Two-way clustering of gene expression profiles by sparse matrix factorization. - Alberto D. Pascual-Montano; Francisco Tirado; Pedro Carmona-Saez; José María Carazo; Roberto D. Pascual-Marqui (CSB Workshops, 2005)

Knowledge Discovery in the Identification of Differentially Expressed Genes in Tumoricidal Macrophage. - A. Fazel Famili; Ziying Liu; Pedro Carmona-Saez; Alaka Mullick (IDA, 2005)

Integrated analysis of gene expression by association rules discovery. - Pedro Carmona-Saez; Monica Chagoyen; Andrés Rodríguez Moreno; Oswaldo Trelles; José María Carazo; Alberto D. Pascual-Montano (BMC Bioinform., 2006)

Biclustering of gene expression data by non-smooth non-negative matrix factorization. - Pedro Carmona-Saez; Roberto D. Pascual-Marqui; Francisco Tirado; José María Carazo; Alberto D. Pascual-Montano (BMC Bioinform., 2006)

A literature-based similarity metric for biological processes. - Monica Chagoyen; Pedro Carmona-Saez; Concha Gil; José María Carazo; Alberto D. Pascual-Montano (BMC Bioinform., 2006)

Discovering semantic features in the literature: a foundation for building functional associations. - Monica Chagoyen; Pedro Carmona-Saez; Hagit Shatkay; José María Carazo; Alberto D. Pascual-Montano (BMC Bioinform., 2006)

bioNMF: a versatile tool for non-negative matrix factorization in biology. - Alberto D. Pascual-Montano; Pedro Carmona-Saez; Monica Chagoyen; Francisco Tirado; José María Carazo; Roberto D. Pascual-Marqui (BMC Bioinform., 2006)

ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data. - Federico Abascal; Pedro Carmona-Saez; José María Carazo; Alberto D. Pascual-Montano (Bioinform., 2008)

bioNMF: a web-based tool for nonnegative matrix factorization in biology. - Edgardo Mejía-Roa; Pedro Carmona-Saez; Rubén Nogales; Cesar Vicente; Miguel Vázquez; X. Y. Yang; Carlos García 001; Francisco Tirado; Alberto D. Pascual-Montano (Nucleic Acids Res., 2008)

GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information. - Rubén Nogales-Cadenas; Pedro Carmona-Saez; Miguel Vázquez; Cesar Vicente; Xiaoyuan Yang 001; Francisco Tirado; José María Carazo; Alberto D. Pascual-Montano (Nucleic Acids Res., 2009)

SENT: semantic features in text. - Miguel Vázquez; Pedro Carmona-Saez; Rubén Nogales-Cadenas; Monica Chagoyen; Francisco Tirado; José María Carazo; Alberto D. Pascual-Montano (Nucleic Acids Res., 2009)

Rbbt: A Framework for Fast Bioinformatics Development with Ruby. - Miguel Vázquez; Rubén Nogales; Pedro Carmona-Saez; Alberto Pascual; Juan Pavón (IWPACBB, 2010)

MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures. - Miguel Vázquez; Rubén Nogales-Cadenas; Javier Arroyo; Pedro Botías; Raul García; José María Carazo; Francisco Tirado; Alberto D. Pascual-Montano; Pedro Carmona-Saez (Nucleic Acids Res., 2010)

Finding closed frequent item sets by intersecting transactions. - Christian Borgelt; Xiaoyuan Yang 001; Rubén Nogales-Cadenas; Pedro Carmona-Saez; Alberto D. Pascual-Montano (EDBT, 2011)

Metagene projection characterizes GEN2.2 and CAL-1 as relevant human plasmacytoid dendritic cell models. - Pedro Carmona-Saez; Nieves Varela; María José Luque; Daniel Toro-Domínguez; Jordi Martorell-Marugan; Marta E. Alarcón-Riquelme; Concepción Marañón (Bioinform., 2017)

MetaGenyo: a web tool for meta-analysis of genetic association studies. - Jordi Martorell-Marugan; Daniel Toro-Domínguez; Marta E. Alarcón-Riquelme; Pedro Carmona-Saez (BMC Bioinform., 2017)

mCSEA: detecting subtle differentially methylated regions. - Jordi Martorell-Marugan; Víctor González-Rumayor; Pedro Carmona-Saez (Bioinform., 2019)

ImaGEO: integrative gene expression meta-analysis from GEO database. - Daniel Toro-Domínguez; Jordi Martorell-Marugan; Raúl López-Domínguez; Adrián García-Moreno; Víctor González-Rumayor; Marta E. Alarcón-Riquelme; Pedro Carmona-Saez (Bioinform., 2019)

A survey of gene expression meta-analysis: methods and applications. - Daniel Toro-Domínguez; Juan Antonio Villatoro-García; Jordi Martorell-Marugan; Yolanda Román-Montoya; Marta E. Alarcón-Riquelme; Pedro Carmona-Saez (Briefings Bioinform., 2021)

DREIMT: a drug repositioning database and prioritization tool for immunomodulation. - Kevin Troulé; Hugo López-Fernández; Santiago García-Martín; Miguel Reboiro-Jato; Carlos Carretero-Puche; Jordi Martorell-Marugan; Guillermo Martín-Serrano; Pedro Carmona-Saez; Daniel Glez-Peña; Fátima Al-Shahrour; Gonzalo Gómez-López (Bioinform., 2021)

A comprehensive database for integrated analysis of omics data in autoimmune diseases. - Jordi Martorell-Marugan; Raúl López-Domínguez; Adrián García-Moreno; Daniel Toro-Domínguez; Juan Antonio Villatoro-García; Guillermo Barturen; Adoración Martín-Gómez; Kevin Troulé; Gonzalo Gómez-López; Fátima Al-Shahrour; Víctor González-Rumayor; María Peña-Chilet; et al. (BMC Bioinform., 2021)

Scoring personalized molecular portraits identify Systemic Lupus Erythematosus subtypes and predict individualized drug responses, symptomatology and disease progression. - Daniel Toro-Domínguez; Jordi Martorell-Marugan; Manuel Martínez-Bueno; Raúl López-Domínguez; Elena Carnero-Montoro; Guillermo Barturen; Daniel Goldman; Michelle Petri; Pedro Carmona-Saez; Marta E. Alarcón-Riquelme (Briefings Bioinform., 2022)

sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms. - Ernesto Aparicio-Puerta; Cristina Gómez-Martín; Stavros Giannoukakos; José María Medina; Chantal Scheepbouwer; Adrián García-Moreno; Pedro Carmona-Saez; Bastian Fromm; Michiel Pegtel; Andreas Keller; Juan Antonio Marchal; Michael Hackenberg (Nucleic Acids Res., 2022)

Differential diagnosis of systemic lupus erythematosus and Sjögren's syndrome using machine learning and multi-omics data. - Jordi Martorell-Marugan; Marco Chierici; Giuseppe Jurman; Marta E. Alarcón-Riquelme; Pedro Carmona-Saez (Comput. Biol. Medicine, 2023)

Response to the letter 'testing the effectiveness of MyPROSLE in classifying patients with lupus nephritis'. - Daniel Toro-Domínguez; Jordi Martorell-Marugan; Manuel Martínez-Bueno; Raúl López-Domínguez; Elena Carnero-Montoro; Guillermo Barturen; Daniel Goldman; Michelle Petri; Pedro Carmona-Saez; Marta E. Alarcón-Riquelme (Briefings Bioinform., 2023)

Explainable deep neural networks for predicting sample phenotypes from single-cell transcriptomics. - Jordi Martorell-Marugan; Raúl López-Domínguez; Juan Antonio Villatoro-García; Daniel Toro-Domínguez; Marco Chierici; Giuseppe Jurman; Pedro Carmona-Saez (Briefings Bioinform., 2024)