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

Fornes O, Castro-Mondragon JA, Khan A, van der Lee R, Zhang X, Richmond PA, Modi BP, Correard S, Gheorghe M, Baranašić D, Santana-Garcia W, Tan G, Chèneby J, Ballester B, Parcy F, Sandelin A, Lenhard B, Wasserman WW, Mathelier A. Fornes O, et al. Nucleic Acids Res. 2020 Jan 8;48(D1):D87-D92. doi: 10.1093/nar/gkz1001. Nucleic Acids Res. 2020. PMID: 31701148 Free PMC article.

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A GO catalogue of human DNA-binding transcription factors.

Lovering RC, Gaudet P, Acencio ML, Ignatchenko A, Jolma A, Fornes O, Kuiper M, Kulakovskiy IV, Lægreid A, Martin MJ, Logie C. Lovering RC, et al. Among authors: fornes o. Biochim Biophys Acta Gene Regul Mech. 2021 Nov-Dec;1864(11-12):194765. doi: 10.1016/j.bbagrm.2021.194765. Epub 2021 Oct 18. Biochim Biophys Acta Gene Regul Mech. 2021. PMID: 34673265

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Biologically relevant transfer learning improves transcription factor binding prediction.

Novakovsky G, Saraswat M, Fornes O, Mostafavi S, Wasserman WW. Novakovsky G, et al. Among authors: fornes o. Genome Biol. 2021 Sep 27;22(1):280. doi: 10.1186/s13059-021-02499-5. Genome Biol. 2021. PMID: 34579793 Free PMC article.

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Networks of ProteinProtein Interactions: From Uncertainty to Molecular Details.

Garcia-Garcia J, Bonet J, Guney E, Fornes O, Planas J, Oliva B. Garcia-Garcia J, et al. Among authors: fornes o. Mol Inform. 2012 May;31(5):342-62. doi: 10.1002/minf.201200005. Epub 2012 Apr 30. Mol Inform. 2012. PMID: 27477264 Review.

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

Poglayen D, Marín-López MA, Bonet J, Fornes O, Garcia-Garcia J, Planas-Iglesias J, Segura J, Oliva B, Fernandez-Fuentes N. Poglayen D, et al. Among authors: fornes o. Biochem Soc Trans. 2016 Jun 15;44(3):917-24. doi: 10.1042/BST20150001. Biochem Soc Trans. 2016. PMID: 27284060 Review.

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Cross-species examination of X-chromosome inactivation highlights domains of escape from silencing.

Balaton BP, Fornes O, Wasserman WW, Brown CJ. Balaton BP, et al. Among authors: fornes o. Epigenetics Chromatin. 2021 Feb 17;14(1):12. doi: 10.1186/s13072-021-00386-8. Epigenetics Chromatin. 2021. PMID: 33597016 Free PMC article.

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JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles.

Castro-Mondragon JA, Riudavets-Puig R, Rauluseviciute I, Berhanu Lemma R, Turchi L, Blanc-Mathieu R, Lucas J, Boddie P, Khan A, Manosalva Pérez N, Fornes O, Leung TY, Aguirre A, Hammal F, Schmelter D, Baranasic D, Ballester B, Sandelin A, Lenhard B, Vandepoele K, Wasserman WW, Parcy F, Mathelier A. Castro-Mondragon JA, et al. Among authors: fornes o. Nucleic Acids Res. 2022 Jan 7;50(D1):D165-D173. doi: 10.1093/nar/gkab1113. Nucleic Acids Res. 2022. PMID: 34850907 Free PMC article.

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Human progranulin-expressing mice as a novel tool for the development of progranulin-modulating therapeutics.

Petkau TL, Life B, Lu G, Yang J, Fornes O, Wasserman W, Simpson EM, Leavitt BR. Petkau TL, et al. Among authors: fornes o. Neurobiol Dis. 2021 Jun;153:105314. doi: 10.1016/j.nbd.2021.105314. Epub 2021 Feb 24. Neurobiol Dis. 2021. PMID: 33636385 Free article.

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

Richmond PA, Av-Shalom TV, Fornes O, Modi B, Elliott AM, Wasserman WW. Richmond PA, et al. Among authors: fornes o. Hum Mutat. 2021 Apr;42(4):346-358. doi: 10.1002/humu.24163. Epub 2021 Feb 10. Hum Mutat. 2021. PMID: 33368787 Free PMC article.

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Linkage analysis identifies an isolated strabismus locus at 14q12 overlapping with FOXG1 syndrome region.

Ye XC, Roslin NM, Paterson AD, Lyons CJ, Pegado V, Richmond P, Shyr C, Fornes O, Han X, Higginson M, Ross CJ, Giaschi D, Gregory-Evans C, Patel MS, Wasserman WW. Ye XC, et al. Among authors: fornes o. J Med Genet. 2022 Jan;59(1):46-55. doi: 10.1136/jmedgenet-2020-107226. Epub 2020 Nov 30. J Med Genet. 2022. PMID: 33257509 Free PMC article.

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