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Featured Article
https://doi.org/10.12688/f1000research.24427.1
Research Article metrics
Annotation and curation of human genomic variations: an ELIXIR Implementation Study
[version 1; peer review: 2 approved with reservations]
Alessia David, Valérie Barbié, Marcella Attimonelli, Roberto Preste, Enni Makkonen, Heidi Marjonen, Mats Lindstedt, Kati Kristiansson, Sarah E. Hunt, Fiona Cunningham, Ilkka Lappalainen, Michael J.E. Sternberg
Peer Reviewers Invited
  • Funders
  • ELIXIR
  • Imperial College London
  • European Molecular Biology Laboratory
PUBLISHED 08 Oct 2020
https://doi.org/10.12688/f1000research.168288.1
Opinion Article metrics
Fostering and sustaining collaborative innovation: Insights from ELIXIR Europe's life science Communities
[version 1; peer review: 1 approved]
Clare Garrard, Katharina F Heil, Maria Cristina Aspromonte, Bérénice Batut, Magda Chegkazi, John M Hancock, Elaine Harrison, Naveed Ishaque, Giselle Kerry, Eija Korpelainen, Jerry Lanfear, Corinne Martin, Sebastian Schaaf, Serena Scollen, Yun-Yun Tseng, Sameer Velankar, Juan Antonio Vizcaíno, Robert M Waterhouse, Egon Willighagen, Niklas Blomberg, Peter Maccallum
Peer Reviewers Amany Gouda-Vossos
  • Funder
  • This work was funded by ELIXIR, the research infrastructure for life science data. Specifically, parts of the work received funding from the European Union’s research and innovation programme under grant agreement 871075 (CONVERGE) and 676559 (EXCELERATE).
PUBLISHED 09 Sep 2025
https://doi.org/10.12688/f1000research.144515.2
Opinion Article metrics
Revised
Establishing the ELIXIR Microbiome Community
[version 2; peer review: 2 approved, 1 approved with reservations]
Robert D. Finn, Bachir Balech, Josephine Burgin, Physilia Chua, Erwan Corre, Cymon J. Cox, Claudio Donati, Vitor Martins dos Santos, Bruno Fosso, John Hancock, Katharina F. Heil, Naveed Ishaque, Varsha Kale, Benoit J. Kunath, Claudine Médigue, Teresa Nogueira, Evangelos Pafilis, Graziano Pesole, Lorna Richardson, Monica Santamaria, Nikolaos Strepis, Tim Van Den Bossche, Juan Antonio Vizcaíno, Haris Zafeiropoulos, Nils P. Willassen, Eric Pelletier, Bérénice Batut
Peer Reviewers Charlie Pauvert; Almut Heinken; Lauren Lui
  • Funders
  • CnrBiomics
  • Fundação para a Ciência e a Tecnologia
  • ELIXIRxNextGenIT
  • National Research Fund Luxembourg
  • Research Foundation Flanders
  • Biotechnology and Biological Sciences Research Council
LATEST VERSION PUBLISHED 08 Sep 2025
https://doi.org/10.12688/f1000research.166538.1
Review metrics
White paper: standards for handling and analyzing plant pan-genomes
[version 1; peer review: 2 approved with reservations]
Marc C. Heuermann, Pedro Barros, Sebastian Beier, Heidrun Gundlach, Jorge Alvarez-Jarreta, Keywan Hassani-Pak, Patrick König, Anne Fiebig, Tim Godec, Kristina Gruden, Nadja Nolte, Marko Petek, Uwe Scholz, Maja Zagorščak, Klaas Vandepoele, Michiel Van Bel
Peer Reviewers Sunil Kumar Sahu; Xiaoming Xie
  • Funders
  • ELIXIR under the call for proposals on Biodiversity, Food Safety and Pathogens
  • Federal Ministry of Education and Research
PUBLISHED 28 Jul 2025
https://doi.org/10.12688/f1000research.158264.3
Method Article metrics
Revised
Using text-mining to measure the scientific impact and legacy of ELIXIR, a distributed research infrastructure for life science data
[version 3; peer review: 2 approved, 1 approved with reservations]
Francesca De Leo, Erika Balsyte, Robert Petryszak, Marilena D’Ambrosio, Chiara Bruno, Martin Cook, Ivan Mičetić, Corinne S. Martin
Peer Reviewers Helen M. Berman; Shuichi Kawashima; Alfonso Valencia
  • Funders
  • Italian Ministry for Universities and Research (National Recovery and Resilience Plan M4C2)
  • European Union (Horizon Programmes)
  • ELIXIR, the research infrastructure for life science data
LATEST VERSION PUBLISHED 22 Apr 2025
https://doi.org/10.12688/f1000research.146301.2
Opinion Article metrics
Revised
A research data management (RDM) community for ELIXIR
[version 2; peer review: 2 approved]
Flora D'Anna, Niclas Jareborg, Mijke Jetten, Minna Ahokas, Pinar Alper, Robert Andrews, Korbinian Bösl, Teresa D’Altri, Daniel Faria, Nazeefa Fatima, Siiri Fuchs, Clare Garrard, Wei Gu, Katharina F. Heil, Yvonne Kallberg, Flavio Licciulli, Nils-Christian Lübke, Ana M. P. Melo, Ivan Mičetić, Jorge Oliveira, Anastasis Oulas, Patricia M. Palagi, Krzysztof Poterlowicz, Xenia Perez-Sitja, Patrick Ruch, Susanna-Assunta Sansone, Helena Schnitzer, Celia van Gelder, Thanasis Vergoulis, Daniel Wibberg, Ulrike Wittig, Brane Leskošek, Jiri Vondrasek, Munazah Andrabi
Peer Reviewers Jeff Christiansen; Sara El Gebali
  • Funders
  • ELIXIR-CONVERGE: European Union’s Horizon 2020 programme
  • FAIRplus: European Union’s Horizon 2020 programme
LATEST VERSION PUBLISHED 30 Sep 2024
https://doi.org/10.12688/f1000research.153895.1
Opinion Article metrics
From the establishment of a national bioinformatics society to the development of a national bioinformatics infrastructure
[version 1; peer review: 3 approved with reservations]
Bogdan Mirăuță, Cătălina Zenoaga-Barbăroșie, Monica Abrudan, Marius Mihășan, Mădălina Giurgiu, Daria Mihalachi, Michalis-Daniel Lazăr, RSBI Members, Horia L. Banciu
Peer Reviewers Francis Ouellette; Federico Zambelli; Carol Goble
  • Funder
  • EEA Grants/Norway Grants (Bioinformatics Capacity Building Human Genomics, an RSBI and ELIXIR Norway bilateral project)
PUBLISHED 03 Sep 2024
https://doi.org/10.12688/f1000research.126734.2
Opinion Article metrics
Revised
Systems Biology in ELIXIR: modelling in the spotlight
[version 2; peer review: 2 approved, 1 approved with reservations]
Vitor Martins dos Santos, Mihail Anton, Barbara Szomolay, Marek Ostaszewski, Ilja Arts, Rui Benfeitas, Victoria Dominguez Del Angel, Elena Domínguez-Romero, Polonca Ferk, Dirk Fey, Carole Goble, Martin Golebiewski, Kristina Gruden, Katharina F. Heil, Henning Hermjakob, Pascal Kahlem, Maria I. Klapa, Jasper Koehorst, Alexey Kolodkin, Martina Kutmon, Brane Leskošek, Sébastien Moretti, Wolfgang Müller, Marco Pagni, Tadeja Rezen, Miguel Rocha, Damjana Rozman, David Šafránek, William T. Scott, Rahuman S. Malik Sheriff, Maria Suarez Diez, Kristel Van Steen, Hans V Westerhoff, Ulrike Wittig, Katherine Wolstencroft, Anze Zupanic, Chris T. Evelo, John M. Hancock
Peer Reviewers Yoram Vodovotz; Herbert Sauro; Ioannis Androulakis
  • Funder
  • EPAnEk-NSRF
LATEST VERSION PUBLISHED 31 May 2024
https://doi.org/10.12688/f1000research.133724.2
Opinion Article metrics
Revised
The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity
[version 2; peer review: 3 approved]
Robert M. Waterhouse, Anne-Françoise Adam-Blondon, Bachir Balech, Endre Barta, Physilia Ying Shi Chua, Valeria Di Cola, Katharina F. Heil, Graham M. Hughes, Lars S. Jermiin, Matúš Kalaš, Jerry Lanfear, Evangelos Pafilis, Patricia M. Palagi, Aristotelis C. Papageorgiou, Joana Paupério, Fotis Psomopoulos, Niels Raes, Josephine Burgin, Toni Gabaldón
Peer Reviewers Patrick Comer; Abigail Benson and Stephen Formel; Cher FY Chow
  • Funders
  • Swiss State Secretariat for Education, Research and Innovation (SERI)
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
LATEST VERSION PUBLISHED 22 May 2024
https://doi.org/10.12688/f1000research.129720.2
Opinion Article metrics
Revised
Ten recommendations for organising bioimaging data for archival
[version 2; peer review: 3 approved, 1 approved with reservations]
Paul K. Korir, Andrii Iudin, Sriram Somasundharam, Simone Weyand, Osman Salih, Matthew Hartley, Ugis Sarkans, Ardan Patwardhan, Gerard J. Kleywegt
Peer Reviewers Sjors Scheres; Kenneth H. L. Ho; Sylvia Emmanuelle Le Dévédec; William T. Katz and Virginia Scarlett
  • Funders
  • EMBL
  • UKRI-MRC with co-funding from UKRI-BBSRC
  • Wellcome Trust
LATEST VERSION PUBLISHED 27 Feb 2024
https://doi.org/10.12688/f1000research.142165.1
Research Article metrics AWAITING PEER REVIEW
A survey into the contribution of regional/national pathogen data platforms and on the resources needed to develop and maintain them
[version 1; peer review: awaiting peer review]
Aitana Neves, Nils P Willassen, Erik Hjerde, Isabel Cuesta, Corinne S Martin, Heleri Inno, Diana Pilvar, Kim Ng, David Salgado, Jacques van Helden, Wei Gu, Marina Popleteeva, Joaquin Dopazo, Timotej Šuri, Jan Pačes, Cezary Mazurek, Krzysztof Kurowski, Natalia Koralewska, Gunter Maier, ELIXIR CONVERGE WP9 community
Peer Reviewers Invited
  • Funder
  • Horizon 2020
PUBLISHED 14 Dec 2023
https://doi.org/10.12688/f1000research.74502.2
Opinion Article metrics
Revised
ELIXIR and Toxicology: a community in development
[version 2; peer review: 2 approved]
Marvin Martens, Rob Stierum, Emma L. Schymanski, Chris T. Evelo, Reza Aalizadeh, Hristo Aladjov, Kasia Arturi, Karine Audouze, Pavel Babica, Karel Berka, Jos Bessems, Ludek Blaha, Evan E. Bolton, Montserrat Cases, Dimitrios Ε. Damalas, Kirtan Dave, Marco Dilger, Thomas Exner, Daan P. Geerke, Roland Grafström, Alasdair Gray, John M. Hancock, Henner Hollert, Nina Jeliazkova, Danyel Jennen, Fabien Jourdan, Pascal Kahlem, Jana Klanova, Jos Kleinjans, Todor Kondic, Boï Kone, Iseult Lynch, Uko Maran, Sergio Martinez Cuesta, Hervé Ménager, Steffen Neumann, Penny Nymark, Herbert Oberacher, Noelia Ramirez, Sylvie Remy, Philippe Rocca-Serra, Reza M. Salek, Brett Sallach, Susanna-Assunta Sansone, Ferran Sanz, Haralambos Sarimveis, Sirarat Sarntivijai, Tobias Schulze, Jaroslav Slobodnik, Ola Spjuth, Jonathan Tedds, Nikolaos Thomaidis, Ralf J.M. Weber, Gerard J.P. van Westen, Craig E. Wheelock, Antony J. Williams, Hilda Witters, Barbara Zdrazil, Anže Županič, Egon L. Willighagen
Peer Reviewers Christopher Southan; Marta Eide
  • Funders
  • Eesti Teadusagentuur
  • Bundesministerium für Bildung und Forschung
  • LIFE programme
  • Miguel Servet
  • Agence Nationale de la Recherche
  • Horizon 2020
  • Stiftelsen Forska Utan Djurförsök
  • Wellcome Trust
  • Umweltbundesamt
  • H2020 Marie Skłodowska-Curie Actions
  • European Regional Development Fund
LATEST VERSION PUBLISHED 03 Oct 2023
https://doi.org/10.12688/f1000research.128167.2
Policy Brief metrics
Revised
The road to success: drawing parallels between 'road' and 'research data' infrastructures to foster understanding between service providers, funders and policymakers
[version 2; peer review: 2 approved]
Rob W.W. Hooft, Elaine Harrison, Corinne S. Martin
Peer Reviewers Frédéric Sgard; Silvia Vignetti
  • Funders
  • ELIXIR
  • Horizon 2020
LATEST VERSION PUBLISHED 22 Aug 2023
https://doi.org/10.12688/f1000research.51747.1
Opinion Article metrics
The future of food and nutrition in ELIXIR
[version 1; peer review: 2 approved with reservations]
Bachir Balech, Lorraine Brennan, Enrique Carrillo de Santa Pau, Duccio Cavalieri, Susan Coort, Domenica D’Elia, Lars Ove Dragsted, Tome Eftimov, Chris T. Evelo, Polonca Ferk, Paul Finglas, Agnese Gori, John Hancock, Matúš Kalaš, Barbara Koroušić Seljak, Carl Lachat, Brane Leskošek, Edoardo Pasolli, Graziano Pesole, Karl Presser, Anna Sandionigi, Monica Santamaria, Duygu Dede Şener, Maria Traka, Guy Vergères, Karin L. Zimmermann, Jildau Bouwman
Peer Reviewers Graham King; Anu Bansal
PUBLISHED 25 Aug 2022
https://doi.org/10.12688/f1000research.108804.2
Opinion Article metrics
Revised
Making European performance and impact assessment frameworks for research infrastructures glocal
[version 2; peer review: 2 approved]
Ana M.P. Melo, Sofia Oliveira, Jorge S. Oliveira, Corinne S. Martin, Ricardo B. Leite
Peer Reviewers Eugénio Campos Ferreira; Enrico Guarini and Marialuisa Lavitrano
  • Funders
  • ELIXIR
  • H2020 Research Infrastructures
  • Foundation for Science and Technology - Portugal
LATEST VERSION PUBLISHED 02 Aug 2022
https://doi.org/10.12688/f1000research.73825.2
Opinion Article metrics
Revised
Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR
[version 2; peer review: 2 approved]
Robert M. Waterhouse, Anne-Françoise Adam-Blondon, Donat Agosti, Petr Baldrian, Bachir Balech, Erwan Corre, Robert P. Davey, Henrik Lantz, Graziano Pesole, Christian Quast, Frank Oliver Glöckner, Niels Raes, Anna Sandionigi, Monica Santamaria, Wouter Addink, Jiri Vohradsky, Amandine Nunes-Jorge, Nils Peder Willassen, Jerry Lanfear
Peer Reviewers Donald Hobern; Anders Andersson
  • Funders
  • Grantová Agentura České Republiky
  • Norges Forskningsråd
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
  • Ministry of Education, Youth and Sports of the Czech Republic
  • Horizon 2020
  • Arcadia Fund
  • Biotechnology and Biological Sciences Research Council
LATEST VERSION PUBLISHED 01 Aug 2022
https://doi.org/10.12688/f1000research.122312.1
Opinion Article metrics
Community-driven ELIXIR activities in single-cell omics
[version 1; peer review: 2 approved with reservations]
Paulo Czarnewski, Ahmed Mahfouz, Raffaele A. Calogero, Patricia M. Palagi, Laura Portell-Silva, Asier Gonzalez-Uriarte, Charlotte Soneson, Tony Burdett, Barbara Szomolay, Pavankumar Videm, Hans-Rudolf Hotz, Irene Papatheodorou, John M. Hancock, Björn Grüning, Wilfried Haerty, Roland Krause, Salvador Capella-Gutierrez, Brane Leskošek, Luca Alessandri, Maddalena Arigoni, Tadeja Rezen, Alexander Botzki, Polonca Ferk, Jessica Lindvall, Katharina F. Heil, Naveed Ishaque, Eija Korpelainen
Peer Reviewers Xiao-Yang Zhao; Feng Zhu
  • Funders
  • ELIXIR
  • Knut och Alice Wallenbergs Stiftelse
PUBLISHED 29 Jul 2022
https://doi.org/10.12688/f1000research.109080.2
Opinion Article metrics
Revised
Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR
[version 2; peer review: 2 approved]
Sebastian Beier, Anne Fiebig, Cyril Pommier, Isuru Liyanage, Matthias Lange, Paul J. Kersey, Stephan Weise, Richard Finkers, Baron Koylass, Timothee Cezard, Mélanie Courtot, Bruno Contreras-Moreira, Guy Naamati, Sarah Dyer, Uwe Scholz
Peer Reviewers Boas Pucker and Alenka Hafner; Micha M. Bayer
  • Funders
  • ELIXIR
  • Bundesministerium für Bildung und Forschung
  • Horizon 2020 Framework Programme
LATEST VERSION PUBLISHED 19 May 2022
https://doi.org/10.12688/f1000research.74024.1
Research Article metrics
eTRANSAFE: Building a sustainable framework to share reproducible drug safety knowledge with the public domain
[version 1; peer review: 2 approved]
Sirarat Sarntivijai, Niklas Blomberg, Katharina B. Lauer, Katharine Briggs, Thomas Steger-Hartmann, Johan van der Lei, John-Michael Sauer, Richard Liwski, Miranda Mourby, Montse Camprubi, The eTRANSAFE Consortium
Peer Reviewers Merran Smith; Ishwar Chandramouliswaran
  • Funders
  • Innovative Medicines Initiative
  • Horizon 2020
PUBLISHED 07 Mar 2022
https://doi.org/10.12688/f1000research.54159.1
Opinion Article metrics
Perspectives on automated composition of workflows in the life sciences
[version 1; peer review: 2 approved]
Anna-Lena Lamprecht, Magnus Palmblad, Jon Ison, Veit Schwämmle, Mohammad Sadnan Al Manir, Ilkay Altintas, Christopher J. O. Baker, Ammar Ben Hadj Amor, Salvador Capella-Gutierrez, Paulos Charonyktakis, Michael R. Crusoe, Yolanda Gil, Carole Goble, Timothy J. Griffin, Paul Groth, Hans Ienasescu, Pratik Jagtap, Matúš Kalaš, Vedran Kasalica, Alireza Khanteymoori, Tobias Kuhn, Hailiang Mei, Hervé Ménager, Steffen Möller, Robin A. Richardson, Vincent Robert, Stian Soiland-Reyes, Robert Stevens, Szoke Szaniszlo, Suzan Verberne, Aswin Verhoeven, Katherine Wolstencroft
Peer Reviewers Pinar Alper; Rafael Ferreira da Silva
  • Funder
  • European Commission Horizon 2020 Framework Programme
PUBLISHED 07 Sep 2021
https://doi.org/10.12688/f1000research.54071.1
Data Note metrics
Organizing knowledge to enable faster data interpretation in COVID-19 research
[version 1; peer review: 2 approved with reservations]
Joseph Hearnshaw, Marco Brandizi, Ajit Singh, Chris Rawlings, Keywan Hassani-Pak
Peer Reviewers Justin Reese; Keith Hall
  • Funder
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 30 Jul 2021
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