Computational Biology

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Mostrant 61 - 90 resultats de 180

2021

A catalogue of 863 Rett-syndrome-causing MECP2 mutations and lessons learned from data integration

Scientific Data

F. Ehrhart, A. Jacobsen, M. Rigau, M. Bosio, R. Kaliyaperumal, J. F. J. Laros, E. L. Willighagen, A. Valencia, M. Roos, S. Capella-Gutierrez, L. M. G. Curfs, and C. T. Evelo
COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

Molecular Systems Biology

M. Ostaszewski, A. Niarakis, A. Mazein, I. Kuperstein, R. Phair, A. Orta‐Resendiz, V. Singh, S. Sadat Aghamiri, M. Luis Acencio, E. Glaab, et al.
Systems biology at the giga-scale: Large multiscale models of complex, heterogeneous multicellular systems

Current Opinion in Systems Biology

A. Montagud, M. Ponce-de-Leon, and A. Valencia
BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems

Lecture Notes in Computer Science

G. Saxena, M. Ponce-de-Leon, A. Montagud, D. Vicente Dorca, and A. Valencia
COVID-19 Flow-Maps an open geographic information system on COVID-19 and human mobility for Spain

Scientific Data

M. Ponce De Leon, J. del Valle, J. Maria Fernández, M. Bernardo, D. Cirillo, J. Sánchez-Valle, M. Smith, S. Capella-Gutierrez, T. Gullón, and A. Valencia
DOME: recommendations for supervised machine learning validation in biology

Nature Methods

I. Walsh, D. Fishman, D. Garcia-Gasulla, T. Titma, G. Pollastri, E. Capriotti, R. Casadio, S. Capella-Gutierrez, D. Cirillo, A. Del Conte, A. C. Dimopoulos, V. Dominguez Del Angel, J. Dopazo, P. Fariselli, J. Maria Fernández, F. Huber, A. Kreshuk, T. Lenaerts, P. Luigi Martelli, A. Navarro, P. Ó. Broin, J. Piñero, D. Piovesan, M. Reczko, F. Ronzano, V. Satagopam, C. Savojardo, V. Spiwok, M. Antonio Tangaro, G. Tartari, D. Salgado, A. Valencia, F. Zambelli, J. Harrow, F. E. Psomopoulos, and S. C. E. Tosatto
MAX mutant small-cell lung cancers exhibit impaired activities of MGA-dependent noncanonical polycomb repressive complex

Proceedings of the National Academy of Sciences

P. Llabata, M. Torres-Diz, A. Gomez, L. Tomas-Daza, O. A. Romero, J. Grego-Bessa, P. Llinas-Arias, A. Valencia, M. Esteller, B. M. Javierre, X. Zhang, and M. Sanchez-Cespedes
The multilayer community structure of medulloblastoma

iScience

I. Núñez-Carpintero, M. Petrizzelli, A. Zinovyev, D. Cirillo, and A. Valencia
Artificial Intelligence–Aided Precision Medicine for COVID-19: Strategic Areas of Research and Development

Journal of Medical Internet Research

E. Santus, N. Marino, D. Cirillo, E. Chersoni, A. Montagud, A. Santuccion Chadha, A. Valencia, K. Hughes, and C. Lindvall
Artificial intelligence in cancer research: learning at different levels of data granularity

Molecular Oncology

D. Cirillo, I. Núñez-Carpintero, and A. Valencia
Simulating SARS-CoV-2 epidemics by region-specific variables and modeling contact tracing app containment

Nature Digital Medicine

A. Ferrari, E. Santus, D. Cirillo, M. Ponce De Leon, N. Marino, M. Teresa Ferretti, A. Santuccion Chadha, N. Mavridis, and A. Valencia

2020

COVID-19 and beyond: a call for action and audacious solidarity to all the citizens and nations, it is humanity’s fight

F1000Research

C. Auffray, R. Balling, N. Blomberg, M. C. Bonaldo, B. Boutron, S. Brahmachari, C. Brechot, A. Cesario, S-J. Chen, K. Clément, D. Danilenko, A. Di Meglio, A. Gelemanović, C. Goble, T. Gojobori, J. D. Goldman, M. Goldman, Y-K. Guo, J. Heath, L. Hood, P. Hunter, L. Jin, H. Kitano, B. Knoppers, D. Lancet, C. Larue, M. Lathrop, M. Laville, A. B. Lindner, A. Magnan, A. Metspalu, E. Morin, L. F. P. Ng, L. Nicod, D. Noble, L. Nottale, H. Nowotny, T. Ochoa, I. N. Okeke, T. Oni, P. Openshaw, M. Oztürk, S. Palkonen, J. T. Paweska, C. Pison, M. H. Polymeropoulos, C. Pristipino, U. Protzer, J. Roca, D. Rozman, M. Santolini, F. Sanz, G. Scambia, E. Segal, I. Serageldin, M. Bento Soares, P. Sterk, S. Sugano, G. Superti-Furga, D. Supple, J. Tegner, M. Uhlen, A. Urbani, A. Valencia, V. Valentini, S. van der Werf, M. Vinciguerra, O. Wolkenhauer, and E. Wouters
Sex differences in oncogenic mutational processes

Nature Communications

C. H. Li, S. D. Prokopec, R. X. Sun, F. Yousif, N. Schmitz, P. C. Boutros, and
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Nature Communications

M. H. Bailey, W. U. Meyerson, L. Jonathan Dursi, L-B. Wang, G. Dong, W-W. Liang, A. Weerasinghe, S. Li, Y. Li, S. Kelso, G. Saksena, K. Ellrott, M. C. Wendl, D. A. Wheeler, G. Getz, J. T. Simpson, M. B. Gerstein, and L. Ding
INforE: Interactive Cross-platform Analytics for Everyone

CIKM '20: The 29th ACM International Conference on Information and Knowledge ManagementProceedings of the 29th ACM International Conference on Information & Knowledge Management

N. Giatrakos, D. Arnu, T. Bitsakis, A. Deligiannakis, M. Garofalakis, R. Klinkenberg, A. Konidaris, A. Kontaxakis, Y. Kotidis, V. Samoladas, A. Simitsis, G. Stamatakis, F. Temme, M. Torok, E. Yaqub, A. Montagud, M. Ponce-de-Leon, H. Arndt, and S. Burkard
How to Design AI-Driven Clinical Trials in Nuclear Medicine

Seminars in Nuclear Medicine

G. Delso, D. Cirillo, J. D. Kaggie, A. Valencia, U. Metser, and P. Veit-Haibach
GOPHER, an HPC Framework for Large Scale Graph Exploration and Inference

High Performance Computing. ISC High Performance 2020. Lecture Notes in Computer Science

M. JosepFabregó, X. Teruel, V. Gimenez-Abalos, D. Cirillo, D. Garcia-Gasulla, S. Alvarez-Napagao, M. Garcia-Gasulla, E. Ayguadé, and A. Valencia
Sex and gender differences and biases in artificial intelligence for biomedicine and healthcare

Nature Digital Medicine

D. Cirillo, S. Catuara-Solarz, C. Morey, E. Guney, L. Subirats, S. Mellino, A. Gigante, A. Valencia, M. José Rementeria, A. Santuccion Chadha, and N. Mavridis
Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships

Nature Communications

J. Sánchez-Valle, H. Tejero, J. María Fernández, D. Juan, B. Urda-García, S. Capella-Gutierrez, F. Al-Shahrour, R. Tabarés-Seisdedos, A. Baudot, V. Pancaldi, and A. Valencia
Pan-cancer analysis of whole genomes

Nature

2019

Reconstructing complex lineage trees from scRNA-seq data using MERLoTAbstract

Nucleic Acids Research

G. R. Parra, N. Papadopoulos, L. Ahumada-Arranz, J. El Kholtei, N. Mottelson, Y. Horokhovsky, B. Treutlein, and J. Soeding
Local frustration around enzyme active sitesSignificance

Proceedings of the National Academy of Sciences

M. I. Freiberger, B. A. Guzovsky, P. G. Wolynes, G. R. Parra, and D. U. Ferreiro
PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processesAbstractSummaryAvailability and implementationSupplementary information

Bioinformatics

N. Papadopoulos, P. R. Gonzalo, and J. Söding
Personalization of Logical Models With Multi-Omics Data Allows Clinical Stratification of Patients

Frontiers in Physiology

J. Béal, A. Montagud, P. Traynard, E. Barillot, and L. Calzone
PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling

Bioinformatics

G. Letort, A. Montagud, G. Stoll, R. Heiland, E. Barillot, P. Macklin, A. Zinovyev, and L. Calzone
On the inconsistent treatment of gene-protein-reaction rules in context-specific metabolic models

Bioinformatics

M. Ponce De Leon, I. Apaolaza, A. Valencia, and F. J. Planes
Patient Dossier: Healthcare queries over distributed resources

PLoS computational biology

M. Vázquez, and A. Valencia
The bio.tools registry of software tools and data resources for the life sciences

Genome Biology

J. Ison, H. Ienasescu, P. Chmura, E. Rydza, H. Ménager, M. Kalaš, V. Schwämmle, B. Grüning, N. Beard, R. Lopez, S. Duvaud, H. Stockinger, B. Persson, R. Svobodová Vařeková, T. Raček, J. Vondrášek, H. Peterson, A. Salumets, I. Jonassen, R. Hooft, T. Nyrönen, A. Valencia, S. Capella, J. Gelpí, F. Zambelli, B. Savakis, B. Leskošek, K. Rapacki, C. Blanchet, R. Jimenez, A. Oliveira, G. Vriend, O. Collin, J. van Helden, P. Løngreen, and S. Brunak
Precision medicine needs pioneering clinical bioinformaticians

Briefings in Bioinformatics

G. Gómez-López, J. Dopazo, J. C. Cigudosa, A. Valencia, and F. Al-Shahrour
Molecular Inverse Comorbidity between Alzheimer’s Disease and Lung Cancer: New Insights from Matrix Factorization

International Journal of Molecular Sciences

A. Greco, J. Sanchez Valle, V. Pancaldi, A. Baudot, E. Barillot, M. Caselle, A. Valencia, A. Zinovyev, and L. Cantini

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