{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,15]],"date-time":"2026-03-15T13:25:55Z","timestamp":1773581155866,"version":"3.50.1"},"reference-count":170,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2024,9,9]],"date-time":"2024-09-09T00:00:00Z","timestamp":1725840000000},"content-version":"vor","delay-in-days":252,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000921","name":"European Cooperation in Science and Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000921","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Research on animal venoms and their components spans multiple disciplines, including biology, biochemistry, bioinformatics, pharmacology, medicine, and more. Manipulating and analyzing the diverse array of data required for venom research can be challenging, and relevant tools and resources are often dispersed across different online platforms, making them less accessible to nonexperts. In this article, we address the multifaceted needs of the scientific community involved in venom and toxin-related research by identifying and discussing web resources, databases, and tools commonly used in this field. We have compiled these resources into a comprehensive table available on the VenomZone website (https:\/\/venomzone.expasy.org\/10897). Furthermore, we highlight the challenges currently faced by researchers in accessing and using these resources and emphasize the importance of community-driven interdisciplinary approaches. We conclude by underscoring the significance of enhancing standards, promoting interoperability, and encouraging data and method sharing within the venom research community.<\/jats:p>","DOI":"10.1093\/gigascience\/giae054","type":"journal-article","created":{"date-parts":[[2024,9,9]],"date-time":"2024-09-09T12:55:31Z","timestamp":1725886531000},"source":"Crossref","is-referenced-by-count":6,"title":["Web of venom: exploration of big data resources in animal toxin research"],"prefix":"10.1093","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3060-2507","authenticated-orcid":false,"given":"Giulia","family":"Zancolli","sequence":"first","affiliation":[{"name":"Department of Ecology and Evolution, University of Lausanne , 1015 Lausanne , Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7462-8226","authenticated-orcid":false,"given":"Bj\u00f6rn Marcus","family":"von\u00a0Reumont","sequence":"additional","affiliation":[{"name":"Goethe University Frankfurt, Faculty of Biological Sciences , 60438 Frankfurt , Germany"},{"name":"LOEWE Centre for Translational Biodiversity Genomics , 60325 Frankfurt , Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9916-8465","authenticated-orcid":false,"given":"Gregor","family":"Anderluh","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry , 1000 Ljubljana , Slovenia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5241-7770","authenticated-orcid":false,"given":"Figen","family":"Caliskan","sequence":"additional","affiliation":[{"name":"Department of Biology, Faculty of Science, Eskisehir Osmangazi University , 26040 Eski\u015fehir , Turkey"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6296-7132","authenticated-orcid":false,"given":"Maria Luisa","family":"Chiusano","sequence":"additional","affiliation":[{"name":"Department of Agricultural Sciences, University Federico II of Naples , 80055 Portici, Naples , Italy"},{"name":"Department of Research Infrastructures for Marine Biological Resources , Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples , Italy"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-5629-0882","authenticated-orcid":false,"given":"Jacob","family":"Fr\u00f6hlich","sequence":"additional","affiliation":[{"name":"Veterinary Center for Resistance Research (TZR), Freie Universit\u00e4t Berlin , 14163 Berlin , Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2785-145X","authenticated-orcid":false,"given":"Evroula","family":"Hapeshi","sequence":"additional","affiliation":[{"name":"Department of Health Sciences, School of Life and Health Sciences, University of Nicosia , 1700 Nicosia , Cyprus"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1998-4033","authenticated-orcid":false,"given":"Benjamin-Florian","family":"Hempel","sequence":"additional","affiliation":[{"name":"Veterinary Center for Resistance Research (TZR), Freie Universit\u00e4t Berlin , 14163 Berlin , Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7739-080X","authenticated-orcid":false,"given":"Maria P","family":"Ikonomopoulou","sequence":"additional","affiliation":[{"name":"Madrid Institute of Advanced Studies in Food , Precision Nutrition & Aging Program, 28049 Madrid , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7456-8390","authenticated-orcid":false,"given":"Florence","family":"Jungo","sequence":"additional","affiliation":[{"name":"SIB Swiss Institute of Bioinformatics , Swiss-Prot Group, 1211 Geneva , Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0630-0541","authenticated-orcid":false,"given":"Pascale","family":"Marchot","sequence":"additional","affiliation":[{"name":"Laboratory Architecture et Fonction des Macromol\u00e9cules Biologiques, Aix-Marseille University , Centre National de la Recherche Scientifique, Facult\u00e9 des Sciences, Campus Luminy, 13288 Marseille , France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3175-5372","authenticated-orcid":false,"given":"Tarcisio Mendes","family":"de\u00a0Farias","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolution, University of Lausanne , 1015 Lausanne , Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2532-6763","authenticated-orcid":false,"given":"Maria Vittoria","family":"Modica","sequence":"additional","affiliation":[{"name":"Department of Biology and Evolution of Marine Organisms , Stazione Zoologica Anton Dohrn, 00198 Rome , Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9928-9294","authenticated-orcid":false,"given":"Yehu","family":"Moran","sequence":"additional","affiliation":[{"name":"Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem , 9190401 Jerusalem , Israel"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3852-1974","authenticated-orcid":false,"given":"Ayse","family":"Nalbantsoy","sequence":"additional","affiliation":[{"name":"Engineering Faculty, Bioengineering Department, Ege University , 35100 Bornova -Izmir, Turkey"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4675-8995","authenticated-orcid":false,"given":"Jan","family":"Proch\u00e1zka","sequence":"additional","affiliation":[{"name":"Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences , 252 50 Vestec , Czech Republic"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2749-8588","authenticated-orcid":false,"given":"Andrea","family":"Tarallo","sequence":"additional","affiliation":[{"name":"Institute of Research on Terrestrial Ecosystems (IRET) , National Research Council (CNR), 73100 Lecce , Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8935-8938","authenticated-orcid":false,"given":"Fiorella","family":"Tonello","sequence":"additional","affiliation":[{"name":"Neuroscience Institute , National Research Council (CNR), 35131 Padua , Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3636-5805","authenticated-orcid":false,"given":"Rui","family":"Vitorino","sequence":"additional","affiliation":[{"name":"Department of Medical Sciences, iBiMED, University of Aveiro , 3810-193 Aveiro , Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9202-1797","authenticated-orcid":false,"given":"Mark Lawrence","family":"Zammit","sequence":"additional","affiliation":[{"name":"Department of Clinical Pharmacology & Therapeutics, Faculty of Medicine & Surgery, University of Malta , 2090 Msida , Malta"},{"name":"Malta National Poisons Centre , Malta Life Sciences Park, 3000 San \u0120wann , Malta"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1328-1732","authenticated-orcid":false,"given":"Agostinho","family":"Antunes","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto , 4450-208 Porto , Portugal"},{"name":"Department of Biology, Faculty of Sciences, University of Porto , 4169-007 Porto , Portugal"}]}],"member":"286","published-online":{"date-parts":[[2024,9,9]]},"reference":[{"key":"2024090912551860000_bib1","doi-asserted-by":"publisher","first-page":"666","DOI":"10.3390\/toxins11110666","article-title":"The diversity of venom: the importance of behavior and venom system morphology in understanding its ecology and evolution","volume":"11","author":"Schendel","year":"2019","journal-title":"Toxins"},{"key":"2024090912551860000_bib2","doi-asserted-by":"publisher","first-page":"790","DOI":"10.1038\/nrd1197","article-title":"Therapeutic potential of venom peptides","volume":"2","author":"Lewis","year":"2003","journal-title":"Nat Rev Drug Discov"},{"key":"2024090912551860000_bib3","doi-asserted-by":"publisher","first-page":"842","DOI":"10.1126\/science.aau7761","article-title":"Venoms to the rescue","volume":"361","author":"Holford","year":"2018","journal-title":"Science"},{"key":"2024090912551860000_bib4","doi-asserted-by":"publisher","first-page":"114096","DOI":"10.1016\/j.bcp.2020.114096","article-title":"Animal toxins\u2014nature's evolutionary-refined toolkit for basic research and drug discovery","volume":"181","author":"Herzig","year":"2020","journal-title":"Biochem Pharmacol"},{"key":"2024090912551860000_bib5","doi-asserted-by":"publisher","first-page":"1874","DOI":"10.2174\/0929867324666170605091546","article-title":"Snake venom: from deadly toxins to life-saving therapeutics","volume":"24","author":"Waheed","year":"2017","journal-title":"Curr Med Chem"},{"key":"2024090912551860000_bib6","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1080\/15569543.2022.2084418","article-title":"Snake venom toxins targeting the central nervous system","volume":"42","author":"Talukdar","year":"2023","journal-title":"Toxin Rev"},{"key":"2024090912551860000_bib7","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1038\/s41570-022-00393-7","article-title":"The chemistry of snake venom and its medicinal potential","volume":"6","author":"Oliveira","year":"2022","journal-title":"Nat Rev Chem"},{"key":"2024090912551860000_bib8","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1159\/000048065","article-title":"Diagnostic uses of snake venom","volume":"31","author":"Marsh","year":"2001","journal-title":"Pathophysiol Haemos Thromb"},{"key":"2024090912551860000_bib9","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1016\/j.biocel.2018.09.011","article-title":"Snake venom components in medicine: from the symbolic rod of Asclepius to tangible medical research and application","volume":"104","author":"Estev\u00e3o-Costa","year":"2018","journal-title":"Int J Biochem Cell Biol"},{"key":"2024090912551860000_bib10","doi-asserted-by":"publisher","first-page":"191","DOI":"10.3390\/toxins4030191","article-title":"Spider-venom peptides as bioinsecticides","volume":"4","author":"Windley","year":"2012","journal-title":"Toxins"},{"key":"2024090912551860000_bib11","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1146\/annurev-ento-120811-153650","article-title":"Spider-venom peptides: structure, pharmacology, and potential for control of insect pests","volume":"58","author":"King","year":"2013","journal-title":"Annu Rev Entomol"},{"key":"2024090912551860000_bib12","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1146\/annurev-animal-021419-083626","article-title":"Omics technologies for profiling toxin diversity and evolution in snake venom: impacts on the discovery of therapeutic and diagnostic agents","volume":"8","author":"Modahl","year":"2020","journal-title":"Annu Rev Anim Biosci"},{"key":"2024090912551860000_bib13","doi-asserted-by":"publisher","first-page":"13315","DOI":"10.1074\/jbc.R109.076596","article-title":"Use of venom peptides to probe ion channel structure and function","volume":"285","author":"Dutertre","year":"2010","journal-title":"J Biol Chem"},{"key":"2024090912551860000_bib14","doi-asserted-by":"publisher","first-page":"giac048","DOI":"10.1093\/gigascience\/giac048","article-title":"Modern venomics\u2014current insights, novel methods, and future perspectives in biological and applied animal venom research","volume":"11","author":"von\u00a0Reumont","year":"2022","journal-title":"Gigascience"},{"key":"2024090912551860000_bib15","author":"VenomZone Web Resources"},{"key":"2024090912551860000_bib16","doi-asserted-by":"publisher","first-page":"giab019","DOI":"10.1093\/gigascience\/giab019","article-title":"The new COST Action European Venom Network (EUVEN)\u2014synergy and future perspectives of modern venomics","volume":"10","author":"Modica","year":"2021","journal-title":"Gigascience"},{"key":"2024090912551860000_bib17","doi-asserted-by":"publisher","first-page":"D543","DOI":"10.1093\/nar\/gkab1038","article-title":"The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences","volume":"50","author":"Perez-Riverol","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib18","doi-asserted-by":"publisher","first-page":"1074","DOI":"10.1093\/bioinformatics\/btx661","article-title":"ArachnoServer 3.0: an online resource for automated discovery, analysis and annotation of spider toxins","volume":"34","author":"Pineda","year":"2018","journal-title":"Bioinformatics"},{"key":"2024090912551860000_bib19","doi-asserted-by":"publisher","first-page":"D325","DOI":"10.1093\/nar\/gkr886","article-title":"ConoServer: updated content, knowledge, and discovery tools in the conopeptide database","volume":"40","author":"Kaas","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib20","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1016\/j.toxicon.2012.03.010","article-title":"The UniProtKB\/Swiss-Prot Tox-Prot program: a central hub of integrated venom protein data","volume":"60","author":"Jungo","year":"2012","journal-title":"Toxicon"},{"key":"2024090912551860000_bib21","doi-asserted-by":"publisher","first-page":"W216","DOI":"10.1093\/nar\/gkab225","article-title":"Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users","volume":"49","author":"Duvaud","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib22","doi-asserted-by":"publisher","first-page":"D520","DOI":"10.1093\/nar\/gky949","article-title":"Protein Data Bank: the single global archive for 3D macromolecular structure data","volume":"47","author":"wwPDB Consortium","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib23","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1007\/978-1-0716-0270-6_14","article-title":"BioMagResBank (BMRB) as a resource for structural biology","volume-title":"Structural Bioinformatics: Methods and Protocols","author":"Romero","year":"2020"},{"key":"2024090912551860000_bib24","doi-asserted-by":"publisher","first-page":"D456","DOI":"10.1093\/nar\/gkad1019","article-title":"EMDB\u2014The Electron Microscopy Data Bank","volume":"52","author":"The wwPDB Consortium","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib25","doi-asserted-by":"publisher","first-page":"eadf4936","DOI":"10.1126\/sciadv.adf4936","article-title":"Cryo-EM analysis of scorpion toxin binding to ryanodine receptors reveals subconductance that is abolished by PKA phosphorylation","volume":"9","author":"Haji-Ghassemi","year":"2023","journal-title":"Sci Adv"},{"key":"2024090912551860000_bib26","doi-asserted-by":"publisher","first-page":"4543","DOI":"10.1038\/s41467-022-32174-7","article-title":"The molecular mechanism of snake short-chain \u03b1-neurotoxin binding to muscle-type nicotinic acetylcholine receptors","volume":"13","author":"Nys","year":"2022","journal-title":"Nat Commun"},{"key":"2024090912551860000_bib27","doi-asserted-by":"publisher","first-page":"D439","DOI":"10.1093\/nar\/gkab1061","article-title":"AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models","volume":"50","author":"Varadi","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib28","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"2024090912551860000_bib29","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"Kyoto Encyclopedia of Genes and Genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib30","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat Genet"},{"key":"2024090912551860000_bib31","doi-asserted-by":"publisher","first-page":"D1373","DOI":"10.1093\/nar\/gkac956","article-title":"PubChem 2023 update","volume":"51","author":"Kim","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib32","doi-asserted-by":"publisher","first-page":"e4776","DOI":"10.1002\/pro.4776","article-title":"Kalium 3.0 is a comprehensive depository of natural, artificial, and labeled polypeptides acting on potassium channels","volume":"32","author":"Krylov","year":"2023","journal-title":"Protein Sci"},{"key":"2024090912551860000_bib33","doi-asserted-by":"publisher","first-page":"D454","DOI":"10.1093\/nar\/gkx1084","article-title":"KNOTTIN: the database of inhibitor cystine knot scaffold after 10 years, toward a systematic structure modeling","volume":"46","author":"Postic","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib34","doi-asserted-by":"publisher","first-page":"e4566","DOI":"10.1002\/pro.4566","article-title":"ScrepYard: an online resource for disulfide-stabilized tandem repeat peptides","volume":"32","author":"Liu","year":"2023","journal-title":"Protein Sci"},{"key":"2024090912551860000_bib35","doi-asserted-by":"publisher","first-page":"262","DOI":"10.3390\/toxins2020261","article-title":"Animal toxins: how is complexity represented in databases?","volume":"2","author":"Jungo","year":"2010","journal-title":"Toxins"},{"key":"2024090912551860000_bib36","doi-asserted-by":"publisher","first-page":"356","DOI":"10.1016\/j.toxicon.2005.12.001","article-title":"SCORPION2: a database for structure-function analysis of scorpion toxins","volume":"47","author":"Tan","year":"2006","journal-title":"Toxicon"},{"key":"2024090912551860000_bib37","doi-asserted-by":"publisher","first-page":"D293","DOI":"10.1093\/nar\/gkm832","article-title":"ATDB: a uni-database platform for animal toxins","volume":"36","author":"He","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib38","doi-asserted-by":"publisher","first-page":"327","DOI":"10.3390\/metabo10080327","article-title":"VenoMS\u2014a website for the low molecular mass compounds in spider venoms","volume":"10","author":"Forster","year":"2020","journal-title":"Metabolites"},{"key":"2024090912551860000_bib39","doi-asserted-by":"publisher","first-page":"D928","DOI":"10.1093\/nar\/gku1004","article-title":"T3DB: the toxic exposome database","volume":"43","author":"Wishart","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib40","author":"VenomZone"},{"key":"2024090912551860000_bib41","doi-asserted-by":"publisher","first-page":"W345","DOI":"10.1093\/nar\/gkac247","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update","volume":"50","author":"The Galaxy Community","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib42","doi-asserted-by":"publisher","first-page":"1058","DOI":"10.1101\/gr.276251.121","article-title":"Snake venom gene expression is coordinated by novel regulatory architecture and the integration of multiple co-opted vertebrate pathways","volume":"32","author":"Perry","year":"2022","journal-title":"Genome Res"},{"key":"2024090912551860000_bib43","doi-asserted-by":"publisher","first-page":"2434","DOI":"10.1016\/j.cub.2016.07.038","article-title":"The deep origin and recent loss of venom toxin genes in rattlesnakes","volume":"26","author":"Dowell","year":"2016","journal-title":"Curr Biol"},{"key":"2024090912551860000_bib44","doi-asserted-by":"publisher","first-page":"20651","DOI":"10.1073\/pnas.1314702110","article-title":"The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system","volume":"110","author":"Vonk","year":"2013","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024090912551860000_bib45","doi-asserted-by":"publisher","first-page":"590","DOI":"10.1101\/gr.240952.118","article-title":"The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes","volume":"29","author":"Schield","year":"2019","journal-title":"Genome Res"},{"key":"2024090912551860000_bib46","doi-asserted-by":"crossref","first-page":"163","DOI":"10.3389\/fevo.2019.00163","article-title":"The significance of comparative genomics in modern evolutionary venomics","volume":"7","author":"Drukewitz","year":"2019","journal-title":"Front Ecol Evol"},{"key":"2024090912551860000_bib47","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Trinity: Reconstructing a full-length transcriptome without a genome from RNA-seq data","volume":"29","author":"Grabherr","year":"2011","journal-title":"Nat Biotechnol"},{"key":"2024090912551860000_bib48","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat Methods"},{"key":"2024090912551860000_bib49","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"Kim","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2024090912551860000_bib50","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2024090912551860000_bib51","doi-asserted-by":"publisher","first-page":"R36","DOI":"10.1186\/gb-2013-14-4-r36","article-title":"TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions","volume":"14","author":"Kim","year":"2013","journal-title":"Genome Biol"},{"key":"2024090912551860000_bib52","doi-asserted-by":"publisher","first-page":"657240","DOI":"10.3389\/fpls.2021.657240","article-title":"Comparison of short-read sequence aligners indicates strengths and weaknesses for biologists to consider","volume":"12","author":"Musich","year":"2021","journal-title":"Front Plant Sci"},{"key":"2024090912551860000_bib53","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1186\/s13059-020-1935-5","article-title":"Opportunities and challenges in long-read sequencing data analysis","volume":"21","author":"Amarasinghe","year":"2020","journal-title":"Genome Biol"},{"key":"2024090912551860000_bib54","doi-asserted-by":"publisher","first-page":"1348","DOI":"10.1038\/s41587-021-01108-x","article-title":"Nanopore sequencing technology, bioinformatics and applications","volume":"39","author":"Wang","year":"2021","journal-title":"Nat Biotechnol"},{"key":"2024090912551860000_bib55","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1038\/s41587-023-02100-3","article-title":"Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy","volume":"42","author":"Larivi\u00e8re","year":"2024","journal-title":"Nat Biotechnol"},{"key":"2024090912551860000_bib56","doi-asserted-by":"publisher","first-page":"D988","DOI":"10.1093\/nar\/gkab1049","article-title":"Ensembl 2022","volume":"50","author":"Cunningham","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib57","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1038\/s41586-021-03451-0","article-title":"Towards complete and error-free genome assemblies of all vertebrate species","volume":"592","author":"Rhie","year":"2021","journal-title":"Nature"},{"key":"2024090912551860000_bib58","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1146\/annurev-animal-090414-014900","article-title":"The Genome 10\u00a0K Project: a way forward","volume":"3","author":"Koepfli","year":"2015","journal-title":"Annu Rev Anim Biosci"},{"key":"2024090912551860000_bib59","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1071\/IS16059","article-title":"Advancing genomics through the Global Invertebrate Genomics Alliance (GIGA)","volume":"31","author":"Voolstra","year":"2017","journal-title":"Invert Systematics"},{"key":"2024090912551860000_bib60","doi-asserted-by":"publisher","first-page":"4325","DOI":"10.1073\/pnas.1720115115","article-title":"Earth BioGenome Project: sequencing life for the future of life","volume":"115","author":"Lewin","year":"2018","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024090912551860000_bib61","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1016\/j.tree.2021.11.008","article-title":"The era of reference genomes in conservation genomics","volume":"37","author":"Formenti","year":"2022","journal-title":"Trends Ecol Evol"},{"key":"2024090912551860000_bib62","doi-asserted-by":"publisher","first-page":"e2115642118","DOI":"10.1073\/pnas.2115642118","article-title":"Sequence locally, think globally: the Darwin Tree of Life Project","volume":"119","author":"The Darwin Tree of Life Project Consortium","year":"2022","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024090912551860000_bib63","doi-asserted-by":"publisher","first-page":"1311","DOI":"10.1126\/science.1251385","article-title":"Comparative genomics reveals insights into avian genome evolution and adaptation","volume":"346","author":"Zhang","year":"2014","journal-title":"Science"},{"key":"2024090912551860000_bib64","doi-asserted-by":"publisher","first-page":"8270","DOI":"10.1038\/s41467-023-44080-7","article-title":"Topological structures and syntenic conservation in sea anemone genomes","volume":"14","author":"Zimmermann","year":"2023","journal-title":"Nat Commun"},{"key":"2024090912551860000_bib65","doi-asserted-by":"publisher","first-page":"jkad107","DOI":"10.1093\/g3journal\/jkad107","article-title":"Chromosome-level genome assembly of hydractinia symbiolongicarpus","volume":"13","author":"Kon-Nanjo","year":"2023","journal-title":"G3 (Bethesda)"},{"key":"2024090912551860000_bib66","doi-asserted-by":"publisher","first-page":"592","DOI":"10.1038\/nature08830","article-title":"The dynamic genome of Hydra","volume":"464","author":"Chapman","year":"2010","journal-title":"Nature"},{"key":"2024090912551860000_bib67","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1126\/science.1139158","article-title":"Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization","volume":"317","author":"Putnam","year":"2007","journal-title":"Science"},{"key":"2024090912551860000_bib68","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1038\/nature10249","article-title":"Using the Acropora digitifera genome to understand coral responses to environmental change","volume":"476","author":"Shinzato","year":"2011","journal-title":"Nature"},{"key":"2024090912551860000_bib69","doi-asserted-by":"publisher","first-page":"11893","DOI":"10.1073\/pnas.1513318112","article-title":"The genome of Aiptasia, a sea anemone model for coral symbiosis","volume":"112","author":"Baumgarten","year":"2015","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024090912551860000_bib70","doi-asserted-by":"publisher","first-page":"e13288","DOI":"10.7554\/eLife.13288","article-title":"Comparative genomics explains the evolutionary success of reef-forming corals","volume":"5","author":"Bhattacharya","year":"2016","journal-title":"eLife"},{"key":"2024090912551860000_bib71","doi-asserted-by":"publisher","first-page":"1193","DOI":"10.1038\/nature07415","article-title":"Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals","volume":"455","author":"Grimson","year":"2008","journal-title":"Nature"},{"key":"2024090912551860000_bib72","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1101\/gr.162503.113","article-title":"Cnidarian microRNAs frequently regulate targets by cleavage","volume":"24","author":"Moran","year":"2014","journal-title":"Genome Res"},{"key":"2024090912551860000_bib73","doi-asserted-by":"publisher","first-page":"639","DOI":"10.1101\/gr.162529.113","article-title":"Evolutionary conservation of the eumetazoan gene regulatory landscape","volume":"24","author":"Schwaiger","year":"2014","journal-title":"Genome Res"},{"key":"2024090912551860000_bib74","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1101\/gr.277040.122","article-title":"A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state","volume":"33","author":"Cazet","year":"2023","journal-title":"Genome Res"},{"key":"2024090912551860000_bib75","doi-asserted-by":"publisher","first-page":"574925","DOI":"10.3389\/fphar.2020.574925","article-title":"How the toxin got its toxicity","volume":"11","author":"Jackson","year":"2020","journal-title":"Front Pharmacol"},{"key":"2024090912551860000_bib76","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1186\/s12915-023-01656-5","article-title":"Prevalent bee venom genes evolved before the aculeate stinger and eusociality","volume":"21","author":"Koludarov","year":"2023","journal-title":"BMC Biol"},{"key":"2024090912551860000_bib77","doi-asserted-by":"publisher","first-page":"4861","DOI":"10.1038\/s41467-023-40550-0","article-title":"Domain loss enabled evolution of novel functions in the snake three-finger toxin gene superfamily","volume":"14","author":"Koludarov","year":"2023","journal-title":"Nat Commun"},{"key":"2024090912551860000_bib78","doi-asserted-by":"publisher","first-page":"D1062","DOI":"10.1093\/nar\/gkab966","article-title":"PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies","volume":"50","author":"Fuentes","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib79","doi-asserted-by":"publisher","first-page":"giad116","DOI":"10.1093\/gigascience\/giad116","article-title":"ToxCodAn-genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages","volume":"13","author":"Nachtigall","year":"2024","journal-title":"Gigascience"},{"key":"2024090912551860000_bib80","doi-asserted-by":"publisher","first-page":"e2313440121","DOI":"10.1073\/pnas.2313440121","article-title":"The genetic regulatory architecture and epigenomic basis for age-related changes in rattlesnake venom","volume":"121","author":"Hogan","year":"2024","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024090912551860000_bib81","doi-asserted-by":"publisher","first-page":"W774","DOI":"10.1093\/nar\/gkac238","article-title":"WashU Epigenome Browser update 2022","volume":"50","author":"Li","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib82","doi-asserted-by":"publisher","first-page":"762","DOI":"10.1016\/j.celrep.2016.12.063","article-title":"A tissue-mapped axolotl de novo transcriptome enables identification of limb regeneration factors","volume":"18","author":"Bryant","year":"2017","journal-title":"Cell Rep"},{"key":"2024090912551860000_bib83","doi-asserted-by":"publisher","first-page":"e5428","DOI":"10.7717\/peerj.5428","article-title":"The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly","volume":"6","author":"MacManes","year":"2018","journal-title":"PeerJ"},{"key":"2024090912551860000_bib84","doi-asserted-by":"publisher","first-page":"W29","DOI":"10.1093\/nar\/gkr367","article-title":"HMMER web server: interactive sequence similarity searching","volume":"39","author":"Finn","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib85","doi-asserted-by":"publisher","first-page":"D344","DOI":"10.1093\/nar\/gkaa977","article-title":"The InterPro protein families and domains database: 20 years on","volume":"49","author":"Blum","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib86","doi-asserted-by":"publisher","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","article-title":"Pfam: the protein families database in 2021","volume":"49","author":"Mistry","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib87","doi-asserted-by":"publisher","first-page":"D384","DOI":"10.1093\/nar\/gkac1096","article-title":"The conserved domain database in 2023","volume":"51","author":"Wang","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib88","doi-asserted-by":"publisher","DOI":"10.1021\/acsomega.4c01959","article-title":"Unveiling encrypted antimicrobial peptides from cephalopods\u2019 salivary glands: a proteolysis-driven virtual approach","author":"Ag\u00fcero-Chapin","year":"2024","journal-title":"ACS Omega"},{"key":"2024090912551860000_bib89","doi-asserted-by":"publisher","first-page":"e5361","DOI":"10.7717\/peerj.5361","article-title":"Venomix: a simple bioinformatic pipeline for identifying and characterizing toxin gene candidates from transcriptomic data","volume":"6","author":"Macrander","year":"2018","journal-title":"PeerJ"},{"key":"2024090912551860000_bib90","doi-asserted-by":"publisher","first-page":"e90","DOI":"10.7717\/peerj-cs.90","article-title":"Machine learning can differentiate venom toxins from other proteins having non-toxic physiological functions","volume":"2","author":"Gacesa","year":"2016","journal-title":"Peer J Comput Sci"},{"key":"2024090912551860000_bib91","doi-asserted-by":"publisher","first-page":"e7200","DOI":"10.7717\/peerj.7200","article-title":"TOXIFY: a deep learning approach to classify animal venom proteins","volume":"7","author":"Cole","year":"2019","journal-title":"PeerJ"},{"key":"2024090912551860000_bib92","doi-asserted-by":"publisher","first-page":"bbae094","DOI":"10.1093\/bib\/bbae094","article-title":"DeTox: a pipeline for the detection of toxins in venomous organisms","volume":"25","author":"Ringeval","year":"2024","journal-title":"Briefings Bioinf"},{"key":"2024090912551860000_bib93","doi-asserted-by":"publisher","first-page":"5159","DOI":"10.1093\/bioinformatics\/btaa656","article-title":"ToxDL: deep learning using primary structure and domain embeddings for assessing protein toxicity","volume":"36","author":"Pan","year":"2021","journal-title":"Bioinformatics"},{"key":"2024090912551860000_bib94","doi-asserted-by":"publisher","first-page":"W84","DOI":"10.1093\/nar\/gky350","article-title":"PANNZER2: a rapid functional annotation web server","volume":"46","author":"T\u00f6r\u00f6nen","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib95","doi-asserted-by":"publisher","first-page":"e2111392119","DOI":"10.1073\/pnas.2111392119","article-title":"Convergent evolution of venom gland transcriptomes across Metazoa","volume":"119","author":"Zancolli","year":"2022","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024090912551860000_bib96","doi-asserted-by":"publisher","first-page":"18083","DOI":"10.1038\/s41598-020-75048-y","article-title":"Physiological demands and signaling associated with snake venom production and storage illustrated by transcriptional analyses of venom glands","volume":"10","author":"Perry","year":"2020","journal-title":"Sci Rep"},{"key":"2024090912551860000_bib97","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1186\/1471-2164-15-366","article-title":"Dramatic expansion of the black widow toxin arsenal uncovered by multi-tissue transcriptomics and venom proteomics","volume":"15","author":"Haney","year":"2014","journal-title":"BMC Genomics"},{"key":"2024090912551860000_bib98","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1038\/nbt.3519","article-title":"Near-optimal probabilistic RNA-seq quantification","volume":"34","author":"Bray","year":"2016","journal-title":"Nat Biotechnol"},{"key":"2024090912551860000_bib99","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"2024090912551860000_bib100","doi-asserted-by":"publisher","first-page":"585","DOI":"10.3390\/toxins15090585","article-title":"De novo assembly of venom gland transcriptome of Tropidolaemus wagleri (Temple pit viper, Malaysia) and insights into the origin of its major toxin, waglerin","volume":"15","author":"Tan","year":"2023","journal-title":"Toxins"},{"key":"2024090912551860000_bib101","doi-asserted-by":"publisher","first-page":"170643","DOI":"10.1016\/j.peptides.2021.170643","article-title":"Transcriptomic and proteomic analyses of venom glands from scorpions Liocheles australasiae, Mesobuthus martensii, and Scorpio maurus palmatus","volume":"146","author":"So","year":"2021","journal-title":"Peptides"},{"key":"2024090912551860000_bib102","doi-asserted-by":"publisher","first-page":"345","DOI":"10.3390\/toxins15050345","article-title":"Antimicrobial peptide arsenal predicted from the venom gland transcriptome of the tropical trap-jaw ant Odontomachus chelifer","volume":"15","author":"Menk","year":"2023","journal-title":"Toxins"},{"key":"2024090912551860000_bib103","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1016\/j.ygeno.2018.11.012","article-title":"Comparative transcriptome analyses of venom glands from three scorpionfishes","volume":"111","author":"Xie","year":"2019","journal-title":"Genomics"},{"key":"2024090912551860000_bib104","doi-asserted-by":"publisher","first-page":"429","DOI":"10.3390\/toxins15070429","article-title":"Intersexual differences in the gene expression of Phoneutria depilata (Araneae, Ctenidae) toxins revealed by venom gland transcriptome analyses","volume":"15","author":"Ram\u00edrez","year":"2023","journal-title":"Toxins"},{"key":"2024090912551860000_bib105","doi-asserted-by":"publisher","first-page":"2873","DOI":"10.3390\/ijms21082873","article-title":"Bioinformatics methods for mass spectrometry-based proteomics data analysis","volume":"21","author":"Chen","year":"2020","journal-title":"Int J Mol Sci"},{"key":"2024090912551860000_bib106","doi-asserted-by":"publisher","first-page":"3551","DOI":"10.1002\/(SICI)1522-2683(19991201)20:18%3c3551::AID-ELPS3551%3e3.0.CO;2-2","article-title":"Probability-based protein identification by searching sequence databases using mass spectrometry data","volume":"20","author":"Perkins","year":"1999","journal-title":"Electrophoresis"},{"key":"2024090912551860000_bib107","doi-asserted-by":"publisher","first-page":"M111.010587","DOI":"10.1074\/mcp.M111.010587","article-title":"PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification","volume":"11","author":"Zhang","year":"2012","journal-title":"Mol Cell Proteomics"},{"key":"2024090912551860000_bib108","doi-asserted-by":"publisher","first-page":"15","DOI":"10.3390\/proteomes9010015","article-title":"Proteome discoverer\u2014a community enhanced data processing suite for protein informatics","volume":"9","author":"Orsburn","year":"2021","journal-title":"Proteomes"},{"key":"2024090912551860000_bib109","doi-asserted-by":"publisher","first-page":"976","DOI":"10.1016\/1044-0305(94)80016-2","article-title":"An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database","volume":"5","author":"Eng","year":"1994","journal-title":"J Am Soc Mass Spectrom"},{"key":"2024090912551860000_bib110","doi-asserted-by":"publisher","first-page":"13.20.1","DOI":"10.1002\/0471250953.bi1320s40","article-title":"Advanced peptide and protein identification software","volume":"40","author":"Bern","year":"2012","journal-title":"Curr Protoc Bioinformatics"},{"key":"2024090912551860000_bib111","doi-asserted-by":"publisher","first-page":"1059","DOI":"10.1038\/nbt.4236","article-title":"Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine","volume":"36","author":"Chi","year":"2018","journal-title":"Nat Biotechnol"},{"key":"2024090912551860000_bib112","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1038\/nmeth.4256","article-title":"MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry\u2013based proteomics","volume":"14","author":"Kong","year":"2017","journal-title":"Nat Methods"},{"key":"2024090912551860000_bib113","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1038\/nbt.3109","article-title":"PeptideShaker enables reanalysis of MS-derived proteomics data sets","volume":"33","author":"Vaudel","year":"2015","journal-title":"Nat Biotechnol"},{"key":"2024090912551860000_bib114","doi-asserted-by":"publisher","first-page":"1367","DOI":"10.1038\/nbt.1511","article-title":"MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification","volume":"26","author":"Cox","year":"2008","journal-title":"Nat Biotechnol"},{"key":"2024090912551860000_bib115","doi-asserted-by":"publisher","first-page":"966","DOI":"10.1093\/bioinformatics\/btq054","article-title":"Skyline: an open source document editor for creating and analyzing targeted proteomics experiments","volume":"26","author":"MacLean","year":"2010","journal-title":"Bioinformatics"},{"key":"2024090912551860000_bib116","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/s41592-019-0638-x","article-title":"DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput","volume":"17","author":"Demichev","year":"2020","journal-title":"Nat Methods"},{"key":"2024090912551860000_bib117","doi-asserted-by":"publisher","first-page":"1563","DOI":"10.1038\/s41587-021-00968-7","article-title":"MaxDIA enables library-based and library-free data-independent acquisition proteomics","volume":"39","author":"Sinitcyn","year":"2021","journal-title":"Nat Biotechnol"},{"key":"2024090912551860000_bib118","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1038\/nmeth.3234","article-title":"DIA mass spectrometry","volume":"12","author":"Doerr","year":"2015","journal-title":"Nat Methods"},{"key":"2024090912551860000_bib119","doi-asserted-by":"publisher","first-page":"1885","DOI":"10.1007\/s13361-015-1204-0","article-title":"Novor: real-time peptide de novo sequencing software","volume":"26","author":"Ma","year":"2015","journal-title":"J Am Soc Mass Spectrom"},{"key":"2024090912551860000_bib120","doi-asserted-by":"publisher","first-page":"i183","DOI":"10.1093\/bioinformatics\/btz366","article-title":"pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework","volume":"35","author":"Yang","year":"2019","journal-title":"Bioinformatics"},{"key":"2024090912551860000_bib121","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1186\/s40409-017-0135-6","article-title":"It is time for top-down venomics","volume":"23","author":"Melani","year":"2017","journal-title":"J Venom Anim Toxins Incl Trop Dis"},{"key":"2024090912551860000_bib122","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1038\/nmeth.3959","article-title":"OpenMS: a flexible open-source software platform for mass spectrometry data analysis","volume":"13","author":"R\u00f6st","year":"2016","journal-title":"Nat Methods"},{"key":"2024090912551860000_bib123","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1038\/s41587-023-01690-2","article-title":"Integrative analysis of multimodal mass spectrometry data in MZmine 3","volume":"41","author":"Schmid","year":"2023","journal-title":"Nat Biotechnol"},{"key":"2024090912551860000_bib124","doi-asserted-by":"publisher","first-page":"2772","DOI":"10.1074\/mcp.M110.002766","article-title":"Deconvolution and database search of complex tandem mass spectra of intact proteins","volume":"9","author":"Liu","year":"2010","journal-title":"Mol Cell Proteomics"},{"key":"2024090912551860000_bib125","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1007\/978-1-4939-6747-6_23","article-title":"Data conversion with ProteoWizard msConvert","volume-title":"Proteomics: Methods and Protocols","author":"Adusumilli","year":"2017"},{"key":"2024090912551860000_bib126","doi-asserted-by":"publisher","first-page":"M111.008524","DOI":"10.1074\/mcp.M111.008524","article-title":"Protein identification using top-down spectra","volume":"11","author":"Liu","year":"2012","journal-title":"Mol Cell Proteomics"},{"key":"2024090912551860000_bib127","doi-asserted-by":"publisher","first-page":"464","DOI":"10.1007\/s13361-013-0789-4","article-title":"MASH Suite: a user-friendly and versatile software interface for high-resolution mass spectrometry data interpretation and visualization","volume":"25","author":"Guner","year":"2014","journal-title":"J Am Soc Mass Spectrom"},{"key":"2024090912551860000_bib128","doi-asserted-by":"publisher","first-page":"3082","DOI":"10.1021\/acs.analchem.5b03963","article-title":"pTop 1.0: a high-accuracy and high-efficiency search engine for intact protein identification","volume":"88","author":"Sun","year":"2016","journal-title":"Anal Chem"},{"key":"2024090912551860000_bib129","doi-asserted-by":"publisher","first-page":"1309","DOI":"10.1093\/bioinformatics\/btw806","article-title":"A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra","volume":"33","author":"Kou","year":"2017","journal-title":"Bioinformatics"},{"key":"2024090912551860000_bib130","doi-asserted-by":"publisher","first-page":"3495","DOI":"10.1093\/bioinformatics\/btw398","article-title":"TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization","volume":"32","author":"Kou","year":"2016","journal-title":"Bioinformatics"},{"key":"2024090912551860000_bib131","doi-asserted-by":"publisher","first-page":"909","DOI":"10.1038\/nmeth.4388","article-title":"Informed-Proteomics: open-source software package for top-down proteomics","volume":"14","author":"Park","year":"2017","journal-title":"Nat Methods"},{"key":"2024090912551860000_bib132","doi-asserted-by":"publisher","first-page":"e73957","DOI":"10.1371\/journal.pone.0073957","article-title":"In silico approach for predicting toxicity of peptides and proteins","volume":"8","author":"Gupta","year":"2013","journal-title":"PLoS One"},{"key":"2024090912551860000_bib133","doi-asserted-by":"publisher","first-page":"bbac174","DOI":"10.1093\/bib\/bbac174","article-title":"ToxinPred2: an improved method for predicting toxicity of proteins","volume":"23","author":"Sharma","year":"2022","journal-title":"Brief Bioinform"},{"key":"2024090912551860000_bib134","doi-asserted-by":"publisher","first-page":"e45012","DOI":"10.1371\/journal.pone.0045012","article-title":"Towards the improved discovery and design of functional peptides: common features of diverse classes permit generalized prediction of bioactivity","volume":"7","author":"Mooney","year":"2012","journal-title":"PLoS One"},{"key":"2024090912551860000_bib135","doi-asserted-by":"publisher","first-page":"W449","DOI":"10.1093\/nar\/gkw329","article-title":"PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex","volume":"44","author":"Lamiable","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib136","doi-asserted-by":"publisher","first-page":"W432","DOI":"10.1093\/nar\/gkad376","article-title":"PEP-FOLD4: a pH-dependent force field for peptide structure prediction in aqueous solution","volume":"51","author":"Rey","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib137","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1038\/s41592-022-01488-1","article-title":"ColabFold: making protein folding accessible to all","volume":"19","author":"Mirdita","year":"2022","journal-title":"Nat Methods"},{"key":"2024090912551860000_bib138","doi-asserted-by":"publisher","first-page":"871","DOI":"10.1126\/science.abj8754","article-title":"Accurate prediction of protein structures and interactions using a three-track neural network","volume":"373","author":"Baek","year":"2021","journal-title":"Science"},{"key":"2024090912551860000_bib139","doi-asserted-by":"publisher","first-page":"1511","DOI":"10.1038\/nprot.2012.085","article-title":"Template-based protein structure modeling using the RaptorX web server","volume":"7","author":"K\u00e4llberg","year":"2012","journal-title":"Nat Protoc"},{"key":"2024090912551860000_bib140","doi-asserted-by":"publisher","first-page":"981","DOI":"10.1038\/s41592-020-0955-0","article-title":"MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets","volume":"17","author":"Choi","year":"2020","journal-title":"Nat Methods"},{"key":"2024090912551860000_bib141","doi-asserted-by":"publisher","first-page":"D521","DOI":"10.1093\/nar\/gkl923","article-title":"HMDB: the Human Metabolome Database","volume":"35","author":"Wishart","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib142","doi-asserted-by":"publisher","first-page":"161","DOI":"10.3390\/toxins15020161","article-title":"Metabolome-based classification of snake venoms by bioinformatic tools","volume":"15","author":"Alonso","year":"2023","journal-title":"Toxins"},{"key":"2024090912551860000_bib143","doi-asserted-by":"publisher","first-page":"828","DOI":"10.1038\/nbt.3597","article-title":"Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking","volume":"34","author":"Wang","year":"2016","journal-title":"Nat Biotechnol"},{"key":"2024090912551860000_bib144","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1016\/j.drudis.2021.10.003","article-title":"Paracelsus\u2019 legacy in the faunal realm: drugs deriving from animal toxins","volume":"27","author":"Fischer","year":"2022","journal-title":"Drug Discov Today"},{"key":"2024090912551860000_bib145","doi-asserted-by":"publisher","first-page":"27","DOI":"10.3390\/life11010027","article-title":"Biological nanopores: engineering on demand","volume":"11","author":"Crnkovi\u0107","year":"2021","journal-title":"Life"},{"key":"2024090912551860000_bib146","doi-asserted-by":"publisher","first-page":"D837","DOI":"10.1093\/nar\/gku892","article-title":"CancerPPD: a database of anticancer peptides and proteins","volume":"43","author":"Tyagi","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib147","doi-asserted-by":"publisher","first-page":"D1212","DOI":"10.1093\/nar\/gkac1004","article-title":"canSAR: update to the cancer translational research and drug discovery knowledgebase","volume":"51","author":"di\u00a0Micco","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib148","doi-asserted-by":"publisher","first-page":"21341","DOI":"10.1038\/s41598-022-25530-6","article-title":"ApInAPDB: a database of apoptosis-inducing anticancer peptides","volume":"12","author":"Faraji","year":"2022","journal-title":"Sci Rep"},{"key":"2024090912551860000_bib149","doi-asserted-by":"publisher","first-page":"W502","DOI":"10.1093\/nar\/gkaa327","article-title":"PaccMann: a web service for interpretable anticancer compound sensitivity prediction","volume":"48","author":"Cadow","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib150","doi-asserted-by":"publisher","first-page":"167528","DOI":"10.1016\/j.jmb.2022.167528","article-title":"EviCor: interactive web platform for exploration of molecular features and response to anti-cancer drugs","volume":"434","author":"Petrov","year":"2022","journal-title":"J Mol Biol"},{"key":"2024090912551860000_bib151","doi-asserted-by":"publisher","first-page":"150065","DOI":"10.1038\/sdata.2015.65","article-title":"VenomKB, a new knowledge base for facilitating the validation of putative venom therapies","volume":"2","author":"Romano","year":"2015","journal-title":"Sci Data"},{"key":"2024090912551860000_bib152","doi-asserted-by":"publisher","first-page":"D44","DOI":"10.1093\/nar\/gkad902","article-title":"The SIB Swiss Institute of Bioinformatics Semantic Web of data","volume":"52","author":"SIB Swiss Institute of Bioinformatics RDF Group Members","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib153","doi-asserted-by":"publisher","first-page":"baz106","DOI":"10.1093\/database\/baz106","article-title":"Enabling semantic queries across federated bioinformatics databases","volume":"2019","author":"Sima","year":"2019","journal-title":"Database"},{"key":"2024090912551860000_bib154","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1186\/s13321-021-00515-1","article-title":"IDSM ChemWebRDF: sPARQLing small-molecule datasets","volume":"13","author":"Galgonek","year":"2021","journal-title":"J Cheminform"},{"key":"2024090912551860000_bib155","doi-asserted-by":"publisher","first-page":"D1038","DOI":"10.1093\/nar\/gkac972","article-title":"The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease","volume":"51","author":"Groza","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib156","doi-asserted-by":"publisher","first-page":"D758","DOI":"10.1093\/nar\/gkw1116","article-title":"The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching","volume":"45","author":"Howe","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib157","doi-asserted-by":"publisher","first-page":"iyac035","DOI":"10.1093\/genetics\/iyac035","article-title":"FlyBase: a guided tour of highlighted features","volume":"220","author":"Gramates","year":"2022","journal-title":"Genetics"},{"key":"2024090912551860000_bib158","doi-asserted-by":"publisher","first-page":"W270","DOI":"10.1093\/nar\/gkr366","article-title":"SwissDock, a protein-small molecule docking web service based on EADock DSS","volume":"39","author":"Grosdidier","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib159","doi-asserted-by":"publisher","first-page":"1829","DOI":"10.1021\/acs.jproteome.2c00020","article-title":"PPI-affinity: a web tool for the prediction and optimization of protein\u2013peptide and protein\u2013protein binding affinity","volume":"21","author":"Romero-Molina","year":"2022","journal-title":"J Proteome Res"},{"key":"2024090912551860000_bib160","doi-asserted-by":"publisher","first-page":"5465","DOI":"10.1038\/s41467-021-25772-4","article-title":"A deep-learning framework for multi-level peptide\u2013protein interaction prediction","volume":"12","author":"Lei","year":"2021","journal-title":"Nat Commun"},{"key":"2024090912551860000_bib161","doi-asserted-by":"publisher","first-page":"934","DOI":"10.1021\/acs.jafc.1c06110","article-title":"Integration of molecular docking analysis and molecular dynamics simulations for studying food proteins and bioactive peptides","volume":"70","author":"Vidal-Limon","year":"2022","journal-title":"J Agric Food Chem"},{"key":"2024090912551860000_bib162","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1002\/ddr.21456","article-title":"Harnessing snake venom phospholipases A2 to novel approaches for overcoming antibiotic resistance","volume":"80","author":"Almeida","year":"2019","journal-title":"Drug Dev Res"},{"key":"2024090912551860000_bib163","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1016\/j.tibs.2018.12.004","article-title":"Friends or foes? Emerging impacts of biological toxins","volume":"44","author":"Clark","year":"2019","journal-title":"Trends Biochem Sci"},{"key":"2024090912551860000_bib164","doi-asserted-by":"publisher","DOI":"10.1093\/actrade\/9780198779575.003.0001","article-title":"The data explosion","volume-title":"Big Data: A Very Short Introduction","author":"Holmes","year":"2017"},{"key":"2024090912551860000_bib170_871_075824","doi-asserted-by":"publisher","DOI":"10.1038\/s41597-024-03669-3","article-title":"Assessing semantic interoperability in environmental 1 sciences: variety of approaches and semantic artefacts","author":"Di\u00a0Muri","year":"2024","journal-title":"Scientific Data"},{"key":"2024090912551860000_bib165","doi-asserted-by":"publisher","first-page":"D347","DOI":"10.1093\/nar\/gkw918","article-title":"Ontobee: a linked ontology data server to support ontology term dereferencing, linkage, query and integration","volume":"45","author":"Ong","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib166","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1007\/s13721-024-00442-9","article-title":"Comparative evaluation of multiomics integration tools for the study of prediabetes: insights into the earliest stages of type 2 diabetes mellitus","volume":"13","author":"Emam","year":"2024","journal-title":"Netw Model Anal Health Inform Bioinforma"},{"key":"2024090912551860000_bib167","doi-asserted-by":"publisher","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci Data"},{"key":"2024090912551860000_bib168","doi-asserted-by":"publisher","first-page":"W541","DOI":"10.1093\/nar\/gkr469","article-title":"BioPortal: enhanced functionality via new web services from the National Center for Biomedical Ontology to access and use ontologies in software applications","volume":"39","author":"Whetzel","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2024090912551860000_bib169","doi-asserted-by":"publisher","DOI":"10.2777\/54599","article-title":"Directorate-General for Research and Innovation. Turning FAIR into reality\u2014final report and action plan from the European Commission expert group on FAIR data","author":"European Commission","year":"2018"}],"container-title":["GigaScience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/gigascience\/article-pdf\/doi\/10.1093\/gigascience\/giae054\/59057107\/giae054.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gigascience\/article-pdf\/doi\/10.1093\/gigascience\/giae054\/59057107\/giae054.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,9]],"date-time":"2024-09-09T12:55:40Z","timestamp":1725886540000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gigascience\/article\/doi\/10.1093\/gigascience\/giae054\/7753515"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024]]},"references-count":170,"URL":"https:\/\/doi.org\/10.1093\/gigascience\/giae054","relation":{},"ISSN":["2047-217X"],"issn-type":[{"value":"2047-217X","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024]]},"published":{"date-parts":[[2024]]},"article-number":"giae054"}}