All papers authored by Irene Papatheodorou
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2023
Heather R. Jackson 
,
Luca Miglietta,
Dominic Habgood-Coote,
Giselle D’Souza,
Priyen Shah,
Samuel Nichols,
Ortensia Vito ,
Oliver Powell,
Maisey Salina Davidson,
Chisato Shimizu,
Philipp K. A. Agyeman ,
Coco R. Beudeker,
Karen Brengel-Pesce,
Enitan D. Carrol,
Michael J. Carter
and 37 other authors
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,
Luca Miglietta,
Dominic Habgood-Coote,
Giselle D’Souza,
Priyen Shah,
Samuel Nichols,
Ortensia Vito ,
Oliver Powell,
Maisey Salina Davidson,
Chisato Shimizu,
Philipp K. A. Agyeman ,
Coco R. Beudeker,
Karen Brengel-Pesce,
Enitan D. Carrol,
Michael J. Carter
and 37 other authors
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2022
Matthew Thakur ,
Alex Bateman ,
Cath Brooksbank,
Mallory Freeberg ,
Melissa Harrison,
Matthew Hartley,
Thomas Keane ,
Gerard Kleywegt,
Andrew Leach ,
Mariia Levchenko ,
Sarah Morgan,
Ellen M. McDonagh ,
Sandra Orchard ,
Irene Papatheodorou ,
Sameer Velankar
and 4 other authors
,
Alex Bateman ,
Cath Brooksbank,
Mallory Freeberg ,
Melissa Harrison,
Matthew Hartley,
Thomas Keane ,
Gerard Kleywegt,
Andrew Leach ,
Mariia Levchenko ,
Sarah Morgan,
Ellen M. McDonagh ,
Sandra Orchard ,
Irene Papatheodorou ,
Sameer Velankar
and 4 other authors
EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2022
Download from doi.org
Noah Fahlgren ,
Muskan Kapoor ,
Galabina Yordanova ,
Irene Papatheodorou ,
Jamie Waese ,
Benjamin Cole ,
Peter Harrison ,
Doreen Ware ,
Timothy Tickle ,
Benedict Paten ,
Tony Burdett ,
Christine G. Elsik ,
Christopher K. Tuggle ,
Nicholas J. Provart
,
Muskan Kapoor ,
Galabina Yordanova ,
Irene Papatheodorou ,
Jamie Waese ,
Benjamin Cole ,
Peter Harrison ,
Doreen Ware ,
Timothy Tickle ,
Benedict Paten ,
Tony Burdett ,
Christine G. Elsik ,
Christopher K. Tuggle ,
Nicholas J. Provart
Toward a data infrastructure for the Plant Cell Atlas
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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
and 12 other authors
,
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
and 12 other authors
Community-driven ELIXIR activities in single-cell omics
Download from f1000research.com
Mathias Walzer ,
David García-Seisdedos ,
Ananth Prakash ,
Paul Brack,
Peter Crowther,
Robert L. Graham,
Nancy George,
Suhaib Mohammed,
Pablo Moreno ,
Irene Papathedourou,
Irene Papatheodorou ,
Simon J. Hubbard ,
Juan Antonio Vizcaíno
Download from www.nature.com
,
David García-Seisdedos ,
Ananth Prakash ,
Paul Brack,
Peter Crowther,
Robert L. Graham,
Nancy George,
Suhaib Mohammed,
Pablo Moreno ,
Irene Papathedourou,
Irene Papatheodorou ,
Simon J. Hubbard ,
Juan Antonio Vizcaíno
Download from www.nature.com
2021
Pablo Moreno ,
Silvie Fexova,
Nancy George,
Jonathan R. Manning ,
Zhichiao Miao ,
Suhaib Mohammed,
Alfonso Muñoz-Pomer,
Anja Fullgrabe ,
Yalan Bi,
Natassja Bush,
Haider Iqbal,
Upendra Kumbham,
Andrey Solovyev,
Lingyun Zhao,
Ananth Prakash
and 19 other authors
,
Silvie Fexova,
Nancy George,
Jonathan R. Manning ,
Zhichiao Miao ,
Suhaib Mohammed,
Alfonso Muñoz-Pomer,
Anja Fullgrabe ,
Yalan Bi,
Natassja Bush,
Haider Iqbal,
Upendra Kumbham,
Andrey Solovyev,
Lingyun Zhao,
Ananth Prakash
and 19 other authors
Expression Atlas update: gene and protein expression in multiple species
Download from doi.org
Chengxin Dai,
Anja Füllgrabe ,
Julianus Pfeuffer,
Elizaveta M. Solovyeva ,
Jingwen Deng,
Pablo Moreno ,
Selvakumar Kamatchinathan,
Deepti Jaiswal Kundu,
Nancy George ,
Silvie Fexova,
Björn Grüning ,
Melanie Christine Föll,
Johannes Griss ,
Marc Vaudel ,
Enrique Audain
and 25 other authors
,
Julianus Pfeuffer,
Elizaveta M. Solovyeva ,
Jingwen Deng,
Pablo Moreno ,
Selvakumar Kamatchinathan,
Deepti Jaiswal Kundu,
Nancy George ,
Silvie Fexova,
Björn Grüning ,
Melanie Christine Föll,
Johannes Griss ,
Marc Vaudel ,
Enrique Audain
and 25 other authors
A proteomics sample metadata representation for multiomics integration and big data analysis
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Nurlan Kerimov ,
James D. Hayhurst,
Kateryna Peikova,
Jonathan R. Manning ,
Peter Walter,
Liis Kolberg ,
Marija Samoviča,
Manoj Pandian Sakthivel,
Ivan Kuzmin ,
Stephen J. Trevanion,
Tony Burdett,
Simon Jupp ,
Helen Parkinson,
Irene Papatheodorou ,
Andrew D. Yates
and 2 other authors
,
James D. Hayhurst,
Kateryna Peikova,
Jonathan R. Manning ,
Peter Walter,
Liis Kolberg ,
Marija Samoviča,
Manoj Pandian Sakthivel,
Ivan Kuzmin ,
Stephen J. Trevanion,
Tony Burdett,
Simon Jupp ,
Helen Parkinson,
Irene Papatheodorou ,
Andrew D. Yates
and 2 other authors
A compendium of uniformly processed human gene expression and splicing quantitative trait loci
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Pablo Moreno ,
Ni Huang,
Jonathan R. Manning ,
Suhaib Mohammed,
Andrey Solovyev,
Krzysztof Polanski ,
Wendi Bacon,
Ruben Chazarra,
Carlos Talavera-López ,
Maria A. Doyle,
Guilhem Marnier,
Björn Grüning ,
Helena Rasche ,
Nancy George ,
Silvie Korena Fexova
and 8 other authors
,
Ni Huang,
Jonathan R. Manning ,
Suhaib Mohammed,
Andrey Solovyev,
Krzysztof Polanski ,
Wendi Bacon,
Ruben Chazarra,
Carlos Talavera-López ,
Maria A. Doyle,
Guilhem Marnier,
Björn Grüning ,
Helena Rasche ,
Nancy George ,
Silvie Korena Fexova
and 8 other authors
User-friendly, scalable tools and workflows for single-cell RNA-seq analysis
Download from www.nature.com
2020
Anja Füllgrabe ,
Nancy George,
Matthew Green,
Parisa Nejad ,
Laura Huerta ,
Norman Morrison ,
Richard H. Scheuermann ,
Deanne Taylor ,
Nicole Vasilevsky ,
Nils Gehlenborg ,
Jim Kent,
John Marioni ,
Sarah Teichmann ,
Irene Papatheodorou ,
Bruce Aronow
and 5 other authors
,
Nancy George,
Matthew Green,
Parisa Nejad ,
Laura Huerta ,
Norman Morrison ,
Richard H. Scheuermann ,
Deanne Taylor ,
Nicole Vasilevsky ,
Nils Gehlenborg ,
Jim Kent,
John Marioni ,
Sarah Teichmann ,
Irene Papatheodorou ,
Bruce Aronow
and 5 other authors
Guidelines for reporting single-cell RNA-seq experiments
Download from www.nature.com
Marcela K. Tello-Ruiz ,
Sushma Naithani ,
Parul Gupta,
Andrew Olson,
Sharon Wei,
Justin Preece,
Yinping Jiao,
Bo Wang,
Kapeel Chougule,
Priyanka Garg,
Justin Elser,
Sunita Kumari,
Vivek Kumar,
Bruno Contreras-Moreira,
Guy Naamati
and 14 other authors
,
Sushma Naithani ,
Parul Gupta,
Andrew Olson,
Sharon Wei,
Justin Preece,
Yinping Jiao,
Bo Wang,
Kapeel Chougule,
Priyanka Garg,
Justin Elser,
Sunita Kumari,
Vivek Kumar,
Bruno Contreras-Moreira,
Guy Naamati
and 14 other authors
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research
Download from academic.oup.com
Mehmet Tekman ,
Bérénice Batut ,
Alexander Ostrovsky ,
Christophe Antoniewski ,
Dave Clements ,
Fidel Ramirez ,
Graham J. Etherington ,
Hans-Rudolf Hotz ,
Jelle Scholtalbers ,
Jonathan R. Manning ,
Lea Bellenger ,
Maria A. Doyle ,
Mohammad Heydarian ,
Ni Huang ,
Nicola Soranzo
and 8 other authors
,
Bérénice Batut ,
Alexander Ostrovsky ,
Christophe Antoniewski ,
Dave Clements ,
Fidel Ramirez ,
Graham J. Etherington ,
Hans-Rudolf Hotz ,
Jelle Scholtalbers ,
Jonathan R. Manning ,
Lea Bellenger ,
Maria A. Doyle ,
Mohammad Heydarian ,
Ni Huang ,
Nicola Soranzo
and 8 other authors
A single-cell RNA-sequencing training and analysis suite using the Galaxy framework
Download from academic.oup.com
Mary J. Goldman ,
Junjun Zhang ,
Nuno A. Fonseca ,
Isidro Cortés-Ciriano ,
Qian Xiang ,
Brian Craft,
Elena Piñeiro-Yáñez ,
Brian D. O’Connor,
Wojciech Bazant,
Elisabet Barrera,
Alfonso Muñoz-Pomer,
Robert Petryszak,
Anja Füllgrabe ,
Fatima Al-Shahrour ,
Maria Keays
and 9 other authors
,
Junjun Zhang ,
Nuno A. Fonseca ,
Isidro Cortés-Ciriano ,
Qian Xiang ,
Brian Craft,
Elena Piñeiro-Yáñez ,
Brian D. O’Connor,
Wojciech Bazant,
Elisabet Barrera,
Alfonso Muñoz-Pomer,
Robert Petryszak,
Anja Füllgrabe ,
Fatima Al-Shahrour ,
Maria Keays
and 9 other authors
A user guide for the online exploration and visualization of PCAWG data
Download from www.nature.com
2019
John E. Collins,
Richard J. White ,
Nicole Staudt,
Ian M. Sealy ,
Ian Packham,
Neha Wali,
Catherine Tudor ,
Cecilia Mazzeo,
Angela Green,
Emma Siragher,
Edward Ryder,
Jacqueline K. White,
Irene Papatheodoru ,
Amy Tang ,
Anja Füllgrabe
and 11 other authors
,
Nicole Staudt,
Ian M. Sealy ,
Ian Packham,
Neha Wali,
Catherine Tudor ,
Cecilia Mazzeo,
Angela Green,
Emma Siragher,
Edward Ryder,
Jacqueline K. White,
Irene Papatheodoru ,
Amy Tang ,
Anja Füllgrabe
and 11 other authors
Common and distinct transcriptional signatures of mammalian embryonic lethality
Download from www.nature.com
2018
Pablo Moreno ,
Luca Pireddu ,
Pierrick Roger ,
Nuwan Goonasekera,
Enis Afgan ,
Marius van den Beek ,
Sijin He ,
Anders Larsson ,
Christoph Ruttkies ,
Daniel Schober ,
David Johnson ,
Philippe Rocca-Serra ,
Ralf Jm M. Weber ,
Bjoern Gruening ,
Reza M. Salek
and 5 other authors
,
Luca Pireddu ,
Pierrick Roger ,
Nuwan Goonasekera,
Enis Afgan ,
Marius van den Beek ,
Sijin He ,
Anders Larsson ,
Christoph Ruttkies ,
Daniel Schober ,
David Johnson ,
Philippe Rocca-Serra ,
Ralf Jm M. Weber ,
Bjoern Gruening ,
Reza M. Salek
and 5 other authors
Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud
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