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Employment (2)

University of British Columbia: Vancouver, British Columbia, CA

2020-06-01 to present | Research Associate (Medical Genetics)
Employment
Source: Self-asserted source
Oriol Fornés

University of British Columbia: Vancouver, BC, CA

2015-06-01 to 2020-05-31 | PostDoctoral Fellow (Medical Genetics)
Employment
Source: Self-asserted source
Oriol Fornés

Education and qualifications (3)

Universitat Pompeu Fabra: Barcelona, Catalunya, ES

2008-09 to 2015-02 | PhD in Biomedicine (Experimental and Health Sciences)
Education
Source: Self-asserted source
Oriol Fornés

Universitat Pompeu Fabra: Barcelona, Catalunya, ES

2006-09 to 2008-10 | Master in Bioinformatics for Health Sciences (Experimental and Health Sciences)
Education
Source: Self-asserted source
Oriol Fornés

Universitat Pompeu Fabra: Barcelona, Catalunya, ES

2001-09 to 2006-09 | Bachelor's degree in Human Biology (Experimental and Health Sciences)
Education
Source: Self-asserted source
Oriol Fornés

Works (31)

Transcriptional reprogramming by mutated IRF4 in lymphoma

Nature Communications
2023-11-07 | Journal article
Contributors: Nikolai Schleussner; Pierre Cauchy; Vedran Franke; Maciej Giefing; Oriol Fornes; Naveen Vankadari; Salam A. Assi; Mariantonia Costanza; Marc A. Weniger; Altuna Akalin et al.
Source: check_circle
Crossref

JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles

2023-10-31 | Other
Contributors: Ieva Rauluseviciute; Romain Blanc Mathieu; Oriol Fornes; Morten Johansen; Rafael Riudavets Puig; Jeremy LUCAS; Jaime Castro-Mondragon; Katalin Ferenc; Vipin Kumar; Roza Berhanu Lemma et al.
Source: check_circle
Crossref

SBILib: a handle for protein modeling and engineering

Bioinformatics
2023-10-03 | Journal article
Contributors: Patrick Gohl; Jaume Bonet; Oriol Fornes; Joan Planas-Iglesias; Narcís Fernandez-Fuentes; Baldo Oliva; Lenore Cowen
Source: check_circle
Crossref

OnTarget: in silico design of MiniPromoters for targeted delivery of expression

Nucleic Acids Research
2023-07-05 | Journal article
Contributors: Oriol Fornes; Tamar V Av-Shalom; Andrea J Korecki; Rachelle A Farkas; David J Arenillas; Anthony Mathelier; Elizabeth M Simpson; Wyeth W Wasserman
Source: check_circle
Crossref

ExplaiNN: interpretable and transparent neural networks for genomics

Genome Biology
2023-06-27 | Journal article
Contributors: Gherman Novakovsky; Oriol Fornes; Manu Saraswat; Sara Mostafavi; Wyeth W. Wasserman
Source: check_circle
Crossref

Refining the genomic determinants underlying escape from X-chromosome inactivation

NAR Genomics and Bioinformatics
2023-03-29 | Journal article
Contributors: Samantha Peeters; Tiffany Leung; Oriol Fornes; Rachelle A Farkas; Wyeth W Wasserman; Carolyn J Brown
Source: check_circle
Crossref

ExplaiNN: interpretable and transparent neural networks for genomics

2022-05-22 | Preprint
Contributors: Gherman Novakovsky; Oriol Fornes; Manu Saraswat; Sara Mostafavi; Wyeth W. Wasserman
Source: check_circle
Crossref

Biologically relevant transfer learning improves transcription factor binding prediction

Genome Biology
2021-12 | Journal article
Contributors: Gherman Novakovsky; Manu Saraswat; Oriol Fornes; Sara Mostafavi; Wyeth W. Wasserman
Source: check_circle
Crossref

In silico discovery of small molecules for efficient stem cell differentiation into definitive endoderm

2021-10-09 | Other
Contributors: Gherman Novakovsky; Shugo Sasaki; Oriol Fornes; Meltem E. Omur; Helen Huang; Nathaniel Lim; Artem Cherkasov; Paul Pavlidis; Sara Mostafavi; Francis C. Lynn et al.
Source: check_circle
Crossref

Human MiniPromoters for ocular-rAAV expression in ON bipolar, cone, corneal, endothelial, Müller glial, and PAX6 cells

Gene Therapy
2021-06-02 | Journal article
Contributors: Andrea J. Korecki; Jorge L. Cueva-Vargas; Oriol Fornes; Jessica Agostinone; Rachelle A. Farkas; Jack W. Hickmott; Siu Ling Lam; Anthony Mathelier; Michelle Zhou; Wyeth W. Wasserman et al.
Source: check_circle
Crossref

On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction

NAR Genomics and Bioinformatics
2021-04-09 | Journal article
Contributors: Bernat Anton; Mireia Besalú; Oriol Fornes; Jaume Bonet; Alexis Molina; Ruben Molina-Fernandez; Gemma De las Cuevas; Narcis Fernandez-Fuentes; Baldo Oliva
Source: check_circle
Crossref

Biologically-relevant transfer learning improves transcription factor binding prediction

2020-12-22 | Other
Contributors: Gherman Novakovsky; Manu Saraswat; Oriol Fornes; Sara Mostafavi; Wyeth W. Wasserman
Source: check_circle
Crossref

A GO catalogue of human DNA-binding transcription factors

2020-10-28 | Preprint
Contributors: Ruth C. Lovering; Pascale Gaudet; Marcio L. Acencio; Alex Ignatchenko; Arttu Jolma; Oriol Fornes; Martin Kuiper; Ivan V. Kulakovskiy; Astrid Lægreid; Maria J. Martin et al.
Source: check_circle
Crossref

On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF

NAR Genomics and Bioinformatics
2020-09-01 | Journal article
Contributors: Alberto Meseguer; Filip Årman; Oriol Fornes; Ruben Molina-Fernández; Jaume Bonet; Narcis Fernandez-Fuentes; Baldo Oliva
Source: check_circle
Crossref

GeneBreaker - Variant simulation to improve the diagnosis of Mendelian rare genetic diseases

2020-05-30 | Preprint
Contributors: Phillip A. Richmond; Tamar V. Av-Shalom; Oriol Fornes; Bhavi Modi; Alison M. Elliott; Wyeth W. Wasserman
Source: check_circle
Crossref

Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study

Genome Biology
2020-05-11 | Journal article
Part of ISSN: 1474-760X
Source: Self-asserted source
Oriol Fornés

JASPAR 2020: update of the open-access database of transcription factor binding profiles

Nucleic Acids Research
2019-11-08 | Journal article
Contributors: Oriol Fornes; Jaime A Castro-Mondragon; Aziz Khan; Robin van der Lee; Xi Zhang; Phillip A Richmond; Bhavi P Modi; Solenne Correard; Marius Gheorghe; Damir Baranašić et al.
Source: check_circle
Crossref

Gene expression models based on transcription factor binding events confer insight into functional cis-regulatory variants

Bioinformatics
2019-08-01 | Journal article
Part of ISSN: 1367-4803
Part of ISSN: 1460-2059
Source: Self-asserted source
Oriol Fornés

New MiniPromoter Ple345 (NEFL) Drives Strong and Specific Expression in Retinal Ganglion Cells of Mouse and Primate Retina

Human Gene Therapy
2019-03-18 | Journal article
Part of ISSN: 1043-0342
Part of ISSN: 1557-7422
Source: Self-asserted source
Oriol Fornés

JASPAR 2018: Update of the open-access database of transcription factor binding profiles and its web framework

Nucleic Acids Research
2018 | Journal article
EID:

2-s2.0-85040936337

Contributors: Khan, A.; Fornes, O.; Stigliani, A.; Gheorghe, M.; Castro-Mondragon, J.A.; Van Der Lee, R.; Bessy, A.; Chèneby, J.; Kulkarni, S.R.; Tan, G. et al.
Source: Self-asserted source
Oriol Fornés via Scopus - Elsevier

MANTA2, update of the Mongo database for the analysis of transcription factor binding site alterations

Scientific data
2018 | Journal article
EID:

2-s2.0-85058515138

Contributors: Fornes, O.; Gheorghe, M.; Richmond, P.A.; Arenillas, D.J.; Wasserman, W.W.; Mathelier, A.
Source: Self-asserted source
Oriol Fornés via Scopus - Elsevier

c-Myc is a novel Leishmania virulence factor by proxy that targets the host miRNA system and is essential for survival in human macrophages

Journal of Biological Chemistry
2018-08 | Journal article
Contributors: Lucie Colineau; Ulrike Lambertz; Oriol Fornes; Wyeth W. Wasserman; Neil E. Reiner
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

Nature Communications
2016 | Journal article
EID:

2-s2.0-84984705713

Contributors: Sieberts, S.K.; Zhu, F.; García-García, J.; Stahl, E.; Pratap, A.; Pandey, G.; Pappas, D.; Aguilar, D.; Anton, B.; Bonet, J. et al.
Source: Self-asserted source
Oriol Fornés via Scopus - Elsevier

Evaluating the impact of single nucleotide variants on transcription factor binding

Nucleic Acids Research
2016 | Journal article
EID:

2-s2.0-85016141829

Contributors: Shi, W.; Fornes, O.; Mathelier, A.; Wasserman, W.W.
Source: Self-asserted source
Oriol Fornés via Scopus - Elsevier

InteractoMIX: A suite of computational tools to exploit interactomes in biological and clinical research

Biochemical Society Transactions
2016 | Journal article
EID:

2-s2.0-85009754217

Contributors: Manuel, A.M.-L.; Javier, G.-G.; Joan, P.-I.; Narcis, F.-F.; Poglayen, D.; Bonet, J.; Fornes, O.; Segura, J.; Oliva, B.
Source: Self-asserted source
Oriol Fornés via Scopus - Elsevier

JASPAR 2016: A major expansion and update of the open-access database of transcription factor binding profiles

Nucleic Acids Research
2016 | Journal article
EID:

2-s2.0-84976884426

Contributors: Mathelier, A.; Fornes, O.; Arenillas, D.J.; Chen, C.-Y.; Denay, G.; Lee, J.; Shi, W.; Shyr, C.; Tan, G.; Worsley-Hunt, R. et al.
Source: Self-asserted source
Oriol Fornés via Scopus - Elsevier

On the use of knowledge-based potentials for the evaluation of models of protein-protein, protein-DNA, and protein-RNA interactions

Advances in Protein Chemistry and Structural Biology
2014 | Book
EID:

2-s2.0-84896281598

Contributors: Fornes, O.; Garcia-Garcia, J.; Bonet, J.; Oliva, B.
Source: Self-asserted source
Oriol Fornés via Scopus - Elsevier

Networks of protein-protein interactions: From uncertainty to molecular details

Molecular Informatics
2012 | Journal article
EID:

2-s2.0-84861087763

Contributors: Garcia-Garcia, J.; Bonet, J.; Guney, E.; Fornes, O.; Planas, J.; Oliva, B.
Source: Self-asserted source
Oriol Fornés via Scopus - Elsevier

Backup in gene regulatory networks explains differences between binding and knockout results

Molecular Systems Biology
2009 | Journal article
EID:

2-s2.0-67650663220

Contributors: Gitter, A.; Siegfried, Z.; Klutstein, M.; Fornes, O.; Oliva, B.; Simon, I.; Bar-Joseph, Z.
Source: Self-asserted source
Oriol Fornés via Scopus - Elsevier

ModLink+: Improving fold recognition by using protein-protein interactions

Bioinformatics
2009 | Journal article
EID:

2-s2.0-66349097903

Contributors: Fornes, O.; Aragues, R.; Espadaler, J.; Marti-Renom, M.A.; Sali, A.; Oliva, B.
Source: Self-asserted source
Oriol Fornés via Scopus - Elsevier

Knowledge environments representing molecular entities for the virtual physiological human

Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences
2008 | Journal article
EID:

2-s2.0-48349143152

Contributors: Hofmann-Apitius, M.; Fluck, J.; Furlong, L.; Fornes, O.; Kolářik, C.; Hanser, S.; Boeker, M.; Schulz, S.; Sanz, F.; Klinger, R. et al.
Source: Self-asserted source
Oriol Fornés via Scopus - Elsevier

Peer review (1 review for 1 publication/grant)

Review activity for Faculty Opinions (1)