Strengthening bioinformatics education: e-learning initiatives across ELIXIR Nodes and Communities.

Zahn-Zabala M, Ahokas M, Batut B, Beier S, Botzki A, Cardona A, Gruden K, Korpelainen E, Lehtivaara M, Leskosek B, Mirăuță B, Mishra A, Pommier C, Poterlowicz K, Rasche H, Sand O, Waterhouse R, Wittke S, Zenoaga-Barbăroșie C, Anton M, Wibberg D.

F1000Research, 2025

doi:10.12688/f1000research.173116.1.

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2024.

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.

Nucleic acids research, 2025

doi:10.1093/nar/gkae1089.

Competencies for bioinformatics core facility scientists: extension of the ISCB competency framework for bioinformatics.

Lloret-Llinares M, Carvajal-López P, Downing T, Gogol M, Ho Sui S, Nonell L, Paladin L, Reid AJ, Pomann GM, Brooksbank C.

Bioinformatics advances, 2025

doi:10.1093/bioadv/vbaf206.

Gene–environment interactions in shaping human health and disease

Foreman AL, Araújo D, Mishra A.

2024

doi:10.6019/tol.gene-envt-interaction2024-t.2024.00001.1.

Molecular building blocks of life

Mishra A.

2024

doi:10.6019/tol.molbuildblocks-t.2024.00001.1.

Making bioinformatics training FAIR: the EMBL-EBI training portal.

Swan AL, Broadbent A, Singh Gaur P, Mishra A, Gurwitz K, Mithani A, Morgan SL, Malhotra G, Brooksbank C.

Frontiers in bioinformatics, 2024

doi:10.3389/fbinf.2024.1347168.

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2023.

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.

Nucleic acids research, 2024

doi:10.1093/nar/gkad1088.

The ISCB competency framework v. 3: a revised and extended standard for bioinformatics education and training.

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

Bioinformatics advances, 2024

doi:10.1093/bioadv/vbae166.

Abalone peptide increases stress resilience and cost-free longevity via SKN-1-governed transcriptional metabolic reprogramming in C. elegans.

Wang Q, Wang L, Huang Z, Xiao Y, Liu M, Liu H, Yu Y, Liang M, Luo N, Li K, Mishra A, Huang Z.

Aging cell, 2023

doi:10.1111/acel.14046.

Data-driven plant sciences: A curated collection of EMBL-EBI on-demand training

Mishra A.

2023

doi:10.6019/tol.datadrivenplantsciences-t.2023.00001.1.

Making bioinformatics training FAIR: the EMBL-EBI training portal

Swan A, Broadbent A, Gaur PS, Mishra A, Gurwitz K, Mithani A, Morgan S, Malhotra G, Brooksbank C.

Preprint, 2023

doi:10.5281/zenodo.10391149.

"Be sustainable": EOSC-Life recommendations for implementation of FAIR principles in life science data handling.

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, Grüning 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, Sánchez-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.

The EMBO journal, 2023

doi:10.15252/embj.2023115008.

Methods in Bioinformatics

Larionov A, Lock A, Luck K, Ly T, Mishra A, Moore B, Perfetto L, Rausch T, Tischer C.

2022

doi:10.6019/tol.methodsbioinformatics-t.2022.00001.1.

Introduction to multiomics data integration and visualisation

Cortes-Ciriano I, Korcsmáros T, Mishra A, Petsalaki E.

2022

doi:10.6019/tol.multiomicsintegration22-t.2022.00001.1.

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

Huang Z, Ma L, Mishra A, Turnbull JE, Tu H.

Frontiers in pharmacology, 2022

doi:10.3389/fphar.2022.1029752.

Cancer genomics: course materials

Gerstung M, Mishra A.

2022

doi:10.6019/tol.cancergenomics-t.2021.00001.1.

Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses.

Bacon W, Holinski A, Pujol M, Wilmott M, Morgan SL, European Molecular Biology Laboratory—European Bioinformatics Institute Training Team.

PLoS computational biology, 2022

doi:10.1371/journal.pcbi.1010220.

Correction: Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries.

Moore B, Carvajal-López 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.

PLoS computational biology, 2022

doi:10.1371/journal.pcbi.1010197.

Introduction to CATH database: Quick tour

Waman V, Silitoe I, Mishra A, Orengo C.

2021

doi:10.6019/tol.cathdb-t.2021.00001.1.

A guide to...: Introducing concepts and resources in bioinformatics

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’Donovan C, Harrus D, Zaru R, Pearce M, Eduardo Ribas C, Sweeney B, Swan A, Mishra A.

2021

doi:10.6019/tol.guidewebinarseries-t.2021.00001.1.

Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries.

Moore B, Carvajal-López 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.

PLoS computational biology, 2021

doi:10.1371/journal.pcbi.1009218.

Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops.

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, Vázquez-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.

PLoS computational biology, 2021

doi:10.1371/journal.pcbi.1009056.

Wheat genomics and breeding: bridging the gap.

Hussain B, Akpınar 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, Gálvez 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.

Preprint, 2021

doi:10.31220/agrirxiv.2021.00039.

Human epidermal stem cell differentiation is modulated by specific lipid subspecies.

Vietri Rudan M, Mishra A, Klose C, Eggert US, Watt FM.

Proceedings of the National Academy of Sciences of the United States of America, 2020

doi:10.1073/pnas.2011310117.

A framework to assess the quality and impact of bioinformatics training across ELIXIR.

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, Leskošek B, Lindvall JM, Marek D, Martinez PA, Muyldermans T, Nygård S, Palagi PM, Peterson H, Psomopoulos F, Spiwok V, van Gelder CWG, Via A, Vidak M, Wibberg D, Morgan SL, Rustici G.

PLoS computational biology, 2020

doi:10.1371/journal.pcbi.1007976.

Ten simple rules for making training materials FAIR.

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.

PLoS computational biology, 2020

doi:10.1371/journal.pcbi.1007854.

Microarray-Based Quality Assessment as a Supporting Criterion for de novo Transcriptome Assembly Selection.

Carvajal-Lopez P, Von Borstel FD, Torres A, Rustici G, Gutierrez J, Romero-Vivas E.

IEEE/ACM transactions on computational biology and bioinformatics, 2018

doi:10.1109/tcbb.2018.2860997.

EMBL-EBI resources: An introduction

Gopalasingam P.

2018

doi:10.6019/tol.intr-ebi-res-w.2015.00001.1.

10th Anniversary Treasure Hunt

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.

2017

doi:10.6019/tol.treasure-t.2017.00001.1.

Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat.

Leach LJ, Belfield EJ, Jiang C, Brown C, Mithani A, Harberd NP.

BMC genomics, 2014

doi:10.1186/1471-2164-15-276.

Microarray-based ultra-high resolution discovery of genomic deletion mutations.

Belfield EJ, Brown C, Gan X, Jiang C, Baban D, Mithani A, Mott R, Ragoussis J, Harberd NP.

BMC genomics, 2014

doi:10.1186/1471-2164-15-224.