We aim to rapidly publish high impact research publications and openly share our data as part of our commitment to supporting pre-competitive research in drug discovery. We also publish review articles on relevant topics in drug discovery.
Research publications
Associations on the Fly, a new feature aiming to facilitate exploration of the Open Targets Platform evidence
Cruz-Castillo, C., et al.
Bioinformatics
Open Access
Full text available (Europe PMC)
Preprint available
Decoding MASLD Progression: A Molecular Trajectory-Based Framework for Modelling Disease Dynamics
Kamzolas, I. et al.
bioRxiv
Temporal trends in novel drug target discovery reveal the increasing importance of human genetic data
Falaguera, M. et al.
Research Square
Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery
Buniello, A et al.
Nucleic Acids Research
Simulating CD8 T Cell Exhaustion: A Comprehensive Approach
Manrique-Rincon, A. et al.
bioRxiv
Open Access
DOI: 10.1101/2024.09.06.611697
Preprint available
Genetic factors associated with reasons for clinical trial stoppage
Razuvayevskaya, O et al.
Nature Genetics
Open Access
Full text available (Europe PMC)
Preprint available
USP18 modulates lupus risk via negative regulation of interferon response
Freimann, K. et al.
medRxiv
Open Access
Full text available (Europe PMC)
Preprint available
Predicted mechanistic impacts of human protein missense variants
Janes, J. et al.
bioRxiv
Open Access
Full text available (Europe PMC)
Preprint available
Single-cell and spatial transcriptomics analysis of non-small cell lung cancer
De Zuani, M., Xue, H. et al.
Nature Communications
Acquisition of epithelial plasticity in human chronic liver disease
Gribben, C. et al.
Nature
ProtVar: mapping and contextualizing human missense variation
Stephenson, JD. et al
Nucleic Acids Research
An atlas of protein-protein associations of human tissues prioritizes candidate disease genes
Laman Trip, DS. et al
bioRxiv
CATD: a reproducible pipeline for selecting cell-type deconvolution methods across tissues
Vathrakokoili Pournara, A et al.
Bioinformatics Advances
Open Access
Full text available (Europe PMC)
Preprint available
scSNV-seq: high-throughput phenotyping of single nucleotide variants by coupled single-cell genotyping and transcriptomics
Cooper, SE., Coelho, MA., Strauss, ME., et al.
Genome Biology
A comprehensive clinically informed map of dependencies in cancer cells and framework for target prioritization
Pacini, C. et al.
Cancer Cell
Integrated Proteomics analysis of baseline protein expression in pig tissues
Wang, S. et al
J. Proteome Res.
Open Access
Full text available (Europe PMC)
Preprint available
An Alzheimer's disease-associated common regulatory variant in PTK2B has causal effects on microglial function
Bello, E. et al.
bioRxiv
Integrative GWAS and co-localisation analysis suggests novel genes associated with age-related multimorbidity
West, C. et al.
Scientific Data
eQTL Catalogue 2023: New datasets, X chromosome QTLs, and improved detection and visualisation of transcript-level QTLs
Kerimov, N et al.
PLOS Genetics
Single-cell RNA sequencing reveals dysregulated cellular programmes in the inflamed epithelium of Crohns disease patients
Krzak, M., Alegbe, T., Taylor, L. et al.
medRxiv
Open Access
DOI: 10.1101/2023.09.06.23295056
Preprint available
HNRNPH1 regulates the neuroprotective cold-shock protein RBM3 expression through poison exon exclusion
Lin, JQ, Khuperkar, D. et al
EMBO Journal
Screening for functional regulatory variants in open chromatin using GenIE-ATAC
Cooper, S et al.
Nucleic Acids Research
CRISPR-Cas9 genetic screen leads to the discovery of L-Moses, a KAT2B inhibitor that attenuates Tunicamycin-mediated neuronal cell death
Pavlou, S. et al
Scientific Reports
Network expansion of genetic associations defines a pleiotropy map of human cell biology
Barrio-Hernandez, I. et al
Nature Genetics
Open Access
Full text available (Europe PMC)
Preprint available
Base editing screens map mutations affecting interferon-_ signaling in cancer
Coelho, M et al.
Cancer Cell
Open Access
Full text available (Europe PMC)
Preprint available
The next-generation Open Targets Platform: reimagined, redesigned, rebuilt
Ochoa, D et al.
Nucleic Acids Research
Integrated View of Baseline Protein Expression in Human Tissues
Prakash, A et al.
Journal of Proteome Research
The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource
Sollis, E et al.
Nucleic Acids Research
Derivation of nociceptive sensory neurons from hiPSCs with early patterning and temporally controlled NEUROG2 overexpression
Plumbly, W et al.
Cell Reports Methods
Single-cell transcriptomics defines an improved, validated monoculture protocol for differentiation of human iPSC to microglia
Washer, S et al.
Scientific Reports
Human genetics evidence supports two-thirds of the 2021 FDA-approved drugs
Ochoa, D et al.
Nature Reviews Drug Discovery
Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues
Shengbo, W et al.
PLOS Computational Biology
Immune disease risk variants regulate gene expression dynamics during CD4+ T cell activation
Soskic, B, Cano-Gamez, E et al.
Nature Genetics
Open Access
DOI: 10.1038/s41588-022-01066-3
Preprint available
Robust temporal map of human in vitro myelopoiesis using single-cell genomics
Alsinet, C et al.
Nature Communications
Open Access
Full text available (Europe PMC)
Preprint available
Whole-exome sequencing identifies rare genetic variants associated with human plasma metabolites
Bomba, L et al.
American Journal of Human Genetics
An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci
Mountjoy, E et al.
Nature Genetics
A compendium of uniformly processed human gene expression and splicing quantitative trait loci
Kerimov, N et al.
Nature Genetics
A proteome-wide genetic investigation identifies several SARS-CoV-2-exploited host targets of clinical relevance
Anisul, M et al.
eLife
The PROTACtable genome
Schneider, M et al.
Nature Reviews Drug Discovery
A map of transcriptional heterogeneity and regulatory variation in human microglia
Young, A M H et al.
Nature Genetics
Integrated cross-study datasets of genetic dependencies in cancer
Pacini, C et al.
Nature Communications
Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation
Jerber, J et al.
Nature Genetics
Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer’s disease risk genes
Schwartzentruber, J et al.
Nature Genetics
Open Targets Platform: supporting systematic drug–target identification and prioritisation
Ochoa, D et al.
Nucleic Acids Research
Screening for functional transcriptional and splicing regulatory variants with GenIE
Cooper, S et al.
Nucleic Acids Research
Project Score database: a resource for investigating cancer cell dependencies and prioritizing therapeutic targets
Dwane, L et al.
Nucleic Acids Research
Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics
Ghoussaini, M et al.
Nucleic Acids Research
Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms
Gordon, D et al.
Science
Single-Cell Transcriptomics of Parkinson’s Disease Human In Vitro Models Reveals Dopamine Neuron-Specific Stress Responses
Fernandes, H et al.
Cell Reports
Using Reactome to build an autophagy mechanism knowledgebase
Varusai, TM et al.
Autophagy
CELLector: Genomics-Guided Selection of Cancer In Vitro Models
Najgebauer, H et al.
Cell Systems
Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4+ T cells to cytokines
Cano-Gamez, E et al.
Nature Communications
The Open Targets post-GWAS analysis pipeline
Peat, G et al.
Bioinformatics
Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets
Dempster JM & Pacini C et al.
Nature Communications
Chromatin activity at GWAS loci identifies T cell states driving complex immune diseases
Soskic B et al.
Nature Genetics
A cellular census of human lungs identifies novel cell states in health and in asthma
Vieira Braga, FA et al.
Nature Medicine
Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR-Cas9 screening
Picco, G et al.
Nature Communications
Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens
Behan F et al.
Nature
The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019
Buniello, A et al.
Nucleic Acids Research
ChEMBL: towards direct deposition of bioassay data
Mendez, D et al.
Nucleic Acids Research
Open Targets Platform: new developments and updates two years on
Carvalho-Silva, D et al.
Nucleic Acids Research
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes
Meldal, B et al.
Nucleic Acids Research
The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers
Sondka, Z et al.
Nature Reviews Cancer
Uncovering new disease indications for G-protein coupled receptors and their endogenous ligands
Freudenberg, JM et al.
BMC Bioinformatics
Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting
Iorio, F et al.
BMC Genomics
Pathway-based dissection of the genomic heterogeneity of cancer hallmarks’ acquisition with SLAPenrich
Iorio, F et al.
Scientific Reports
Interleukins and their signaling pathways in the Reactome biological pathway database
Jupe, S et al.
The Journal of Allergy and Clinical Immunology
Designing an intuitive web application for drug discovery scientists
Karamanis, N et al.
Drug Discovery Today
Expression Atlas: gene and protein expression across multiple studies and organisms
Papatheodorou, I et al.
Nucleic Acids Research
Comparison, alignment, and synchronization of cell line information between CLO and EFO
Ong, E et al.
BMC Bioinformatics
Uncovering novel repositioning opportunities using the Open Targets platform
Khaladkar, M et al.
Drug Discovery Today
In silico prediction of novel therapeutic targets using gene–disease association data
Ferrero, E et al.
Journal of Translational Medicine
Reactome enhanced pathway visualization
Sidiropoulos, K et al.
Bioinformatics
ProtVista: visualization of protein sequence annotations
Watkins, X et al.
Bioinformatics
Reactome pathway analysis: a high-performance in-memory approach
Fabregat, A et al.
BMC Bioinformatics
Open Targets: a platform for therapeutic target identification and validation
Koscielny, G et al.
Nucleic Acids Research
Transcription factor activities enhance markers of drug sensitivity in cancer
Garcia-Alonso, L et al.
Cancer Research
Fine-mapping inflammatory bowel disease loci to single-variant resolution
Huang, H et al.
Nature
Literature evidence in open targets - a target validation platform
Kafkas, S et al.
Journal of Biomedical Semantics volume
TnT: a set of libraries for visualizing trees and track-based annotations for the web
Pignatelli, M
Bioinformatics (Oxford, England)
Warped Matrix Factorisation for Multi-view Data Integration
Pratanwanich, N et al.
Part of the Lecture Notes in Computer Science book series
Webulous and the Webulous Google Add-On - a web service and application for ontology building from templates
Jupp, S et al.
Journal of Biomedical Semantics
Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation
Sarntivijai, S et al.
Journal of Biomedical Semantics
Review articles
Computational estimation of quality and clinical relevance of cancer cell lines
Trastulla, L et al.
Molecular Systems Biology
Mining a GWAS of Severe Covid-19
Karim, M et al.
The New England Journal of Medicine
From GWAS to Function: Using Functional Genomics to Identify the Mechanisms Underlying Complex Diseases
Cano-Gamez, E & Trynka, G
Frontiers in Genetics
Ten simple rules for making training materials FAIR
Garcia, L et al.
PLoS Computational Biology
Ten simple rules for delivering live distance training in bioinformatics across the globe using webinars
Carvalho-Silva, D et al.
PLoS Computational Biology
Computational approaches for interpreting scRNAâ€seq data
Rostom, R et al.
Febs Letters
Harnessing public domain data to discover and validate therapeutic targets
Reisdorf WC et al.
Expert Opinion on Drug Discovery
The impact of rare and low-frequency genetic variants in common disease
Bomba, L et al.
Genome Biology
Use of Biomedical Ontologies for Integration of Biological Knowledge for Learning and Prediction of Adverse Drug Reactions
Zaman, S et al.
Gene Regulation and Systems Biology
Genetics and immunity in the era of single-cell genomics
Vieira Braga FA et al.
Human Molecular Genetics
Using human genetics to make new medicines
Barrett, JC et al.
Nature Reviews Genetics
Understanding inflammatory bowel disease via immunogenetics
de Lange, KM et al.
Journal of Autoimmunity
Strategies for fine-mapping complex traits
Spain, SL et al.
Human Molecular Genetics
Associated publications
EMBL's European Bioinformatics Institute (EMBL-EBI) in 2024
Thakur, M. et al.
Nucleic Acids Research
Base editing screens define the genetic landscape of cancer drug resistance mechanisms
Coelho, M et al.
Nature Genetics
Archetypes of Open Science Partnerships: connecting aims and means in open biomedical research collaborations
Norn, MT. et al
Humanities and Social Sciences Communications
Can AlphaFold's breakthrough in protein structure help decode the fundamental principles of adaptive cellular immunity?
McMaster, B. et al.
Nat Methods
CMAT: ClinVar Mapping and Annotation Toolkit
Shen, A. et al.
Bioinformatics Advances
Towards a structurally resolved human protein interaction network
Burke, DF, Bryant, P, Barrio-Hernandez, I, Memon, D, Pozzati, G, et al.
Nat Struct Mol Biol
EMBL's European Bioinformatics Institute (EMBL-EBI) in 2023
Thakur, M. et al.
Nucleic Acids Research