Oriol Fornes
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JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework
A Khan, O Fornes, A Stigliani, M Gheorghe, JA Castro-Mondragon, ...
Nucleic acids research 46 (D1), D260-D266, 2018
JASPAR 2020: update of the open-access database of transcription factor binding profiles
O Fornes, JA Castro-Mondragon, A Khan, R Van der Lee, X Zhang, ...
Nucleic acids research 48 (D1), D87-D92, 2020
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles
A Mathelier, O Fornes, DJ Arenillas, C Chen, G Denay, J Lee, W Shi, ...
Nucleic acids research 44 (D1), D110-D115, 2016
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles
JA Castro-Mondragon, R Riudavets-Puig, I Rauluseviciute, ...
Nucleic acids research 50 (D1), D165-D173, 2022
Backup in gene regulatory networks explains differences between binding and knockout results
A Gitter, Z Siegfried, M Klutstein, O Fornes, B Oliva, I Simon, Z Bar‐Joseph
Molecular systems biology 5 (1), 276, 2009
Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis
SK Sieberts, F Zhu, J García-García, E Stahl, A Pratap, G Pandey, ...
Nature communications 7, 12460, 2016
Evaluating the impact of single nucleotide variants on transcription factor binding
W Shi, O Fornes, A Mathelier, WW Wasserman
Nucleic acids research 44 (21), 10106-10116, 2016
Knowledge environments representing molecular entities for the virtual physiological human
M Hofmann-Apitius, J Fluck, L Furlong, O Fornes, C Kolářik, S Hanser, ...
Philosophical Transactions of the Royal Society A: Mathematical, Physical …, 2008
Networks of Protein-Protein Interactions: From Uncertainty to Molecular Details
J Garcia‐Garcia, J Bonet, E Guney, O Fornes, J Planas, B Oliva
Molecular Informatics 31 (5), 342-362, 2012
On the use of knowledge-based potentials for the evaluation of models of protein–protein, protein–DNA, and protein–RNA interactions
O Fornes, J Garcia-Garcia, J Bonet, B Oliva
Advances in protein chemistry and structural biology 94, 77-120, 2014
Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study
G Ambrosini, I Vorontsov, D Penzar, R Groux, O Fornes, DD Nikolaeva, ...
Genome biology 21 (1), 1-18, 2020
Cross-species examination of X-chromosome inactivation highlights domains of escape from silencing
BP Balaton, O Fornes, WW Wasserman, CJ Brown
Epigenetics & chromatin 14 (1), 1-17, 2021
New MiniPromoter Ple345 (NEFL) Drives Strong and Specific Expression in Retinal Ganglion Cells of Mouse and Primate Retina
EM Simpson, AJ Korecki, O Fornes, TJ McGill, JL Cueva-Vargas, ...
Human gene therapy 30 (3), 257-272, 2019
ModLink+: improving fold recognition by using protein–protein interactions
O Fornes, R Aragues, J Espadaler, MA Marti-Renom, A Sali, B Oliva
Bioinformatics 25 (12), 1506-1512, 2009
c-Myc is a novel Leishmania virulence factor by proxy that targets the host miRNA system and is essential for survival in human macrophages
L Colineau, U Lambertz, O Fornes, WW Wasserman, NE Reiner
Journal of Biological Chemistry 293 (33), 12805-12819, 2018
Gene expression models based on transcription factor binding events confer insight into functional cis-regulatory variants
W Shi, O Fornes, WW Wasserman
Bioinformatics 35 (15), 2610-2617, 2019
MANTA2, update of the Mongo database for the analysis of transcription factor binding site alterations
O Fornes, M Gheorghe, PA Richmond, DJ Arenillas, WW Wasserman, ...
Scientific data 5 (1), 1-7, 2018
Biologically relevant transfer learning improves transcription factor binding prediction
G Novakovsky, M Saraswat, O Fornes, S Mostafavi, WW Wasserman
Genome biology 22 (1), 1-25, 2021
A GO catalogue of human DNA-binding transcription factors
RC Lovering, P Gaudet, ML Acencio, A Ignatchenko, A Jolma, O Fornes, ...
Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1864 (11-12 …, 2021
SPServer: split-statistical potentials for the analysis of protein structures and protein–protein interactions
J Aguirre-Plans, A Meseguer, R Molina-Fernandez, MA Marín-López, ...
BMC bioinformatics 22 (1), 1-13, 2021
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