Valencia, Alfonso

GENCODE: The reference human genome annotation for The ENCODE Project

Harrow, J., Frankish, A., Gonzalez, J. M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B. L., Barrell, D., Zadissa, A., Searle, S., et al. (2012) · Genome Research

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 4,585

The repertoire of mutational signatures in human cancer

Alexandrov, L. B., Kim, J., Haradhvala, N. J., Huang, M. N., Tian Ng, A. W., Wu, Y., Boot, A., Covington, K. R., Gordenin, D. A., Bergstrom, E. N., et al. (2020) · Nature

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 3,496

Pan-cancer analysis of whole genomes

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S.-M., Aikata, H., et al. (2020) · Nature

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 3,064

Expanded encyclopaedias of DNA elements in the human and mouse genomes

The ENCODE Project Consortium, Abascal, F., Acosta, R., Addleman, N. J., Adrian, J., Afzal, V., Ai, R., Aken, B., Akiyama, J. A., Jammal, O. A., et al. (2020) · Nature

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 2,378

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

Astle, W. J., Elding, H., Jiang, T., Allen, D., Ruklisa, D., Mann, A. L., Mead, D., Bouman, H., Riveros-Mckay, F., Kostadima, M. A., et al. (2016) · Cell

Genetic Associations and EpidemiologyGenetic Mapping and Diversity in Plants and Animals

Cited by 1,224

The evolutionary history of 2,658 cancers

Gerstung, M., Jolly, C., Leshchiner, I., Dentro, S. C., Gonzalez, S., Rosebrock, D., Mitchell, T. J., Rubanova, Y., Anur, P., Yu, K., et al. (2020) · Nature

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 1,057

Patterns of somatic structural variation in human cancer genomes

Li, Y., Roberts, N. D., Wala, J. A., Shapira, O., Schumacher, S. E., Kumar, K., Khurana, E., Waszak, S., Korbel, J. O., Haber, J. E., et al. (2020) · Nature

Cancer Genomics and DiagnosticsGenomic variations and chromosomal abnormalities

Cited by 867

Correlated mutations and residue contacts in proteins

Göbel, U., Sander, C., Schneider, R., & Valencia, A. (1994) · Proteins Structure Function and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 863

An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins.

Bork, P., Sander, C., & Valencia, A. (1992) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 811

Distinct DNA methylomes of newborns and centenarians

Heyn, H., Li, N., Ferreira, H. J., Moran, S., Pisano, D. G., Gomez, A., Diez, J., Sanchez-Mut, J. V., Setien, F., Carmona, F. J., et al. (2012) · Proceedings of the National Academy of Sciences

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 802

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Cortés-Ciriano, I., Lee, J. J.-K., Xi, R., Jain, D., Jung, Y. L., Yang, L., Gordenin, D., Klimczak, L. J., Zhang, C.-Z., Pellman, D. S., et al. (2020) · Nature Genetics

Cancer Genomics and DiagnosticsGenomic variations and chromosomal abnormalities

Cited by 712

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

Chen, L., Ge, B., Casale, F. P., Vasquez, L., Kwan, T., Garrido-Martín, D., Watt, S., Yan, Y., Kundu, K., Ecker, S., et al. (2016) · Cell

Genetic Associations and EpidemiologyEpigenetics and DNA Methylation

Cited by 679

A structural biology community assessment of AlphaFold2 applications

Akdel, M., Pires, D. E. V., Pardo, E. P., Jänes, J., Zalevsky, A. O., Mészáros, B., Bryant, P., Good, L. L., Laskowski, R. A., Pozzati, G., et al. (2022) · Nature Structural & Molecular Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 675

Emerging methods in protein co-evolution

de Juan, D., Pazos, F., & Valencia, A. (2013) · Nature Reviews Genetics

Protein Structure and DynamicsGenomics and Phylogenetic Studies

Cited by 607

Sex and gender differences and biases in artificial intelligence for biomedicine and healthcare

Cirillo, D., Catuara-Solarz, S., Morey, C., Guney, E., Subirats, L., Mellino, S., Gigante, A., Valencia, A., Rementeria, M. J., Chadha, A. S., et al. (2020) · npj Digital Medicine

Sex and Gender in HealthcareArtificial Intelligence in Healthcare and Education

Cited by 553

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

Rodriguez-Martin, B., Alvarez, E. G., Baez-Ortega, A., Zamora, J., Supek, F., Demeulemeester, J., Santamarina, M., Ju, Y. S., Temes, J., Garcia-Souto, D., et al. (2020) · Nature Genetics

Genomic variations and chromosomal abnormalitiesCancer Genomics and Diagnostics

Cited by 451

Towards FAIR Principles for Research Software

Lamprecht, A.-L., Garcia, L., Kuzak, M., Martinez, C., Arcila, R., Martin Del Pico, E., Dominguez Del Angel, V., van de Sandt, S., Ison, J., Martinez, P. A., et al. (2020) · Data Science

Scientific Computing and Data ManagementResearch Data Management Practices

Cited by 322

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

Akdemir, K. C., Le, V. T., Chandran, S., Li, Y., Verhaak, R. G., Beroukhim, R., Campbell, P. J., Chin, L., Dixon, J. R., Futreal, P. A., et al. (2020) · Nature Genetics

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 283

Information retrieval and text mining technologies for chemistry

Krallinger, M., Rabal, O., Lourenço, A., Oyarzabal, J., & Valencia, A. (2017) · Chemical Reviews

Biomedical Text Mining and OntologiesComputational Drug Discovery Methods

Cited by 281

APPRIS: annotation of principal and alternative splice isoforms

Rodriguez, J. M., Maietta, P., Ezkurdia, I., Pietrelli, A., Wesselink, J.-J., Lopez, G., Valencia, A., & Tress, M. L. (2013) · Nucleic Acids Research

RNA Research and SplicingGenomics and Phylogenetic Studies

Cited by 232

Linking genes to literature: text mining, information extraction, and retrieval applications for biology

Krallinger, M., Valencia, A., & Hirschman, L. (2008) · Genome Biology

Biomedical Text Mining and OntologiesBioinformatics and Genomic Networks

Cited by 231

Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia

Ferreira, P. G., Jares, P., Rico, D., Gómez-López, G., Martínez-Trillos, A., Villamor, N., Ecker, S., González-Pérez, A., Knowles, D. G., Monlong, J., et al. (2014) · Genome Research

Chronic Lymphocytic Leukemia ResearchLymphoma Diagnosis and Treatment

Cited by 214

The BLUEPRINT Data Analysis Portal

Fernández, J. M., de la Torre, V., Richardson, D., Royo, R., Puiggròs, M., Moncunill, V., Fragkogianni, S., Clarke, L., Flicek, P., Rico, D., et al. (2016) · Cell Systems

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 151

Mortality in Persons With Autism Spectrum Disorder or Attention-Deficit/Hyperactivity Disorder: A Systematic Review and Meta-analysis

Catalá-López, F., Hutton, B., Page, M. J., Driver, J. A., Ridao, M., Alonso-Arroyo, A., Valencia, A., Macías Saint-Gerons, D., & Tabarés-Seisdedos, R. (2022) · JAMA Pediatrics

Autism Spectrum Disorder ResearchAttention Deficit Hyperactivity Disorder

Cited by 148