Computational Biology

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Showing 91 - 120 results of 171

2018

Comprehensive Characterization of Cancer Driver Genes and Mutations

Cell

M. H. Bailey, C. Tokheim, E. Porta-Pardo, S. Sengupta, D. Bertrand, A. Weerasinghe, A. Colaprico, M. C. Wendl, J. Kim, B. Reardon, et al.

2017

Inferring repeat-protein energetics from evolutionary information

PLOS Computational Biology

R. Espada, G. R. Parra, T. Mora, A. M. Walczak, and D. U. Ferreiro
Conceptual and computational framework for logical modelling of biological networks deregulated in diseases

Briefings in Bioinformatics

A. Montagud, P. Traynard, L. Martignetti, E. Bonnet, E. Barillot, A. Zinovyev, and L. Calzone
Four simple recommendations to encourage best practices in research software

F1000Research

R. C. Jiménez, M. Kuzak, M. Alhamdoosh, M. Barker, B. Batut, M. Borg, S. Capella-Gutierrez, N. Chue Hong, M. Cook, M. Corpas, M. Flannery, L. Garcia, J L. Gelpí, S. Gladman, C. Goble, M. González Ferreiro, A. Gonzalez-Beltran, P. C. Griffin, B. Grüning, J. Hagberg, P. Holub, R. Hooft, J. Ison, D. S. Katz, B. Leskošek, F. López Gómez, L. J. Oliveira, D. Mellor, R. Mosbergen, N. Mulder, Y. Perez-Riverol, R. Pergl, H. Pichler, B. Pope, F. Sanz, M. V. Schneider, V. Stodden, R. Suchecki, R. Svobodová Vařeková, H-A. Talvik, I. Todorov, A. Treloar, S. Tyagi, M. van Gompel, D. Vaughan, A. Via, X. Wang, N. S. Watson-Haigh, and S. Crouch
Automatic identification of informative regions with epigenomic changes associated to hematopoiesis

Nucleic Acids Research

E. Carrillo-de-Santa-Pau, D. Juan, V. Pancaldi, F. Were, I. Martin-Subero, D. Rico, and A. Valencia
Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types

Genome Biology

S. Ecker, L. Chen, V. Pancaldi, F. O. Bagger, J. María Fernández, E. Carrillo d Pau, D. Juan, A. L. Mann, S. Watt, F. Paolo Casale, N. Sidiropoulos, N. Rapin, A. Merkel, H. G. Stunnenberg, O. Stegle, M. Frontini, K. Downes, T. Pastinen, T. W. Kuijpers, D. Rico, A. Valencia, S. Beck, N. Soranzo, and D. S. Paul
Discovering the 3′ UTR-mediated regulation of alpha-synuclein

Nucleic Acids Research

D. Marchese, T. Botta-Orfila, D. Cirillo, J. Antonio Rodriguez, C. Maria Livi, R. Fernández-Santiago, M. Ezquerra, M. J. Martí, E. Bechara, and G. Gaetano Tartaglia
Epigenetic and Transcriptional Variability Shape Phenotypic Plasticity

BioEssays

S. Ecker, V. Pancaldi, A. Valencia, S. Beck, and D. S. Paul
Docking-based modeling of protein-protein interfaces for extensive structural and functional characterization of missense mutations

PLOS ONE

D. Barradas-Bautista, and J. Fernández-Recio
The Functional Impact of Alternative Splicing in Cancer

Cell Reports

H. Climente-González, E. Porta-Pardo, A. Godzik, and E. Eyras
Comparison of algorithms for the detection of cancer drivers at subgene resolution

Nature Methods

E. Porta-Pardo, A. Kamburov, D. Tamborero, T. Pons, D. Grases, A. Valencia, N. López-Bigas, G. Getz, and A. Godzik
APPRIS 2017: principal isoforms for multiple gene sets

Nucleic Acids Research

J. ManuelRodriguez, J. Rodriguez-Rivas, T. Di Domenico, J. Vázquez, A. Valencia, and M. L. Tress
Information Retrieval and Text Mining Technologies for Chemistry

Chemical Reviews

M. Krallinger, O. Rabal, A. Lourenço, J. Oyarzabal, and A. Valencia
Anorexia nervosa and cancer: a protocol for a systematic review and meta-analysis of observational studies

Systematic Reviews

F. Catalá-López, B. Hutton, J. A. Driver, M. Ridao, J. M. Valderas, R. Gènova-Maleras, J. Forés-Martos, A. Alonso-Arroyo, D. Macías Saint-Gerons, E. Vieta, A. Valencia, and R. Tabarés-Seisdedos
A molecular hypothesis to explain direct and inverse co-morbidities between Alzheimer’s Disease, Glioblastoma and Lung cancer

Scientific Reports

J. Sánchez-Valle, H. Tejero, K. Ibáñez, J. Luis Portero, M. Krallinger, F. Al-Shahrour, R. Tabarés-Seisdedos, A. Baudot, and A. Valencia
Cancer and central nervous system disorders: protocol for an umbrella review of systematic reviews and updated meta-analyses of observational studies

Systematic Reviews

F. Catalá-López, B. Hutton, J. A. Driver, M. J. Page, M. Ridao, J. M. Valderas, A. Alonso-Arroyo, J. Forés-Martos, S. Martínez, R. Gènova-Maleras, D. Macías-Saint-Gerons, B. Crespo-Facorro, E. Vieta, A. Valencia, and R. Tabarés-Seisdedos
LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes

Nucleic Acids Research

A. Cañada, S. Capella-Gutierrez, O. Rabal, J. Oyarzabal, A. Valencia, and M. Krallinger

2016

INSECT 2.0: a web-server for genome-wide cis -regulatory modules predictionAbstract

Bioinformatics

G. R. Parra, C. O. Rohr, D. Koile, C. Perez-Castro, and P. Yankilevich
Protein Repeats from First PrinciplesAbstract

Scientific Reports

P. Turjanski, G. R. Parra, R. Espada, V. Becher, and D. U. Ferreiro
Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics

Nucleic Acids Research

G. R. Parra, N. P. Schafer, L. G. Radusky, M-Y. Tsai, B. A. Guzovsky, P. G. Wolynes, and D. U. Ferreiro
The BLUEPRINT Data Analysis Portal

Cell Systems

J. MaríaFernández, V. de la Torre, D. Richardson, R. Royo, M. Puiggròs, V. Moncunill, S. Fragkogianni, L. Clarke, P. Flicek, D. Rico, D. Torrents, E. Carrillo d Pau, and A. Valencia

2015

Repeat proteins challenge the concept of structural domains

Biochemical Society Transactions

R. Espada, G. R. Parra, M. J. Sippl, T. Mora, A. M. Walczak, and D. U. Ferreiro
Capturing coevolutionary signals inrepeat proteins

BMC Bioinformatics

R. Espada, G. R. Parra, T. Mora, A. M. Walczak, and D. U. Ferreiro
Structural and Energetic Characterization of the Ankyrin Repeat Protein Family

PLOS Computational Biology

G. R. Parra, R. Espada, N. Verstraete, and D. U. Ferreiro
Conformational heterogeneity enhances protein-protein recognition

XXXVIII Congreso SEBBM. Valencia

C.. Pallara, and J. Fernández-Recio
Identification of near-native protein-protein docking models using structural clustering

XXXVIII Congreso SEBBM. Valencia

S.. Mares-Sámano, and J. Fernández-Recio
Hot-spot interface predictions to identify edgetic mutations

XXXVIII Congreso SEBBM. Valencia

D. Barradas-Bautista, and J. Fernández-Recio
LightDock: a novel protein-protein docking framework for the new challenges in the interactomics era

XXXVIII Congreso SEBBM. Valencia

B.. Jiménez-García, and J. Fernández-Recio
Computational structural analysis and energetics of protein interactions: identifying disease-associated residues

XXXVIII Congreso SEBBM. Valencia

J. Fernández-Recio
Expanding template-based protein-protein complex prediction using ab-initio docking

29th Annual symposium of the Protein Society. Barcelona

S.. Mares-Sámano, L.A.. Rodríguez-Lumbreras, and J. Fernández-Recio

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