A consensus view of protein dynamics. - Manuel Rueda; Carles Ferrer-Costa; Tim Meyer; Alberto Pérez; Jordi Camps; Adam Hospital; Josep Lluis Gelpí; Modesto Orozco (Proc. Natl. Acad. Sci. USA, 2007)

FlexServ: an integrated tool for the analysis of protein flexibility. - Jordi Camps; Oliver Carrillo; Agustí Emperador; Laura Orellana; Adam Hospital; Manuel Rueda; Damjan Cicin-Sain; Marco D'Abramo; Josep Lluis Gelpí; Modesto Orozco (Bioinform., 2009)

Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes. - Manuel Rueda; Giovanni Bottegoni; Ruben Abagyan (J. Chem. Inf. Model., 2009)

SimiCon: a web tool for protein-ligand model comparison through calculation of equivalent atomic contacts. - Manuel Rueda; Vsevolod Katritch; Eugene Raush; Ruben Abagyan (Bioinform., 2010)

Recipes for the Selection of Experimental Protein Conformations for Virtual Screening. - Manuel Rueda; Giovanni Bottegoni; Ruben Abagyan (J. Chem. Inf. Model., 2010)

ALiBERO: Evolving a Team of Complementary Pocket Conformations Rather than a Single Leader. - Manuel Rueda; Maxim Totrov; Ruben Abagyan (J. Chem. Inf. Model., 2012)

Exploring Early Stages of the Chemical Unfolding of Proteins at the Proteome Scale. - Michela Candotti; Alberto Pérez; Carles Ferrer-Costa; Manuel Rueda; Tim Meyer; Josep Lluis Gelpí; Modesto Orozco (PLoS Comput. Biol., 2013)

SG-ADVISER mtDNA: a web server for mitochondrial DNA annotation with data from 200 samples of a healthy aging cohort. - Manuel Rueda; Ali Torkamani (BMC Bioinform., 2017)

From Homology Models to a Set of Predictive Binding Pockets-a 5-HT1A Receptor Case Study. - Dawid Warszycki; Manuel Rueda; Stefan Mordalski; Kurt Kristiansen; Grzegorz Satala; Krzysztof Rataj; Zdzislaw Chilmonczyk; Ingebrigt Sylte; Ruben Abagyan; Andrzej J. Bojarski (J. Chem. Inf. Model., 2017)

A quality control portal for sequencing data deposited at the European genome-phenome archive. - Dietmar Fernández-Orth; Manuel Rueda; Babita Singh; Mauricio Moldes; Aina Jene; Marta Ferri; Claudia Vasallo; Lauren A. Fromont; Arcadi Navarro; Jordi Rambla (Briefings Bioinform., 2022)

Beacon v2 Reference Implementation: a toolkit to enable federated sharing of genomic and phenotypic data. - Manuel Rueda; Roberto Ariosa; Mauricio Moldes; Jordi Rambla (Bioinform., 2022)

The European Genome-phenome Archive in 2021. - Mallory Ann Freeberg; Lauren A. Fromont; Teresa D'altri; Anna Foix Romero; Jorge Izquierdo Ciges; Aina Jene; Giselle Kerry; Mauricio Moldes; Roberto Ariosa; Silvia Bahena; Daniel Barrowdale; Marcos Casado Barbero; et al. (Nucleic Acids Res., 2022)

Convert-Pheno: A software toolkit for the interconversion of standard data models for phenotypic data. - Manuel Rueda; Ivo C. Leist; Ivo Glynne Gut (J. Biomed. Informatics, 2024)

Pheno-Ranker: a toolkit for comparison of phenotypic data stored in GA4GH standards and beyond. - Ivo C. Leist; María Rivas-Torrubia; Marta E. Alarcón-Riquelme; Guillermo Barturen; Ivo Glynne Gut; Manuel Rueda (BMC Bioinform., 2024)