (2024) Biodiversity and poten al func onality of biofilmsediment biotope in La Muerte lagoon, Monegros desert, Spain. Frontiers in Ecology and Evolution, 12.
  14. Bianconi,I. et al. (2024) Characterization of Verona Integron-Encoded Metallo-β-Lactamase-Type Carbapenemase-Producing Escherichia coli Isolates Collected over a 16-Year Period in Bolzano (Northern Italy). Microbial Drug Resistance, 30, 91–100.
  15. Bihani,S. et al. (2024) Metaproteomics for Coinfections in the Upper Respiratory Tract: The Case of COVID-19. In, Salerno,C. (ed), Metaproteomics: Methods and Protocols. Springer US, New York, NY, pp. 165–185.
  16. Bode,C. et al. (2024) Catecholamine treatment induces reversible heart injury and cardiomyocyte gene expression. Intensive Care Medicine Experimental, 12, 48.
  17. Bode,C. et al. (2024) Dynamics of cardiomyocyte gene expression and reversibility of catecholamine-induced heart injury.
  18. Boeckman,J. et al. (2024) Phage DNA Extraction, Genome Assembly, and Genome Closure. In, Tumban,E. (ed), Bacteriophages: Methods and Protocols, Methods in Molecular Biology. Springer US, New York, NY, pp. 125–144.
  19. Boyer,T. and Neronov,A. (2024) Pulsar timing array constraints on the cosmological magnetic field from quark confinement epoch.
  20. Camacho-Beltrán,E. et al. (2024) Complete genome sequence of the Microbacterium enclense bacteriophage phiMiGM15. Microbiology Resource Announcements, 0, e00302–24.
  21. Candeliere,F. et al. (2024) Genomic and functional analysis of the mucinolytic species Clostridium celatum, Clostridium tertium, and Paraclostridium bifermentans. Frontiers in Microbiology, 15.
  22. Carval,T. et al. (2024) Pangeo environment in Galaxy Earth System supported by Fair-Ease Copernicus Meetings.
  23. Castellana,S. et al. (2024) Pannonibacter anstelovis sp. nov. Isolated from Two Cases of Bloodstream Infections in Paediatric Patients. Microorganisms, 12, 799.
  24. Ceylan,F. et al. (2024) Whole-genome resequencing identifies exonic single-nucleotide variations in terpenoid biosynthesis genes of the medicinal and aromatic plant common sage (Salvia officinalis L.). Genetic Resources and Crop Evolution.
  25. Chetverikov,P.E. et al. (2024) Molecular Phylogenetics and Light Microscopy Reveal “True” and “False” Calacarines and Novel Genital Structures in Gall Mites (Acariformes, Eriophyoidea). Forests, 15, 329.
  26. Choudalakis,M. et al. (2024) RepEnTools: an automated repeat enrichment analysis package for ChIP-seq data reveals hUHRF1 Tandem-Tudor domain enrichment in young repeats. Mobile DNA, 15, 6.
  27. Cosenza-Contreras,M. et al. (2024) Proteometabolomics of initial and recurrent glioblastoma highlights an increased immune cell signature with altered lipid metabolism. Neuro-Oncology, 26, 488–502.
  28. Crespo,R. et al. (2024) PCID2 dysregulates transcription and viral RNA processing to promote HIV-1 latency. iScience, 27, 109152.
  29. Croney,K. (2024) Revealing Binding and Unbinding Pathways of Small Molecules and Peptides to Enzymes with Enhanced Sampling Methods. WWU Graduate School Collection.
  30. Darino,M. et al. (2024) Identification and functional characterisation of a locus for target site integration in Fusarium graminearum. Fungal Biology and Biotechnology, 11, 2.
  31. Azevedo,B.L. de et al. (2024) The genomic and phylogenetic analysis of Marseillevirus cajuinensis raises questions about the evolution of Marseilleviridae lineages and their taxonomical organization. Journal of Virology, 0, e00513–24.
  32. Souza,F.D. de et al. (2024) Mitochondrial genome of Hancornia speciosa gomes: intergenic regions containing retrotransposons and predicted genes. Molecular Biology Reports, 51, 132.
  33. Souza,Y.P.A. de et al. (2024) The seeds of Plantago lanceolata comprise a stable core microbiome along a plant richness gradient. Environmental Microbiome, 19, 11.
  34. Dederichs,T.-S. et al. (2024) Nonpreferential but Detrimental Accumulation of Macrophages With Clonal Hematopoiesis-Driver Mutations in Cardiovascular Tissues—Brief Report. Arteriosclerosis, Thrombosis, and Vascular Biology, 44, 690–697.
  35. Dehghanian,F. et al. (2024) ZFP982 confers mouse embryonic stem cell characteristics by regulating expression of Nanog, Zfp42, and Dppa3. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, 1871, 119686.
  36. Delandre,O. et al. (2024) 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. Biology, 13, 89.
  37. Deng,L. et al. (2024) Atlas of cardiac endothelial cell enhancer elements linking the mineralocorticoid receptor to pathological gene expression. Science Advances, 10, eadj5101.
  38. Deng,L. et al. (2024) Massively parallel CRISPR-assisted homologous recombination enables saturation editing of full-length endogenous genes in yeast. Science Advances, 10, eadj9382.
  39. Depari,E.K. et al. (2024) Long-read datasets of Kayu Bawang (Azadirachta excelsa (Jack) Jacobs) from 3 different identified seed stands in Bengkulu (Sumatra), Indonesia and its phylogenetic relationships.
  40. Donátová,K. et al. (2024) 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. International Journal of Molecular Sciences, 25, 2460.
  41. Dossmann,L. et al. (2024) Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons. Communications Biology, 7, 1–12.
  42. Edet,O.U. et al. (2024) Genomic analysis of a spontaneous unifoliate mutant reveals gene candidates associated with compound leaf development in Vigna unguiculata [L] Walp. Scientific Reports, 14, 10654.
  43. Eggenhofer,F. and Siederdissen,C. Höner zu (2024) Evolutionary Structure Conservation and Covariance Scores. In, Lorenz,R. (ed), RNA Folding: Methods and Protocols. Springer US, New York, NY, pp. 255–284.
  44. Ehle,C. et al. (2024) Downregulation of HNF4A enables transcriptomic reprogramming during the hepatic acute-phase response. Communications Biology, 7, 1–14.
  45. Ercole,T.G. et al. (2024) Unveiling Agricultural Biotechnological Prospects: The Draft Genome Sequence of Stenotrophomonas geniculata LGMB417. Current Microbiology, 81, 247.
  46. Ferreira,M.M. et al. (2024) TcSERPIN, an inhibitor that interacts with cocoa defense proteins and has biotechnological potential against human pathogens. Frontiers in Plant Science, 15.
  47. Fischer,J. et al. (2024) Expanding the Scope of Adenoviral Vectors by Utilizing Novel Tools for Recombination and Vector Rescue. Viruses, 16, 658.
  48. Flores Orozco,D. (2024) Evaluation of the long-term effects of anaerobic digestion on bovine manure resistomes and mobilomes and the molecular and microbial mechanisms involved.
  49. Galvis,J. et al. (2024) DIMet: An open-source tool for Differential analysis of targeted Isotope-labeled Metabolomics data. Bioinformatics (Oxford, England), btae282.
  50. Garcia-Fernandez,A. et al. (2024) Antibiotic resistance, plasmids, and virulence-associated markers in human strains of Campylobacter jejuni and Campylobacter coli isolated in Italy. Frontiers in Microbiology, 14.
  51. Gavalda-Garcia,J. et al. (2024) bio2Byte Tools deployment as a Python package and Galaxy tool to predict protein biophysical properties.
  52. Giufrè,M. et al. (2024) Detection of KPC-216, a Novel KPC-3 Variant, in a Clinical Isolate of Klebsiella pneumoniae ST101 Co-Resistant to Ceftazidime-Avibactam and Cefiderocol. Antibiotics, 13, 507.
  53. Glærum,I.L. et al. (2024) Postnatal persistence of hippocampal Cajal-Retzius cells has a crucial role in the establishment of the hippocampal circuit. Development, 151, dev202236.
  54. Gress,C. et al. (2024) Transcriptomic characterization of the human segmental endotoxin challenge model. Scientific Reports, 14, 1721.
  55. Häkkänen,T. et al. (2024) 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. International Journal for Parasitology, 54, 225–231.
  56. Hecht,H. et al. (2024) Quantum chemistry based prediction of electron ionization mass spectra for environmental chemicals.
  57. Heine,S. et al. (2024) Activation of the aryl hydrocarbon receptor improves allergen-specific immunotherapy of murine allergic airway inflammation: a novel adjuvant option? Frontiers in Immunology, 15.
  58. Herwibawa,B. et al. (2024) Association of a Specific OsCULLIN3c Haplotype with Salt Stress Responses in Local Thai Rice. International Journal of Molecular Sciences, 25, 1040.
  59. Hoffmann,U.A. et al. (2024) The role of the 5’ sensing function of ribonuclease E in cyanobacteria. RNA Biology.
  60. Hossain,M.S. et al. (2024) Evaluation of novel pyridoxal isonicotinoyl hydrazone (PIH) derivatives as potential anti-tuberculosis agents: An in silico investigation. International Journal of Quantum Chemistry, 124, e27381.
  61. Hosseinzadeh,S. and Hasanpur,K. (2024) Whole genome discovery of regulatory genes responsible for the response of chicken to heat stress. Scientific Reports, 14, 6544.
  62. Hwang,H.M. et al. (2024) Reduction of APOE accounts for neurobehavioral deficits in fetal alcohol spectrum disorders. Molecular Psychiatry, 1–17.
  63. Ipoutcha,T. et al. (2024) A synthetic biology approach to assemble and reboot clinically relevant Pseudomonas aeruginosa tailed phages. Microbiology Spectrum, 12, e02897–23.
  64. Ishola,O.A. et al. (2024) Comparative Metagenomic Analysis of Bacteriophages and Prophages in Gnotobiotic Mouse Models. Microorganisms, 12, 255.
  65. Jain,K. and Yadav,R. (2024) Human Metagenome Analysis with COVID-19 Infectious Disease. Current Trends in Biotechnology and Pharmacy, 18, 1616–1628.
  66. Jia,C. et al. (2024) Salmonella phylogenomics. In, Mokrousov,I. and Shitikov,E. (eds), Phylogenomics. Academic Press, pp. 267–281.
  67. Joshi,S. and Srivastava,R. (2024) Physicochemical properties and biological efficacy of 30 DYRK2 Inhibitors for the treatment of prostate cancer. Vietnam Journal of Chemistry, n/a.
  68. Joshi,S. and Srivastava,R. (2024) Tracing the pathways and mechanisms involved in medicinal uses of flaxseed with computational methods and bioinformatics tools. Frontiers in Chemistry, 11.
  69. Jovović,L. et al. (2024) De novo transcriptomes of cave and surface isopod crustaceans: insights from 11 species across three suborders. Scientific Data, 11, 595.
  70. Kahraman-Ilıkkan,Ö. (2024) Comparative genomics of four lactic acid bacteria identified with Vitek MS (MALDI-TOF) and whole-genome sequencing. Molecular Genetics and Genomics, 299, 31.
  71. Kalnytska,O. et al. (2024) SORCS2 activity in pancreatic α-cells safeguards insulin granule formation and release from glucose-stressed β-cells. iScience, 27, 108725.
  72. Kandinov,I. et al. (2024) Mini-Multilocus Sequence Typing Scheme for the Global Population of Neisseria gonorrhoeae. International Journal of Molecular Sciences, 25, 5781.
  73. Kostrykin,L. et al. (2024) Enhancing the image analysis community in Galaxy.
  74. Kruk,M.E. et al. (2024) An integrated metaproteomics workflow for studying host-microbe dynamics in bronchoalveolar lavage samples applied to cystic fibrosis disease. mSystems, 0, e00929–23.
  75. Kruse,P. et al. (2024) Synaptopodin Regulates Denervation-Induced Plasticity at Hippocampal Mossy Fiber Synapses. Cells, 13, 114.
  76. Kumawat,K.L. et al. (2024) Association of Reproductive Phenology with Air Temperature in Almond (Prunus dulcis [Mill.] D.A. Webb) Cultivars Under Northwestern Himalayan Conditions. Applied Fruit Science, 66, 581–588.
  77. Lapp,T. et al. (2024) Transcriptional profiling specifies the pathogen-specific human host response to infectious keratitis. Frontiers in Cellular and Infection Microbiology, 13.
  78. Larivière,D. et al. (2024) Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nature Biotechnology, 1–4.
  79. Lasolle,H. et al. (2024) Dual targeting of MAPK and PI3K pathways unlocks redifferentiation of Braf-mutated thyroid cancer organoids. Oncogene, 43, 155–170.
  80. Laurette,P. et al. (2024) In Vivo Silencing of Regulatory Elements Using a Single AAV-CRISPRi Vector. Circulation Research, 134, 223–225.
  81. Leavitt,R.J. et al. (2024) Acute Hypoxia Does Not Alter Tumor Sensitivity to FLASH Radiation Therapy. International Journal of Radiation Oncology*Biology*Physics.
  82. Link,T. (2024) Characterization and habitat adaptation of \textlessem\textgreaterTetragenococcus halophilus\textless/em\textgreater and \textlessem\textgreaterDebaryomyces hansenii\textless/em\textgreater from a lupine seasoning sauce fermentation.
  83. López,M.-E. et al. (2024) Epigenomic and transcriptomic persistence of heat stress memory in strawberry (Fragaria vesca). BMC Plant Biology, 24, 405.
  84. Luenstedt,J. et al. (2024) Partial hepatectomy accelerates colorectal metastasis by priming an inflammatory premetastatic niche in the liver. Frontiers in Immunology, 15.
  85. Maffei,E. et al. (2024) Complete genome sequence of Pseudomonas aeruginosa phage Knedl. Microbiology Resource Announcements, 13, e01174–23.
  86. McCluskey,K. et al. (2024) Predicting the Identities of su(met-2) and met-3 in Neurospora crassa by Genome Resequencing. Fungal Genetics Reports, 67.
  87. McVey,D.G. et al. (2024) Genetic influence on vascular smooth muscle cell apoptosis. Cell Death & Disease, 15, 1–12.
  88. Meem,M.H. et al. (2024) Exploring the anticancer and antibacterial potential of naphthoquinone derivatives: a comprehensive computational investigation. Frontiers in Chemistry, 12.
  89. Mérida-Cerro,J.A. et al. (2024) Rat1 promotes premature transcription termination at R-loops. Nucleic Acids Research, 52, 3623–3635.
  90. Merz,M. et al. (2024) Characterization of the major autolysin (AtlC) of Staphylococcus carnosus. BMC Microbiology, 24, 77.
  91. Miranda,S. et al. (2024) Assessment and Partial Characterization of Candidate Genes in Dihydrochalcone and Arbutin Biosynthesis in an Apple–Pear Hybrid by De Novo Transcriptome Assembly. Journal of Agricultural and Food Chemistry.
  92. Moris,V.C. et al. (2024) Ionizing radiation responses appear incidental to desiccation responses in the bdelloid rotifer Adineta vaga. BMC Biology, 22, 11.
  93. Mostafa,K. et al. (2024) Genome-wide analysis of PvMADS in common bean and functional characterization of PvMADS31 in Arabidopsis thaliana as a player in abiotic stress responses. The Plant Genome, 17, e20432.
  94. Müller,T. et al. (2024) CheRRI—Accurate classification of the biological relevance of putative RNA–RNA interaction sites. GigaScience, 13, giae022.
  95. Nicholson,T.L. et al. (2024) The contribution of BvgR, RisA, and RisS to global gene regulation, intracellular cyclic-di-GMP levels, motility, and biofilm formation in Bordetella bronchiseptica. Frontiers in Microbiology, 15.
  96. Candidatus Methanosphaera massiliense sp. nov., a methanogenic archaeal species found in a human fecal sample and prevalent in pigs and red kangaroos \textbar Microbiology Spectrum (2024).
  97. Effect of Anti‐S100A4 Monoclonal Antibody Treatment on Experimental Skin Fibrosis and Systemic Sclerosis–Specific Transcriptional Signatures in Human Skin - Trinh‐Minh - 2024 - Arthritis & Rheumatology - Wiley Online Library (2024).
  98. Nutrients \textbar Free Full-Text \textbar 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 (2024).
  99. Nugroho,A. et al. (2024) Transcriptome dataset of gall-rust infected Sengon (Falcataria falcata) seedlings using long-read PCR-cDNA sequencing. Data in Brief, 52, 109919.
  100. Nwankwo,C.C. et al. (2024) Metagenomic Study of Bacteria Diversity and Functional Profile in Bulk and Rhizosphere Soils of Fusarium-Wilt Infected Plantain (Musa paradisiaca). Journal of Advances in Microbiology, 24, 77–93.
  101. Oakes,B.J. et al. (2024) Building Domain-Specific Machine Learning Workflows: A Conceptual Framework for the State of the Practice. ACM Transactions on Software Engineering and Methodology, 33, 91:1–91:50.
  102. Oliveira,T.T. et al. (2024) Integrated analysis of RNA-seq datasets reveals novel targets and regulators of COVID-19 severity. Life Science Alliance, 7.
  103. Ostenfeld,L.J. et al. (2024) A hybrid receptor binding protein enables phage F341 infection of Campylobacter by binding to flagella and lipooligosaccharides. Frontiers in Microbiology, 15.
  104. Pachanon,R. et al. (2024) Genomic characterization of carbapenem and colistin-resistant Klebsiella pneumoniae isolates from humans and dogs. Frontiers in Veterinary Science, 11.
  105. Palacios-Rodriguez,A.P. et al. (2024) Antimicrobial Activity of Bacillus amyloliquefaciens BS4 against Gram-Negative Pathogenic Bacteria. Antibiotics, 13, 304.
  106. Pazoki,N. et al. (2024) Elucidating the impact of Y chromosome microdeletions and altered gene expression on male fertility in assisted reproduction. Human Molecular Genetics, ddae086.
  107. Pérez-Sisqués,L. et al. (2024) The Intellectual Disability Risk Gene Kdm5b Regulates Long-Term Memory Consolidation in the Hippocampus. Journal of Neuroscience, 44.
  108. Pfäffle,S.P. et al. (2024) 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. Nutrients, 16, 373.
  109. Pick,K. et al. (2024) Complete genome sequence of Escherichia coli MP1. Microbiology Resource Announcements, 0, e01216–23.
  110. Pilliol,V. et al. (2024) Methanobrevibacter massiliense and Pyramidobacter piscolens Co-Culture Illustrates Transkingdom Symbiosis. Microorganisms, 12, 215.
  111. Pinto,D. et al. (2024) Rescue of Mycobacterium bovis DNA Obtained from Cultured Samples during Official Surveillance of Animal TB: Key Steps for Robust Whole Genome Sequence Data Generation. International Journal of Molecular Sciences, 25, 3869.
  112. Pirnay,J.-P. et al. (2024) Personalized bacteriophage therapy outcomes for 100 consecutive cases: a multicentre, multinational, retrospective observational study. Nature Microbiology, 9, 1434–1453.
  113. Pustam,A. et al. (2024) Whole genome sequencing reveals complex resistome features of Klebsiella pneumoniae isolated from patients at major hospitals in Trinidad, West Indies. Journal of Global Antimicrobial Resistance.
  114. Pyles,R.B. et al. (2024) The altered TBI fecal microbiome is stable and functionally distinct. Frontiers in Molecular Neuroscience, 17.
  115. Qiu,X. et al. (2024) SmCYP71D373 of Salvia miltiorrhiza catalyzes the methyl oxidation reaction of tanshinone IIA-19 position. Industrial Crops and Products, 212, 118323.
  116. Rahman,N. et al. (2024) Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses. Microbial Genomics, 10, 001188.
  117. Ramos,B. and Cunha,M.V. (2024) The mobilome of Staphylococcus aureus from wild ungulates reveals epidemiological links at the animal-human interface. Environmental Pollution, 124241.
  118. Rapp,J. et al. (2024) Oncostatin M Reduces Pathological Neovascularization in the Retina Through Müller Cell Activation. Investigative Ophthalmology & Visual Science, 65, 22.
  119. Robson,J.K. et al. (2024) Environmental regulation of male fertility is mediated through Arabidopsis transcription factors bHLH89, 91, and 10. Journal of Experimental Botany, 75, 1934–1947.
  120. Royaux,C. et al. (2024) Genetic variability of New Caledonian Boeckella De Guerne & Richard, 1889 (Copepoda: Calanoida), with the description of a new species. Journal of Crustacean Biology, 44, ruae001.
  121. Sabala,R.F. et al. (2024) Carbapenem and colistin-resistant hypervirulent Klebsiella pneumoniae: An emerging threat transcending the egyptian food chain. Journal of Infection and Public Health, 17, 1037–1046.
  122. Sageman-Furnas,K. et al. (2024) Detailing Early Shoot Growth Arrest in Kro-0 x BG-5 Hybrids of Arabidopsis thaliana. Plant and Cell Physiology, 65, 420–427.
  123. Salapa,H.E. et al. (2024) hnRNP A1 dysfunction alters RNA splicing and drives neurodegeneration in multiple sclerosis (MS). Nature Communications, 15, 356.
  124. Sarkar,P. et al. (2024) Insights on the comparative affinity of ribonucleic acids with plant-based beta carboline alkaloid, harmine: Spectroscopic, calorimetric and computational evaluation. Heliyon, 0.
  125. Schmidt,C. et al. (2024) A practical guide to bioimaging research data management in core facilities. Journal of Microscopy, 294, 350–371.
  126. Sethi,R. et al. (2024) ezSingleCell: an integrated one-stop single-cell and spatial omics analysis platform for bench scientists. Nature Communications, 15, 5600.
  127. Silva,F.J. et al. (2024) 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. International Journal of Molecular Sciences, 25, 4228.
  128. Singh,P. et al. (2024) Biophysical and structural characterization of tetramethrin serum protein complex and its toxicological implications. Journal of Molecular Recognition, n/a, e3076.
  129. Soggia,G. et al. (2024) Bioelectrochemical protein production valorizing NH3-rich pig manure-derived wastewater and CO2 from anaerobic digestion. Renewable Energy, 120761.
  130. Soleau,N. et al. (2024) 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. International Journal of Molecular Sciences, 25, 5428.
  131. Stillger,M.N. et al. (2024) Neoadjuvant chemo- or chemo-radiation-therapy of pancreatic ductal adenocarcinoma differentially shift ECM composition, complement activation, energy metabolism and ribosomal proteins of the residual tumor mass. International Journal of Cancer, 154, 2162–2175.
  132. Stojkovic,L. et al. (2024) Targeted RNAseq Revealed the Gene Expression Signature of Ferroptosis-Related Processes Associated with Disease Severity in Patients with Multiple Sclerosis. International Journal of Molecular Sciences, 25, 3016.
  133. Strateva,T. and Peykov,S. (2024) First detection of a cefiderocol-resistant and extensively drug-resistant Acinetobacter baumannii clinical isolate in Bulgaria. Acta Microbiologica et Immunologica Hungarica, -1.
  134. Tetzlaff,S. et al. (2024) Small RNAs from mitochondrial genome recombination sites are incorporated into T. gondii mitoribosomes. eLife, 13, e95407.
  135. Thompson,R.M. et al. (2024) Draft genome sequences of five Mycobacterium strains, isolated from Alnus glutinosa root nodules. Microbiology Resource Announcements, 13, e01132–23.
  136. Thongbunrod,N. and Chaiprasert,P. (2024) Potential of enriched and stabilized anaerobic lignocellulolytic fungi coexisting with bacteria and methanogens for enhanced methane production from rice straw. Biomass Conversion and Biorefinery, 14, 8229–8250.
  137. Toth,R. et al. (2024) Divergence within the Taxon ‘Candidatus Phytoplasma asteris’ Confirmed by Comparative Genome Analysis of Carrot Strains. Microorganisms, 12, 1016.
  138. Tóth,K. et al. (2024) Genomic Epidemiology of C2/H30Rx and C1-M27 Subclades of Escherichia coli ST131 Isolates from Clinical Blood Samples in Hungary. Antibiotics, 13, 363.
  139. Trinh-Minh,T. et al. (2024) Effect of Anti-S100A4 Monoclonal Antibody Treatment on Experimental Skin Fibrosis and Systemic Sclerosis–Specific Transcriptional Signatures in Human Skin. Arthritis and Rheumatology, 76, 783–795.
  140. Ummethum,H. (2024) Proximity labeling as a tool to study transcription-replication interference.
  141. Umpeleva,T. et al. (2024) Identification of genetic determinants of bedaquiline resistance in Mycobacterium tuberculosis in Ural region, Russia. Microbiology Spectrum, 12, e03749–23.
  142. Vieira Da Cruz,A. et al. (2024) Pyridylpiperazine efflux pump inhibitor boosts in vivo antibiotic efficacy against K. pneumoniae. EMBO Molecular Medicine, 16, 93–111.
  143. Vieira,T. et al. (2024) Polymyxin Resistance in Salmonella: Exploring Mutations and Genetic Determinants of Non-Human Isolates. Antibiotics, 13, 110.
  144. Volkova,P. et al. (2024) Multi-omics responses of barley seedlings to low and high linear energy transfer irradiation. Environmental and Experimental Botany, 218, 105600.
  145. Vozenin,M.-C. et al. (2024) More May Not be Better: Enhanced Spacecraft Shielding May Exacerbate Cognitive Decrements by Increasing Pion Exposures during Deep Space Exploration. Radiation Research, 201, 93–103.
  146. Wang,Y.-H. et al. (2024) The Genome of Arsenophonus sp. and Its Potential Contribution in the Corn Planthopper, Peregrinus maidis. Insects, 15, 113.
  147. Wang,L. et al. (2024) Growth, Enzymatic, and Transcriptomic Analysis of xyr1 Deletion Reveals a Major Regulator of Plant Biomass-Degrading Enzymes in Trichoderma harzianum. Biomolecules, 14, 148.
  148. Watson,S. et al. (2024) Modification of Seurat v4 for the Development of a Phase Assignment Tool Able to Distinguish between G2 and Mitotic Cells. International Journal of Molecular Sciences, 25, 4589.
  149. Wight,J. et al. (2024) Anthropogenic contamination sources drive differences in antimicrobial-resistant Escherichia coli in three urban lakes. Applied and Environmental Microbiology, 90, e01809–23.
  150. Wight,J. et al. (2024) Anthropogenic contamination sources drive differences in antimicrobial-resistant Escherichia coli in three urban lakes. Applied and Environmental Microbiology, 0, e01809–23.
  151. Willnow,P. and Teleman,A.A. (2024) Nuclear position and local acetyl-CoA production regulate chromatin state. Nature, 1–9.
  152. Wurzbacher,C.E. et al. (2024) 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. Scientific Reports, 14, 5741.
  153. Zafar,Z. et al. (2024) Identification of the odorant binding proteins of Western Flower Thrips (Frankliniella occidentalis), characterization and binding analysis of FoccOBP3 with molecular modelling, molecular dynamics simulations and a confirmatory field trial. Journal of Biomolecular Structure and Dynamics, 0, 1–16.
  154. Zaman,B. et al. (2024) Tolperisone hydrochloride improves motor functions in Parkinson’s disease via MMP-9 inhibition and by downregulating p38 MAPK and ERK1/2 signaling cascade. Biomedicine & Pharmacotherapy, 174, 116438.
  155. Zhang,G. et al. (2024) Complete Mitochondrial Genomes of Nedyopus patrioticus: New Insights into the Color Polymorphism of Millipedes. Current Issues in Molecular Biology, 46, 2514–2527.
  156. Zhang,G. et al. (2024) The First Complete Mitochondrial Genome of the Genus Litostrophus: Insights into the Rearrangement and Evolution of Mitochondrial Genomes in Diplopoda. Genes, 15, 254.
  157. Zhao,R. et al. (2024) An RRM domain protein SOE suppresses transgene silencing in rice. New Phytologist, n/a.
  158. Zhu,T. et al. (2024) The BAS chromatin remodeler determines brassinosteroid-induced transcriptional activation and plant growth in Arabidopsis. Developmental Cell, 59, 924–939.e6.


  1. В,С.М. et al. (2023) ВЫЧИСЛИТЕЛЬНЫЙ АНАЛИЗ СТРУКТУРНОГО CОСТАВА ГЕНОМОВ КОРОНАВИРУСОВ. Доклады Белорусского государственного университета информатики и радиоэлектроники, 21, 104–113.
  2. Acebal,M.C. et al. (2023) Embryogenesis of a calanoid copepod analyzed by transcriptomics. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 45, 101054.
  3. Agboli,E. et al. (2023) Interaction of Mesonivirus and Negevirus with arboviruses and the RNAi response in Culex tarsalis-derived cells. Parasites & Vectors, 16, 361.
  4. Ahmad,N. et al. (2023) Biosynthetic Potential of Hypogymnia Holobionts: Insights into Secondary Metabolite Pathways. Journal of Fungi, 9, 546.
  5. Ahmed,N.A. et al. (2023) Safety assessment of Enterococcus lactis strains complemented with comparative genomics analysis reveals probiotic and safety characteristics of the entire species. BMC Genomics, 24, 667.
  6. Multimodal epigenetic changes and altered NEUROD1 chromatin binding in the mouse hippocampus underlie FOXG1 syndrome (2023) Proceedings of the National Academy of Sciences, 120, e2122467120.
  7. Alvandi,H. et al. (2023) Pathovar-Specific PCR Method for Detection and Identification of Xanthomonas translucens pv. undulosa. Plant Disease.
  8. Ambros,C.L. and Ehrmann,M.A. (2023) Distribution, inducibility, and characteristics of Latilactobacillus curvatus temperate phages. Microbiome Research Reports, 2, 34.
  9. Anbazhagan,S. et al. (2023) Comparative genomics of Brucella abortus and Brucella melitensis unravels the gene sharing, virulence factors and SNP diversity among the standard, vaccine and field strains. International Microbiology.
  10. Andrade,L. et al. (2023) Assessing Antimicrobial and Metal Resistance Genes in Escherichia Coli from Domestic Groundwater Supplies in Rural Ireland. SSRN Electronic Journal.
  11. Annor,S.D. et al. (2023) Melibiose–X-Gal–MacConkey Agar for Presumptive Differentiation of Escherichia albertii from E. coli and Salmonella from Poultry Meat. Applied Microbiology, 3, 119–130.
  12. Apostolakos,I. et al. (2023) Genomic and Phenotypic Characterization of Mastitis-Causing Staphylococci and Probiotic Lactic Acid Bacteria Isolated from Raw Sheep’s Milk. International Journal of Molecular Sciences, 24, 13883.
  13. Arcari,G. et al. (2023) Ceftazidime–avibactam resistance in Klebsiella pneumoniae sequence type 37: a decade of persistence and concealed evolution. Microbial Genomics, 9, 000931.
  14. Arcari,G. et al. (2023) Genotypic Evolution of Klebsiella pneumoniae Sequence Type 512 during Ceftazidime/Avibactam, Meropenem/Vaborbactam, and Cefiderocol Treatment, Italy. Emerging Infectious Diseases, 29, 2266.
  15. Arcari,G. et al. (2023) Multiplicity of blaKPC Genes and pKpQIL Plasmid Plasticity in the Development of Ceftazidime-Avibactam and Meropenem Coresistance in Klebsiella pneumoniae Sequence Type 307. Antimicrobial Agents and Chemotherapy, 0, e00368–23.
  16. Aribisala,J.O. et al. (2023) Cheminformatics identification of phenolics as modulators of key penicillin−binding proteins of Escherichia coli towards interventive antibacterial therapy. Molecular Simulation, 0, 1–17.
  17. Arnold,N.D. et al. (2023) Isolation, biochemical characterization, and genome sequencing of two high‐quality genomes of a novel chitinolytic Jeongeupia species. MicrobiologyOpen, 12, e1372.
  18. Bafna,A. et al. (2023) Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock. Genome Research, genome;gr.277581.122v2.
  19. Baig,D.I. et al. (2023) 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. PLOS ONE, 18, e0286428.
  20. Silva,I. Batista da et al. (2023) Discovery of putative long non-coding RNAs expressed in the eyes of Astyanax mexicanus (Actinopterygii: Characidae). Scientific Reports, 13, 12051.
  21. Bazukyan,I. et al. (2023) In Silico Probiogenomic Characterization of Lactobacillus delbrueckii subsp. lactis A4 Strain Isolated from an Armenian Honeybee Gut. Insects, 14, 540.
  22. Beck,C. et al. (2023) Trimannose-coupled antimiR-21 for macrophage-targeted inhalation treatment of acute inflammatory lung damage. Nature Communications, 14, 4564.
  23. Beerling,D. et al. (2023) Enhanced weathering in the U.S. Corn Belt delivers carbon removal with agronomic benefits.
  24. Belair,M. et al. (2023) Botryosphaeriaceae gene machinery: Correlation between diversity and virulence. Fungal Biology, 127, 1010–1031.
  25. Ben-Oz,B.M. et al. (2023) A dual role of RBM42 in modulating splicing and translation of CDKN1A/p21 during DNA damage response. Nature Communications, 14, 7628.
  26. Bennett-Keki,S. et al. (2023) Sex-biased gene expression in nutrient-sensing pathways. Proceedings of the Royal Society B: Biological Sciences, 290, 20222086.
  27. Bennett-Keki,S. et al. (2023) Sex-biased gene expression in nutrient-sensing pathways. Proceedings of the Royal Society B: Biological Sciences, 290, 20222086.
  28. Bordel,S. et al. (2023) Genome sequence analysis and characterization of Bacillus altitudinis B12, a polylactic acid- and keratin-degrading bacterium. Molecular Genetics and Genomics, 298, 389–398.
  29. Bordel,S. et al. (2023) Genome sequence analysis and characterization of Bacillus altitudinis B12, a polylactic acid- and keratin-degrading bacterium. Molecular Genetics and Genomics, 298, 389–398.
  30. Boutigny,A.-L. et al. (2023) Direct Xylella fastidiosa whole genome sequencing from various plant species using targeted enrichment. Journal of Microbiological Methods, 208, 106719.
  31. Braga,P.R.C. et al. (2023) 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. Journal of Global Antimicrobial Resistance, 35, 198–201.
  32. Breidenbach,J.D. (2023) Harmful Algal Bloom Toxin Aerosol Exposure and Airway Inflammation.
  33. Broche,J. et al. (2023) Genome-wide deposition of 6-methyladenine in human DNA reduces the viability of HEK293 cells and directly influences gene expression. Communications Biology, 6, 1–12.
  34. Brück,P. et al. (2023) Ploidy in Vibrio natriegens: Very Dynamic and Rapidly Changing Copy Numbers of Both Chromosomes. Genes, 14, 1437.
  35. Bruno,F. et al. (2023) Collisions of RNA polymerases behind the replication fork promote alternative RNA splicing in newly replicated chromatin. Molecular Cell, S1097–2765(23)01012–2.
  36. Buchacher,T. et al. (2023) PIM kinases regulate early human Th17 cell differentiation. Cell Reports, 42, 113469.
  37. Camargo,C.H. et al. (2023) Genomic analysis and antimicrobial activity of β-lactam/β-lactamase inhibitors and other agents against KPC-producing Klebsiella pneumoniae clinical isolates from Brazilian hospitals. Scientific Reports, 13, 14603.
  38. Camargo,C.H. et al. (2023) Genomics and Antimicrobial Susceptibility of Clinical Pseudomonas aeruginosa Isolates from Hospitals in Brazil. Pathogens, 12, 918.
  39. Capitani,V. et al. (2023) Genome-Based Retrospective Analysis of a Providencia stuartii Outbreak in Rome, Italy: Broad Spectrum IncC Plasmids Spread the NDM Carbapenemase within the Hospital. Antibiotics, 12, 943.
  40. Capra,E. et al. (2023) CpG DNA methylation changes during epididymal sperm maturation in bulls. Epigenetics & Chromatin, 16, 20.
  41. Chanama,M. et al. (2023) Comparative genome features and secondary metabolite biosynthetic potential of Kutzneria chonburiensis and other species of the genus Kutzneria. Scientific Reports, 13, 8794.
  42. USP7/Maged1-mediated H2A monoubiquitination in the paraventricular thalamus: an epigenetic mechanism involved in cocaine use disorder (2023) Nature Communications, 14, 8481.
  43. Cherrad,S. et al. (2023) New insights from short and long reads sequencing to explore cytochrome b variants in Plasmopara viticola populations collected from vineyards and related to resistance to complex III inhibitors. PLOS ONE, 18, e0268385.
  44. Cigana,K.\textless1994\textgreater (2023) Monitoraggio della comunità microbiologica durante un processo di fermentazione anaerobica di scarti vitivinicoli.
  45. Corneo,A. (2023) Proceedings of 2023 International Camellia Congress in Italy.
  46. Cosenza-Contreras,M. et al. (2023) Proteometabolomics of initial and recurrent glioblastoma highlights an increased immune cell signature with altered lipid metabolism. Neuro-Oncology, noad208.
  47. Čupić,M. et al. (2023) The first cavefish in the Dinaric Karst? Cave colonization made possible by phenotypic plasticity in Telestes karsticus. Zoological Research, 44, 821–833.
  48. Davasaz Tabrizi,E. et al. (2023) Bioinformatic challenge on prostate cancer and urinary microbiome. Revista Latinoamericana de Hipertensión, 18, 266–273.
  49. Andrade,T.S. de et al. (2023) Whole genome sequencing of Bacillus anthracis isolated from animal in the 1960s, Brazil, belonging to the South America subclade. Comparative Immunology, Microbiology and Infectious Diseases, 100, 102027.
  50. Jesus Bertani,A.M. de et al. (2023) Whole genome sequence analysis of the first reported isolate of Salmonella Agona carrying blaCTX-M-55 gene in Brazil. Scientific Reports, 13, 2299.
  51. Carmo Santos,M.L. do et al. (2023) Proteomics analysis reveals three potential cacao target that interacts with Moniliophthora perniciosa NEP during witches broom disease. Physiological and Molecular Plant Pathology, 124, 101946.
  52. Dziuba,M.V. et al. (2023) Silent gene clusters encode magnetic organelle biosynthesis in a non-magnetotactic phototrophic bacterium. The ISME Journal, 17, 326–339.
  53. Emser,S.V. et al. (2023) Mitochondrial polymorphism m.3017C\textgreaterT of SHLP6 relates to heterothermy. Frontiers in Physiology, 14.
  54. Esha,N.J.I. et al. (2023) Exploring the potential of fluoro-flavonoid derivatives as anti-lung cancer agents: DFT, molecular docking, and molecular dynamics techniques. International Journal of Quantum Chemistry, n/a, e27274.
  55. Farias,K.S. et al. (2023) BASIDIN as a New Protein Effector of the Phytopathogen Causing Witche’s Broom Disease in Cocoa. International Journal of Molecular Sciences, 24, 11714.
  56. Farmiloe,G. et al. (2023) Structural Evolution of Gene Promoters Driven by Primate-Specific KRAB Zinc Finger Proteins. Genome Biology and Evolution, 15, evad184.
  57. Fatima,A. and Khan,M.A. (2023) Book of Abstracts of the 1st Colloquium for Bioinformatics Learning, Education, and Training. F1000Research, 12, 70.
  58. Fernández-Díaz,M. et al. (2023) Draft Genome Sequence of an Isolate of Genotype VII Newcastle Disease Virus Isolated from an Outbreak in Fighting Cock in Peru. Microbiology Resource Announcements, 12, e01293–22.
  59. Ferreira,T. (2023) Avaliação da expressão diferencial em Physcomitrium patens na busca das adaptações moleculares responsivas na arquitetura dos órgãos reprodutivos.
  60. Figiel,M. et al. (2023) Zinc controls operator affinity of human transcription factor YY1 by mediating dimerization via its N-terminal region. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 1866, 194905.
  61. Fischer,S. et al. (2023) Peptide-mediated inhibition of the transcriptional regulator Elongin BC induces apoptosis in cancer cells. Cell Chemical Biology, 30, 766–779.e11.
  62. Gains,A.F. et al. (2023) Identification of a Czc-like operon of the periodontal pathobiont P. gingivalis involved in metal ion efflux. Anaerobe, 80, 102696.
  63. Galgano,M. et al. (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. Antibiotics, 12, 436.
  64. Goossens,P. et al. (2023) Obligate biotroph downy mildew consistently induces near-identical protective microbiomes in Arabidopsis thaliana. Nature Microbiology, 8, 2349–2364.
  65. Gosch,A. et al. (2023) Spitting in the wind?—The challenges of RNA sequencing for biomarker discovery from saliva. International Journal of Legal Medicine.
  66. Guerler,A. et al. (2023) Fast and accurate genome-wide predictions and structural modeling of protein–protein interactions using Galaxy. BMC Bioinformatics, 24, 263.
  67. Gussak,A. et al. (2023) Precision Genome Engineering in Streptococcus suis Based on a Broad-Host-Range Vector and CRISPR-Cas9 Technology. ACS Synthetic Biology.
  68. Han,Z. et al. (2023) DNA-directed termination of RNA polymerase II transcription. Molecular Cell, 83, 3253–3267.e7.
  69. Härdtner,C. et al. (2023) A comparative gene expression matrix in Apoe-deficient mice identifies unique and atherosclerotic disease stage-specific gene regulation patterns in monocytes and macrophages. Atherosclerosis, 371, 1–13.
  70. Hassan,Z. et al. (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. Phytopathogenomics and Disease Control, 2, 1–12.
  71. Hedhly,A. et al. (2023) S-Locus Genotyping in Japanese Plum by High Throughput Sequencing Using a Synthetic S-Loci Reference Sequence. International Journal of Molecular Sciences, 24, 3932.
  72. Heß,D. et al. (2023) The impact of salt stress on the physiology and the transcriptome of the model streptophyte green alga Chara braunii. Physiologia Plantarum, 175, e14123.
  73. Heß,D. et al. (2023) Insight into the nodal cells transcriptome of the streptophyte green alga Chara braunii S276. Physiologia Plantarum, 175, e14025.
  74. Hodzhev,Y. (2023) Analysis of blood microbiome dysbiosis in pulmonary sarcoidosis by decision tree model. Biotechnology & Biotechnological Equipment, 37, 2283133.
  75. Hosseinzadeh,S. and Hasanpur,K. (2023) Gene expression networks and functionally enriched pathways involved in the response of domestic chicken to acute heat stress. Frontiers in Genetics, 14.
  76. Howard,M. et al. (2023) Complete genome sequence of a human bacteremia isolate of Kalamiella piersonii. Microbiology Resource Announcements, 0, e00293–23.
  77. Huang,Y.-H. et al. (2023) A translational regulator MHZ9 modulates ethylene signaling in rice. Nature Communications, 14, 4674.
  78. Huszarik,M. et al. (2023) External DNA contamination and efficiency of bleach decontamination for arthropod diet analysis. Environmental DNA, 5, 540–550.
  79. Ilikkan,Ö. (2023) Laktik Asit Bakterilerinde Tetrasiklin Direncinin Fenotipik ve Tüm Genom Dizilerinde in silico Genotipik Olarak Araştırılması. Journal of the Institute of Science and Technology, 13, 932–940.
  80. Iniesta-Pallarés,M. et al. (2023) Changes in rice rhizosphere and bulk soil bacterial communities in the Doñana wetlands at different growth stages. Applied Soil Ecology, 190, 105013.
  81. Ioos,R. et al. (2023) Harnessing the power of comparative genomics to support the distinction of sister species within Phyllosticta and development of highly specific detection of Phyllosticta citricarpa causing citrus black spot by real-time PCR. PeerJ, 11, e16354.
  82. Izquierdo-Lara,R.W. et al. (2023) Rise and fall of SARS-CoV-2 variants in Rotterdam: Comparison of wastewater and clinical surveillance. Science of The Total Environment, 873, 162209.
  83. izzo,annalisa et al. (2023) Nucleophosmin 1 cooperates with the methyltransferase DOT1L to regulate H3K79me2 levels and DNA satellites expression at peri-nucleolar heterochromatin In Review.
  84. Jaki,L. et al. (2023) Total escape of SARS-CoV-2 from dual monoclonal antibody therapy in an immunocompromised patient. Nature Communications, 14, 1999.
  85. Javed,M. et al. (2023) Unraveling the transcriptional network regulated by miRNAs in blast-resistant and blast-susceptible rice genotypes during Magnaporthe oryzae interaction. Gene, 886, 147718.
  86. Jeon,G.-T. et al. (2023) Tailored Multiplex Real-Time RT-PCR with Species-Specific Internal Positive Controls for Detecting SARS-CoV-2 in Canine and Feline Clinical Samples. Animals, 13, 602.
  87. Jesudoss Chelladurai,J.R.J. et al. (2023) Comparative Genomic Analysis and Species Delimitation: A Case for Two Species in the Zoonotic Cestode Dipylidium caninum. Pathogens, 12, 675.
  88. Jhinjharia,D. et al. (2023) A high-throughput structural dynamics approach for identification of potential agonists of FFAR4 for type 2 diabetes mellitus therapy. Journal of Biomolecular Structure and Dynamics, 0, 1–21.
  89. Kandinov,I. et al. (2023) Azithromycin Susceptibility Testing and Molecular Investigation of Neisseria gonorrhoeae Isolates Collected in Russia, 2020–2021. Antibiotics, 12, 170.
  90. Kandinov,I. et al. (2023) Emergence of Azithromycin-Resistant Neisseria gonorrhoeae Isolates Belonging to the NG-MAST Genogroup 12302 in Russia. Microorganisms, 11, 1226.
  91. Karthik,K. et al. (2023) Foremost report of the whole genome of Spirabiliibacterium mucosae from India and comparative genomics of the novel genus Spirabiliibacterium. Gene, 867, 147359.
  92. Kefi,A. (2023) Improving the Human Genome Annotation Using Integrative Analysis and Deep Learning Methods.
  93. Khan,U.M. et al. (2023) Comparative phylogenomic insights of KCS and ELO gene families in Brassica species indicate their role in seed development and stress responsiveness. Scientific Reports, 13, 3577.
  94. Khine,N.O. et al. (2023) Comparative genomic analysis of Colistin resistant Escherichia coli isolated from pigs, a human and wastewater on colistin withdrawn pig farm. Scientific Reports, 13, 5124.
  95. Kmeli,N. et al. (2023) Genome-wide characterization of Ficus carica MADS-box transcription factors with a focus on their roles during fruit development. Horticulture, Environment, and Biotechnology.
  96. Kocsmár,É. et al. (2023) Proteome alterations in human autopsy tissues in relation to time after death. Cellular and Molecular Life Sciences, 80, 117.
  97. Kohler,D. et al. (2023) MSstatsShiny: A GUI for Versatile, Scalable, and Reproducible Statistical Analyses of Quantitative Proteomic Experiments. Journal of Proteome Research, 22, 551–556.
  98. Lamas,A. et al. (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. Frontiers in Microbiology, 14.
  99. Lapadula,W.J. and Juri Ayub,M. (2023) Ribosome inactivating proteins in insects: HGT, gene expression, and functional implications. Gene, 877, 147547.
  100. Le Corre,L. and Padovani,D. (2023) Mechanism-based and computational modeling of hydrogen sulfide biogenesis inhibition: interfacial inhibition. Scientific Reports, 13, 7287.
  101. Lee,C. et al. (2023) Global and local functions of the Fused kinase ortholog CdaH in intracellular patterning in Tetrahymena. Journal of Cell Science, 137, jcs261256.
  102. Lenz,M. et al. (2023) The Amyloid Precursor Protein Regulates Synaptic Transmission at Medial Perforant Path Synapses. Journal of Neuroscience, 43, 5290–5304.
  103. Lenz,M. et al. (2023) Denervated mouse CA1 pyramidal neurons express homeostatic synaptic plasticity following entorhinal cortex lesion. Frontiers in Molecular Neuroscience, 16.
  104. Li,Y. et al. (2023) Proteogenomic data and resources for pan-cancer analysis. Cancer Cell, 41, 1397–1406.
  105. Liu,L. et al. (2023) A comprehensive review of bioinformatics tools for chromatin loop calling. Briefings in Bioinformatics, bbad072.
  106. Livingstone,M. et al. (2023) De Novo Whole-Genome Sequencing of Two Pathogenic Pasteurella multocida Type D:6 Strains Isolated from Pigs. Microbiology Resource Announcements, 12, e00098–23.
  107. Maki,J.J. et al. (2023) Species Delineation and Comparative Genomics within the Campylobacter ureolyticus Complex. Journal of Clinical Microbiology, 61, e00046–23.
  108. Manna,P.T. et al. (2023) Endosomal vesicle fusion machinery is involved with the contractile vacuole in Dictyostelium discoideum. Journal of Cell Science, 136, jcs260477.
  109. Mathlouthi,N.E.H. et al. (2023) Colorectal Cancer Archaeome: A Metagenomic Exploration, Tunisia. Current Issues in Molecular Biology, 45, 7572–7581.
  110. Mathura,S.R. et al. (2023) Characterization and expression analysis of SnRK2, PYL, and ABF/ AREB/ ABI5 gene families in sweet potato. PLOS ONE, 18, e0288481.
  111. Mathura,S.R. et al. (2023) Genome-wide Identification of the Auxin Transporter Gene Families in Sweet Potato (Ipomoea batatas) and their Expression During Tuberization. Tropical Plant Biology.
  112. Mehta,S. et al. (2023) A Galaxy of informatics resources for MS-based proteomics. Expert Review of Proteomics, 0, 1–16.
  113. Métris,K.L. and Métris,J. (2023) Aircraft surveys for air eDNA: probing biodiversity in the sky. PeerJ, 11, e15171.
  114. Mohamed,N.A. et al. (2023) Candidate miRNAs from Oryza sativa for Silencing the Rice Tungro Viruses. Agriculture, 13, 651.
  115. Mohebifar,H. et al. (2023) Construction and analysis of pseudogene-related ceRNA network in breast cancer. Scientific Reports, 13, 21874.
  116. Moris,V.C. et al. (2023) Intrasexual cuticular hydrocarbon dimorphism in a wasp sheds light on hydrocarbon biosynthesis genes in Hymenoptera. Communications Biology, 6, 1–15.
  117. Myacheva,K. et al. (2023) CRISPRi screening identifies CASP8AP2 as an essential viability factor in lung cancer controlling tumor cell death via the AP-1 pathway. Cancer Letters, 552, 215958.
  118. Nielsen,C.M. et al. (2023) Delayed boosting improves human antigen-specific Ig and B cell responses to the RH5.1/AS01_\textrmB malaria vaccine. JCI Insight, 8.
  119. Characterization of the Italian population of Ciborinia camelliae (2023).
  120. Proceedings of the Joint 3rd International Conference on Bioinformatics and Data Science (ICBDS 2022), ISBN 9789464631630 - Better Read Than Dead Bookstore Newtown (2023).
  121. Oger,F. et al. (2023) β-Cell–Specific E2f1 Deficiency Impairs Glucose Homeostasis, β-Cell Identity, and Insulin Secretion. Diabetes, 72, 1112–1126.
  122. Ohta,T. and Shiwa,Y. (2023) Hybrid Genome Assembly of Short and Long Reads in Galaxy. In, Arakawa,K. (ed), Nanopore Sequencing: Methods and Protocols, Methods in Molecular Biology. Springer US, New York, NY, pp. 15–30.
  123. Olagoke,O.C. et al. (2023) RPS6 transcriptional modulation in neural tissues of Nauphoeta cinerea during streptozotocin-associated sugar metabolism impairment. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, 263, 110785.
  124. Oliveira, et al. (2023) Cocoa apoplastome contains defense proteins against pathogens.
  125. Palecanda,S. et al. (2023) Increasing complexity of opsin expression across stomatopod development. Ecology and Evolution, 13, e10121.
  126. Palecanda,S. et al. (2023) Molecular Evolution of Malacostracan Short Wavelength Sensitive Opsins. Journal of Molecular Evolution.
  127. Pannhorst,K. et al. (2023) The non-classical major histocompatibility complex II protein SLA-DM is crucial for African swine fever virus replication. Scientific Reports, 13, 10342.
  128. Patel,U. et al. (2023) Bioprospecting phytochemicals of Rosmarinus officinalis L. for targeting SARS-CoV-2 main protease (Mpro): a computational study. Journal of Molecular Modeling, 29, 161.
  129. Pelos,G. et al. (2023) Fast proliferating and slowly migrating non-small cell lung cancer cells are vulnerable to decitabine and retinoic acid combinatorial treatment. International Journal of Cancer.
  130. Peschel,C. (2023) Molekulare Mechanismen der pharmakologischen Resistenz kolorektaler Karzinomzelllinien gegen das Chemotherapieregime FOLFIRI.
  131. Phillip,S. et al. (2023) Molecular Characterizations of the Coagulase-Negative Staphylococci Species Causing Urinary Tract Infection in Tanzania: A Laboratory-Based Cross-Sectional Study. Pathogens, 12, 180.
  132. Pimentel,L.G.P. et al. (2023) Description of eight new mitochondrial genomes for the genus Neoarius and phylogenetic considerations for the family Ariidae (Siluriformes). Genomics & Informatics, 21, e51.
  133. Plaza,D.F. et al. (2023) A genomic platform for surveillance and antigen discovery in Plasmodium spp. using long-read amplicon sequencing. Cell Reports Methods, 0.
  134. Potgieter,M.G. et al. (2023) MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets. PLOS Computational Biology, 19, e1011163.
  135. Pustam,A. et al. (2023) Comparative genomics and virulome analysis reveal unique features associated with clinical strains of Klebsiella pneumoniae and Klebsiella quasipneumoniae from Trinidad, West Indies. PLOS ONE, 18, e0283583.
  136. Rapp,J. et al. (2023) STAT3 signaling induced by the IL-6 family of cytokines modulates angiogenesis. Journal of Cell Science, 136, jcs260182.
  137. Rehm,T.M. (2023) Analyse des Replikationszyklus von nicht-melanozytären Hautkrebs-assoziierten beta-humanen Papillomviren in humanen Keratinozyten.
  138. Reyes,B.M.D. et al. (2023) Characterization of the microbiota dynamics associated with Moniliophthora roreri, causal agent of cocoa frosty pod rot disease, reveals new viral species. Frontiers in Microbiology, 13.
  139. Riesle,A.J. et al. (2023) Activator-blocker model of transcriptional regulation by pioneer-like factors. Nature Communications, 14, 5677.
  140. Ristinmaa,A.S. et al. (2023) Resin acids play key roles in shaping microbial communities during degradation of spruce bark. Nature Communications, 14, 8171.
  141. Robson,J.K. et al. (2023) Environmental regulation of male fertility is mediated through Arabidopsis bHLH89, 91 and 10. Journal of Experimental Botany, erad480.
  142. Rogg,M. et al. (2023) A YAP/TAZ–ARHGAP29–RhoA Signaling Axis Regulates Podocyte Protrusions and Integrin Adhesions. Cells, 12, 1795.
  143. Roux,H.M. et al. (2023) DNA ultra-sensitive quantification, a technology for studying HIV unintegrated linear DNA. Cell Reports Methods, 3, 100443.
  144. SAKAMOTO,H. et al. (2023) Detection of domestic cat hepadnavirus by next-generation sequencing and epidemiological survey in Japan. The Journal of Veterinary Medical Science, 85, 642–646.
  145. Sánchez-León,I. et al. (2023) Heteroresistance to Colistin in Clinical Isolates of Klebsiella pneumoniae Producing OXA-48. Antibiotics, 12, 1111.
  146. Schiml,V.C. et al. (2023) Integrative meta-omics in Galaxy and beyond. Environmental Microbiome, 18, 56.
  147. Schoof,M. et al. (2023) Mouse models of pediatric high-grade gliomas with MYCN amplification reveal intratumoral heterogeneity and lineage signatures. Nature Communications, 14, 7717.
  148. Schüle,K.M. et al. (2023) Eomes restricts Brachyury functions at the onset of mouse gastrulation. Developmental Cell, 0.
  149. Schwabenland,M. et al. (2023) Neonatal immune challenge poses a sex-specific risk for epigenetic microglial reprogramming and behavioral impairment. Nature Communications, 14, 2721.
  150. Seckin Dinler,B. et al. (2023) The regulation of glutathione s-transferases by gibberellic acid application in salt treated maize leaves. Physiology and Molecular Biology of Plants, 29, 69–85.
  151. Semenzato,G. et al. (2023) 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. International Journal of Molecular Sciences, 24, 4845.
  152. Senft,R.A. et al. (2023) A biologist’s guide to planning and performing quantitative bioimaging experiments. PLOS Biology, 21, e3002167.
  153. Shankar,M. et al. (2023) Structure and Energetics of Serum Protein Complex of Tea Adulterant Dye Bismarck Brown Y using Experimental and Computational Methods. Computational Biology and Chemistry, 107976.
  154. Sharaf,A. et al. (2023) Bridging the gap in African biodiversity genomics and bioinformatics. Nature Biotechnology, 41, 1348–1354.
  155. Sheikh,T.M.M. et al. (2023) Volatile Organic Compounds Emitted by the Biocontrol Agent Pythium oligandrum Contribute to Ginger Plant Growth and Disease Resistance. Microbiology Spectrum, 0, e01510–23.
  156. Shi,S. et al. (2023) Modeling bile duct ischemia and reoxygenation injury in human cholangiocyte organoids for screening of novel cholangio-protective agents. eBioMedicine, 88, 104431.
  157. Siatra,P. et al. (2023) Return of the Tbx5; lineage-tracing reveals ventricular cardiomyocyte-like precursors in the injured adult mammalian heart. npj Regenerative Medicine, 8, 1–15.
  158. Somashekhar,R. et al. (2023) Proceedings of the Joint 3rd International Conference on Bioinformatics and Data Science (ICBDS 2022) Springer Nature.
  159. Soorni,A. et al. (2023) Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa. BMC Plant Biology, 23, 3.
  160. Sozzoni,M. et al. (2023) A Chromosome-Level Reference Genome for the Black-Legged Kittiwake (Rissa tridactyla), a Declining Circumpolar Seabird. Genome Biology and Evolution, 15, evad153.
  161. Spanò,R. et al. (2023) Comparative Analysis of Bioactive Compounds in Two Globe Artichoke Ecotypes Sanitized and Non-Sanitized from Viral Infections. Plants, 12, 1600.
  162. Strateva,T. et al. (2023) Analysis of biofilm formation in nosocomial Stenotrophomonas maltophilia isolates collected in Bulgaria: An 11-year study (2011–2022). Acta Microbiologica et Immunologica Hungarica, 70, 11–21.
  163. Strateva,T. et al. (2023) Genotypic and phenotypic insights into virulence factors of nosocomial Stenotrophomonas maltophilia isolates collected in Bulgaria (2011–2022). Acta Microbiologica et Immunologica Hungarica, -1.
  164. Subramoney,K. et al. (2023) SARS-CoV-2 spike protein diversity at an intra-host level, among SARS-CoV-2 infected individuals in South Africa, 2020 to 2022. PLOS ONE, 18, e0286373.
  165. Sundar,S. (2023) In-silico transcriptome analysis of antibiotic-treated Mycobacterium tuberculosis identifies novel antibiotic resistance factors. Indian Journal of Tuberculosis.
  166. Suzuki,M. et al. (2023) Genomic Epidemiological Analysis of Antimicrobial-Resistant Bacteria with Nanopore Sequencing. In, Arakawa,K. (ed), Nanopore Sequencing: Methods and Protocols, Methods in Molecular Biology. Springer US, New York, NY, pp. 227–246.
  167. Tajuddin,S. et al. (2023) Genomic analysis and biological characterization of a novel Schitoviridae phage infecting Vibrio alginolyticus. Applied Microbiology and Biotechnology, 107, 749–768.
  168. Taylor,R.E. et al. (2023) WHIRLY proteins maintain seed longevity by effects on seed oxygen signalling during imbibition. Biochemical Journal, 480, 941–956.
  169. Thompson,R.M. et al. (2023) Draft genome sequence of Amycolatopsis camponoti RTGN1, a bacterial endophyte isolated from Alnus glutinosa root nodules. Microbiology Resource Announcements, 13, e00470–23.
  170. Thompson,R.M. et al. (2023) Draft genome sequence of Streptomyces poriferorum RTGN2, a bacterial endophyte isolated from Alnus glutinosa root nodules. Microbiology Resource Announcements, 13, e00486–23.
  171. Trifonova,A. et al. (2023) Combination of two rare mutations in the SARS-CoV-2 M gene in patients with severe and prolonged COVID-19. Infectious Diseases, 0, 1–5.
  172. Valadez-Moctezuma,E. et al. (2023) The first transcriptomic analyses of fruits and cladodes for comparison between three species of Opuntia. Genetic Resources and Crop Evolution, 70, 951–970.
  173. Valadez-Moctezuma,E. et al. (2023) The de novo transcriptome assembly of Agave angustifolia Haw, mining for carbohydrates and cellulose synthesis genes profiling, and molecular markers development. Plant Biotechnology Reports.
  174. Vergata,C. et al. (2023) How does particulate matter affect plant transcriptome and microbiome? Environmental and Experimental Botany, 209, 105313.
  175. Viljoen,N. et al. (2023) A rabies-related lyssavirus from a Nycticeinops schlieffeni bat with neurological signs, South Africa. Microbiology Resource Announcements, 12, e00621–23.
  176. Vitali,F. et al. (2023) Employing Genome Mining to Unveil a Potential Contribution of Endophytic Bacteria to Antimicrobial Compounds in the Origanum vulgare L. Essential Oil. Antibiotics, 12, 1179.
  177. Voelker,J. et al. (2023) The terpene synthase genes of Melaleuca alternifolia (tea tree) and comparative gene family analysis among Myrtaceae essential oil crops. Plant Systematics and Evolution, 309, 13.
  178. Vorobyeva,N.E. et al. (2023) Su(Hw) interacts with Combgap to establish long-range chromatin contacts In Review.
  179. Voronezhskaya,V. et al. (2023) Multi-Omics Analysis of Vicia cracca Responses to Chronic Radiation Exposure in the Chernobyl Exclusion Zone. Plants, 12, 2318.
  180. Vukovikj,M. et al. (2023) In-depth genetic characterization of the SARS-CoV-2 pandemic in a two-year frame in North Macedonia using second and third generation sequencing technologies. Frontiers in Virology, 2.
  181. Wang,J. et al. (2023) A systems-level mass spectrometry-based technique for accurate and sensitive quantification of the RNA cap epitranscriptome. Nature Protocols, 1–28.
  182. Weber,L.M. et al. (2023) The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain. Nucleic Acids Research, 51, 574–594.
  183. Wein,S. (2023) Analysis of RNA Sequences and Modifications Using NASE. In, Oliveira,P.H. (ed), Computational Epigenomics and Epitranscriptomics, Methods in Molecular Biology. Springer US, New York, NY, pp. 225–239.
  184. Werner,J. et al. (2023) 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. Neoplasia, 36, 100871.
  185. Whitmore,L. et al. (2023) Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA. Nature Ecology & Evolution, 1–16.
  186. Williams,S.E. et al. (2023) Discovery and biosynthetic assessment of ’Streptomyces ortus’ sp. nov. isolated from a deep-sea sponge. Microbial Genomics, 9, mgen000996.
  187. Wittke,S. et al. (2023) EODIE — Earth Observation Data Information Extractor. SoftwareX, 23, 101421.
  188. Wolf,J. et al. (2023) Transcriptional Profiling Identifies Prognostic Gene Signatures for Conjunctival Extranodal Marginal Zone Lymphoma. Biomolecules, 13, 115.
  189. Xu,F. et al. (2023) Reprogramming of the transcriptome after heat stress mediates heat hormesis in Caenorhabditis elegans. Nature Communications, 14, 1–16.
  190. Yan,Y. et al. (2023) DIET-like mutualism of Geobacter and methanogens at specific electrode potential boosts production of both methane and hydrogen from propionate. Water Research, 235, 119911.
  191. Yousif,M. et al. (2023) SARS-CoV-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses. Nature Communications, 14, 6325.
  192. Yusuf,A.J. et al. (2023) Exploring Scutellaria baicalensis bioactives as EGFR tyrosine kinase inhibitors: Cheminformatics and molecular docking studies. Informatics in Medicine Unlocked, 43, 101406.
  193. Zerouki,C. et al. (2023) Whole-genome sequence and mass spectrometry study of the snow blight fungus Phacidium infestans (Karsten) DSM 5139 growing at freezing temperatures. Molecular Genetics and Genomics.
  194. Zhang,Z. et al. (2023) NFATc1 Is a Central Mediator of EGFR-Induced ARID1A Chromatin Dissociation During Acinar Cell Reprogramming. Cellular and Molecular Gastroenterology and Hepatology.
  195. Zilbauer,M. et al. (2023) A Roadmap for the Human Gut Cell Atlas. Nature Reviews Gastroenterology & Hepatology, 1–18.
  196. Zinati,Z. and Nazari,L. (2023) Deciphering the molecular basis of abiotic stress response in cucumber (Cucumis sativus L.) using RNA-Seq meta-analysis, systems biology, and machine learning approaches. Scientific Reports, 13, 12942.
  197. Zirngibl,M.-E. et al. (2023) Triose phosphate export from chloroplasts and cellular sugar content regulate anthocyanin biosynthesis during high light acclimation. Plant Communications, 4, 100423.
  198. Mohsenin,H. et al. (2023) PenTag, a Versatile Platform for Synthesizing Protein‐Polymer Biohybrid Materials. Advanced Functional Materials.


  1. Achom,M. et al. (2022) Plant circadian clock control of Medicago truncatula nodulation via regulation of nodule cysteine-rich peptides. Journal of Experimental Botany, 73, 2142–2156.
  2. Aciole Barbosa,D. et al. (2022) Transcriptomic Profiling and Microsatellite Identification in Cobia (Rachycentron canadum), Using High-Throughput RNA Sequencing. Marine Biotechnology, 24, 255–262.
  3. Ali,O. et al. (2022) Transcriptome-wide modulation by Sargassum vulgare and Acanthophora spicifera extracts results in a prime-triggered plant signaling cascade in tomato and sweet pepper. AoB PLANTS, plac046.
  4. Ali,O. et al. (2022) Transcriptomic changes induced by applications of a commercial extract of Ascophyllum nodosum on tomato plants. Scientific Reports, 12, 1–13.
  5. Amaral, et al. (2022) TcTI, a Kunitz-type trypsin inhibitor from cocoa associated with defense against pathogens. Scientific Reports, 12.
  6. Arcari,G. et al. (2022) Interplay between Klebsiella pneumoniae producing KPC-31 and KPC-3 under treatment with high dosage meropenem: a case report. European Journal of Clinical Microbiology & Infectious Diseases, 41, 495–500.
  7. Ardisasmita,A.I. et al. (2022) A comprehensive transcriptomic comparison of hepatocyte model systems improves selection of models for experimental use. Communications Biology, 5, 1–15.
  8. Ashrafi,S. et al. (2022) Two New Rhizobiales Species Isolated from Root Nodules of Common Sainfoin (Onobrychis viciifolia) Show Different Plant Colonization Strategies. Microbiology Spectrum, 0, e01099–22.
  9. Bamford,C.G.G. et al. (2022) Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. Viruses, 14, 325.
  10. Blacklock,E. (2022) Examination of crustacean immune responses through dsRNA-nanoparticle injection and phylogenetic analysis.
  11. Bokharaie,H. et al. (2022) Analysis of Alternative mRNA Splicing in Vemurafenib-Resistant Melanoma Cells. Biomolecules, 12.
  12. Borchel,A. et al. (2022) Sex differences in the early life stages of the salmon louse Lepeophtheirus salmonis (Copepoda: Caligidae). PLOS ONE, 17, e0266022.
  13. Bozan,M. et al. (2022) Whole-genome sequence of the filamentous diazotrophic cyanobacterium Tolypothrix sp. PCC 7712 and its comparison with non-diazotrophic Tolypothrix sp. PCC 7601. Frontiers in Microbiology, 13.
  14. Bray,S. et al. (2022) Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease. Journal of Cheminformatics, 14, 22.
  15. Breidenbach,J.D. et al. (2022) Microcystin-LR aerosol induces inflammatory responses in healthy human primary airway epithelium. Environment International, 169, 107531.
  16. Colin,L. et al. (2022) What’s left in the tank? Identification of non-ascribed aquarium’s coral collections with DNA barcodes as part of an integrated diagnostic approach. Conservation Genetics Resources.
  17. Deng,S. et al. (2022) LAMP Assay for Distinguishing Fusarium oxysporum and Fusarium commune in Lotus (Nelumbo nucifera) Rhizomes. Plant Disease, 106, 231–246.
  18. Dias,D. et al. (2022) Pathogenicity of Shiga toxin-producing Escherichia coli (STEC) from wildlife: Should we care? Science of The Total Environment, 812, 152324.
  19. Dugar,G. et al. (2022) A chromosomal loop anchor mediates bacterial genome organization. Nature Genetics, 1–8.
  20. Eisenhardt,A.E. et al. (2022) Genotyping of Circulating Free DNA Enables Monitoring of Tumor Dynamics in Synovial Sarcomas. Cancers, 14, 2078.
  21. Ereqat,S. et al. (2022) Association of DNA methylation and genetic variations of the \textlessem\textgreaterAPOE\textless/em\textgreater gene with the risk of diabetic dyslipidemia. Biomedical Reports, 17, 1–10.
  22. Fahrner,M. et al. (2022) Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework. GigaScience, 11.
  23. Farrell,J.A. et al. (2022) Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water. Molecular Ecology Resources, 22, 2471–2493.
  24. Feng,S. et al. (2022) Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors. Nature Communications, 13, 3808.
  25. Formenti,G. et al. (2022) Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs. Bioinformatics, 38, 4214–4216.
  26. Fröhlich,K. et al. (2022) Benchmarking of analysis strategies for data-independent acquisition proteomics using a large-scale dataset comprising inter-patient heterogeneity. Nature Communications, 13, 2622.
  27. Gallus,M.K. et al. (2022) Fructobacillus cardui sp. nov., isolated from a thistle (Carduus nutans) flower. International Journal of Systematic and Evolutionary Microbiology, 72, 005553.
  28. Gao,M. et al. (2022) Pluripotency factors determine gene expression repertoire at zygotic genome activation. Nature Communications, 13.
  29. Guindo,C.O. et al. (2022) A Tetragenococcus halophilus human gut isolate. Current Research in Microbial Sciences, 3, 100112.
  30. Jarvis,E.D. et al. (2022) Semi-automated assembly of high-quality diploid human reference genomes. Nature, 611, 519–531.
  31. Jdeed,S. et al. (2022) Redistribution of the SWI/SNF Complex Dictates Coordinated Transcriptional Control over Epithelial–Mesenchymal Transition of Normal Breast Cells through TGF-β Signaling. Cells, 11, 2633.
  32. Katsanos,D. and Barkoulas,M. (2022) Targeted DamID in C. elegans reveals a direct role for LIN-22 and NHR-25 in antagonizing the epidermal stem cell fate. Science Advances, 8.
  33. Kavas,M. et al. (2022) Genome-wide analysis of DUF221 domain-containing gene family in common bean and identification of its role on abiotic and phytohormone stress response. Genetic Resources and Crop Evolution.
  34. Kim,S.G. et al. (2022) Complete Genome Sequence of Metabacillus litoralis Strain NCTR108, Isolated from Commercial Tattoo Ink. Microbiology Resource Announcements, 0, e00794–22.
  35. Kim,S.G. et al. (2022) Complete Genome Sequence of Terrisporobacter glycolicus Strain WW3900, Isolated from Influent Wastewater at a Research Center with Multiple-Species Research Animal Facilities. Microbiology Resource Announcements, 0, e00859–22.
  36. Klaas,M. et al. (2022) Olfactomedin-4 improves cutaneous wound healing by promoting skin cell proliferation and migration through POU5F1/OCT4 and ESR1 signalling cascades. Cellular and Molecular Life Sciences, 79, 157.
  37. Koeppel,K.N. et al. (2022) SARS-CoV-2 Reverse Zoonoses to Pumas and Lions, South Africa. Viruses, 14, 120.
  38. Kumar,A. et al. (2022) An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy. GigaScience, 12, giad028.
  39. Kumaran,S. et al. (2022) In vitro and in silico analysis of Brilliant Black degradation by Actinobacteria and a Paraburkholderia sp. Genomics, 114, 110266.
  40. Kumar Halder,S. et al. (2022) Oxa-376 and Oxa-530 variants of β-lactamase: computational study uncovers potential therapeutic targets of Acinetobacter baumannii. RSC Advances, 12, 24319–24338.
  41. Latif,M.U. et al. (2022) NFATc1 signaling drives chronic ER stress responses to promote NAFLD progression. Gut.
  42. Lee,D.-W. et al. (2022) Genomic epidemiology of SARS- CoV-2 Omicron variants in the Republic of Korea. Scientific Reports, 12, 22414.
  43. Liu,M. et al. (2022) Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy. Nature Communications, 13, 3776.
  44. Lopez-Santamarina,A. et al. (2022) Evaluation of the potential prebiotic effect of Himanthalia elongata, an Atlantic brown seaweed, in an in vitro model of the human distal colon. Food Research International, 156, 111156.
  45. Lucaci,A.G. et al. (2022) RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis. bioRxiv.
  46. Mack,H.I.D. et al. (2022) Regulation of fatty acid desaturase- and immunity gene-expression by mbk-1/DYRK1A in Caenorhabditis elegans. BMC Genomics, 23.
  47. Martin,D.P. et al. (2022) Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA. 1 that likely impact Spike function. bioRxiv.
  48. McDonald,M.S. et al. (2022) Ultraviolet vision in larval Neogonodactylus oerstedii. Journal of Experimental Biology, 225, jeb243256.
  49. McDonald,M.S. et al. (2022) Ultraviolet vision in larval Neogonodactylus oerstedii. Journal of Experimental Biology.
  50. Mehta,S. et al. (2022) Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations. Viruses, 14, 2205.
  51. Meier,R. et al. (2022) 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. Blood Cancer Journal, 12, 1–13.
  52. Mevada,V. et al. (2022) Variant Analysis and Strategic Clustering to Sub-Lineage of Double Mutant Strain B.1.617 of SARS-CoV-2. COVID, 2, 513–531.
  53. Mitrofanov,A. et al. (2022) CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection. Bioinformatics, 38, ii42–ii48.
  54. Mossad,O. et al. (2022) Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N6-carboxymethyllysine. Nature Neuroscience, 1–11.
  55. Napoli,A. et al. (2022) Absence of increased genomic variants in the cyanobacterium Chroococcidiopsis exposed to Mars-like conditions outside the space station. Scientific Reports, 12, 8437.
  56. Nasereddin,A. et al. (2022) Concurrent molecular characterization of sand flies and Leishmania parasites by amplicon-based next-generation sequencing. Parasites & Vectors, 15, 262.
  57. Nasereddin,A. et al. (2022) Identification of SARS-CoV-2 Variants of Concern Using Amplicon Next-Generation Sequencing. Microbiology Spectrum, 10, e00736–22.
  58. Ngo,V. et al. (2022) Histone Deacetylase 6 Inhibitor JS28 Prevents Pathological Gene Expression in Cardiac Myocytes. Journal of the American Heart Association, 11, e025857.
  59. Nührenberg,T.G. et al. (2022) Impact of high platelet turnover on the platelet transcriptome: Results from platelet RNA-sequencing in patients with sepsis. PLOS ONE, 17, e0260222.
  60. Patat,A.S. et al. (2022) Construction and characterization of a de novo draft genome of garden cress (Lepidium sativum L.). Functional & Integrative Genomics.
  61. Pérez-Schindler,J. et al. (2022) Characterization of regulatory transcriptional mechanisms in hepatocyte lipotoxicity. Scientific Reports, 12, 11477.
  62. Pinter,N. et al. (2022) MaxQuant and MSstats in Galaxy Enable Reproducible Cloud-Based Analysis of Quantitative Proteomics Experiments for Everyone. Journal of Proteome Research.
  63. Ragot,R. and Villemur,R. (2022) eDNA profiling of mammals, birds, and fish of surface waters by mitochondrial metagenomics: application for source tracking of fecal contamination in surface waters. Environmental monitoring and assessment, 194, 1–13.
  64. Sabbaghian,A. et al. (2022) A panel of blood-derived miRNAs with a stable expression pattern as a potential pan-cancer detection signature. Frontiers in Molecular Biosciences, 9.
  65. Sacco,F. et al. (2022) An outbreak sustained by ST15 Klebsiella pneumoniae carrying 16S rRNA methyltransferases and blaNDM: evaluation of the global dissemination of these resistance determinants. International Journal of Antimicrobial Agents, 60, 106615.
  66. Saragih,F.A.S. et al. (2022) The potential of bacterial key species as a tool for monitoring peatland quality. IOP Conference Series: Earth and Environmental Science, 1025, 012007.
  67. Semenzato,G. et al. (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. Microorganisms, 10, 919.
  68. Shi,S. et al. (2022) Recapitulating Cholangiopathy-Associated Necroptotic Cell Death In Vitro Using Human Cholangiocyte Organoids. Cellular and Molecular Gastroenterology and Hepatology, 13, 541–564.
  69. Singh,A. and Upadhyay,A.K. (2022) Identification and annotation of peptide allergens in Prunus dulcis In Review.
  70. Soriano-Sexto,A. et al. (2022) Identification of Clinical Variants beyond the Exome in Inborn Errors of Metabolism. International Journal of Molecular Sciences, 23, 12850.
  71. Stephen Jr,D.B. et al. (2022) Comparative genomics of the black rot pathogen Xanthomonas campestris pv. campestris and non-pathogenic co-inhabitant Xanthomonas melonis from Trinidad reveal unique pathogenicity determinants and secretion system profiles. PeerJ, 9, e12632.
  72. Subramoney,K. et al. (2022) Identification of SARS-CoV-2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021. Journal of Medical Virology, 94, 3676–3684.
  73. Sun,Q. et al. (2022) STENCIL: A web templating engine for visualizing and sharing life science datasets. PLOS Computational Biology, 18, e1009859.
  74. Tabarelli,M. et al. (2022) Chasing Consistency: An Update of the TCP Gene Family of Malus × Domestica. Genes, 13, 1696.
  75. Tsai,H.-Y. et al. (2022) Biogenesis of C. elegans spermatogenesis small RNAs is initiated by a zc3h12a-like ribonuclease. Science Advances, 8, eabm0699.
  76. Vaquero-Sedas,M.I. and Vega-Palas,M.A. (2022) Epigenetic nature of Arabidopsis thaliana telomeres. Plant Physiology, kiac471.
  77. Verma,D. et al. (2022) Identification Of Taxa and Functional Pathway Information Of Mycobacterium tuberculosis Microbiome And High Throughput Simulation Studies With Mycobacteriophage.
  78. VijayKrishna,N. et al. (2022) Expanding the Galaxy’s reference data. Bioinformatics Advances, 2, vbac030.
  79. Wadhawan,A.D. (2022) Investigating the determinants of Enterococcus faecalis virulence in Drosophila melanogaster.
  80. Werner,E. et al. (2022) The Mitochondrial RNA Granule is Necessary for Parkinsonism-Associated Metal Toxicity. bioRxiv.
  81. Wittenburg,P. et al. (2022) Canonical Workflows to Make Data FAIR. Data Intelligence, 4, 286–305.
  82. Wolf,J. et al. (2022) In-Depth Molecular Profiling Specifies Human Retinal Microglia Identity. Frontiers in Immunology, 13.
  83. Wolf,J. et al. (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. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 1868, 166340.
  84. Wolf,J. et al. (2022) Deciphering the Molecular Signature of Human Hyalocytes in Relation to Other Innate Immune Cell Populations. Investigative Ophthalmology & Visual Science, 63, 9.
  85. Wolf,J. et al. (2022) The Human Eye Transcriptome Atlas: A searchable comparative transcriptome database for healthy and diseased human eye tissue. Genomics, 110286.
  86. Yuan,J. et al. (2022) Ezh2 competes with p53 to license lncRNA Neat1 transcription for inflammasome activation. Cell Death & Differentiation, 29, 2009–2023.
  87. Zebua,P.K. et al. (2022) Bacterial key species candidates for biomonitoring peatland burnt in the Giam Siak Kecil-Bukit Batu biosphere reserve, Riau. IOP Conference Series: Earth and Environmental Science, 1025, 012023.
  88. Zhang,T. et al. (2022) Replication collisions induced by de-repressed S-phase transcription are connected with malignant transformation of adult stem cells. Nature Communications, 13, 6907.
  89. Zhuang,X. et al. (2022) Time- and Stimulus-Dependent Characteristics of Innate Immune Cells in Organ-Cultured Human Corneal Tissue. Journal of Innate Immunity, 14, 98–111.


  1. Aggarwal,D. et al. (2021) The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities. The Lancet Microbe.
  2. Alcaraz,A.J.G. et al. (2021) Development of a Comprehensive Toxicity Pathway Model for 17α-Ethinylestradiol in Early Life Stage Fathead Minnows (Pimephales promelas). Environmental Science & Technology, 55, 5024–5036.
  3. Ali,R. et al. (2021) Characterization of the Virome Associated With Haemagogus Mosquitoes in Trinidad, West Indies.
  4. Apostolakos,I. et al. (2021) Occurrence of Colibacillosis in Broilers and Its Relationship With Avian Pathogenic Escherichia coli (APEC) Population Structure and Molecular Characteristics. 8.
  5. Bamford,C.G.G. et al. (2021) Collaboration Between Host and Viral Factors Shape SARS-CoV-2 Evolution.
  6. Bandyopadhyay,S. et al. (2021) Polypharmacology of some medicinal plant metabolites against SARS-CoV-2 and host targets: Molecular dynamics evaluation of NSP9 RNA binding protein. 1–17.
  7. Barbosa,D.A. et al. (2021) New Putative Long Non-Coding RNAs (lncRNA) Revealed by Pan-Transcriptome of the Emerging Human Pathogenic Fungus Talaromyces Marneffei.
  8. Baron,S.A. et al. (2021) Multidrug-Resistant Klebsiella pneumoniae Clones from Wild Chimpanzees and Termites in Senegal. 65.
  9. Barragán-Rosillo,A.C. et al. (2021) Genome accessibility dynamics in response to phosphate limitation is controlled by the PHR1 family of transcription factors in Arabidopsis. 118, e2107558118.
  10. Bartas,M. et al. (2021) The Changes in the p53 Protein across the Animal Kingdom Point to Its Involvement in Longevity. 22, 8512.
  11. Batut,B. et al. (2021) RNA-Seq Data Analysis in Galaxy. In, Picardi,E. (ed), RNA Bioinformatics, Methods in Molecular Biology. Springer US, New York, NY, pp. 367–392.
  12. Bauer,T.L. et al. (2021) Functional Analysis of Non-Genetic Resistance to Platinum in Epithelial Ovarian Cancer Reveals a Role for the MBD3-NuRD Complex in Resistance Development. 13, 3801.
  13. Bayona-Feliu,A. et al. (2021) The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts. 53, 1050–1063.
  14. Bossche,T.V.D. et al. (2021) Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows. bioRxiv, 2021.03.05.433915.
  15. Broche,J. et al. (2021) Genome-wide investigation of the dynamic changes of epigenome modifications after global DNA methylation editing. Nucleic Acids Research, 49, 158–176.
  16. Camargo Romera,P. (2021) Isoform 2 of DLG2 gene as a possible candidate tumour suppressor of neuroblastoma.
  17. Carattoli,A. et al. (2021) Evolutionary Trajectories toward Ceftazidime-Avibactam Resistance in Klebsiella pneumoniae Clinical Isolates. 65.
  18. Chen,D.-B. et al. (2021) First complete mitochondrial genome of Rhodinia species (Lepidoptera: Saturniidae): genome description and phylogenetic implication. 1–10.
  19. Chiara,M. et al. (2021) Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. Briefings in Bioinformatics, 22, 616–630.
  20. Cordellier,M. et al. (2021) Next-generation sequencing of DNA from resting eggs: signatures of eutrophication in a lake’s sediment. Zoology, 125895.
  21. Cova,G. et al. (2021) Helios represses megakaryocyte priming in hematopoietic stem and progenitor cells. 218.
  22. Darkow,E. et al. (2021) Small Conductance Ca2 +-Activated K+ (SK) Channel mRNA Expression in Human Atrial and Ventricular Tissue: Comparison Between Donor, Atrial Fibrillation and Heart Failure Tissue. Frontiers in Physiology, 12.
  23. Delroisse,J. et al. (2021) Photophore Distribution and Enzymatic Diversity Within the Photogenic Integument of the Cookie-Cutter Shark Isistius brasiliensis (Chondrichthyes: Dalatiidae). 8.
  24. Dorone,Y. et al. (2021) A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation. Cell, 184, 4284–4298.e27.
  25. Dvir,S. et al. (2021) Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells. 35, 109198.
  26. Estell,C. et al. (2021) ZC3H4 restricts non-coding transcription in human cells. 10.
  27. Faddetta,T. et al. (2021) The endophytic microbiota of Citrus limon is transmitted from seed to shoot highlighting differences of bacterial and fungal community structures. 11.
  28. Fahrner,M. et al. (2021) A Systematic Evaluation of Semispecific Peptide Search Parameter Enables Identification of Previously Undescribed N-Terminal Peptides and Conserved Proteolytic Processing in Cancer Cell Lines. Proteomes, 9, 26.
  29. Fell,C.W. et al. (2021) FIBCD1 is a Conserved Receptor for Chondroitin Sulphate Proteoglycans of the Brain Extracellular Matrix and a Candidate Gene for a Complex Neurodevelopmental Disorder.
  30. Feng,S. et al. (2021) Scarless engineering of the Drosophila genome near any site-specific integration site. 217.
  31. Fiedler,G. et al. (2021) Taxonomic Evaluation of the Heyndrickxia (Basonym Bacillus) sporothermodurans Group (H. sporothermodurans, H. vini, H. oleronia) Based on Whole Genome Sequences. 9, 246.
  32. Föll,M.C. et al. (2021) Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: A case study of an urothelial cancer cohort analyzed in the Galaxy framework. bioRxiv, 2021.08.09.455649.
  33. Friedrich,S. et al. (2021) Identification of pathological transcription in autosomal dominant polycystic kidney disease epithelia. 11.
  34. Friedrich,M. et al. (2021) Tryptophan metabolism drives dynamic immunosuppressive myeloid states in IDH-mutant gliomas. Nature Cancer, 1–18.
  35. Genolet,O. et al. (2021) Identification of X-chromosomal genes that drive sex differences in embryonic stem cells through a hierarchical CRISPR screening approach. 22.
  36. Gessara,I. et al. (2021) Highly Efficient Genome Modification of Cultured Primordial Germ Cells with Lentiviral Vectors to Generate Transgenic Songbirds. 16, 784–796.
  37. Gilbertson,S.E. and Weinmann,A.S. (2021) Conservation and divergence in gene regulation between mouse and human immune cells deserves equal emphasis. Trends in Immunology, 42, 1077–1087.
  38. Gjaltema,R.A.F. et al. (2021) Distal and proximal cis-regulatory elements sense X-chromosomal dosage and developmental state at theXistlocus.
  39. Glaros,V. et al. (2021) Limited access to antigen drives generation of early B cell memory while restraining the plasmablast response. 54, 2005–2023.e10.
  40. Greve,G. et al. (2021) Decitabine Induces Gene Derepression on Monosomic Chromosomes: In Vitro and In Vivo Effects in Adverse-Risk Cytogenetics AML. Cancer Research, 81, 834–846.
  41. Gu,Q. et al. (2021) Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine. PLOS Computational Biology, 17, e1009014.
  42. Hering,S. et al. (2021) Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species. 71.
  43. Hesse,M. et al. (2021) Proximity to injury, but neither number of nuclei nor ploidy define pathological adaptation and plasticity in cardiomyocytes. Journal of Molecular and Cellular Cardiology, 152, 95–104.
  44. Hetz,S.A. and Horn,M.A. (2021) Burkholderiaceae Are Key Acetate Assimilators During Complete Denitrification in Acidic Cryoturbated Peat Circles of the Arctic Tundra. 12.
  45. Hildebrandt,S. et al. (2021) ActivinA Induced SMAD1/5 Signaling in an iPSC Derived EC Model of Fibrodysplasia Ossificans Progressiva (FOP) Can Be Rescued by the Drug Candidate Saracatinib. Stem Cell Reviews and Reports, 17, 1039–1052.
  46. Hölper,J.E. et al. (2021) A Genome-Wide CRISPR/Cas9 Screen Reveals the Requirement of Host Sphingomyelin Synthase 1 for Infection with Pseudorabies Virus Mutant gD–Pass. 13, 1574.
  47. Kaiser,V.B. et al. (2021) Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome.
  48. Katsanos,D. et al. (2021) Gene expression profiling of epidermal cell types in C. elegans using Targeted DamID. 148.
  49. Kavas,M. et al. (2021) Genome-wide identification of the BURP domain-containing genes in Phaseolus vulgaris. 27, 1885–1902.
  50. Kimura,K. et al. (2021) Overexpression of human BAG3P209L in mice causes restrictive cardiomyopathy. Nature Communications, 12, 3575.
  51. King,T.L. et al. (2021) Resistome of a carbapenemase-producing novel ST232 Klebsiella michiganensis isolate from urban hospital effluent in South Africa. 24, 321–324.
  52. Klein,A. et al. (2021) Pruriception and neuronal coding in nociceptor subtypes in human and nonhuman primates. 10.
  53. Kowalski,J. et al. (2021) Eplerenone Improves Pulmonary Vascular Remodeling and Hypertension by Inhibition of the Mineralocorticoid Receptor in Endothelial Cells. Hypertension, 78, 456–465.
  54. Kumar,A. et al. (2021) The Polycomb group methyltransferase StE(z)2 and deposition of H3K27me3 and H3K4me3 regulate the expression of tuberization genes in potato. Journal of Experimental Botany, 72, 426–444.
  55. Kumar,A. et al. (2021) Tool recommender system in Galaxy using deep learning. GigaScience, 10.
  56. Li,X.-Y. et al. (2021) The mitochondrial genome of Qinghuang_1, the first modern improved strain of Chinese oak silkworm, Antheraea pernyi (Lepidoptera: Saturniidae). 7, 233–243.
  57. Liu,Z. et al. (2021) DenovoProfiling: a webserver for de novo generated molecule library profiling. Research Square.
  58. Luo,X. et al. (2021) 3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis. Cell, 184, 723–740.e21.
  59. Macnee,M. et al. (2021) SimText: a text mining framework for interactive analysis and visualization of similarities among biomedical entities. Bioinformatics.
  60. Maier,W. et al. (2021) Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring. bioRxiv, 2021.03.25.437046.
  61. Maier,W. et al. (2021) Ready-to-use public infrastructure for global SARS-CoV-2 monitoring. Nature Biotechnology, 1–2.
  62. Marisaldi,L. et al. (2021) De novo transcriptome assembly, functional annotation and characterization of the Atlantic bluefin tuna (Thunnus thynnus) larval stage. Marine Genomics, 58, 100834.
  63. Martins Rodrigues,C. et al. (2021) DataPLANT – Ein NFDI-Konsortium der Pflanzen-Grundlagenforschung.
  64. Mauer,K.M. et al. (2021) Genomics and transcriptomics of epizoic Seisonidea (Rotifera, syn. Syndermata) reveal strain formation and gradual gene loss with growing ties to the host. 22.
  65. Mehta,S. et al. (2021) ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework. F1000Research, 10, 103.
  66. Mehta,S. et al. (2021) Updates on metaQuantome Software for Quantitative Metaproteomics. Journal of Proteome Research.
  67. Migur,A. et al. (2021) The temperature-regulated DEAD-box RNA helicase CrhR interactome: autoregulation and photosynthesis-related transcripts. Journal of Experimental Botany.
  68. Mootapally,C. et al. (2021) Sediment Plasmidome of the Gulfs of Kathiawar Peninsula and Arabian Sea: Insights Gained from Metagenomics Data. Microbial Ecology, 81, 540–548.
  69. Moreno,P. et al. (2021) Expression Atlas update: gene and protein expression in multiple species. Nucleic Acids Research, 50, D129–D140.
  70. Moreno,P. et al. (2021) User-friendly, scalable tools and workflows for single-cell RNA-seq analysis. Nature Methods.
  71. Morsli,M. et al. (2021) Direct Diagnosis of Echovirus 12 Meningitis Using Metagenomic Next Generation Sequencing. Pathogens, 10, 610.
  72. Musmeci,E. et al. (2021) Draft Genome Sequence of the Mucin Degrader Clostridium tertium WC0709. 10.
  73. Nagy,N.A. et al. (2021) Draft genome of a biparental beetle species, Lethrus apterus. BMC Genomics, 22, 301.
  74. Naimi,S. et al. (2021) Direct impact of commonly used dietary emulsifiers on human gut microbiota. Microbiome, 9, 66.
  75. Niemöller,C. et al. (2021) Bisulfite-free epigenomics and genomics of single cells through methylation-sensitive restriction. Communications Biology, 4, 1–10.
  76. Oselusi,S.O. et al. (2021) Cheminformatic Characterization of Natural Antimicrobial Products for the Development of New Lead Compounds. 26, 3970.
  77. Ostrovsky,A. et al. (2021) Using Galaxy to Perform Large-Scale Interactive Data Analyses—An Update. Current Protocols, 1, e31.
  78. Page-Karjian,A. et al. (2021) Fibropapillomatosis and Chelonid Alphaherpesvirus 5 Infection in Kemp’s Ridley Sea Turtles (Lepidochelys kempii). Animals, 11, 3076.
  79. Pallares-Vega,R. et al. (2021) Temperature and Nutrient Limitations Decrease Transfer of Conjugative IncP-1 Plasmid pKJK5 to Wild Escherichia coli Strains. 12.
  80. Pelletier,D. et al. (2021) A Standardized Workflow Based on the STAVIRO Unbaited Underwater Video System for Monitoring Fish and Habitat Essential Biodiversity Variables in Coastal Areas. 8.
  81. Pérez-Schindler,J. et al. (2021) Discovery of lipotoxicity-sensitive transcription factors in non-alcoholic steatohepatitis.
  82. Pérez-Schindler,J. et al. (2021) RNA-bound PGC-1{}upalpha controls gene expression in liquid-like nuclear condensates. 118, e2105951118.
  83. Pessoa Rodrigues,C. et al. (2021) Histone H4 lysine 16 acetylation controls central carbon metabolism and diet-induced obesity in mice. Nature Communications, 12, 6212.
  84. Peters,K. et al. (2021) Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid. 11.
  85. Phan,I.Q. et al. (2021) The transcriptome of Balamuthia mandrillaris trophozoites for structure-guided drug design. Scientific Reports, 11.
  86. Pinter,S. et al. (2021) A functional LSD1 coregulator screen reveals a novel transcriptional regulatory cascade connecting R-loop homeostasis with epigenetic regulation. Nucleic Acids Research, 49, 4350–4370.
  87. Poulose,N. et al. (2021) VPRBP functions downstream of the androgen receptor and OGT to restrict p53 activation in prostate cancer.
  88. Rajczewski,A.T. et al. (2021) A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19). Clinical Proteomics, 18, 15.
  89. Ranchou-Peyruse,M. et al. (2021) Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer. 12.
  90. Rauschmeier,R. et al. (2021) Cell-intrinsic functions of the transcription factor Bhlhe40 in activated B cells and T follicular helper cells restrain the germinal center reaction and prevent lymphomagenesis. bioRxiv, 2021.03.12.435122.
  91. Rogg,M. et al. (2021) SRGAP1 Controls Small Rho GTPases To Regulate Podocyte Foot Process Maintenance. 32, 563–579.
  92. Roncoroni,M. et al. (2021) A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive. Bioinformatics.
  93. Roquis,D. et al. (2021) Genomic impact of stress-induced transposable element mobility in Arabidopsis. 49, 10431–10447.
  94. Saleh,O. et al. (2021) Nascent Transcript Sequencing for the Mapping of Promoters in thaliana Mitochondria. In, Methods in Molecular Biology. Springer US, pp. 279–300.
  95. Simon-Chica,A. et al. (2021) Novel insights into the electrophysiology of murine cardiac macrophages: relevance of voltage-gated potassium channels. Cardiovascular Research.
  96. Soares,M.A.F. et al. (2021) Hierarchical reactivation of transcription during mitosis-to-G1 transition by Brn2 and Ascl1 in neural stem cells. 35, 1020–1034.
  97. Spradling,T.A. et al. (2021) Mitochondrial genome of Geomydoecus aurei, a pocket-gopher louse. 16, e0254138.
  98. Stachurová,T. et al. (2021) Beta-lactam resistance development during the treatment processes of municipal wastewater treatment plants. Chemosphere, 280, 130749.
  99. Stein,C.M. et al. (2021) Single-cell omics: Overview, analysis, and application in biomedical science.
  100. Sun,S.-W. et al. (2021) The complete mitochondrial genome of the wild silkmoth Antheraea yamamai from Heilongjiang, China (Lepidoptera: Saturniidae). 6, 2209–2211.
  101. Tosar,J. et al. (2021) RI-SEC-seq: Comprehensive Profiling of Nonvesicular Extracellular RNAs with Different Stabilities. 11.
  102. Tu,Z. et al. (2021) Molecular Physiological Characterization of a High Heat Resistant Spore Forming Bacillus subtilis Food Isolate. 9, 667.
  103. Videm,P. et al. (2021) ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data. GigaScience, 10.
  104. Villa,T. et al. (2021) Data from crosslinking and analysis of cDNAs (CRAC) of Nab3 in yeast cells expressing a circular ncRNA decoy. Data in Brief, 35, 106951.
  105. Voelker,J. et al. (2021) A high-quality draft genome for Melaleuca alternifolia (tea tree): a new platform for evolutionary genomics of myrtaceous terpene-rich species. 2021, 1–15.
  106. Volkova,P.Y. et al. (2021) Radiosensitivity of herbaceous plants to chronic radiation exposure: Field study in the Chernobyl exclusion zone. 777, 146206.
  107. Weigang,S. et al. (2021) Within-host evolution of SARS-CoV-2 in an immunosuppressed COVID-19 patient: a source of immune escape variants.
  108. Weterings,V. et al. (2021) Duration of Colonisation With Extended-spectrum Beta-lactamase-producing Escherichia Coli: Results of an Open Cohort Study With Dutch Nursing Home Residents (2013 – 2019). Research Square.
  109. Wichers,J.S. et al. (2021) Common virulence gene expression in adult first-time infected malaria patients and severe cases. 10.
  110. Winkler,M.A. and Pan,A.A. (2021) Gene Homologies Identified between Trypanosoma cruzi Antigen 36 and Mammalian TRIM21 Genes Using Bioinformatics Analysis.
  111. Wolf,J. et al. (2021) 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. bioRxiv, 2021.05.10.443381.
  112. Wolfien,M. et al. (2021) Single-Cell RNA Sequencing Procedures and Data Analysis. Exon Publications, pp. 19–35.
  113. Yanta,C.A. et al. (2021) CryptoGenotyper: A new bioinformatics tool for rapid Cryptosporidium identification. Food and Waterborne Parasitology, 23, e00115.
  114. Yol,E. et al. (2021) A High-Density SNP Genetic Map Construction Using ddRAD-Seq and Mapping of Capsule Shattering Trait in Sesame. 12.
  115. Yu,Y. et al. (2021) Bromodomain-containing proteins BRD1, BRD2, and BRD13 are core subunits of SWI/SNF complexes and vital for their genomic targeting in Arabidopsis. Molecular Plant, 14, 888–904.
  116. Zhuang,X. et al. (2021) Time- and Stimulus-Dependent Characteristics of Innate Immune Cells in Organ-Cultured Human Corneal Tissue. 1–14.


  1. Afouda,P. et al. (2020) Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates. Microorganisms, 8, 1522.
  2. Ahmed,S. et al. (2020) High prevalence of mcr-1 -encoded colistin resistance in commensal Escherichia coli from broiler chicken in Bangladesh. Scientific Reports, 10, 18637.
  3. Baker,D. et al. (2020) No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics. PLOS Pathogens, 16, e1008643.
  4. Bazzucchi,M. et al. (2020) Near-complete nucleotide sequence of a border disease virus genotype BDV-7 isolate from Italy. Archives of Virology, 165, 3007–3009.
  5. Blomberg,N. and Lauer,K.B. (2020) Connecting data, tools and people across Europe: ELIXIR’s response to the COVID-19 pandemic. European Journal of Human Genetics, 1–5.
  6. Bohlender,L.L. et al. (2020) Stable Protein Sialylation in Physcomitrella. Frontiers in Plant Science, 11.
  7. Boneva,S. et al. (2020) 3′ MACE RNA-sequencing allows for transcriptome profiling in human tissue samples after long-term storage. Laboratory Investigation, 1–11.
  8. Boneva,S. et al. (2020) MACE RNA sequencing analysis of conjunctival squamous cell carcinoma and papilloma using formalin-fixed paraffin-embedded tumor tissue. Scientific Reports, 10, 21292.
  9. Boneva,S.K. et al. (2020) Transcriptional Profiling Uncovers Human Hyalocytes as a Unique Innate Immune Cell Population. Frontiers in Immunology, 11.
  10. Bose,S. et al. (2020) tRNA ADENOSINE DEAMINASE 3 is required for telomere maintenance in Arabidopsis thaliana. Plant Cell Reports, 39, 1669–1685.
  11. Bray,S.A. et al. (2020) The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform. Journal of Cheminformatics, 12, 40.
  12. Bray,S.A. et al. (2020) Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial. Journal of Cheminformatics, 12, 54.
  13. Buhl,M. and Marschal,M. (2020) Prevotella vespertina sp. nov., isolated from an abscess of a hospital patient. International Journal of Systematic and Evolutionary Microbiology.
  14. Buttimer,C. et al. (2020) Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus. 9, 352.
  15. Buttimer,C. et al. (2020) Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus. Antibiotics, 9, 352.
  16. Candeliere,F. et al. (2020) Draft Genome Sequences of 12 Leuconostoc carnosum Strains Isolated from Cooked Ham Packaged in a Modified Atmosphere and from Fresh Sausages. Microbiology Resource Announcements, 9.
  17. Cantarella,S. (2020) Insights into Alu retrotransposons: mechanism of Alu transcriptome alteration in response to virus infection and novel effects on gene expression.
  18. Čermák,V. et al. (2020) Unexpected variations in posttranscriptional gene silencing induced by differentially produced dsRNAs in tobacco cells. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 1863, 194647.
  19. Chiara,M. et al. (2020) Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. Briefings in Bioinformatics.
  20. Dad,A. et al. (2020) Molecular analysis of GPI-anchor biosynthesis pathway genes in rat strains used for the Pig-a gene mutation assay. Mutation Research/Genetic Toxicology and Environmental Mutagenesis, 858-860, 503256.
  21. Deng,L. et al. (2020) Gene expression in immortalized versus primary isolated cardiac endothelial cells. Scientific Reports, 10, 1–9.
  22. Dhamija,S. et al. (2020) A pan-cancer analysis reveals nonstop extension mutations causing SMAD4 tumour suppressor degradation. Nature Cell Biology, 22, 999–1010.
  23. Di Dalmazi,G. et al. (2020) DNA Methylation of Steroidogenic Enzymes in Benign Adrenocortical Tumors: New Insights in Aldosterone-Producing Adenomas. The Journal of Clinical Endocrinology & Metabolism, 105, e4605–e4615.
  24. Dorn,A. et al. (2020) LINC00261 Is Differentially Expressed in Pancreatic Cancer Subtypes and Regulates a Pro-Epithelial Cell Identity. Cancers, 12, 1227.
  25. Espíndola-Hernández,P. et al. (2020) Genomic Evidence for Sensorial Adaptations to a Nocturnal Predatory Lifestyle in Owls. Genome Biology and Evolution, 12, 1895–1908.
  26. Estrada Mallarino,L. et al. (2020) Nephronophthisis gene products display RNA-binding properties and are recruited to stress granules. Scientific Reports, 10, 15954.
  27. Farmiloe,G. et al. (2020) Widespread correlation of KRAB zinc finger protein binding with brain-developmental gene expression patterns. Philosophical Transactions of the Royal Society B: Biological Sciences, 375, 20190333.
  28. Feldker,N. et al. (2020) Genome-wide cooperation of EMT transcription factor ZEB1 with YAP and AP-1 in breast cancer. The EMBO Journal, n/a, e103209.
  29. Fernandes,M. (2020) GuavaDB: O BANCO DE DADOS DA GENÔMICA DE Psidium guajava L.
  30. Foschini,M.P. et al. (2020) Methylation Profile of X-Chromosome–Related Genes in Male Breast Cancer. Frontiers in Oncology, 10.
  31. Gaafar,Y.Z.A. and Ziebell,H. (2020) Novel targets for engineering Physostegia chlorotic mottle and tomato brown rugose fruit virus-resistant tomatoes: in silico prediction of tomato microRNA targets. PeerJ, 8, e10096.
  32. Gao,L. et al. (2020) Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms. bioRxiv, 2020.04.27.064386.
  33. Gao,M. et al. (2020) Pluripotency factors select gene expression repertoire at Zygotic Genome Activation. bioRxiv, 2020.02.16.949362.
  34. Garrido,J. et al. (2020) Identification and validation of reference genes for RT-qPCR normalization in wheat meiosis. Scientific Reports, 10, 1–12.
  35. Genolet,O. et al. (2020) Identification of X-chromosomal genes that drive global X-dosage effects in mammals. bioRxiv, 2020.03.09.983544.
  36. Greenfield,G. et al. (2020) Modification of the Histone Landscape with JAK Inhibition in Myeloproliferative Neoplasms. Cancers, 12, 2669.
  37. Guendel,F. et al. (2020) Group 3 Innate Lymphoid Cells Program a Distinct Subset of IL-22BP-Producing Dendritic Cells Demarcating Solitary Intestinal Lymphoid Tissues. Immunity, 53, 1015–1032.e8.
  38. Hahn,A. et al. (2020) DNA Methyltransferase 1 (DNMT1) Function Is Implicated in the Age-Related Loss of Cortical Interneurons. Frontiers in Cell and Developmental Biology, 8.
  39. Hernández,I. et al. (2020) Design of Bacterial Strain-Specific qPCR Assays Using NGS Data and Publicly Available Resources and Its Application to Track Biocontrol Strains. Frontiers in Microbiology, 11.
  40. Hesse,M. et al. (2020) Proximity to injury, but neither number of nuclei nor ploidy define pathological adaptation and plasticity in cardiomyocytes. Journal of Molecular and Cellular Cardiology.
  41. Hille,L. et al. (2020) Ultrastructural, transcriptional, and functional differences between human reticulated and non-reticulated platelets. Journal of Thrombosis and Haemostasis, 18, 2034–2046.
  42. Hofacker,D. et al. (2020) Engineering of Effector Domains for Targeted DNA Methylation with Reduced Off-Target Effects. International Journal of Molecular Sciences, 21, 502.
  43. Jalili,V. et al. (2020) The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Research, 48, W395–W402.
  44. Kumar,A. et al. (2020) Community Research Amid COVID-19 Pandemic: Genomics Analysis of SARS-CoV-2 over Public GALAXY server. Preprints.
  45. Kumar,A. et al. (2020) The Polycomb group methyltransferase StE(z)2 and deposition of H3K27me3 and H3K4me3 regulate the expression of tuberization genes in potato. 72, 426–444.
  46. Kumaran,S. et al. (2020) Draft genome sequence of Kocuria indica DP-K7, a methyl red degrading actinobacterium. 3 Biotech, 10, 175.
  47. Lahm,H. et al. (2020) Congenital heart disease risk loci identified by genome-wide association study in European patients. The Journal of Clinical Investigation.
  48. Lahm,H. et al. (2020) Genome-wide association study in European patients with congenital heart disease identifies risk loci for transposition of the great arteries and anomalies of the thoracic arteries and veins and expression of discovered candidate genes in the developing heart. bioRxiv, 2020.06.19.161067.
  49. Lange,C. et al. (2020) Expression of the COVID-19 receptor ACE2 in the human conjunctiva. Journal of Medical Virology, n/a.
  50. Lastic, et al. (2020) Entropic Ranks: A Methodology for Enhanced, Threshold-Free, Information-Rich Data Partition and Interpretation. Preprints.
  51. Lezameta,L. et al. (2020) Draft Genome Sequence of a New Delhi Metallo-β-Lactamase (NDM-1)-Producing Providencia stuartii Strain Isolated in Lima, Peru. Microbiology Resource Announcements, 9.
  53. Lodewijk,G.A. et al. (2020) Evolution of human brain size-associated NOTCH2NL genes proceeds towards reduced protein levels. Molecular Biology and Evolution.
  54. Lopez-Delisle,L. et al. (2020) pyGenomeTracks: reproducible plots for multivariate genomic data sets. Bioinformatics.
  55. Lother,A. et al. (2020) Diabetes changes gene expression but not DNA methylation in cardiac cells. Journal of Molecular and Cellular Cardiology, 0.
  56. Ma,J. et al. (2020) Somatostatin 3 loss of function impairs the innate immune response to intestinal inflammation. Aquaculture and Fisheries.
  57. Martinez-Fabregas,J. et al. (2020) CDK8 Fine-Tunes IL-6 Transcriptional Activities by Limiting STAT3 Resident Time at the Gene Loci. Cell Reports, 33, 108545.
  58. Marzoli,F. et al. (2020) Next generation sequencing study on RNA viruses of Vespa velutina and Apis mellifera sharing the same foraging area. Transboundary and Emerging Diseases, n/a.
  59. McErlean,P. et al. (2020) Epigenetic alterations underlie airway macrophage differentiation and phenotype during lung fibrosis. bioRxiv, 2020.12.04.410191.
  60. McGill,M.M. et al. (2020) The sex-specific role of p38 MAP kinase in CNS autoimmunity is regulated by estrogen receptor alpha. Journal of Neuroimmunology, 342, 577209.
  61. McGowan,T. et al. (2020) Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration. GigaScience, 9.
  62. Mehta,S. et al. (2020) Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform. Proteomes, 8, 15.
  63. Miao,Z. et al. (2020) Putative cell type discovery from single-cell gene expression data. arXiv.
  64. Morandi,L. et al. (2020) An Evolutionary Cancer Epigenetic Approach Revealed DNA Hypermethylation of Ultra-Conserved Non-Coding Elements in Squamous Cell Carcinoma of Different Mammalian Species. Cells, 9, 2092.
  65. Müller-Ruch,U. et al. (2020) GLP: A requirement in cell therapies - perspectives for the cardiovascular field. Advanced Drug Delivery Reviews.
  66. Müller,S. et al. (2020) SNP dependent modulation of circulating miRNAs from the miR25/93/106 cluster in patients undergoing weight loss. Gene, 753, 144787.
  67. The importance of incorporating transcript information in CLIP-seq data analysis (2020).
  68. Núñez-Sánchez,M.A. et al. (2020) Characterizing Phage-Host Interactions in a Simplified Human Intestinal Barrier Model. Microorganisms, 8, 1374.
  69. Oeyen,J.P. et al. (2020) Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera. Genome Biology and Evolution, 12, 1099–1188.
  70. Parenti,I. et al. (2020) MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome. Cell Reports, 31, 107647.
  71. Qi,W. et al. (2020) A secreted endoribonuclease ENDU-2 from the soma protects germline immortality in C. elegans. bioRxiv, 2020.12.04.408260.
  72. Rasche,H. and Hiltemann,S. (2020) Galactic Circos: User-friendly Circos plots within the Galaxy platform. GigaScience, 9.
  73. Rasche,H. and Gruening,B.A. (2020) Training Infrastructure as a Service. bioRxiv, 2020.08.23.263509.
  74. Riediger,M. et al. (2020) Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq). 33, 248–269.
  75. Roland Wirth (2020) Microbiomes in Supragingival Biofilms and Saliva of Adolescent Patients with Induced and Naturally Occurring Gingivitis Relative to Gingival Health. Research Square.
  76. Sabrina,K. (2020) Statistical models to capture protein-RNA interaction footprints from truncation-based CLIP-seq data.
  77. Sajulga,R. et al. (2020) Survey of metaproteomics software tools for functional microbiome analysis. PLOS ONE, 15, e0241503.
  78. Sauriol,A. et al. (2020) Modeling the Diversity of Epithelial Ovarian Cancer through Ten Novel Well Characterized Cell Lines Covering Multiple Subtypes of the Disease. Cancers, 12, 2222.
  79. Schäfer,R.A. et al. (2020) GLASSGo in Galaxy: high-throughput, reproducible and easy-to-integrate prediction of sRNA homologs. Bioinformatics.
  80. Schlecht,A. et al. (2020) Transcriptomic Characterization of Human Choroidal Neovascular Membranes Identifies Calprotectin as a Novel Biomarker for Patients with Age-related Macular Degeneration. The American Journal of Pathology.
  81. Senapathi,T. et al. (2020) BRIDGE: An Open Platform for Reproducible Protein-Ligand Simulations and Free Energy of Binding Calculations. Bio-protocol, 10, e3731–e3731.
  82. Tangaro,M.A. et al. (2020) Laniakea: an open solution to provide Galaxy “on-demand” instances over heterogeneous cloud infrastructures. GigaScience, 9.
  83. Teixeira Pereira,B.F. (2020) A comprehensive analysis of Med12 controlled (l)ncRNAs and characterization of a novel Sall1 antisense transcript.
  84. Tekman,M. et al. (2020) A single-cell RNA-sequencing training and analysis suite using the Galaxy framework. GigaScience, 9.
  85. Uellendahl-Werth,F. et al. (2020) A benchmark of hemoglobin blocking during library preparation for mRNA-Sequencing of human blood samples. Scientific Reports, 10, 1–10.
  86. Valsecchi,C.I.K. et al. (2020) RNA nucleation by MSL2 induces selective X chromosome compartmentalization. Nature.
  87. Villa,T. et al. (2020) Degradation of Non-coding RNAs Promotes Recycling of Termination Factors at Sites of Transcription. Cell Reports, 32, 107942.
  88. Von Suchodoletz,D. et al. (2020) Lessons learned from Virtualized Research Environments in today’s scientific compute infrastructures. In, E-Science-Tage 2019. University Library Heidelberg.
  89. Winkler,R. and Rosas-Román,I. (2020) Contrast Optimization of Mass Spectrometry Imaging (MSI) Data Visualization by Threshold Intensity Quantization (TrIQ). ChemRxiv.
  90. Wirth,R. et al. (2020) Chlorella vulgaris and Its Phycosphere in Wastewater: Microalgae-Bacteria Interactions During Nutrient Removal. Frontiers in Bioengineering and Biotechnology, 8.
  91. Witmer,K. et al. (2020) An epigenetic map of malaria parasite development from host to vector. Scientific Reports, 10, 6354.
  92. Wolf,J. et al. (2020) Corneal tissue induces transcription of metallothioneins in monocyte-derived human macrophages. Molecular Immunology, 128, 188–194.
  93. Wolf,J. et al. (2020) Transcriptional characterization of conjunctival melanoma identifies the cellular tumor microenvironment and prognostic gene signatures. Scientific Reports, 10, 17022.
  94. Yoshida,N. and Kaito,C. (2020) Dataset for de novo transcriptome assembly of the African bullfrog Pyxicephalus adspersus. Data in Brief, 30, 105388.
  95. Zavala-Alvarado,C. et al. (2020) The transcriptional response of pathogenic Leptospira to peroxide reveals new defenses against infection-related oxidative stress. PLOS Pathogens, 16, e1008904.


  2. Ahmad,M. et al. (2019) Development of novel microsatellite markers for Alkanna tinctoria by comparative transcriptomics. Applications in Plant Sciences, 7, e11296.
  3. Bagnacani,A. et al. (2019) Tools for Understanding miRNA–mRNA Interactions for Reproducible RNA Analysis. In, Lai,X. et al. (eds), Computational Biology of Non-Coding RNA: Methods and Protocols, Methods in Molecular Biology. Springer New York, New York, NY, pp. 199–214.
  5. Brunet,M.A. and Roucou,X. (2019) Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames. JoVE (Journal of Visualized Experiments), e59589.
  6. Busch,A. et al. (2019) iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites. Methods.
  7. Davey,N.E. et al. (2019) An intrinsically disordered proteins community for ELIXIR. F1000Research, 8, 1753.
  8. Emperle,M. et al. (2019) Mutations of R882 change flanking sequence preferences of the DNA methyltransferase DNMT3A and cellular methylation patterns. Nucleic Acids Research.
  9. Espenshade,J. et al. (2019) Influence of Urbanization on Epiphytic Bacterial Communities of the Platanus × hispanica Tree Leaves in a Biennial Study. Frontiers in Microbiology, 10.
  10. Etherington,G.J. et al. (2019) A Galaxy-based training resource for single-cell RNA-sequencing quality control and analyses. GigaScience, 8.
  11. Fallmann,J. et al. (2019) The RNA workbench 2.0: next generation RNA data analysis. Nucleic Acids Research.
  12. Föll,M.C. et al. (2019) Accessible and reproducible mass spectrometry imaging data analysis in Galaxy. GigaScience, 8.
  13. Forth,L.F. and Höper,D. (2019) Highly efficient library preparation for Ion Torrent sequencing using Y-adapters. BioTechniques.
  14. Gener,A.R. and Kimata,J.T. (2019) Full-coverage native RNA sequencing of HIV-1 viruses. bioRxiv, 845610.
  15. Gissi,D.B. et al. (2019) 13-gene DNA Methylation Analysis from Oral Brushing: A Promising Non Invasive Tool in the Follow-up of Oral Cancer Patients. Journal of Clinical Medicine, 8, 2107.
  16. Haas,M. et al. (2019) ΔN-Tp63 Mediates Wnt/β-Catenin-Induced Inhibition of Differentiation in Basal Stem Cells of Mucociliary Epithelia. Cell Reports, 28, 3338–3352.e6.
  17. Hamprecht,A. et al. (2019) Candida auris in Germany and Previous Exposure to Foreign Healthcare. Emerging Infectious Diseases, 25, 1763–1765.
  18. Holthausen Bermejo,R. (2019) A workflow-based algorithm for tracing Computational Synteny Blocks along different species.
  19. Jude,B.A. (2019) Draft Genome Sequence of a Chitinimonas Species from Hudson Valley Waterways That Expresses Violacein Pigment. Microbiology Resource Announcements, 8, e00683–19, /mra/8/35/MRA.00683–19.atom.
  20. Kalmbach,A. et al. (2019) Genome-Wide Analysis of the Nucleosome Landscape in Individuals with Coffin-Siris Syndrome. Cytogenetic and Genome Research, 159, 1–11.
  21. Kolosov,D. and O’Donnell,M.J. (2019) Malpighian tubules of caterpillars: blending RNAseq and physiology to reveal regional functional diversity and novel epithelial ion transport control mechanisms. Journal of Experimental Biology, 222.
  22. Lambrecht,S.J. et al. (2019) Interplay and Targetome of the Two Conserved Cyanobacterial sRNAs Yfr1 and Yfr2 in Prochlorococcus MED4. Scientific Reports, 9, 1–15.
  23. Larsen,F.T. et al. (2019) Identification and tissue-expression profiling of novel chicken c-type lectin-like domain containing proteins as potential targets for carbohydrate-based vaccine strategies. Molecular Immunology, 114, 216–225.
  24. Lengfelder,I. et al. (2019) Complex Bacterial Consortia Reprogram the Colitogenic Activity of Enterococcus faecalis in a Gnotobiotic Mouse Model of Chronic, Immune-Mediated Colitis. Frontiers in Immunology, 10.
  25. Lother,A. et al. (2019) Endothelial cell mineralocorticoid receptors oppose VEGF-induced gene expression and angiogenesis. Journal of Endocrinology, 240, 15–26.
  26. Owen,N. and Moosajee,M. (2019) RNA-sequencing in ophthalmology research: considerations for experimental design and analysis. Therapeutic Advances in Ophthalmology, 11, 251584141983546.
  27. Papatheodorou,I. et al. (2019) Expression Atlas update: from tissues to single cells. Nucleic Acids Research.
  28. Perez‐Riverol,Y. and Moreno,P. (2019) Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines. PROTEOMICS, n/a, 1900147.
  29. Prislan,I. et al. (2019) Proof of concept web application for understanding the energetic basis of oligonucleotide unfolding. RSC Advances, 9, 41453–41461.
  30. Rasche,H. and Europe,G.P. (2019) Community, Training, Infrastructure, and Users. F1000Research, 8.
  31. Rauschmeier,R. et al. (2019) Bhlhe40 and Bhlhe41 transcription factors regulate alveolar macrophage self-renewal and identity. The EMBO Journal, 0, e101233.
  32. Sánchez,L.F.H. et al. (2019) PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping. GigaScience, 8.
  33. Senapathi,T. et al. (2019) Biomolecular Reaction & Interaction Dynamics Global Environment (BRIDGE). Bioinformatics.
  34. Sharma,Y. et al. (2019) A pan-cancer analysis of synonymous mutations. Nature Communications, 10.
  35. Szachniuk,M. (2019) RNApolis: Computational Platform for RNA Structure Analysis. Foundations of Computing and Decision Sciences, 44, 241–257.
  36. Tari,M. et al. (2019) U2AF65 assemblies drive sequence-specific splice site recognition. EMBO reports, 20, e47604.
  37. Teikari,J.E. et al. (2019) Insight into the genome and brackish water adaptation strategies of toxic and bloom-forming Baltic Sea Dolichospermum sp. UHCC 0315. Scientific Reports, 9, 4888.
  38. Torres-Paz,J. et al. (2019) Maternally regulated gastrulation as a source of variation contributing to cavefish forebrain evolution. eLife, 8, e50160.
  39. Wibberg,D. et al. (2019) The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR. F1000Research, 8, 1877.
  40. Wirth,R. et al. (2019) Characterization of Core Microbiomes and Functional Profiles of Mesophilic Anaerobic Digesters Fed With Chlorella vulgaris Green Microalgae and Maize Silage. Frontiers in Energy Research, 7.
  41. Wolfien,M. et al. (2019) Workflow Development for the Functional Characterization of ncRNAs. In, Lai,X. et al. (eds), Computational Biology of Non-Coding RNA: Methods and Protocols, Methods in Molecular Biology. Springer New York, New York, NY, pp. 111–132.
  42. Wylie,K.M. et al. (2019) Whole-Genome Sequencing of Klebsiella pneumoniae Isolates to Track Strain Progression in a Single Patient With Recurrent Urinary Tract Infection. Frontiers in Cellular and Infection Microbiology, 9.
  43. Youssar,L. et al. (2019) Intercellular communication is required for trap formation in the nematode-trapping fungus Duddingtonia flagrans. PLOS Genetics, 15, e1008029.


  1. Batut,B. et al. (2018) ASaiM: a Galaxy-based framework to analyze microbiota data. GigaScience, 7.
  2. Batut,B. et al. (2018) Community-Driven Data Analysis Training for Biology. Cell Systems, 6, 752–758.e1.
  3. Blagitko-Dorfs,N. et al. (2018) Combination treatment of acute myeloid leukemia cells with DNMT and HDAC inhibitors: predominant synergistic gene downregulation associated with gene body demethylation. Leukemia, 1.
  4. Bovio,P.P. et al. (2018) Differential Methylation of H3K79 Reveals DOT1L Target Genes and Function in the Cerebellum In Vivo. Molecular Neurobiology.
  5. Chen,Q. et al. (2018) Versatile interactions and bioinformatics analysis of noncoding RNAs. Briefings in Bioinformatics.
  6. Eggenhofer,F. et al. (2018) CMV - Visualization for RNA and Protein family models and their comparisons. Bioinformatics.
  7. Konovalovas,A. (2018) Molecular determinants of Totiviridae family viruses of Saccharomyces sensu stricto clade.
  8. Kumar,P. et al. (2018) QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics. Journal of Proteome Research.
  9. Nekrutenko,A. et al. (2018) Biology needs evolutionary software tools: Let’s build them right. Molecular Biology and Evolution.
  10. Retamal-Morales,G. et al. (2018) Draft genome sequence of Rhodococcus erythropolis B7g, a biosurfactant producing actinobacterium. Journal of Biotechnology, 280, 38–41.
  11. Thanki,A.S. et al. (2018) Aequatus: An open-source homology browser. GigaScience.
  12. Weise,S.C. et al. (2018) FOXG1 Regulates PRKAR2B Transcriptionally and Posttranscriptionally via miR200 in the Adult Hippocampus. Molecular Neurobiology.
  13. Wolff,J. et al. (2018) Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization. Nucleic Acids Research, 46, W11–W16.
  14. Wright*,P.R. et al. (2018) Structure and Interaction Prediction in Prokaryotic RNA Biology. Microbiology Spectrum, 6.


  1. Grüning,B.A. et al. (2017) The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. Nucleic Acids Research, 45, W560–W566.
  2. Wołkowicz,T. (2017) The utility and perspectives of NGS-based methods in BSL-3 and BSL-4 laboratory – sequencing and analysis strategies. Briefings in Functional Genomics.