Irene Papatheodorou (I Papatheodorou, Irene Papatheodoru)

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 26

Top Topics

Idiopathic Pulmonary Fibrosis

Gene Expression

Top Venues

Nature communications

BMC medical informatics and decision making

NAR genomics and bioinformatics

Bioinformatics advances

This page only lists publications with an associated author ORCID identifier.

Publications

Anna Vathrakokoili-Pournara, Zhichiao Miao, Ozgur Yilimaz Beker, Nadja Nolte, Alvis Brazma, Irene Papatheodorou
CATD: a reproducible pipeline for selecting cell-type deconvolution methods across tissues. Bioinformatics advances 4 (1) (2024)
Francesca Nadalin, M J Marzi, M Pirra Piscazzi, Patricio Fuentes-Bravo, Simone Proccacia, M Climent, P Bonetti, C Rubolino, B Giuliani, Irene Papatheodorou, John C Marioni, Francesco Nicassio
Multi-omic lineage tracing predicts the transcriptional, epigenetic and genetic determinants of cancer evolution. Nature communications 15 (1) (2024)
Anna Vathrakokoili-Pournara, Zhichiao Miao, Ozgur Yilimaz Beker, Nadja Nolte, Alvis Brazma, Irene Papatheodorou
CATD: a reproducible pipeline for selecting cell-type deconvolution methods across tissues. Bioinformatics advances 4 (1) (2024)
Anna Vathrakokoili-Pournara, Zhichiao Miao, Ozgur Yilimaz Beker, Nadja Nolte, Alvis Brazma, Irene Papatheodorou
CATD: a reproducible pipeline for selecting cell-type deconvolution methods across tissues. Bioinformatics advances 4 (1) (2024)
Madhulika Mishra, Lucas Barck, Pablo Moreno, Guillaume Heger, Yuyao Song, Janet M Thornton, Irene Papatheodorou
SelectBCM tool: a batch evaluation framework to select the most appropriate batch-correction methods for bulk transcriptome analysis. NAR genomics and bioinformatics 5 (1) (2023)
Albert Burger, Richard A Baldock, David J Adams, Shahida Din, Irene Papatheodorou, Michael Glinka, Bill Hill, Derek Houghton, Mehran Sharghi, Michael Wicks, Mark J Arends
Towards a clinically-based common coordinate framework for the human gut cell atlas: the gut models. BMC medical informatics and decision making 23 (1) (2023)
Madhulika Mishra, Lucas Barck, Pablo Moreno, Guillaume Heger, Yuyao Song, Janet M Thornton, Irene Papatheodorou
SelectBCM tool: a batch evaluation framework to select the most appropriate batch-correction methods for bulk transcriptome analysis. NAR genomics and bioinformatics 5 (1) (2023)
Iona Campbell, Michael Glinka, Fadlo Shaban, Kathryn J Kirkwood, Francesca Nadalin, David Adams, Irene Papatheodorou, Albert Burger, Richard A Baldock, Mark J Arends, Shahida Din
The Promise of Single-Cell RNA Sequencing to Redefine the Understanding of Crohn's Disease Fibrosis Mechanisms. Journal of clinical medicine 12 (12) (2023)
Madhulika Mishra, Lucas Barck, Pablo Moreno, Guillaume Heger, Yuyao Song, Janet M Thornton, Irene Papatheodorou
SelectBCM tool: a batch evaluation framework to select the most appropriate batch-correction methods for bulk transcriptome analysis. NAR genomics and bioinformatics 5 (1) (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 Kwame Abayie Agyeman, Coco R Beudeker, Karen Brengel-Pesce, Enitan D Carrol, Michael J Carter, Tisham De, Irini Eleftheriou, Marieke Emonts, Cristina Epalza, Pantelis Georgiou, Ronald De Groot, Katy Fidler, Colin Fink, Daniëlle van Keulen, Taco Kuijpers, Henriette A Moll, Irene Papatheodorou, Stephane Paulus, Marko Pokorn, Andrew J Pollard, Irene Rivero-Calle, Pablo Rojo, Fatou Secka, Luregn J Schlapbach, Adriana H Tremoulet, Maria Tsolia, Effua Usuf, Michiel Van Der Flier, Ulrich von Both, Clementien Vermont, Shunmay Yeung, Dace Zavadska, Werner Zenz, Lachlan J M Coin, Aubrey Cunnington, Jane C Burns, Victoria Wright, Federico Martinon-Torres, Jethro Adam Herberg, Jesus Rodriguez Manzano, Myrsini Kaforou, Michael Levin, null null
Diagnosis of multisystem inflammatory syndrome in children by a whole-blood transcriptional signature. Journal of the Pediatric Infectious Diseases Society (2023)
Albert Burger, Richard A Baldock, David J Adams, Shahida Din, Irene Papatheodorou, Michael Glinka, Bill Hill, Derek Houghton, Mehran Sharghi, Michael Wicks, Mark J Arends
Towards a clinically-based common coordinate framework for the human gut cell atlas: the gut models. BMC medical informatics and decision making 23 (1) (2023)
Iona Campbell, Michael Glinka, Fadlo Shaban, Kathryn J Kirkwood, Francesca Nadalin, David Adams, Irene Papatheodorou, Albert Burger, Richard A Baldock, Mark J Arends, Shahida Din
The Promise of Single-Cell RNA Sequencing to Redefine the Understanding of Crohn's Disease Fibrosis Mechanisms. Journal of clinical medicine 12 (12) (2023)
Matthias Zilbauer, Kylie Renee James, Mandeep Kaur, Sebastian Pott, Zhixin Li, Albert Burger, Jay R Thiagarajah, Joseph Burclaff, Frode L Jahnsen, Francesca Perrone, Alexander D Ross, Gianluca Matteoli, Nathalie Stakenborg, Tomohisa Sujino, Andreas E Moor, Raquel Bartolomé Casado, Espen S Bækkevold, Ran Zhou, Bingqing Xie, Ken S Lau, Shahida Din, Scott T Magness, Qiuming Yao, Semir Beyaz, Mark J Arends, Alexandre Denadai-Souza, Lori A Coburn, Jellert T Gaublomme, Richard A Baldock, Irene Papatheodorou, José Ordovas-Montañes, Guy E Boeckxstaens, Anna Hupalowska, Sarah A Teichmann, Aviv Regev, Ramnik J Xavier, Alison Simmons, Michael Paul Snyder, Keith T Wilson, null null, null null
A Roadmap for the Human Gut Cell Atlas. Nature reviews. Gastroenterology & hepatology (2023)
Albert Burger, Richard A Baldock, David J Adams, Shahida Din, Irene Papatheodorou, Michael Glinka, Bill Hill, Derek Houghton, Mehran Sharghi, Michael Wicks, Mark J Arends
Towards a clinically-based common coordinate framework for the human gut cell atlas: the gut models. BMC medical informatics and decision making 23 (1) (2023)
Yuyao Song, Zhichiao Miao, Alvis Brazma, Irene Papatheodorou
Benchmarking strategies for cross-species integration of single-cell RNA sequencing data. Nature communications 14 (1) (2023)
Albert Burger, Richard A Baldock, David J Adams, Shahida Din, Irene Papatheodorou, Michael Glinka, Bill Hill, Derek Houghton, Mehran Sharghi, Michael Wicks, Mark J Arends
Towards a clinically-based common coordinate framework for the human gut cell atlas: the gut models. BMC medical informatics and decision making 23 (1) (2023)
Matthew Thakur, Alex Bateman, Cath Brooksbank, Mallory Ann Freeberg, Melissa Harrison, Matthew Hartley, Thomas M Keane, Gerard Kleywegt, Andrew Leach, Mariia Levchenko, Sarah Morgan, Ellen M McDonagh, Sandra E Orchard, Irene Papatheodorou, Sameer Velankar, Juan Antonio Vizcaino, Rick Witham, Barbara Zdrazil, Johanna McEntyre
EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022. Nucleic acids research (2022)
Mathias Walzer, David García-Seisdedos, Ananth Prakash, Paul Brack, Peter Crowther, Robert L Graham, Nancy George, Suhaib Mohammed, Pablo Moreno, Irene Papatheodorou, Simon J Hubbard, Juan Antonio Vizcaino
Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas. Scientific data 9 (1) (2022)
Pablo Moreno, Ni Huang, Jonathan R Manning, Suhaib Mohammed, Andrey Solovyev, Krzysztof Polański, Wendi Bacon, Ruben Chazarra, Carlos Talavera-López, Maria A Doyle, Guilhem Marnier, Bjoern Andreas Gruening, Helena Rasche, Nancy George, Silvie Korena Fexova, Mohamed Alibi, Zhichiao Miao, Yasset Perez Riverol, Maximilian Haeussler, Alvis Brazma, Sarah A Teichmann, Kerstin B Meyer, Irene Papatheodorou
User-friendly, scalable tools and workflows for single-cell RNA-seq analysis. Nature methods 18 (4) (2021)
Andrew F Jarnuczak, Hanna Najgebauer, Mitra Parissa Barzine, Deepti J Kundu, Fatemeh Ghavidel, Yasset Perez Riverol, Irene Papatheodorou, Alvis Brazma, Juan Antonio Vizcaino
An integrated landscape of protein expression in human cancer. Scientific data 8 (1) (2021)
Pablo Moreno, Silvie Fexova, Nancy George, Jonathan R Manning, Zhichiao Miao, Suhaib Mohammed, Alfonso Muñoz-Pomer, Anja Füllgrabe, Yalan Bi, Natassja Bush, Haider Iqbal, Upendra Kumbham, Andrey Solovyev, Lingyun Zhao, Ananth Prakash, David García-Seisdedos, Deepti J 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 Meyer, Tony Burdett, John C Marioni, Sarah Teichmann, Juan Antonio Vizcaino, Alvis Brazma, Irene Papatheodorou
Expression Atlas update: gene and protein expression in multiple species. Nucleic acids research (2021)
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, Daniel R Zerbino, Kaur Alasoo
A compendium of uniformly processed human gene expression and splicing quantitative trait loci. Nature genetics 53 (9) (2021)
Anja Füllgrabe, Nancy George, Matthew Green, Parisa Nejad, Bruce J Aronow, Silvie Korena Fexova, Clay Fischer, Mallory Ann Freeberg, Laura Huerta, Norman Morrison, Richard H Scheuermann, Deanne M Taylor, Nicole A Vasilevsky, Laura Clarke, Nils Gehlenborg, Jim Kent, John C Marioni, Sarah A Teichmann, Alvis Brazma, Irene Papatheodorou
Guidelines for reporting single-cell RNA-seq experiments. Nature biotechnology 38 (12) (2021)
Chengxin Dai, Anja Füllgrabe, Julianus Pfeuffer, Elizaveta M Solovyeva, Jingwen Deng, Pablo Moreno, Selvakumar Kamatchinathan, Deepti Jaiswal Kundu, Nancy George, Silvie Fexova, Bjoern Andreas Gruening, Melanie Christine Föll, Johannes Griss, Marc Vaudel, Enrique Audain, Marie Locard-Paulet, Michael Turewicz, Martin Eisenacher, Julian Uszkoreit, Tim Van Den Bossche, Veit Schwämmle, Henry Webel, Stefan Schulze, David Bouyssié, Savita Jayaram, Vinay Kumar Duggineni, Patroklos Samaras, Mathias Wilhelm, Meena Choi, Mingxun Wang, Oliver Kohlbacher, Alvis Brazma, Irene Papatheodorou, Nuno Bandeira, Eric W Deutsch, Juan Antonio Vizcaino, Mingze Bai, Timo Sachsenberg, Lev I Levitsky, Yasset Perez Riverol
A proteomics sample metadata representation for multiomics integration and big data analysis. Nature communications 12 (1) (2021)
Mary J Goldman, Junjun Zhang, Nuno A Fonseca, Isidro Cortes-Ciriano, Linda Xiang, Brian Craft, Elena Piñeiro-Yañez, Brian D O'Connor, Wojciech Bazant, Elisabet Barrera, Alfonso Muñoz-Pomer, Robert Petryszak, Anja Füllgrabe, Fátima Al-Shahrour, Maria Keays, David Haussler, John N Weinstein, Wolfgang Huber, Alfonso Valencia, Peter J Park, Irene Papatheodorou, Jingchun Zhu, Vincent Ferretti, Miguel Vazquez
A user guide for the online exploration and visualization of PCAWG data. Nature communications 11 (1) (2020)
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 Papatheodorou, Amy Tang, Anja Füllgrabe, Konstantinos Billis, Stefan H Geyer, Wolfgang J Weninger, Antonella Galli, Myriam Hemberger, Derek L Stemple, Elizabeth J Robertson, James C Smith, Timothy Mohun, David J Adams, Elisabeth M Busch-Nentwich
Common and distinct transcriptional signatures of mammalian embryonic lethality. Nature communications 10 (1) (2019)