Author details

Full Name

Irene Papatheodorou

Affiliation

ORCID

Career Start Year

2004

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37992296	Expression Atlas update: insights from sequencing data at both bulk and single cell level.	Nucleic Acids Res	2024
36793076	Towards a clinically-based common coordinate framework for the human gut cell atlas: the gut models.	BMC Med Inform Decis Mak	2023
36200899	Toward a data infrastructure for the Plant Cell Atlas.	Plant Physiol	2023
38020918	Canonical Wnt and TGF-Î²/BMP signaling enhance melanocyte regeneration but suppress invasiveness, migration, and proliferation of melanoma cells.	Front Cell Dev Biol	2023
37838716	Benchmarking strategies for cross-species integration of single-cell RNA sequencing data.	Nat Commun	2023
36577097	Integrated View of Baseline Protein Expression in Human Tissues.	J Proteome Res	2023
36879900	SelectBCM tool: a batch evaluation framework to select the most appropriate batch-correction methods for bulk transcriptome analysis.		2023
37258747	A Roadmap for the Human Gut Cell Atlas.	Nat Rev Gastroenterol Hepatol	2023
37255317	Diagnosis of Multisystem Inflammatory Syndrome in Children by a Whole-Blood Transcriptional Signature.	J Pediatric Infect Dis Soc	2023
36477213	EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022.	Nucleic Acids Res	2023
37373578	The Promise of Single-Cell RNA Sequencing to Redefine the Understanding of Crohn's Disease Fibrosis Mechanisms.	J Clin Med	2023
35223842	Brain Regeneration Resembles Brain Cancer at Its Early Wound Healing Stage and Diverges From Cancer Later at Its Proliferation and Differentiation Stages.	Front Cell Dev Biol	2022
35714157	Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues.	PLoS Comput Biol	2022
35701420	Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas.	Sci Data	2022
35046942	Single-Cell Analysis Reveals the Immune Characteristics of Myeloid Cells and Memory T Cells in Recovered COVID-19 Patients With Different Severities.	Front Immunol	2022
35239393	Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly.	Science	2022
34850121	Expression Atlas update: gene and protein expression in multiple species.	Nucleic Acids Res	2022
35086829	The discovAIR project: a roadmap towards the Human Lung Cell Atlas.	Eur Respir J	2022
34429851	PathExNET: A tool for extracting pathway expression networks from gene expression statistics.	Computational and Structural Biotechnology Journal	2021
33893311	An integrated landscape of protein expression in human cancer.	Sci Data	2021
33782609	User-friendly, scalable tools and workflows for single-cell RNA-seq analysis.	Nat Methods	2021
33995899	DRscDB: A single-cell RNA-seq resource for data mining and data comparison across species.	Comput Struct Biotechnol J	2021
34244710	UCSC Cell Browser: visualize your single-cell data.	Bioinformatics	2021
33170273	Gramene 2021: harnessing the power of comparative genomics and pathways for plant research.	Nucleic Acids Res	2021
33211879	From ArrayExpress to BioStudies.	Nucleic Acids Res	2021
34675242	Meta-analysis of COVID-19 single-cell studies confirms eight key immune responses.	Sci Rep	2021
34615866	A proteomics sample metadata representation for multiomics integration and big data analysis.	Nat Commun	2021
34493866	A compendium of uniformly processed human gene expression and splicing quantitative trait loci.	Nat Genet	2021
33163496	Comparative Transcriptome Analysis of the Regenerating Zebrafish Telencephalon Unravels a Resource With Key Pathways During Two Early Stages and Activation of Wnt/Î²-Catenin Signaling at the Early Wound Healing Stage.	Frontiers in Cell and Developmental Biology	2020
32424270	Putative cell type discovery from single-cell gene expression data.	Nat Methods	2020
31680153	Plant Reactome: a knowledgebase and resource for comparative pathway analysis.	Nucleic Acids Res	2020
31665515	Expression Atlas update: from tissues to single cells.	Nucleic Acids Res	2020
33188371	Guidelines for reporting single-cell RNA-seq experiments.	Nat Biotechnol	2020
33079170	A single-cell RNA-sequencing training and analysis suite using the Galaxy framework.	Gigascience	2020
32636365	A user guide for the online exploration and visualization of PCAWG data.	Nat Commun	2020
30357387	ArrayExpress update - from bulk to single-cell expression data.	Nucleic Acids Res	2019
29165610	Gramene 2018: unifying comparative genomics and pathway resources for plant research.	Nucleic Acids Res	2018
29165655	Expression Atlas: gene and protein expression across multiple studies and organisms.	Nucleic Acids Res	2018
27899665	Open Targets: a platform for therapeutic target identification and validation.	Nucleic Acids Res	2017
25901272	Linking gene expression to phenotypes via pathway information.	J Biomed Semantics	2015
25064569	Comparison of the mammalian insulin signalling pathway to invertebrates in the context of FOXO-mediated ageing.		2014
25232726	Interplay of dFOXO and two ETS-family transcription factors determines lifespan in Drosophila melanogaster.	PLoS Genetics	2014
24531613	MDL-1, a growth- and tumor-suppressor, slows aging and prevents germline hyperplasia and hypertrophy in C. elegans.	Aging	2014
24516399	DAF-16/FoxO directly regulates an atypical AMP-activated protein kinase gamma isoform to mediate the effects of insulin/IGF-1 signaling on aging in Caenorhabditis elegans.	PLoS Genetics	2014
24932005	Using association rule mining to determine promising secondary phenotyping hypotheses.	Bioinformatics	2014
23624434	Transcriptional feedback in the insulin signalling pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster.	Molecular BioSystems	2013
23251396	Using answer set programming to integrate RNA expression with signalling pathway information to infer how mutations affect ageing.	PLoS ONE	2012
21694719	Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling.	Molecular Systems Biology	2011
21115530	Computational biology for ageing.	Philosophical Transactions of the Royal Society B: Biological Sciences	2011
19948017	A metadata approach for clinical data management in translational genomics studies in breast cancer.	BMC Med Genomics	2009