JASPAR 2020: update of the open-access database of transcription factor binding profiles
Fornes, Oriol, Castro-Mondragon, Jaime A, Khan, Aziz, van der Lee, Robin, Zhang, Xi, Richmond, Phillip A, Modi, Bhavi P, Correard, Solenne, Gheorghe, Marius, Baranašić, Damir, Santana-Garcia, Walter, Tan, Ge, Chèneby, Jeanne, Ballester, Benoit, Parcy, François, Sandelin, Albin, Lenhard, Boris, Wasserman, Wyeth W, Mathelier, Anthony
Published in Nucleic acids research (08.01.2020)
Published in Nucleic acids research (08.01.2020)
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Journal Article
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework
Khan, Aziz, Fornes, Oriol, Stigliani, Arnaud, Gheorghe, Marius, Castro-Mondragon, Jaime A, van der Lee, Robin, Bessy, Adrien, Chèneby, Jeanne, Kulkarni, Shubhada R, Tan, Ge, Baranasic, Damir, Arenillas, David J, Sandelin, Albin, Vandepoele, Klaas, Lenhard, Boris, Ballester, Benoît, Wasserman, Wyeth W, Parcy, François, Mathelier, Anthony
Published in Nucleic acids research (04.01.2018)
Published in Nucleic acids research (04.01.2018)
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JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles
Castro-Mondragon, Jaime A, Riudavets-Puig, Rafael, Rauluseviciute, Ieva, Berhanu Lemma, Roza, Turchi, Laura, Blanc-Mathieu, Romain, Lucas, Jeremy, Boddie, Paul, Khan, Aziz, Manosalva Pérez, Nicolás, Fornes, Oriol, Leung, Tiffany Y, Aguirre, Alejandro, Hammal, Fayrouz, Schmelter, Daniel, Baranasic, Damir, Ballester, Benoit, Sandelin, Albin, Lenhard, Boris, Vandepoele, Klaas, Wasserman, Wyeth W, Parcy, François, Mathelier, Anthony
Published in Nucleic acids research (07.01.2022)
Published in Nucleic acids research (07.01.2022)
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JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles
Mathelier, Anthony, Fornes, Oriol, Arenillas, David J, Chen, Chih-Yu, Denay, Grégoire, Lee, Jessica, Shi, Wenqiang, Shyr, Casper, Tan, Ge, Worsley-Hunt, Rebecca, Zhang, Allen W, Parcy, François, Lenhard, Boris, Sandelin, Albin, Wasserman, Wyeth W
Published in Nucleic acids research (04.01.2016)
Published in Nucleic acids research (04.01.2016)
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Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study
Ambrosini, Giovanna, Vorontsov, Ilya, Penzar, Dmitry, Groux, Romain, Fornes, Oriol, Nikolaeva, Daria D, Ballester, Benoit, Grau, Jan, Grosse, Ivo, Makeev, Vsevolod, Kulakovskiy, Ivan, Bucher, Philipp
Published in Genome Biology (11.05.2020)
Published in Genome Biology (11.05.2020)
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Journal Article
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework
Khan, Aziz, Fornes, Oriol, Stigliani, Arnaud, Gheorghe, Marius, Castro-Mondragon, Jaime A, van der Lee, Robin, Bessy, Adrien, Chèneby, Jeanne, Kulkarni, Shubhada R, Tan, Ge, Baranasic, Damir, Arenillas, David J, Sandelin, Albin, Vandepoele, Klaas, Lenhard, Boris, Ballester, Benoît, Wasserman, Wyeth W, Parcy, François, Mathelier, Anthony
Published in Nucleic acids research (04.01.2018)
Published in Nucleic acids research (04.01.2018)
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Journal Article
Biologically relevant transfer learning improves transcription factor binding prediction
Novakovsky, Gherman, Saraswat, Manu, Fornes, Oriol, Mostafavi, Sara, Wasserman, Wyeth W
Published in Genome Biology (27.09.2021)
Published in Genome Biology (27.09.2021)
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ExplaiNN: interpretable and transparent neural networks for genomics
Novakovsky, Gherman, Fornes, Oriol, Saraswat, Manu, Mostafavi, Sara, Wasserman, Wyeth W
Published in Genome Biology (27.06.2023)
Published in Genome Biology (27.06.2023)
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Human MiniPromoters for ocular-rAAV expression in ON bipolar, cone, corneal, endothelial, Müller glial, and PAX6 cells
Korecki, Andrea J., Cueva-Vargas, Jorge L., Fornes, Oriol, Agostinone, Jessica, Farkas, Rachelle A., Hickmott, Jack W., Lam, Siu Ling, Mathelier, Anthony, Zhou, Michelle, Wasserman, Wyeth W., Di Polo, Adriana, Simpson, Elizabeth M.
Published in Gene therapy (01.06.2021)
Published in Gene therapy (01.06.2021)
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Human progranulin-expressing mice as a novel tool for the development of progranulin-modulating therapeutics
Petkau, Terri L., Life, Benjamin, Lu, Ge, Yang, Jasmine, Fornes, Oriol, Wasserman, Wyeth, Simpson, Elizabeth M., Leavitt, Blair R.
Published in Neurobiology of disease (01.06.2021)
Published in Neurobiology of disease (01.06.2021)
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SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions
Aguirre-Plans, Joaquim, Meseguer, Alberto, Molina-Fernandez, Ruben, Marín-López, Manuel Alejandro, Jumde, Gaurav, Casanova, Kevin, Bonet, Jaume, Fornes, Oriol, Fernandez-Fuentes, Narcis, Oliva, Baldo
Published in BMC bioinformatics (06.01.2021)
Published in BMC bioinformatics (06.01.2021)
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Cross-species examination of X-chromosome inactivation highlights domains of escape from silencing
Balaton, Bradley P, Fornes, Oriol, Wasserman, Wyeth W, Brown, Carolyn J
Published in Epigenetics & chromatin (17.02.2021)
Published in Epigenetics & chromatin (17.02.2021)
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Structure-based learning to predict and model protein-DNA interactions and transcription-factor co-operativity in cis -regulatory elements
Oriol, Fornes, Alberto, Meseguer, Joachim, Aguirre-Plans, Patrick, Gohl, M, Bota Patricia, Ruben, Molina-Fernández, Jaume, Bonet, Altair, Chinchilla-Hernandez, Ferran, Pegenaute, Oriol, Gallego, Narcis, Fernandez-Fuentes, Baldo, Oliva
Published in NAR genomics and bioinformatics (12.06.2024)
Published in NAR genomics and bioinformatics (12.06.2024)
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On the Use of Knowledge-Based Potentials for the Evaluation of Models of Protein–Protein, Protein–DNA, and Protein–RNA Interactions
Fornes, Oriol, Garcia-Garcia, Javier, Bonet, Jaume, Oliva, Baldo
Published in Advances in Protein Chemistry and Structural Biology (2014)
Published in Advances in Protein Chemistry and Structural Biology (2014)
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Book Chapter
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Knowledge environments representing molecular entities for the virtual physiological human
Hofmann-Apitius, Martin, Fluck, Juliane, Furlong, Laura, Fornes, Oriol, Kolá ik, Corinna, Hanser, Susanne, Boeker, Martin, Schulz, Stefan, Sanz, Ferran, Klinger, Roman, Mevissen, Theo, Gattermayer, Tobias, Oliva, Baldo, Friedrich, Christoph M
Published in Philosophical transactions of the Royal Society of London. Series A: Mathematical, physical, and engineering sciences (13.09.2008)
Published in Philosophical transactions of the Royal Society of London. Series A: Mathematical, physical, and engineering sciences (13.09.2008)
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JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles
Rauluseviciute, Ieva, Riudavets-Puig, Rafael, Blanc-Mathieu, Romain, Castro-Mondragon, Jaime A, Ferenc, Katalin, Kumar, Vipin, Lemma, Roza Berhanu, Lucas, Jérémy, Chèneby, Jeanne, Baranasic, Damir, Khan, Aziz, Fornes, Oriol, Gundersen, Sveinung, Johansen, Morten, Hovig, Eivind, Lenhard, Boris, Sandelin, Albin, Wasserman, Wyeth W, Parcy, François, Mathelier, Anthony
Published in Nucleic acids research (05.01.2024)
Published in Nucleic acids research (05.01.2024)
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SBILib: a handle for protein modeling and engineering
Gohl, Patrick, Bonet, Jaume, Fornes, Oriol, Planas-Iglesias, Joan, Fernandez-Fuentes, Narcís, Oliva, Baldo
Published in Bioinformatics (Oxford, England) (03.10.2023)
Published in Bioinformatics (Oxford, England) (03.10.2023)
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Evaluating the impact of single nucleotide variants on transcription factor binding
Shi, Wenqiang, Fornes, Oriol, Mathelier, Anthony, Wasserman, Wyeth W
Published in Nucleic acids research (01.12.2016)
Published in Nucleic acids research (01.12.2016)
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