Inference of Gene Relations from Microarray Data by Abduction. - Irene Papatheodorou; Antonis C. Kakas; Marek J. Sergot (LPNMR, 2005)

Using association rule mining to determine promising secondary phenotyping hypotheses. - Anika Oellrich; Julius O. B. Jacobsen; Irene Papatheodorou; Damian Smedley (Bioinform., 2014)

Comparison of the mammalian insulin signalling pathway to invertebrates in the context of FOXO-mediated ageing. - Irene Papatheodorou; Rudolfs Petrovs; Janet M. Thornton (Bioinform., 2014)

Linking gene expression to phenotypes via pathway information. - Irene Papatheodorou; Anika Oellrich; Damian Smedley (J. Biomed. Semant., 2015)

Open Targets: a platform for therapeutic target identification and validation. - 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; et al. (Nucleic Acids Res., 2017)

Expression Atlas: gene and protein expression across multiple studies and organisms. - 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; et al. (Nucleic Acids Res., 2018)

Gramene 2018: unifying comparative genomics and pathway resources for plant research. - 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 117; et al. (Nucleic Acids Res., 2018)

ArrayExpress update - from bulk to single-cell expression data. - Awais Athar; Anja Füllgrabe; Nancy George; Haider Iqbal; Laura Huerta; Ahmed Ali 009; Catherine Snow; Nuno A. Fonseca; Robert Petryszak; Irene Papatheodorou; Ugis Sarkans; Alvis Brazma (Nucleic Acids Res., 2019)

Ensembl Genomes 2020 - enabling non-vertebrate genomic research. - 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; et al. (Nucleic Acids Res., 2020)

Plant Reactome: a knowledgebase and resource for comparative pathway analysis. - 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; et al. (Nucleic Acids Res., 2020)

Expression Atlas update: from tissues to single cells. - Irene Papatheodorou; Pablo A. Moreno; Jonathan R. Manning; Alfonso Muñoz-Pomer Fuentes; Nancy George; Silvie Fexova; Nuno A. Fonseca; Anja Füllgrabe; Matthew Green 005; Ni Huang; Laura Huerta; Haider Iqbal; et al. (Nucleic Acids Res., 2020)

UCSC Cell Browser: visualize your single-cell data. - Matthew L. Speir; Aparna Bhaduri; Nikolay S. Markov; Pablo A. Moreno; Tomasz J. Nowakowski; Irene Papatheodorou; Alex A. Pollen; Brian J. Raney; Lucas Seninge; W. James Kent; Maximilian Haeussler (Bioinform., 2021)

From ArrayExpress to BioStudies. - Ugis Sarkans; Anja Füllgrabe; Ahmed Ali 009; Awais Athar; Ehsan Behrangi; Nestor Diaz; Silvie Fexova; Nancy George; Haider Iqbal; Sandeep Kurri; Jhoan Munoz; Juan Camillo Rada; et al. (Nucleic Acids Res., 2021)

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. - Marcela K. Tello-Ruiz; Sushma Naithani; Parul Gupta; Andrew Olson; Sharon Wei; Justin Preece; Yinping Jiao; Bo Wang 117; Kapeel Chougule; Priyanka Garg; Justin Elser; Sunita Kumari; et al. (Nucleic Acids Res., 2021)

Expression Atlas update: gene and protein expression in multiple species. - Pablo A. 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; et al. (Nucleic Acids Res., 2022)

Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues. - Shengbo Wang; David García-Seisdedos; Ananth Prakash; Deepti Jaiswal Kundu; Andrew Collins 003; Nancy George; Silvie Fexova; Pablo A. Moreno; Irene Papatheodorou; Andrew R. Jones; Juan Antonio Vizcaíno (PLoS Comput. Biol., 2022)

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022. - 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; et al. (Nucleic Acids Res., 2023)

RNAget: an API to securely retrieve RNA quantifications. - 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; et al. (Bioinform., 2023)

Towards a clinically-based common coordinate framework for the human gut cell atlas: the gut models. - 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 (BMC Medical Informatics Decis. Mak., 2023)