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

por Shi, Wenqiang, Fornes, Oriol, Wasserman, Wyeth W
Publicado 2019

Evaluating the impact of single nucleotide variants on transcription factor binding

por Shi, Wenqiang, Fornes, Oriol, Mathelier, Anthony, Wasserman, Wyeth W.
Publicado 2016

ExplaiNN: interpretable and transparent neural networks for genomics

por Novakovsky, Gherman, Fornes, Oriol, Saraswat, Manu, Mostafavi, Sara, Wasserman, Wyeth W.
Publicado 2023

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

por Balaton, Bradley P., Fornes, Oriol, Wasserman, Wyeth W., Brown, Carolyn J.
Publicado 2021

Biologically relevant transfer learning improves transcription factor binding prediction

por Novakovsky, Gherman, Saraswat, Manu, Fornes, Oriol, Mostafavi, Sara, Wasserman, Wyeth W.
Publicado 2021

SBILib: a handle for protein modeling and engineering

por Gohl, Patrick, Bonet, Jaume, Fornes, Oriol, Planas-Iglesias, Joan, Fernandez-Fuentes, Narcís, Oliva, Baldo
Publicado 2023

Refining the genomic determinants underlying escape from X-chromosome inactivation

por Peeters, Samantha, Leung, Tiffany, Fornes, Oriol, Farkas, Rachelle A, Wasserman, Wyeth W, Brown, Carolyn J
Publicado 2023

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

por Gitter, Anthony, Siegfried, Zehava, Klutstein, Michael, Fornes, Oriol, Oliva, Baldo, Simon, Itamar, Bar-Joseph, Ziv
Publicado 2009

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

por Fornes, Oriol, Gheorghe, Marius, Richmond, Phillip A., Arenillas, David J., Wasserman, Wyeth W., Mathelier, Anthony
Publicado 2018

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

por Meseguer, Alberto, Årman, Filip, Fornes, Oriol, Molina-Fernández, Ruben, Bonet, Jaume, Fernandez-Fuentes, Narcis, Oliva, Baldo
Publicado 2020

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

por Richmond, Phillip A., Av‐Shalom, Tamar V., Fornes, Oriol, Modi, Bhavi, Elliott, Alison M., Wasserman, Wyeth W.
Publicado 2021

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

por Anton, Bernat, Besalú, Mireia, Fornes, Oriol, Bonet, Jaume, Molina, Alexis, Molina-Fernandez, Ruben, De las Cuevas, Gemma, Fernandez-Fuentes, Narcis, Oliva, Baldo
Publicado 2021

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

por Fornes, Oriol, Av-Shalom, Tamar V, Korecki, Andrea J, Farkas, Rachelle A, Arenillas, David J, Mathelier, Anthony, Simpson, Elizabeth M, Wasserman, Wyeth W
Publicado 2023

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

por 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
Publicado 2020

SPServer: split-statistical potentials for the analysis of protein structures and protein–protein interactions

por 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
Publicado 2021

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

por Novakovsky, Gherman, Sasaki, Shugo, Fornes, Oriol, Omur, Meltem E., Huang, Helen, Bayly, Carmen L., Zhang, Dahai, Lim, Nathaniel, Cherkasov, Artem, Pavlidis, Paul, Mostafavi, Sara, Lynn, Francis C., Wasserman, Wyeth W.
Publicado 2023

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

por 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.
Publicado 2021

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

por 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.
Publicado 2016

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

por Ye, Xin (Cynthia), Roslin, Nicole M, Paterson, Andrew D, Lyons, Christopher J, Pegado, Victor, Richmond, Phillip, Shyr, Casper, Fornes, Oriol, Han, XiaoHua, Higginson, Michelle, Ross, Colin J, Giaschi, Deborah, Gregory-Evans, Cheryl, Patel, Millan S, Wasserman, Wyeth W
Publicado 2022

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

por 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
Publicado 2018