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ORCIDBibTeX records: Irene Papatheodorou
@article{DBLP:journals/bioinformatics/UpchurchPABBNGKAHRGWABBB23,
author = {Sean Upchurch and
Emilio Palumbo and
Jeremy Adams and
David Bujold and
Guillaume Bourque and
Jared Nedzel and
Keenan Graham and
Meenakshi S. Kagda and
Pedro Assis and
Benjamin Hitz and
Emilio Righi and
Roderic Guig{\'{o}} and
Barbara J. Wold and
Alvis Brazma and
Julia Burchard and
Joe Capka and
Michael Cherry and
Laura Clarke and
Brian Craft and
Manolis Dermitzakis and
Mark Diekhans and
John Dursi and
Michael Sean Fitzsimons and
Zac Flaming and
Romina Garrido and
Alfred Gil and
Paul Godden and
Matt Green and
Mitch Guttman and
Brian Haas and
Max Haeussler and
Bo Li and
Sten Linnarsson and
Adam Lipski and
David Liu and
Simonne Longerich and
David Lougheed and
Jonathan Manning and
John C. Marioni and
Christopher Meyer and
Stephen B. Montgomery and
Alyssa Morrow and
Alfonso Mu{\~{n}}oz{-}Pomer Fuentes and
Jared L. Nedzel and
David Nguyen and
Kevin Osborn and
Francis Ouellette and
Irene Papatheodorou and
Dmitri D. Pervouchine and
Arun K. Ramani and
Jordi Rambla and
Bashir Sadjad and
David Steinberg and
Jeremiah Talkar and
Timothy Tickle and
Kathy Tzeng and
Saman Vaisipour and
Sean Watford and
Barbara Wold and
Zhenyu Zhang and
Jing Zhu},
title = {RNAget: an {API} to securely retrieve {RNA} quantifications},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad126},
doi = {10.1093/BIOINFORMATICS/BTAD126},
timestamp = {Fri, 22 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/UpchurchPABBNGKAHRGWABBB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/midm/BurgerBADPGHHSWA23,
author = {Albert Burger and
Richard A. Baldock and
David J. Adams and
Shahida Din and
Irene Papatheodorou and
Michael Glinka and
Bill Hill and
Derek Houghton and
Mehran Sharghi and
Michael N. Wicks and
Mark J. Arends},
title = {Towards a clinically-based common coordinate framework for the human
gut cell atlas: the gut models},
journal = {{BMC} Medical Informatics Decis. Mak.},
volume = {23},
number = {1},
pages = {36},
year = {2023},
url = {https://doi.org/10.1186/s12911-023-02111-9},
doi = {10.1186/S12911-023-02111-9},
timestamp = {Sat, 11 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/midm/BurgerBADPGHHSWA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ThakurBBFHHKKLLMMOPVVWZM23,
author = {Matthew Thakur and
Alex Bateman and
Cath Brooksbank and
Mallory Ann Freeberg and
Melissa Harrison and
Matthew Hartley and
Thomas M. Keane and
Gerard J. Kleywegt and
Andrew Leach and
Maria Levchenko and
Sarah L. Morgan and
Ellen M. McDonagh and
Sandra E. Orchard and
Irene Papatheodorou and
Sameer Velankar and
Juan Antonio Vizca{\'{\i}}no and
Rick Witham and
Barbara Zdrazil and
Johanna R. McEntyre},
title = {EMBL's European Bioinformatics Institute {(EMBL-EBI)} in 2022},
journal = {Nucleic Acids Res.},
volume = {51},
number = {{D1}},
pages = {9--17},
year = {2023},
url = {https://doi.org/10.1093/nar/gkac1098},
doi = {10.1093/NAR/GKAC1098},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ThakurBBFHHKKLLMMOPVVWZM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/MorenoFGMMMFFBB22,
author = {Pablo A. Moreno and
Silvie Fexova and
Nancy George and
Jonathan R. Manning and
Zhichao Miao and
Suhaib Mohammed and
Alfonso Mu{\~{n}}oz{-}Pomer Fuentes and
Anja F{\"{u}}llgrabe and
Yalan Bi and
Natassja Bush and
Haider Iqbal and
Upendra Kumbham and
Andrey Solovyev and
Lingyun Zhao and
Ananth Prakash and
David Garc{\'{\i}}a{-}Seisdedos and
Deepti Jaiswal Kundu and
Shengbo Wang and
Mathias Walzer and
Laura Clarke and
David Osumi{-}Sutherland and
Marcela Karey Tello{-}Ruiz and
Sunita Kumari and
Doreen Ware and
Jana Eliasova and
Mark J. Arends and
Martijn C. Nawijn and
Kerstin B. Meyer and
Tony Burdett and
John C. Marioni and
Sarah A. Teichmann and
Juan Antonio Vizca{\'{\i}}no and
Alvis Brazma and
Irene Papatheodorou},
title = {Expression Atlas update: gene and protein expression in multiple species},
journal = {Nucleic Acids Res.},
volume = {50},
number = {{D1}},
pages = {129--140},
year = {2022},
url = {https://doi.org/10.1093/nar/gkab1030},
doi = {10.1093/NAR/GKAB1030},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/MorenoFGMMMFFBB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/WangGPKCGFMPJV22,
author = {Shengbo Wang and
David Garc{\'{\i}}a{-}Seisdedos and
Ananth Prakash and
Deepti Jaiswal Kundu and
Andrew Collins and
Nancy George and
Silvie Fexova and
Pablo A. Moreno and
Irene Papatheodorou and
Andrew R. Jones and
Juan Antonio Vizca{\'{\i}}no},
title = {Integrated view and comparative analysis of baseline protein expression
in mouse and rat tissues},
journal = {PLoS Comput. Biol.},
volume = {18},
number = {6},
year = {2022},
url = {https://doi.org/10.1371/journal.pcbi.1010174},
doi = {10.1371/JOURNAL.PCBI.1010174},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/WangGPKCGFMPJV22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SpeirBMMNPPRSKH21,
author = {Matthew L. Speir and
Aparna Bhaduri and
Nikolay S. Markov and
Pablo A. Moreno and
Tomasz J. Nowakowski and
Irene Papatheodorou and
Alex A. Pollen and
Brian J. Raney and
Lucas Seninge and
W. James Kent and
Maximilian Haeussler},
title = {{UCSC} Cell Browser: visualize your single-cell data},
journal = {Bioinform.},
volume = {37},
number = {23},
pages = {4578--4580},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab503},
doi = {10.1093/BIOINFORMATICS/BTAB503},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SpeirBMMNPPRSKH21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/Tello-RuizNGOWP21,
author = {Marcela K. Tello{-}Ruiz and
Sushma Naithani and
Parul Gupta and
Andrew Olson and
Sharon Wei and
Justin Preece and
Yinping Jiao and
Bo Wang and
Kapeel Chougule and
Priyanka Garg and
Justin Elser and
Sunita Kumari and
Vivek Kumar and
Bruno Contreras{-}Moreira and
Guy Naamati and
Nancy George and
Justin Cook and
Dan M. Bolser and
Peter D'Eustachio and
Lincoln D. Stein and
Amit Gupta and
Weijia Xu and
Jennifer Regala and
Irene Papatheodorou and
Paul J. Kersey and
Paul Flicek and
Crispin Taylor and
Pankaj Jaiswal and
Doreen Ware},
title = {Gramene 2021: harnessing the power of comparative genomics and pathways
for plant research},
journal = {Nucleic Acids Res.},
volume = {49},
number = {Database-Issue},
pages = {D1452--D1463},
year = {2021},
url = {https://doi.org/10.1093/nar/gkaa979},
doi = {10.1093/NAR/GKAA979},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/Tello-RuizNGOWP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SarkansF0ABDFGI21,
author = {Ugis Sarkans and
Anja F{\"{u}}llgrabe and
Ahmed Ali and
Awais Athar and
Ehsan Behrangi and
Nestor Diaz and
Silvie Fexova and
Nancy George and
Haider Iqbal and
Sandeep Kurri and
Jhoan Munoz and
Juan Camillo Rada and
Irene Papatheodorou and
Alvis Brazma},
title = {From ArrayExpress to BioStudies},
journal = {Nucleic Acids Res.},
volume = {49},
number = {Database-Issue},
pages = {D1502--D1506},
year = {2021},
url = {https://doi.org/10.1093/nar/gkaa1062},
doi = {10.1093/NAR/GKAA1062},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SarkansF0ABDFGI21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/NaithaniGPDEGDK20,
author = {Sushma Naithani and
Parul Gupta and
Justin Preece and
Peter D'Eustachio and
Justin Elser and
Priyanka Garg and
Daemon A. Dikeman and
Jason Kiff and
Justin Cook and
Andrew Olson and
Sharon Wei and
Marcela K. Tello{-}Ruiz and
Antonio Fabregat Mundo and
Alfonso Mu{\~{n}}oz{-}Pomer Fuentes and
Suhaib Mohammed and
Tiejun Cheng and
Evan Bolton and
Irene Papatheodorou and
Lincoln Stein and
Doreen Ware and
Pankaj Jaiswal},
title = {Plant Reactome: a knowledgebase and resource for comparative pathway
analysis},
journal = {Nucleic Acids Res.},
volume = {48},
number = {Database-Issue},
pages = {D1093--D1103},
year = {2020},
url = {https://doi.org/10.1093/nar/gkz996},
doi = {10.1093/NAR/GKZ996},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/NaithaniGPDEGDK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/HoweCSMAAABBCCC20,
author = {Kevin L. Howe and
Bruno Contreras{-}Moreira and
Nishadi De Silva and
Gareth Maslen and
Wasiu A. Akanni and
James E. Allen and
Jorge {\'{A}}lvarez{-}Jarreta and
Matthieu Barba and
Dan M. Bolser and
Lahcen Cambell and
Manuel Carbajo and
Marc Chakiachvili and
Mikkel B. Christensen and
Carla A. Cummins and
Alayne Cuzick and
Paul Davis and
Silvie Fexova and
Astrid Gall and
Nancy George and
Laurent Gil and
Parul Gupta and
Kim E. Hammond{-}Kosack and
Erin Haskell and
Sarah E. Hunt and
Pankaj Jaiswal and
Sophie H. Janacek and
Paul J. Kersey and
Nick Langridge and
Uma Maheswari and
Thomas Maurel and
Mark D. McDowall and
Benjamin Moore and
Matthieu Muffato and
Guy Naamati and
Sushma Naithani and
Andrew Olson and
Irene Papatheodorou and
Mateus Patricio and
Michael Paulini and
Helder Pedro and
Emily Perry and
Justin Preece and
Marc Rosello and
Matthew Russell and
Vasily Sitnik and
Daniel M. Staines and
Joshua C. Stein and
Marcela K. Tello{-}Ruiz and
Stephen J. Trevanion and
Martin Urban and
Sharon Wei and
Doreen Ware and
Gary Williams and
Andrew D. Yates and
Paul Flicek},
title = {Ensembl Genomes 2020 - enabling non-vertebrate genomic research},
journal = {Nucleic Acids Res.},
volume = {48},
number = {Database-Issue},
pages = {D689--D695},
year = {2020},
url = {https://doi.org/10.1093/nar/gkz890},
doi = {10.1093/NAR/GKZ890},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/HoweCSMAAABBCCC20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/PapatheodorouMM20,
author = {Irene Papatheodorou and
Pablo A. Moreno and
Jonathan R. Manning and
Alfonso Mu{\~{n}}oz{-}Pomer Fuentes and
Nancy George and
Silvie Fexova and
Nuno A. Fonseca and
Anja F{\"{u}}llgrabe and
Matthew Green and
Ni Huang and
Laura Huerta and
Haider Iqbal and
Monica Jianu and
Suhaib Mohammed and
Lingyun Zhao and
Andrew F. Jarnuczak and
Simon Jupp and
John C. Marioni and
Kerstin B. Meyer and
Robert Petryszak and
Cesar Augusto Prada Medina and
Carlos Talavera{-}L{\'{o}}pez and
Sarah A. Teichmann and
Juan Antonio Vizca{\'{\i}}no and
Alvis Brazma},
title = {Expression Atlas update: from tissues to single cells},
journal = {Nucleic Acids Res.},
volume = {48},
number = {Database-Issue},
pages = {D77--D83},
year = {2020},
url = {https://doi.org/10.1093/nar/gkz947},
doi = {10.1093/NAR/GKZ947},
timestamp = {Wed, 24 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/PapatheodorouMM20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AtharFGIHASFPPS19,
author = {Awais Athar and
Anja F{\"{u}}llgrabe and
Nancy George and
Haider Iqbal and
Laura Huerta and
Ahmed Ali and
Catherine Snow and
Nuno A. Fonseca and
Robert Petryszak and
Irene Papatheodorou and
Ugis Sarkans and
Alvis Brazma},
title = {ArrayExpress update - from bulk to single-cell expression data},
journal = {Nucleic Acids Res.},
volume = {47},
number = {Database-Issue},
pages = {D711--D715},
year = {2019},
url = {https://doi.org/10.1093/nar/gky964},
doi = {10.1093/NAR/GKY964},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/AtharFGIHASFPPS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/Tello-RuizNSGCO18,
author = {Marcela K. Tello{-}Ruiz and
Sushma Naithani and
Joshua C. Stein and
Parul Gupta and
Michael Campbell and
Andrew Olson and
Sharon Wei and
Justin Preece and
Matthew J. Geniza and
Yinping Jiao and
Young Koung Lee and
Bo Wang and
Joseph Mulvaney and
Kapeel Chougule and
Justin Elser and
Noor Al{-}Bader and
Sunita Kumari and
James Thomason and
Vivek Kumar and
Daniel M. Bolser and
Guy Naamati and
Electra Tapanari and
Nuno A. Fonseca and
Laura Huerta and
Haider Iqbal and
Maria Keays and
Alfonso Mu{\~{n}}oz{-}Pomer Fuentes and
Y. Amy Tang and
Antonio Fabregat and
Peter D'Eustachio and
Joel Weiser and
Lincoln D. Stein and
Robert Petryszak and
Irene Papatheodorou and
Paul J. Kersey and
Patti Lockhart and
Crispin Taylor and
Pankaj Jaiswal and
Doreen Ware},
title = {Gramene 2018: unifying comparative genomics and pathway resources
for plant research},
journal = {Nucleic Acids Res.},
volume = {46},
number = {Database-Issue},
pages = {D1181--D1189},
year = {2018},
url = {https://doi.org/10.1093/nar/gkx1111},
doi = {10.1093/NAR/GKX1111},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/Tello-RuizNSGCO18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/PapatheodorouFK18,
author = {Irene Papatheodorou and
Nuno A. Fonseca and
Maria Keays and
Y. Amy Tang and
Elisabet Barrera and
Wojciech Bazant and
Melissa L. Burke and
Anja F{\"{u}}llgrabe and
Alfonso Mu{\~{n}}oz{-}Pomer Fuentes and
Nancy George and
Laura Huerta and
Satu Koskinen and
Suhaib Mohammed and
Matthew J. Geniza and
Justin Preece and
Pankaj Jaiswal and
Andrew F. Jarnuczak and
Wolfgang Huber and
Oliver Stegle and
Juan Antonio Vizca{\'{\i}}no and
Alvis Brazma and
Robert Petryszak},
title = {Expression Atlas: gene and protein expression across multiple studies
and organisms},
journal = {Nucleic Acids Res.},
volume = {46},
number = {Database-Issue},
pages = {D246--D251},
year = {2018},
url = {https://doi.org/10.1093/nar/gkx1158},
doi = {10.1093/NAR/GKX1158},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/PapatheodorouFK18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KoscielnyACCFGH17,
author = {Gautier Koscielny and
Peter An and
Denise Carvalho{-}Silva and
Jennifer A. Cham and
Luca Fumis and
Rippa Gasparyan and
Samiul Hasan and
Nikiforos Karamanis and
Michael Maguire and
Eliseo Papa and
Andrea Pierleoni and
Miguel Pignatelli and
Theo Platt and
Francis Rowland and
Priyanka Wankar and
A. Patr{\'{\i}}cia Bento and
Tony Burdett and
Antonio Fabregat and
Simon A. Forbes and
Anna Gaulton and
Cristina Yenyxe Gonz{\'{a}}lez and
Henning Hermjakob and
Anne Hersey and
Steven Jupe and
Senay Kafkas and
Maria Keays and
Catherine Leroy and
Francisco{-}Javier Lopez and
Mar{\'{\i}}a P. Magari{\~{n}}os and
James Malone and
Johanna R. McEntyre and
Alfonso Mu{\~{n}}oz{-}Pomer Fuentes and
Claire O'Donovan and
Irene Papatheodorou and
Helen E. Parkinson and
Barbara Palka and
Justin E. Paschall and
Robert Petryszak and
Naruemon Pratanwanich and
Sirarat Sarntivijai and
Gary Saunders and
Konstantinos Sidiropoulos and
Thomas Smith and
Zbyslaw Sondka and
Oliver Stegle and
Y. Amy Tang and
Edward Turner and
Brendan W. Vaughan and
Olga Vrousgou and
Xavier Watkins and
Maria Jesus Martin and
Philippe Sanseau and
Jessica Vamathevan and
Ewan Birney and
Jeffrey Barrett and
Ian Dunham},
title = {Open Targets: a platform for therapeutic target identification and
validation},
journal = {Nucleic Acids Res.},
volume = {45},
number = {Database-Issue},
pages = {D985--D994},
year = {2017},
url = {https://doi.org/10.1093/nar/gkw1055},
doi = {10.1093/NAR/GKW1055},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KoscielnyACCFGH17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/PapatheodorouOS15,
author = {Irene Papatheodorou and
Anika Oellrich and
Damian Smedley},
title = {Linking gene expression to phenotypes via pathway information},
journal = {J. Biomed. Semant.},
volume = {6},
pages = {17},
year = {2015},
url = {https://doi.org/10.1186/s13326-015-0013-5},
doi = {10.1186/S13326-015-0013-5},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/PapatheodorouOS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OellrichJPS14,
author = {Anika Oellrich and
Julius O. B. Jacobsen and
Irene Papatheodorou and
Damian Smedley},
title = {Using association rule mining to determine promising secondary phenotyping
hypotheses},
journal = {Bioinform.},
volume = {30},
number = {12},
pages = {52--59},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu260},
doi = {10.1093/BIOINFORMATICS/BTU260},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/OellrichJPS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PapatheodorouPT14,
author = {Irene Papatheodorou and
Rudolfs Petrovs and
Janet M. Thornton},
title = {Comparison of the mammalian insulin signalling pathway to invertebrates
in the context of FOXO-mediated ageing},
journal = {Bioinform.},
volume = {30},
number = {21},
pages = {2999--3003},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu493},
doi = {10.1093/BIOINFORMATICS/BTU493},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PapatheodorouPT14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/lpnmr/PapatheodorouKS05,
author = {Irene Papatheodorou and
Antonis C. Kakas and
Marek J. Sergot},
editor = {Chitta Baral and
Gianluigi Greco and
Nicola Leone and
Giorgio Terracina},
title = {Inference of Gene Relations from Microarray Data by Abduction},
booktitle = {Logic Programming and Nonmonotonic Reasoning, 8th International Conference,
{LPNMR} 2005, Diamante, Italy, September 5-8, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3662},
pages = {389--393},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11546207\_33},
doi = {10.1007/11546207\_33},
timestamp = {Sun, 02 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/lpnmr/PapatheodorouKS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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