{"id":147,"date":"2019-06-26T16:23:02","date_gmt":"2019-06-26T16:23:02","guid":{"rendered":"http:\/\/www.ebi.ac.uk\/about\/teams\/training\/publications\/"},"modified":"2021-06-14T12:16:15","modified_gmt":"2021-06-14T12:16:15","slug":"publications","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/about\/teams\/training\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"
\n \n
\n

\n \n Data science for life scientists\n <\/a>\n <\/h3>\n

\n Green A, Tirunagari S, Zane F.\n <\/p>\n

\n \n 2026<\/span>\n <\/p>\n\n

\n doi:10.6019\/tol.data-science-for-life-scientists-course-t.2026.00001.1.\n <\/p>\n <\/article>\n

\n

\n \n Sustainable computing in science\n <\/a>\n <\/h3>\n

\n Lannelongue L, Zane F.\n <\/p>\n

\n \n 2026<\/span>\n <\/p>\n\n

\n doi:10.6019\/tol.sustainable-computing-intro-t.2026.00001.1.\n <\/p>\n <\/article>\n

\n

\n \n An introduction to EMBL-EBI resources\n <\/a>\n <\/h3>\n

\n Zane F, Blackshaw JA, Luciani A, Maga\u00f1a Gomez PG, Mirabueno L, Tejera Hernandez N, Rogers S.\n <\/p>\n

\n \n 2026<\/span>\n <\/p>\n\n

\n doi:10.6019\/tol.intro-ebi-resources-w.2026.00001.1.\n <\/p>\n <\/article>\n

\n

\n \n Data science for life scientists course\n <\/a>\n <\/h3>\n

\n Green A, Zane F.\n <\/p>\n

\n \n 2026<\/span>\n <\/p>\n\n

\n doi:10.6019\/tol.datascience25-t.2025.00001.1.\n <\/p>\n <\/article>\n

\n

\n \n Strengthening bioinformatics education: e-learning initiatives across ELIXIR Nodes and Communities.\n <\/a>\n <\/h3>\n

\n Zahn-Zabala M, Ahokas M, Batut B, Beier S, Botzki A, Cardona A, Gruden K, Korpelainen E, Lehtivaara M, Leskosek B, Mir\u0103u\u021b\u0103 B, Mishra A, Pommier C, Poterlowicz K, Rasche H, Sand O, Waterhouse R, Wittke S, Zenoaga-Barb\u0103ro\u0219ie C, Anton M, Wibberg D.\n <\/p>\n

\n F1000Research, \n 2025<\/span>\n <\/p>\n\n

\n doi:10.12688\/f1000research.173116.1.\n <\/p>\n <\/article>\n

\n

\n \n EMBL's European Bioinformatics Institute (EMBL-EBI) in 2024.\n <\/a>\n <\/h3>\n

\n Thakur M, Brooksbank C, Finn RD, Firth HV, Foreman J, Freeberg M, Gurwitz KT, Harrison M, Hulcoop D, Hunt SE, R Leach A, Levchenko M, Marques D, McDonagh EM, Mithani A, Parkinson H, Perez-Riverol Y, Perova Z, Sarkans U, Tirunagari S, Tzampatzopoulou E, Venkatesan A, Vizcaino JA, Wingfield B, Zdrazil B, McEntyre J.\n <\/p>\n

\n Nucleic acids research, \n 2025<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkae1089.\n <\/p>\n <\/article>\n

\n

\n \n "Smurf Mice": revolutionising our understanding of age-related and end-of-life animal physiology\n <\/a>\n <\/h3>\n

\n Cansell C, Goepp V, Bain F, Todd N, Douard V, Monnoye M, Zane F, Sanchez C, Pietrancosta N, Rovere C, Denis RG, Luquet S, Rera M.\n <\/p>\n

\n Preprint, \n 2025<\/span>\n <\/p>\n\n

\n doi:10.1101\/2025.06.14.659669.\n <\/p>\n <\/article>\n

\n

\n \n Competencies for bioinformatics core facility scientists: extension of the ISCB competency framework for bioinformatics.\n <\/a>\n <\/h3>\n

\n Lloret-Llinares M, Carvajal-L\u00f3pez P, Downing T, Gogol M, Ho Sui S, Nonell L, Paladin L, Reid AJ, Pomann GM, Brooksbank C.\n <\/p>\n

\n Bioinformatics advances, \n 2025<\/span>\n <\/p>\n\n

\n doi:10.1093\/bioadv\/vbaf206.\n <\/p>\n <\/article>\n

\n

\n \n Gene\u2013environment interactions in shaping human health and disease\n <\/a>\n <\/h3>\n

\n Foreman AL, Ara\u00fajo D, Mishra A.\n <\/p>\n

\n \n 2024<\/span>\n <\/p>\n\n

\n doi:10.6019\/tol.gene-envt-interaction2024-t.2024.00001.1.\n <\/p>\n <\/article>\n

\n

\n \n Molecular building blocks of life\n <\/a>\n <\/h3>\n

\n Mishra A.\n <\/p>\n

\n \n 2024<\/span>\n <\/p>\n\n

\n doi:10.6019\/tol.molbuildblocks-t.2024.00001.1.\n <\/p>\n <\/article>\n

\n

\n \n Making bioinformatics training FAIR: the EMBL-EBI training portal.\n <\/a>\n <\/h3>\n

\n Swan AL, Broadbent A, Singh Gaur P, Mishra A, Gurwitz K, Mithani A, Morgan SL, Malhotra G, Brooksbank C.\n <\/p>\n

\n Frontiers in bioinformatics, \n 2024<\/span>\n <\/p>\n\n

\n doi:10.3389\/fbinf.2024.1347168.\n <\/p>\n <\/article>\n

\n

\n \n EMBL's European Bioinformatics Institute (EMBL-EBI) in 2023.\n <\/a>\n <\/h3>\n

\n Thakur M, Buniello A, Brooksbank C, Gurwitz KT, Hall M, Hartley M, Hulcoop DG, Leach AR, Marques D, Martin M, Mithani A, McDonagh EM, Mutasa-Gottgens E, Ochoa D, Perez-Riverol Y, Stephenson J, Varadi M, Velankar S, Vizcaino JA, Witham R, McEntyre J.\n <\/p>\n

\n Nucleic acids research, \n 2024<\/span>\n <\/p>\n\n

\n doi:10.1093\/nar\/gkad1088.\n <\/p>\n <\/article>\n

\n

\n \n The ISCB competency framework v. 3: a revised and extended standard for bioinformatics education and training.\n <\/a>\n <\/h3>\n

\n Brooksbank C, Brazas MD, Mulder N, Schwartz R, Ras V, Morgan SL, Lloret Llinares M, Carvajal L\u00f3pez P, Larcombe L, Ghouila A, Hancocks T, Satagopam V, De Las Rivas J, Mazandu G, Gaeta B.\n <\/p>\n

\n Bioinformatics advances, \n 2024<\/span>\n <\/p>\n\n

\n doi:10.1093\/bioadv\/vbae166.\n <\/p>\n <\/article>\n

\n

\n \n Abalone peptide increases stress resilience and cost-free longevity via SKN-1-governed transcriptional metabolic reprogramming in C. elegans.\n <\/a>\n <\/h3>\n

\n Wang Q, Wang L, Huang Z, Xiao Y, Liu M, Liu H, Yu Y, Liang M, Luo N, Li K, Mishra A, Huang Z.\n <\/p>\n

\n Aging cell, \n 2023<\/span>\n <\/p>\n\n

\n doi:10.1111\/acel.14046.\n <\/p>\n <\/article>\n

\n

\n \n Data-driven plant sciences: A curated collection of EMBL-EBI on-demand training\n <\/a>\n <\/h3>\n

\n Mishra A.\n <\/p>\n

\n \n 2023<\/span>\n <\/p>\n\n

\n doi:10.6019\/tol.datadrivenplantsciences-t.2023.00001.1.\n <\/p>\n <\/article>\n

\n

\n \n Making bioinformatics training FAIR: the EMBL-EBI training portal\n <\/a>\n <\/h3>\n

\n Swan A, Broadbent A, Gaur PS, Mishra A, Gurwitz K, Mithani A, Morgan S, Malhotra G, Brooksbank C.\n <\/p>\n

\n Preprint, \n 2023<\/span>\n <\/p>\n\n

\n doi:10.5281\/zenodo.10391149.\n <\/p>\n <\/article>\n

\n

\n \n "Be sustainable": EOSC-Life recommendations for implementation of FAIR principles in life science data handling.\n <\/a>\n <\/h3>\n

\n David R, Rybina A, Burel JM, Heriche JK, Audergon P, Boiten JW, Coppens F, Crockett S, Exter K, Fahrner S, Fratelli M, Goble C, Gormanns P, Grantner T, Gr\u00fcning B, Gurwitz KT, Hancock JM, Harmse H, Holub P, Juty N, Karnbach G, Karoune E, Keppler A, Klemeier J, Lancelotti C, Legras JL, Lister AL, Longo DL, Ludwig R, Madon B, Massimi M, Matser V, Matteoni R, Mayrhofer MT, Ohmann C, Panagiotopoulou M, Parkinson H, Perseil I, Pfander C, Pieruschka R, Raess M, Rauber A, Richard AS, Romano P, Rosato A, S\u00e1nchez-Pla A, Sansone SA, Sarkans U, Serrano-Solano B, Tang J, Tanoli Z, Tedds J, Wagener H, Weise M, Westerhoff HV, Wittner R, Ewbank J, Blomberg N, Gribbon P.\n <\/p>\n

\n The EMBO journal, \n 2023<\/span>\n <\/p>\n\n

\n doi:10.15252\/embj.2023115008.\n <\/p>\n <\/article>\n

\n

\n \n Methods in Bioinformatics\n <\/a>\n <\/h3>\n

\n Larionov A, Lock A, Luck K, Ly T, Mishra A, Moore B, Perfetto L, Rausch T, Tischer C.\n <\/p>\n

\n \n 2022<\/span>\n <\/p>\n\n

\n doi:10.6019\/tol.methodsbioinformatics-t.2022.00001.1.\n <\/p>\n <\/article>\n

\n

\n \n Introduction to multiomics data integration and visualisation\n <\/a>\n <\/h3>\n

\n Cortes-Ciriano I, Korcsm\u00e1ros T, Mishra A, Petsalaki E.\n <\/p>\n

\n \n 2022<\/span>\n <\/p>\n\n

\n doi:10.6019\/tol.multiomicsintegration22-t.2022.00001.1.\n <\/p>\n <\/article>\n

\n

\n \n Editorial: <i>C. elegans<\/i> as an emerging model of pharmacological innovation.\n <\/a>\n <\/h3>\n

\n Huang Z, Ma L, Mishra A, Turnbull JE, Tu H.\n <\/p>\n

\n Frontiers in pharmacology, \n 2022<\/span>\n <\/p>\n\n

\n doi:10.3389\/fphar.2022.1029752.\n <\/p>\n <\/article>\n

\n

\n \n Cancer genomics: course materials\n <\/a>\n <\/h3>\n

\n Gerstung M, Mishra A.\n <\/p>\n

\n \n 2022<\/span>\n <\/p>\n\n

\n doi:10.6019\/tol.cancergenomics-t.2021.00001.1.\n <\/p>\n <\/article>\n

\n

\n \n Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses.\n <\/a>\n <\/h3>\n

\n Bacon W, Holinski A, Pujol M, Wilmott M, Morgan SL, European Molecular Biology Laboratory\u2014European Bioinformatics Institute Training Team.\n <\/p>\n

\n PLoS computational biology, \n 2022<\/span>\n <\/p>\n\n

\n doi:10.1371\/journal.pcbi.1010220.\n <\/p>\n <\/article>\n

\n

\n \n Correction: Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries.\n <\/a>\n <\/h3>\n

\n Moore B, Carvajal-L\u00f3pez P, Abel Chauke P, Cristancho M, Dominguez Del Angel V, Fernandez-Valverde SL, Ghouila A, Gopalasingam P, Guerfali FZ, Matimba A, Morgan SL, Oliveira G, Ras V, Reyes A, De Las Rivas J, Mulder N.\n <\/p>\n

\n PLoS computational biology, \n 2022<\/span>\n <\/p>\n\n

\n doi:10.1371\/journal.pcbi.1010197.\n <\/p>\n <\/article>\n

\n

\n \n Introduction to CATH database: Quick tour\n <\/a>\n <\/h3>\n

\n Waman V, Silitoe I, Mishra A, Orengo C.\n <\/p>\n

\n \n 2021<\/span>\n <\/p>\n\n

\n doi:10.6019\/tol.cathdb-t.2021.00001.1.\n <\/p>\n <\/article>\n

\n

\n \n A guide to…: Introducing concepts and resources in bioinformatics\n <\/a>\n <\/h3>\n

\n Sarkans U, Madhusoodanan N, Mushtaq A, Petrov A, Griffiths-Jones S, Ontiveros-Palacios N, Nawrocki E, Griss J, Meldal B, Bowler-Barnett E, Paysan-Lafosse T, Armstrong D, Manners E, Hunter F, Cornu H, O\u2019Donovan C, Harrus D, Zaru R, Pearce M, Eduardo Ribas C, Sweeney B, Swan A, Mishra A.\n <\/p>\n

\n \n 2021<\/span>\n <\/p>\n\n

\n doi:10.6019\/tol.guidewebinarseries-t.2021.00001.1.\n <\/p>\n <\/article>\n

\n

\n \n Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries.\n <\/a>\n <\/h3>\n

\n Moore B, Carvajal-L\u00f3pez P, Chauke PA, Cristancho M, Dominguez Del Angel V, Fernandez-Valverde SL, Ghouila A, Gopalasingam P, Guerfali FZ, Matimba A, Morgan SL, Oliveira G, Ras V, Reyes A, De Las Rivas J, Mulder N.\n <\/p>\n

\n PLoS computational biology, \n 2021<\/span>\n <\/p>\n\n

\n doi:10.1371\/journal.pcbi.1009218.\n <\/p>\n <\/article>\n

\n

\n \n Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops.\n <\/a>\n <\/h3>\n

\n Dillon MR, Bolyen E, Adamov A, Belk A, Borsom E, Burcham Z, Debelius JW, Deel H, Emmons A, Estaki M, Herman C, Keefe CR, Morton JT, Oliveira RRM, Sanchez A, Simard A, V\u00e1zquez-Baeza Y, Ziemski M, Miwa HE, Kerere TA, Coote C, Bonneau R, Knight R, Oliveira G, Gopalasingam P, Kaehler BD, Cope EK, Metcalf JL, Robeson Ii MS, Bokulich NA, Caporaso JG.\n <\/p>\n

\n PLoS computational biology, \n 2021<\/span>\n <\/p>\n\n

\n doi:10.1371\/journal.pcbi.1009056.\n <\/p>\n <\/article>\n

\n

\n \n Wheat genomics and breeding: bridging the gap.\n <\/a>\n <\/h3>\n

\n Hussain B, Akp\u0131nar BA, Alaux M, Algharib AM, Sehgal D, Ali Z, Appels R, Aradottir GI, Batley J, Bellec A, Bentley AR, Cagirici HB, Cattivelli L, Choulet F, Cockram J, Desiderio F, Devaux P, Dogramaci M, Dorado G, Dreisigacker S, Edwards D, El-Hassouni K, Eversole K, Fahima T, Figueroa M, G\u00e1lvez S, Gill KS, Govta L, Gul A, Hensel G, Hernandez P, Herrera LC, Ibrahim A, Kilian B, Korzun V, Krugman T, Li Y, Liu S, Mahmoud AF, Morgounov A, Muslu T, Naseer F, Ordon F, Paux E, Perovic D, Reddy GVP, Reif JC, Reynolds M, Roychowdhury R, Rudd J, Sen TZ, Sukumaran S, Tiwari VK, Ullah N, Unver T, Yazar S, Budak H.\n <\/p>\n

\n Preprint, \n 2021<\/span>\n <\/p>\n\n

\n doi:10.31220\/agrirxiv.2021.00039.\n <\/p>\n <\/article>\n

\n

\n \n Human epidermal stem cell differentiation is modulated by specific lipid subspecies.\n <\/a>\n <\/h3>\n

\n Vietri Rudan M, Mishra A, Klose C, Eggert US, Watt FM.\n <\/p>\n

\n Proceedings of the National Academy of Sciences of the United States of America, \n 2020<\/span>\n <\/p>\n\n

\n doi:10.1073\/pnas.2011310117.\n <\/p>\n <\/article>\n

\n

\n \n A framework to assess the quality and impact of bioinformatics training across ELIXIR.\n <\/a>\n <\/h3>\n

\n Gurwitz KT, Singh Gaur P, Bellis LJ, Larcombe L, Alloza E, Balint BL, Botzki A, Dimec J, Dominguez Del Angel V, Fernandes PL, Korpelainen E, Krause R, Kuzak M, Le Pera L, Lesko\u0161ek B, Lindvall JM, Marek D, Martinez PA, Muyldermans T, Nyg\u00e5rd S, Palagi PM, Peterson H, Psomopoulos F, Spiwok V, van Gelder CWG, Via A, Vidak M, Wibberg D, Morgan SL, Rustici G.\n <\/p>\n

\n PLoS computational biology, \n 2020<\/span>\n <\/p>\n\n

\n doi:10.1371\/journal.pcbi.1007976.\n <\/p>\n <\/article>\n

\n

\n \n Ten simple rules for making training materials FAIR.\n <\/a>\n <\/h3>\n

\n Garcia L, Batut B, Burke ML, Kuzak M, Psomopoulos F, Arcila R, Attwood TK, Beard N, Carvalho-Silva D, Dimopoulos AC, Del Angel VD, Dumontier M, Gurwitz KT, Krause R, McQuilton P, Le Pera L, Morgan SL, Rauste P, Via A, Kahlem P, Rustici G, van Gelder CWG, Palagi PM.\n <\/p>\n

\n PLoS computational biology, \n 2020<\/span>\n <\/p>\n\n

\n doi:10.1371\/journal.pcbi.1007854.\n <\/p>\n <\/article>\n

\n

\n \n Microarray-Based Quality Assessment as a Supporting Criterion for de novo Transcriptome Assembly Selection.\n <\/a>\n <\/h3>\n

\n Carvajal-Lopez P, Von Borstel FD, Torres A, Rustici G, Gutierrez J, Romero-Vivas E.\n <\/p>\n

\n IEEE\/ACM transactions on computational biology and bioinformatics, \n 2018<\/span>\n <\/p>\n\n

\n doi:10.1109\/tcbb.2018.2860997.\n <\/p>\n <\/article>\n

\n

\n \n EMBL-EBI resources: An introduction\n <\/a>\n <\/h3>\n

\n Gopalasingam P.\n <\/p>\n

\n \n 2018<\/span>\n <\/p>\n\n

\n doi:10.6019\/tol.intr-ebi-res-w.2015.00001.1.\n <\/p>\n <\/article>\n

\n

\n \n 10th Anniversary Treasure Hunt\n <\/a>\n <\/h3>\n

\n Armstrong D, Burke M, Huerta L, Levchenko M, Mitchell A, Morgan S, Mugumbate G, Mutowo P, Orchard S, Perry E, Pundir S, Richardson L, Tang A.\n <\/p>\n

\n \n 2017<\/span>\n <\/p>\n\n

\n doi:10.6019\/tol.treasure-t.2017.00001.1.\n <\/p>\n <\/article>\n

\n

\n \n Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat.\n <\/a>\n <\/h3>\n

\n Leach LJ, Belfield EJ, Jiang C, Brown C, Mithani A, Harberd NP.\n <\/p>\n

\n BMC genomics, \n 2014<\/span>\n <\/p>\n\n

\n doi:10.1186\/1471-2164-15-276.\n <\/p>\n <\/article>\n

\n

\n \n Microarray-based ultra-high resolution discovery of genomic deletion mutations.\n <\/a>\n <\/h3>\n

\n Belfield EJ, Brown C, Gan X, Jiang C, Baban D, Mithani A, Mott R, Ragoussis J, Harberd NP.\n <\/p>\n

\n BMC genomics, \n 2014<\/span>\n <\/p>\n\n

\n doi:10.1186\/1471-2164-15-224.\n <\/p>\n <\/article>\n <\/div>","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"template-publications.php","meta":{"_acf_changed":false,"footnotes":""},"embl_taxonomy":[],"class_list":["post-147","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/training\/wp-json\/wp\/v2\/pages\/147","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/training\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/training\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/training\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/training\/wp-json\/wp\/v2\/comments?post=147"}],"version-history":[{"count":6,"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/training\/wp-json\/wp\/v2\/pages\/147\/revisions"}],"predecessor-version":[{"id":1496,"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/training\/wp-json\/wp\/v2\/pages\/147\/revisions\/1496"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/training\/wp-json\/wp\/v2\/media?parent=147"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/training\/wp-json\/wp\/v2\/embl_taxonomy?post=147"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}