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1-20 of 46 ARTICLES
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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 Lina Ma; Osamu Ogasawara
  • Funders
  • ELIXIR
  • Imperial College London
  • European Molecular Biology Laboratory
PUBLISHED 08 Oct 2020
https://doi.org/10.12688/f1000research.51747.1
Opinion Article metrics
The future of food and nutrition in ELIXIR [version 1; peer review: 1 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 Reviewer Graham King
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 AWAITING PEER REVIEW
Community-driven ELIXIR activities in single-cell omics [version 1; peer review: awaiting peer review]
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 Invited
  • 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.74502.1
Opinion Article metrics
ELIXIR and Toxicology: a community in development [version 1; peer review: 1 approved, 1 approved with reservations]
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
  • H2020 Marie Skłodowska-Curie Actions
  • Umweltbundesamt
  • European Regional Development Fund
PUBLISHED 08 Nov 2021
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
https://doi.org/10.12688/f1000research.28449.1
Opinion Article metrics
Recommendations for the FAIRification of genomic track metadata [version 1; peer review: 2 approved]
Sveinung Gundersen, Sanjay Boddu, Salvador Capella-Gutierrez, Finn Drabløs, José M. Fernández, Radmila Kompova, Kieron Taylor, Dmytro Titov, Daniel Zerbino, Eivind Hovig
Peer Reviewers Max Haeussler; Granger Sutton
  • Funders
  • ELIXIR
  • ELIXIR Norway
  • ELIXIR Spain
  • INB
  • EMBL-EBI
PUBLISHED 01 Apr 2021
https://doi.org/10.12688/f1000research.27188.1
Software Tool Article metrics
isa4j: a scalable Java library for creating ISA-Tab metadata [version 1; peer review: 2 approved]
Dennis Psaroudakis, Feng Liu, Patrick König, Uwe Scholz, Astrid Junker, Matthias Lange, Daniel Arend
Peer Reviewers Massimiliano Izzo; Nils Hoffmann
  • Funders
  • ELIXIR
  • German Ministry of Education and Research (BMBF)
PUBLISHED 03 Dec 2020
https://doi.org/10.12688/f1000research.25413.2
Research Article metrics
Revised
Biocuration - mapping resources and needs [version 2; peer review: 2 approved]
Alexandra Holinski, Melissa L. Burke, Sarah L. Morgan, Peter McQuilton, Patricia M. Palagi
Peer Reviewers Tanya Berardini; Luana Licata
  • Funder
  • ELIXIR
LATEST VERSION PUBLISHED 02 Dec 2020
https://doi.org/10.12688/f1000research.24956.2
Software Tool Article metrics
Revised
gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler [version 2; peer review: 2 approved]
Liis Kolberg, Uku Raudvere, Ivan Kuzmin, Jaak Vilo, Hedi Peterson
Peer Reviewers Egon L. Willighagen; Ewy Mathe
  • Funders
  • Eesti Teadusagentuur
  • Seventh Framework Programme
  • European Regional Development Fund
LATEST VERSION PUBLISHED 17 Nov 2020
https://doi.org/10.12688/f1000research.24887.1
Opinion Article metrics
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research [version 1; peer review: 2 approved]
David Salgado, Irina M. Armean, Michael Baudis, Sergi Beltran, Salvador Capella-Gutierrez, Denise Carvalho-Silva, Victoria Dominguez Del Angel, Joaquin Dopazo, Laura I. Furlong, Bo Gao, Leyla Garcia, Dietlind Gerloff, Ivo Gut, Attila Gyenesei, Nina Habermann, John M. Hancock, Marc Hanauer, Eivind Hovig, Lennart F. Johansson, Thomas Keane, Jan Korbel, Katharina B. Lauer, Steve Laurie, Brane Leskošek, David Lloyd, Tomas Marques-Bonet, Hailiang Mei, Katalin Monostory, Janet Piñero, Krzysztof Poterlowicz, Ana Rath, Pubudu Samarakoon, Ferran Sanz, Gary Saunders, Daoud Sie, Morris A. Swertz, Kirill Tsukanov, Alfonso Valencia, Marko Vidak, Cristina Yenyxe González, Bauke Ylstra, Christophe Béroud
Peer Reviewers Antonio Rausell; Andrew Lonie
  • Funder
  • ELIXIR Hub
PUBLISHED 13 Oct 2020
https://doi.org/10.12688/f1000research.20244.2
Opinion Article metrics
Revised
The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR [version 2; peer review: 2 approved]
Daniel Wibberg, Bérénice Batut, Peter Belmann, Jochen Blom, Frank Oliver Glöckner, Björn Grüning, Nils Hoffmann, Nils Kleinbölting, René Rahn, Maja Rey, Uwe Scholz, Malvika Sharan, Andreas Tauch, Ulrike Trojahn, Björn Usadel, Oliver Kohlbacher
Peer Reviewers Roland Krause; Loredana Le Pera and Allegra Via
  • Funders
  • Bundesministerium für Bildung und Forschung
  • Ministerium für Innovation, Wissenschaft und Forschung des Landes Nordrhein-Westfalen
LATEST VERSION PUBLISHED 11 Sep 2020
https://doi.org/10.12688/f1000research.20559.1
Opinion Article metrics
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community) [version 1; peer review: 1 approved, 3 approved with reservations]
Christine Orengo, Sameer Velankar, Shoshana Wodak, Vincent Zoete, Alexandre M.J.J. Bonvin, Arne Elofsson, K. Anton Feenstra, Dietland L. Gerloff, Thomas Hamelryck, John M. Hancock, Manuela Helmer-Citterich, Adam Hospital, Modesto Orozco, Anastassis Perrakis, Matthias Rarey, Claudio Soares, Joel L. Sussman, Janet M. Thornton, Pierre Tuffery, Gabor Tusnady, Rikkert Wierenga, Tiina Salminen, Bohdan Schneider
Peer Reviewers Sjoerd Jacob De Vries and Isaure Chauvot de Beauchene; Silvio C.E Tosatto; Roland L. Dunbrack; Andras Fiser
  • Funder
  • ELIXIR
PUBLISHED 22 Apr 2020
https://doi.org/10.12688/f1000research.20136.1
Opinion Article metrics
An intrinsically disordered proteins community for ELIXIR [version 1; peer review: 2 approved]
Norman E. Davey, M. Madan Babu, Martin Blackledge, Alan Bridge, Salvador Capella-Gutierrez, Zsuzsanna Dosztanyi, Rachel Drysdale, Richard J. Edwards, Arne Elofsson, Isabella C. Felli, Toby J. Gibson, Aleksandras Gutmanas, John M. Hancock, Jen Harrow, Desmond Higgins, Cy M. Jeffries, Philippe Le Mercier, Balint Mészáros, Marco Necci, Cedric Notredame, Sandra Orchard, Christos A. Ouzounis, Rita Pancsa, Elena Papaleo, Roberta Pierattelli, Damiano Piovesan, Vasilis J. Promponas, Patrick Ruch, Gabriella Rustici, Pedro Romero, Sirarat Sarntivijai, Gary Saunders, Benjamin Schuler, Malvika Sharan, Denis C. Shields, Joel L. Sussman, Jonathan A. Tedds, Peter Tompa, Michael Turewicz, Jiri Vondrasek, Wim F. Vranken, Bonnie Ann Wallace, Kanin Wichapong, Silvio C. E. Tosatto
Peer Reviewers Iva Pritisanac and Julie Forman-Kay; Osman Ugur Sezerman
  • Funders
  • Vetenskapsrådet
  • BBSRC
  • European Molecular Biology Laboratory
  • Carlsberg Foundation Distinguished Fellowship
  • National Institutes of Health
  • Israel I-CORE Project
  • ELIXIR
  • Danmarks Grundforskningsfond
  • Instruct-ERIC
  • Swiss Federal Government
  • Marie Skłodowska-Curie
  • COST Action BM1405 NGP-net
  • Wellcome Trust
PUBLISHED 15 Oct 2019
https://doi.org/10.12688/f1000research.19427.1
Research Article metrics
Understanding life sciences data curation practices via user research [version 1; peer review: 1 approved, 1 approved with reservations]
Aravind Venkatesan, Nikiforos Karamanis, Michele Ide-Smith, Jonathan Hickford, Johanna McEntyre
Peer Reviewers Lynette Hirschman; Cecilia N. Arighi
  • Funder
  • European Commission
PUBLISHED 11 Sep 2019
https://doi.org/10.12688/f1000research.14613.2
Software Tool Article metrics
Revised
CyTargetLinker app update: A flexible solution for network extension in Cytoscape [version 2; peer review: 2 approved]
Martina Kutmon, Friederike Ehrhart, Egon L. Willighagen, Chris T. Evelo, Susan L. Coort
Peer Reviewers Alex Gutteridge; John H. Morris
  • Funders
  • ELIXIR
  • Dutch Province of Limburg
LATEST VERSION PUBLISHED 13 Aug 2019
1-20 of 46 ARTICLES
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