Irene Papatheodorou

Publication Activity (10 Years)

Years Active: 2005-2023
Publications (10 Years): 15

Top Topics

Comparative Genomics

Gene Expression

Interesting Rules

Top Venues

Nucleic Acids Res.

BMC Medical Informatics Decis. Mak.

J. Biomed. Semant.

Publications

Albert Burger, Richard A. Baldock, David J. Adams, Shahida Din, Irene Papatheodorou, Michael Glinka, Bill Hill, Derek Houghton, Mehran Sharghi, Michael N. Wicks, Mark J. Arends
Towards a clinically-based common coordinate framework for the human gut cell atlas: the gut models. BMC Medical Informatics Decis. Mak. 23 (1) (2023)
Matthew Thakur, Alex Bateman, Cath Brooksbank, Mallory Ann Freeberg, Melissa Harrison, Matthew Hartley, Thomas M. Keane, Gerard J. Kleywegt, Andrew Leach, Maria Levchenko, Sarah L. Morgan, Ellen M. McDonagh, Sandra E. Orchard, Irene Papatheodorou, Sameer Velankar, Juan Antonio Vizcaíno, Rick Witham, Barbara Zdrazil, Johanna R. McEntyre
EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022. Nucleic Acids Res. 51 (D1) (2023)
Sean Upchurch, Emilio Palumbo, Jeremy Adams, David Bujold, Guillaume Bourque, Jared Nedzel, Keenan Graham, Meenakshi S. Kagda, Pedro Assis, Benjamin C. Hitz, Emilio Righi, Roderic Guigó, Barbara J. Wold, Alvis Brazma, Julia Burchard, Joe Capka, Michael Cherry, Laura Clarke, Brian Craft, Manolis Dermitzakis, Mark Diekhans, John Dursi, Michael Sean Fitzsimons, Zac Flaming, Romina Garrido, Alfred Gil, Paul Godden, Matt Green, Mitch Guttman, Brian Haas, Max Haeussler, Bo Li, Sten Linnarsson, Adam Lipski, David Liu, Simonne Longerich, David Lougheed, Jonathan Manning, John C. Marioni, Christopher Meyer, Stephen B. Montgomery, Alyssa Morrow, Alfonso Muñoz-Pomer Fuentes, Jared L. Nedzel, David Nguyen, Kevin Osborn, Francis Ouellette, Irene Papatheodorou, Dmitri D. Pervouchine, Arun K. Ramani, Jordi Rambla, Bashir Sadjad, David Steinberg, Jeremiah Talkar, Timothy Tickle, Kathy Tzeng, Saman Vaisipour, Sean Watford, Barbara Wold, Zhenyu Zhang, Jing Zhu
RNAget: an API to securely retrieve RNA quantifications. Bioinform. 39 (4) (2023)
Pablo Moreno, Silvie Fexova, Nancy George, Jonathan R. Manning, Zhichao Miao, Suhaib Mohammed, Alfonso Muñoz-Pomer Fuentes, Anja Füllgrabe, Yalan Bi, Natassja Bush, Haider Iqbal, Upendra Kumbham, Andrey Solovyev, Lingyun Zhao, Ananth Prakash, David García-Seisdedos, Deepti Jaiswal Kundu, Shengbo Wang, Mathias Walzer, Laura Clarke, David Osumi-Sutherland, Marcela Karey Tello-Ruiz, Sunita Kumari, Doreen Ware, Jana Eliasova, Mark J. Arends, Martijn C. Nawijn, Kerstin B. Meyer, Tony Burdett, John C. Marioni, Sarah A. Teichmann, Juan Antonio Vizcaíno, Alvis Brazma, Irene Papatheodorou
Expression Atlas update: gene and protein expression in multiple species. Nucleic Acids Res. 50 (D1) (2022)
Shengbo Wang, David García-Seisdedos, Ananth Prakash, Deepti Jaiswal Kundu, Andrew Collins, Nancy George, Silvie Fexova, Pablo Moreno, Irene Papatheodorou, Andrew R. Jones, Juan Antonio Vizcaíno
Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues. PLoS Comput. Biol. 18 (6) (2022)
Ugis Sarkans, Anja Füllgrabe, Ahmed Ali, Awais Athar, Ehsan Behrangi, Nestor Diaz, Silvie Fexova, Nancy George, Haider Iqbal, Sandeep Kurri, Jhoan Munoz, Juan Camillo Rada, Irene Papatheodorou, Alvis Brazma
From ArrayExpress to BioStudies. Nucleic Acids Res. 49 (Database-Issue) (2021)
Matthew L. Speir, Aparna Bhaduri, Nikolay S. Markov, Pablo Moreno, Tomasz J. Nowakowski, Irene Papatheodorou, Alex A. Pollen, Brian J. Raney, Lucas Seninge, W. James Kent, Maximilian Haeussler
UCSC Cell Browser: visualize your single-cell data. Bioinform. 37 (23) (2021)
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, Nancy George, Justin Cook, Dan M. Bolser, Peter D'Eustachio, Lincoln D. Stein, Amit Gupta, Weijia Xu, Jennifer Regala, Irene Papatheodorou, Paul J. Kersey, Paul Flicek, Crispin Taylor, Pankaj Jaiswal, Doreen Ware
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Res. 49 (Database-Issue) (2021)
Irene Papatheodorou, Pablo Moreno, Jonathan R. Manning, Alfonso Muñoz-Pomer Fuentes, Nancy George, Silvie Fexova, Nuno A. Fonseca, Anja Füllgrabe, Matthew Green, Ni Huang, Laura Huerta, Haider Iqbal, Monica Jianu, Suhaib Mohammed, Lingyun Zhao, Andrew F. Jarnuczak, Simon Jupp, John C. Marioni, Kerstin B. Meyer, Robert Petryszak, Cesar Augusto Prada Medina, Carlos Talavera-López, Sarah A. Teichmann, Juan Antonio Vizcaíno, Alvis Brazma
Expression Atlas update: from tissues to single cells. Nucleic Acids Res. 48 (Database-Issue) (2020)
Kevin L. Howe, Bruno Contreras-Moreira, Nishadi De Silva, Gareth Maslen, Wasiu A. Akanni, James E. Allen, Jorge Álvarez-Jarreta, Matthieu Barba, Dan M. Bolser, Lahcen Cambell, Manuel Carbajo, Marc Chakiachvili, Mikkel B. Christensen, Carla A. Cummins, Alayne Cuzick, Paul Davis, Silvie Fexova, Astrid Gall, Nancy George, Laurent Gil, Parul Gupta, Kim E. Hammond-Kosack, Erin Haskell, Sarah E. Hunt, Pankaj Jaiswal, Sophie H. Janacek, Paul J. Kersey, Nick Langridge, Uma Maheswari, Thomas Maurel, Mark D. McDowall, Benjamin Moore, Matthieu Muffato, Guy Naamati, Sushma Naithani, Andrew Olson, Irene Papatheodorou, Mateus Patricio, Michael Paulini, Helder Pedro, Emily Perry, Justin Preece, Marc Rosello, Matthew Russell, Vasily Sitnik, Daniel M. Staines, Joshua C. Stein, Marcela K. Tello-Ruiz, Stephen J. Trevanion, Martin Urban, Sharon Wei, Doreen Ware, Gary Williams, Andrew D. Yates, Paul Flicek
Ensembl Genomes 2020 - enabling non-vertebrate genomic research. Nucleic Acids Res. 48 (Database-Issue) (2020)
Sushma Naithani, Parul Gupta, Justin Preece, Peter D'Eustachio, Justin Elser, Priyanka Garg, Daemon A. Dikeman, Jason Kiff, Justin Cook, Andrew Olson, Sharon Wei, Marcela K. Tello-Ruiz, Antonio Fabregat Mundo, Alfonso Muñoz-Pomer Fuentes, Suhaib Mohammed, Tiejun Cheng, Evan Bolton, Irene Papatheodorou, Lincoln Stein, Doreen Ware, Pankaj Jaiswal
Plant Reactome: a knowledgebase and resource for comparative pathway analysis. Nucleic Acids Res. 48 (Database-Issue) (2020)
Awais Athar, Anja Füllgrabe, Nancy George, Haider Iqbal, Laura Huerta, Ahmed Ali, Catherine Snow, Nuno A. Fonseca, Robert Petryszak, Irene Papatheodorou, Ugis Sarkans, Alvis Brazma
ArrayExpress update - from bulk to single-cell expression data. Nucleic Acids Res. 47 (Database-Issue) (2019)
Irene Papatheodorou, Nuno A. Fonseca, Maria Keays, Y. Amy Tang, Elisabet Barrera, Wojciech Bazant, Melissa L. Burke, Anja Füllgrabe, Alfonso Muñoz-Pomer Fuentes, Nancy George, Laura Huerta, Satu Koskinen, Suhaib Mohammed, Matthew J. Geniza, Justin Preece, Pankaj Jaiswal, Andrew F. Jarnuczak, Wolfgang Huber, Oliver Stegle, Juan Antonio Vizcaíno, Alvis Brazma, Robert Petryszak
Expression Atlas: gene and protein expression across multiple studies and organisms. Nucleic Acids Res. 46 (Database-Issue) (2018)
Marcela K. Tello-Ruiz, Sushma Naithani, Joshua C. Stein, Parul Gupta, Michael Campbell, Andrew Olson, Sharon Wei, Justin Preece, Matthew J. Geniza, Yinping Jiao, Young Koung Lee, Bo Wang, Joseph Mulvaney, Kapeel Chougule, Justin Elser, Noor Al-Bader, Sunita Kumari, James Thomason, Vivek Kumar, Daniel M. Bolser, Guy Naamati, Electra Tapanari, Nuno A. Fonseca, Laura Huerta, Haider Iqbal, Maria Keays, Alfonso Muñoz-Pomer Fuentes, Y. Amy Tang, Antonio Fabregat, Peter D'Eustachio, Joel Weiser, Lincoln D. Stein, Robert Petryszak, Irene Papatheodorou, Paul J. Kersey, Patti Lockhart, Crispin Taylor, Pankaj Jaiswal, Doreen Ware
Gramene 2018: unifying comparative genomics and pathway resources for plant research. Nucleic Acids Res. 46 (Database-Issue) (2018)
Gautier Koscielny, Peter An, Denise Carvalho-Silva, Jennifer A. Cham, Luca Fumis, Rippa Gasparyan, Samiul Hasan, Nikiforos Karamanis, Michael Maguire, Eliseo Papa, Andrea Pierleoni, Miguel Pignatelli, Theo Platt, Francis Rowland, Priyanka Wankar, A. Patrícia Bento, Tony Burdett, Antonio Fabregat, Simon A. Forbes, Anna Gaulton, Cristina Yenyxe González, Henning Hermjakob, Anne Hersey, Steven Jupe, Senay Kafkas, Maria Keays, Catherine Leroy, Francisco-Javier Lopez, María P. Magariños, James Malone, Johanna R. McEntyre, Alfonso Muñoz-Pomer Fuentes, Claire O'Donovan, Irene Papatheodorou, Helen E. Parkinson, Barbara Palka, Justin E. Paschall, Robert Petryszak, Naruemon Pratanwanich, Sirarat Sarntivijai, Gary Saunders, Konstantinos Sidiropoulos, Thomas Smith, Zbyslaw Sondka, Oliver Stegle, Y. Amy Tang, Edward Turner, Brendan W. Vaughan, Olga Vrousgou, Xavier Watkins, Maria Jesus Martin, Philippe Sanseau, Jessica Vamathevan, Ewan Birney, Jeffrey Barrett, Ian Dunham
Open Targets: a platform for therapeutic target identification and validation. Nucleic Acids Res. 45 (Database-Issue) (2017)
Irene Papatheodorou, Anika Oellrich, Damian Smedley
Linking gene expression to phenotypes via pathway information. J. Biomed. Semant. 6 (2015)
Irene Papatheodorou, Rudolfs Petrovs, Janet M. Thornton
Comparison of the mammalian insulin signalling pathway to invertebrates in the context of FOXO-mediated ageing. Bioinform. 30 (21) (2014)
Anika Oellrich, Julius O. B. Jacobsen, Irene Papatheodorou, Damian Smedley
Using association rule mining to determine promising secondary phenotyping hypotheses. Bioinform. 30 (12) (2014)
Irene Papatheodorou, Antonis C. Kakas, Marek J. Sergot
Inference of Gene Relations from Microarray Data by Abduction. LPNMR (2005)