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Papatheodorou Group

Decoding phenotypes using single cell genomics

Publications

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Publication year

Expression Atlas in 2026: enabling FAIR and open expression data through community collaboration and integration.

Madrigal P, Thanki AS, Fexova S, Yu ID, Chatzigeorgiou A, Zucchi I, Marugan Calles JC, Vilmovsky L, Khen A, Zhao L, Erdos K, Kurri SR, Selvakumar S, Kumbham U, Prakash A, Wang S, Green A, Ribas CE, Sweeney B, Alegbe T, Suveges D, Hemrom A, Gomez Gutierrez DE, Insua S, Jeffryes M, Pearce M, Basutkar P, Kaforou M, Cunnington A, Levin M, Kumari S, Ware D, Goutte-Gattat D, Röper K, Brown NH, Hu Y, Perrimon N, Papatheodorou I, Brazma A, Hermjakob H, Harrison M, Ocaña D, Ochoa D, McDonagh EM, Bateman A, Keane T, Vizcaíno JA, Ernst C.

Nucleic acids research, 2025

doi:10.1093/nar/gkaf1238.

Gramene 2025: expanded comparative genomics and pathway resources, integrated search, and pan-genome portals for crop research.

Olson A, Kumari S, Wei X, Chougule K, Lu Z, Tello-Ruiz MK, Kumar V, Van Buren P, Olson A, Kim C, Braynen J, Zhang L, Dyer S, Alvarez-Jarreta J, Saraf S, Contreras-Moreira B, Naamati G, Ernst C, Papatheodorou I, George N, Jaiswal P, Naithani S, Gupta P, Elser J, D'Eustachio P, Assmann SM, Ferrero-Serrano Á, Pasha A, Provart N, Gladman N, Ware D.

Nucleic acids research, 2025

doi:10.1093/nar/gkaf1260.

The Biodiversity Cell Atlas: mapping the tree of life at cellular resolution.

Sebé-Pedrós A, Tanay A, Lawniczak MKN, Arendt D, Aerts S, Archibald J, Arnone MI, Blaxter M, Cleves P, Coelho SM, Dias M, Dunn C, Elek A, Frazer J, Gabaldón T, Gillis J, Grau-Bové X, Guigó R, Hobert O, Huerta-Cepas J, Irimia M, Klein A, Lewin H, Lowe CJ, Marlow H, Musser JM, Nagy LG, Najle SR, Pachter L, Paez S, Papatheodorou I, Passalacqua MJ, Rajewsky N, Rhee SY, Richards TA, Sauka-Spengler T, Saunders LM, Seuntjens E, Solana J, Song Y, Technau U, Wang B, Biodiversity Cell Atlas meeting participants.

Nature, 2025

doi:10.1038/s41586-025-09312-4.

Expression Atlas update: insights from sequencing data at both bulk and single cell level.

George N, Fexova S, Fuentes AM, Madrigal P, Bi Y, Iqbal H, Kumbham U, Nolte NF, Zhao L, Thanki AS, Yu ID, Marugan Calles JC, Erdos K, Vilmovsky L, Kurri SR, Vathrakokoili-Pournara A, Osumi-Sutherland D, Prakash A, Wang S, Tello-Ruiz MK, Kumari S, Ware D, Goutte-Gattat D, Hu Y, Brown N, Perrimon N, Vizcaíno JA, Burdett T, Teichmann S, Brazma A, Papatheodorou I.

Nucleic acids research, 2024

doi:10.1093/nar/gkad1021.

A Roadmap for the Human Gut Cell Atlas.

Zilbauer M, James KR, Kaur M, Pott S, Li Z, Burger A, Thiagarajah JR, Burclaff J, Jahnsen FL, Perrone F, Ross AD, Matteoli G, Stakenborg N, Sujino T, Moor A, Bartolome-Casado R, Bækkevold ES, Zhou R, Xie B, Lau KS, Din S, Magness ST, Yao Q, Beyaz S, Arends M, Denadai-Souza A, Coburn LA, Gaublomme JT, Baldock R, Papatheodorou I, Ordovas-Montanes J, Boeckxstaens G, Hupalowska A, Teichmann SA, Regev A, Xavier RJ, Simmons A, Snyder MP, Wilson KT, Gut Cell Atlas Consortium, Human Cell Atlas Gut Biological Network Consortium.

Nature reviews. Gastroenterology & hepatology, 2023

doi:10.1038/s41575-023-00784-1.

Diagnosis of Multisystem Inflammatory Syndrome in Children by a Whole-Blood Transcriptional Signature.

Jackson HR, Miglietta L, Habgood-Coote D, D'Souza G, Shah P, Nichols S, Vito O, Powell O, Davidson MS, Shimizu C, Agyeman PKA, Beudeker CR, Brengel-Pesce K, Carrol ED, Carter MJ, De T, Eleftheriou I, Emonts M, Epalza C, Georgiou P, De Groot R, Fidler K, Fink C, van Keulen D, Kuijpers T, Moll H, Papatheodorou I, Paulus S, Pokorn M, Pollard AJ, Rivero-Calle I, Rojo P, Secka F, Schlapbach LJ, Tremoulet AH, Tsolia M, Usuf E, Van Der Flier M, Von Both U, Vermont C, Yeung S, Zavadska D, Zenz W, Coin LJM, Cunnington A, Burns JC, Wright V, Martinon-Torres F, Herberg JA, Rodriguez-Manzano J, Kaforou M, Levin M.

Journal of the Pediatric Infectious Diseases Society, 2023

doi:10.1093/jpids/piad035.

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022.

Thakur M, Bateman A, Brooksbank C, Freeberg M, Harrison M, Hartley M, Keane T, Kleywegt G, Leach A, Levchenko M, Morgan S, McDonagh EM, Orchard S, Papatheodorou I, Velankar S, Vizcaino JA, Witham R, Zdrazil B, McEntyre J.

Nucleic acids research, 2023

doi:10.1093/nar/gkac1098.

Community-driven ELIXIR activities in single-cell omics

Czarnewski P, Mahfouz A, Calogero RA, Palagi PM, Portell-Silva L, Gonzalez-Uriarte A, Soneson C, Burdett T, Szomolay B, Videm P, Hotz H, Papatheodorou I, Hancock JM, Grüning B, Haerty W, Krause R, Capella-Gutierrez S, Leskošek B, Alessandri L, Arigoni M, Rezen T, Botzki A, Ferk P, Lindvall J, Heil KF, Ishaque N, Korpelainen E.

Preprint, 2022

doi:10.12688/f1000research.122312.1.

Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly.

Li H, Janssens J, De Waegeneer M, Kolluru SS, Davie K, Gardeux V, Saelens W, David FPA, Brbić M, Spanier K, Leskovec J, McLaughlin CN, Xie Q, Jones RC, Brueckner K, Shim J, Tattikota SG, Schnorrer F, Rust K, Nystul TG, Carvalho-Santos Z, Ribeiro C, Pal S, Mahadevaraju S, Przytycka TM, Allen AM, Goodwin SF, Berry CW, Fuller MT, White-Cooper H, Matunis EL, DiNardo S, Galenza A, O'Brien LE, Dow JAT, FCA Consortium§, Jasper H, Oliver B, Perrimon N, Deplancke B, Quake SR, Luo L, Aerts S, Agarwal D, Ahmed-Braimah Y, Arbeitman M, Ariss MM, Augsburger J, Ayush K, Baker CC, Banisch T, Birker K, Bodmer R, Bolival B, Brantley SE, Brill JA, Brown NC, Buehner NA, Cai XT, Cardoso-Figueiredo R, Casares F, Chang A, Clandinin TR, Crasta S, Desplan C, Detweiler AM, Dhakan DB, Donà E, Engert S, Floc'hlay S, George N, González-Segarra AJ, Groves AK, Gumbin S, Guo Y, Harris DE, Heifetz Y, Holtz SL, Horns F, Hudry B, Hung RJ, Jan YN, Jaszczak JS, Jefferis GSXE, Karkanias J, Karr TL, Katheder NS, Kezos J, Kim AA, Kim SK, Kockel L, Konstantinides N, Kornberg TB, Krause HM, Labott AT, Laturney M, Lehmann R, Leinwand S, Li J, Li JSS, Li K, Li K, Li L, Li T, Litovchenko M, Liu HH, Liu Y, Lu TC, Manning J, Mase A, Matera-Vatnick M, Matias NR, McDonough-Goldstein CE, McGeever A, McLachlan AD, Moreno-Roman P, Neff N, Neville M, Ngo S, Nielsen T, O'Brien CE, Osumi-Sutherland D, Özel MN, Papatheodorou I, Petkovic M, Pilgrim C, Pisco AO, Reisenman C, Sanders EN, Dos Santos G, Scott K, Sherlekar A, Shiu P, Sims D, Sit RV, Slaidina M, Smith HE, Sterne G, Su YH, Sutton D, Tamayo M, Tan M, Tastekin I, Treiber C, Vacek D, Vogler G, Waddell S, Wang W, Wilson RI, Wolfner MF, Wong YE, Xie A, Xu J, Yamamoto S, Yan J, Yao Z, Yoda K, Zhu R, Zinzen RP.

Science (New York, N.Y.), 2022

doi:10.1126/science.abk2432.

The discovAIR project: a roadmap towards the Human Lung Cell Atlas.

Luecken MD, Zaragosi LE, Madissoon E, Sikkema L, Firsova AB, De Domenico E, Kümmerle L, Saglam A, Berg M, Gay ACA, Schniering J, Mayr CH, Abalo XM, Larsson L, Sountoulidis A, Teichmann SA, van Eunen K, Koppelman GH, Saeb-Parsy K, Leroy S, Powell P, Sarkans U, Timens W, Lundeberg J, van den Berge M, Nilsson M, Horváth P, Denning J, Papatheodorou I, Schultze JL, Schiller HB, Barbry P, Petoukhov I, Misharin AV, Adcock IM, von Papen M, Theis FJ, Samakovlis C, Meyer KB, Nawijn MC.

The European respiratory journal, 2022

doi:10.1183/13993003.02057-2021.

Expression Atlas update: gene and protein expression in multiple species.

Moreno P, Fexova S, George N, Manning JR, Miao Z, Mohammed S, Muñoz-Pomer A, Fullgrabe A, Bi Y, Bush N, Iqbal H, Kumbham U, Solovyev A, Zhao L, Prakash A, García-Seisdedos D, Kundu DJ, Wang S, Walzer M, Clarke L, Osumi-Sutherland D, Tello-Ruiz MK, Kumari S, Ware D, Eliasova J, Arends MJ, Nawijn MC, Meyer K, Burdett T, Marioni J, Teichmann S, Vizcaíno JA, Brazma A, Papatheodorou I.

Nucleic acids research, 2022

doi:10.1093/nar/gkab1030.

A proteomics sample metadata representation for multiomics integration and big data analysis.

Dai C, Füllgrabe A, Pfeuffer J, Solovyeva EM, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, Locard-Paulet M, Turewicz M, Eisenacher M, Uszkoreit J, Van Den Bossche T, Schwämmle V, Webel H, Schulze S, Bouyssié D, Jayaram S, Duggineni VK, Samaras P, Wilhelm M, Choi M, Wang M, Kohlbacher O, Brazma A, Papatheodorou I, Bandeira N, Deutsch EW, Vizcaíno JA, Bai M, Sachsenberg T, Levitsky LI, Perez-Riverol Y.

Nature communications, 2021

doi:10.1038/s41467-021-26111-3.

A proteomics sample metadata representation for multiomics integration, and big data analysis

Dai C, Füllgrabe A, Pfeuffer J, Solovyeva E, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, Locard-Paulet M, Turewicz M, Eisenacher M, Uszkoreit J, Van Den Bossche T, Schwämmle V, Webel H, Schulze S, Bouyssié D, Jayaram S, Duggineni VK, Samaras P, Wilhelm M, Choi M, Wang M, Kohlbacher O, Brazma A, Papatheodorou I, Bandeira N, Deutsch EW, Vizcaíno JA, Bai M, Sachsenberg T, Levitsky L, Perez-Riverol Y.

Preprint, 2021

doi:10.1101/2021.05.21.445143.

User-friendly, scalable tools and workflows for single-cell RNA-seq analysis.

Moreno P, Huang N, Manning JR, Mohammed S, Solovyev A, Polanski K, Bacon W, Chazarra R, Talavera-López C, Doyle MA, Marnier G, Grüning B, Rasche H, George N, Fexova SK, Alibi M, Miao Z, Perez-Riverol Y, Haeussler M, Brazma A, Teichmann S, Meyer KB, Papatheodorou I.

Nature methods, 2021

doi:10.1038/s41592-021-01102-w.

From ArrayExpress to BioStudies.

Sarkans U, Füllgrabe A, Ali A, Athar A, Behrangi E, Diaz N, Fexova S, George N, Iqbal H, Kurri S, Munoz J, Rada J, Papatheodorou I, Brazma A.

Nucleic acids research, 2021

doi:10.1093/nar/gkaa1062.

Guidelines for reporting single-cell RNA-seq experiments.

Füllgrabe A, George N, Green M, Nejad P, Aronow B, Fexova SK, Fischer C, Freeberg MA, Huerta L, Morrison N, Scheuermann RH, Taylor D, Vasilevsky N, Clarke L, Gehlenborg N, Kent J, Marioni J, Teichmann S, Brazma A, Papatheodorou I.

Nature biotechnology, 2020

doi:10.1038/s41587-020-00744-z.

A user guide for the online exploration and visualization of PCAWG data.

Goldman MJ, Zhang J, Fonseca NA, Cortés-Ciriano I, Xiang Q, Craft B, Piñeiro-Yáñez E, O'Connor BD, Bazant W, Barrera E, Muñoz-Pomer A, Petryszak R, Füllgrabe A, Al-Shahrour F, Keays M, Haussler D, Weinstein JN, Huber W, Valencia A, Park PJ, Papatheodorou I, Zhu J, Ferretti V, Vazquez M.

Nature communications, 2020

doi:10.1038/s41467-020-16785-6.

A single-cell RNA-seq Training and Analysis Suite using the Galaxy Framework

Tekman M, Batut B, Ostrovsky A, Antoniewski C, Clements D, Ramirez F, Etherington GJ, Hotz H, Scholtalbers J, Manning JR, Bellenger L, Doyle MA, Heydarian M, Huang N, Soranzo N, Moreno P, Mautner S, Papatheodorou I, Nekrutenko A, Taylor J, Blankenberg D, Backofen R, Grüning B.

Preprint, 2020

doi:10.1101/2020.06.06.137570.

Expression Atlas update: from tissues to single cells.

Papatheodorou I, Moreno P, Manning J, Fuentes AM, George N, Fexova S, Fonseca NA, Füllgrabe A, Green M, Huang N, Huerta L, Iqbal H, Jianu M, Mohammed S, Zhao L, Jarnuczak AF, Jupp S, Marioni J, Meyer K, Petryszak R, Prada Medina CA, Talavera-López C, Teichmann S, Vizcaino JA, Brazma A.

Nucleic acids research, 2020

doi:10.1093/nar/gkz947.

Ensembl Genomes 2020-enabling non-vertebrate genomic research.

Howe KL, Contreras-Moreira B, De Silva N, Maslen G, Akanni W, Allen J, Alvarez-Jarreta J, Barba M, Bolser DM, Cambell L, Carbajo M, Chakiachvili M, Christensen M, Cummins C, Cuzick A, Davis P, Fexova S, Gall A, George N, Gil L, Gupta P, Hammond-Kosack KE, Haskell E, Hunt SE, Jaiswal P, Janacek SH, Kersey PJ, Langridge N, Maheswari U, Maurel T, McDowall MD, Moore B, Muffato M, Naamati G, Naithani S, Olson A, Papatheodorou I, Patricio M, Paulini M, Pedro H, Perry E, Preece J, Rosello M, Russell M, Sitnik V, Staines DM, Stein J, Tello-Ruiz MK, Trevanion SJ, Urban M, Wei S, Ware D, Williams G, Yates AD, Flicek P.

Nucleic acids research, 2020

doi:10.1093/nar/gkz890.

Common and distinct transcriptional signatures of mammalian embryonic lethality.

Collins JE, White RJ, Staudt N, Sealy IM, Packham I, Wali N, Tudor C, Mazzeo C, Green A, Siragher E, Ryder E, White JK, Papatheodoru I, Tang A, Füllgrabe A, Billis K, Geyer SH, Weninger WJ, Galli A, Hemberger M, Stemple DL, Robertson E, Smith JC, Mohun T, Adams DJ, Busch-Nentwich EM.

Nature communications, 2019

doi:10.1038/s41467-019-10642-x.

Gramene 2018: unifying comparative genomics and pathway resources for plant research.

Tello-Ruiz MK, Naithani S, Stein JC, Gupta P, Campbell M, Olson A, Wei S, Preece J, Geniza MJ, Jiao Y, Lee YK, Wang B, Mulvaney J, Chougule K, Elser J, Al-Bader N, Kumari S, Thomason J, Kumar V, Bolser DM, Naamati G, Tapanari E, Fonseca N, Huerta L, Iqbal H, Keays M, Munoz-Pomer Fuentes A, Tang A, Fabregat A, D'Eustachio P, Weiser J, Stein LD, Petryszak R, Papatheodorou I, Kersey PJ, Lockhart P, Taylor C, Jaiswal P, Ware D.

Nucleic acids research, 2018

doi:10.1093/nar/gkx1111.

A user’s guide to the online resources for data exploration, visualization, and discovery for the Pan-Cancer Analysis of Whole Genomes project (PCAWG)

Goldman M, Zhang J, Fonseca NA, Cortés-Ciriano I, Xiang Q, Craft B, Piñeiro-Yáñez E, O’Connor BD, Bazant W, Barrera E, Muñoz-Pomer A, Petryszak R, Füllgrabe A, Al-Shahrour F, Keays M, Haussler D, Weinstein JN, Huber W, Valencia A, Park PJ, Papatheodorou I, Zhu J, Ferretti V, Vazquez M, on behalf of the PCAWG Portals and Visualization Working Group, the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network.

Preprint, 2017

doi:10.1101/163907.

Open Targets: a platform for therapeutic target identification and validation.

Koscielny G, An P, Carvalho-Silva D, Cham JA, Fumis L, Gasparyan R, Hasan S, Karamanis N, Maguire M, Papa E, Pierleoni A, Pignatelli M, Platt T, Rowland F, Wankar P, Bento AP, Burdett T, Fabregat A, Forbes S, Gaulton A, Gonzalez CY, Hermjakob H, Hersey A, Jupe S, Kafkas Ş, Keays M, Leroy C, Lopez FJ, Magarinos MP, Malone J, McEntyre J, Munoz-Pomer Fuentes A, O'Donovan C, Papatheodorou I, Parkinson H, Palka B, Paschall J, Petryszak R, Pratanwanich N, Sarntivijal S, Saunders G, Sidiropoulos K, Smith T, Sondka Z, Stegle O, Tang YA, Turner E, Vaughan B, Vrousgou O, Watkins X, Martin MJ, Sanseau P, Vamathevan J, Birney E, Barrett J, Dunham I.

Nucleic acids research, 2016

doi:10.1093/nar/gkw1055.

Computational biology for ageing.

Wieser D, Papatheodorou I, Ziehm M, Thornton JM.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2011

doi:10.1098/rstb.2010.0286.

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