Alfonso Valencia

Barcelona Supercomputing Center

Affiliated withBarcelona Supercomputing Center Catalan Institution for Research and Advanced Studies (ICREA)

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 2	2023

Other Publications

Article	Year
Towards the prediction of protein interaction partners using physical docking. Molecular systems biology\| PubMed ID: 21326236	2011
Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature\| PubMed ID: 21642962	2011
Non-coding recurrent mutations in chronic lymphocytic leukaemia. Nature\| PubMed ID: 26200345	2015
The BLUEPRINT Data Analysis Portal. Cell systems\| PubMed ID: 27863955	2016
Cancer and central nervous system disorders: protocol for an umbrella review of systematic reviews and updated meta-analyses of observational studies. Systematic reviews\| PubMed ID: 28376926	2017
Anna Tramontano 1957-2017. Nature structural & molecular biology\| PubMed ID: 28471426	2017
Most Alternative Isoforms Are Not Functionally Important. Trends in biochemical sciences\| PubMed ID: 28483377	2017
LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes. Nucleic acids research\| PubMed ID: 28531339	2017
A molecular hypothesis to explain direct and inverse co-morbidities between Alzheimer's Disease, Glioblastoma and Lung cancer. Scientific reports\| PubMed ID: 28667284	2017
Anorexia nervosa and cancer: a protocol for a systematic review and meta-analysis of observational studies. Systematic reviews\| PubMed ID: 28693568	2017
Risk of mortality among children, adolescents, and adults with autism spectrum disorder or attention deficit hyperactivity disorder and their first-degree relatives: a protocol for a systema... Systematic reviews\| PubMed ID: 28915839	2017
Legacy data sharing to improve drug safety assessment: the eTOX project. Nature reviews. Drug discovery\| PubMed ID: 29026211	2017
Epigenetic and Transcriptional Variability Shape Phenotypic Plasticity. BioEssays : news and reviews in molecular, cellular and developmental biology\| PubMed ID: 29251357	2018
BIOLITMAP: a web-based geolocated, temporal and thematic visualization of the evolution of bioinformatics publications. Bioinformatics (Oxford, England)\| PubMed ID: 30521012	2019
Intronic CNVs and gene expression variation in human populations. PLoS genetics\| PubMed ID: 30677042	2019
Reviewer-coerced citation: case report, update on journal policy and suggestions for future prevention. Bioinformatics (Oxford, England)\| PubMed ID: 30698640	2019
Big data analytics for personalized medicine. Current opinion in biotechnology\| PubMed ID: 30965188	2019
Association of Anorexia Nervosa With Risk of Cancer: A Systematic Review and Meta-analysis. JAMA network open\| PubMed ID: 31173122	2019
Molecular Inverse Comorbidity between Alzheimer's Disease and Lung Cancer: New Insights from Matrix Factorization. International journal of molecular sciences\| PubMed ID: 31247897	2019
Patient Dossier: Healthcare queries over distributed resources. PLoS computational biology\| PubMed ID: 31622330	2019
On the inconsistent treatment of gene-protein-reaction rules in context-specific metabolic models. Bioinformatics (Oxford, England)\| PubMed ID: 31722383	2020
Pathway and network analysis of more than 2500 whole cancer genomes. Nature communications\| PubMed ID: 32024854	2020
Understanding oncogenicity of cancer driver genes and mutations in the cancer genomics era. FEBS letters\| PubMed ID: 32239503	2020
Unveiling new disease, pathway, and gene associations via multi-scale neural network. PloS one\| PubMed ID: 32251458	2020
COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Scientific data\| PubMed ID: 32371892	2020
Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships. Nature communications\| PubMed ID: 32504002	2020
Sex and gender differences and biases in artificial intelligence for biomedicine and healthcare. NPJ digital medicine\| PubMed ID: 32529043	2020
A user guide for the online exploration and visualization of PCAWG data. Nature communications\| PubMed ID: 32636365	2020
Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Scientific data\| PubMed ID: 32678106	2020
LifeTime and improving European healthcare through cell-based interceptive medicine. Nature\| PubMed ID: 32894860	2020
Detection of SARS-CoV-2 in a cat owned by a COVID-19-affected patient in Spain. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 32948692	2020
Pigs are not susceptible to SARS-CoV-2 infection but are a model for viral immunogenicity studies. Transboundary and emerging diseases\| PubMed ID: 33007154	2021
ECCB2020: the 19th European Conference on Computational Biology. Bioinformatics (Oxford, England)\| PubMed ID: 33381810	2020
Simulating SARS-CoV-2 epidemics by region-specific variables and modeling contact tracing app containment. NPJ digital medicine\| PubMed ID: 33446891	2021
Unraveling the molecular basis of host cell receptor usage in SARS-CoV-2 and other human pathogenic β-CoVs. Computational and structural biotechnology journal\| PubMed ID: 33456724	2021
SARS-CoV-2 infection elicits a rapid neutralizing antibody response that correlates with disease severity. Scientific reports\| PubMed ID: 33510275	2021
Artificial intelligence in cancer research: learning at different levels of data granularity. Molecular oncology\| PubMed ID: 33533192	2021
Stable neutralizing antibody levels 6 months after mild and severe COVID-19 episodes. Med (New York, N.Y.)\| PubMed ID: 33554155	2021
Artificial Intelligence-Aided Precision Medicine for COVID-19: Strategic Areas of Research and Development. Journal of medical Internet research\| PubMed ID: 33560998	2021
Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine. Nature\| PubMed ID: 33731935	2021
The eTRANSAFE Project on Translational Safety Assessment through Integrative Knowledge Management: Achievements and Perspectives. Pharmaceuticals (Basel, Switzerland)\| PubMed ID: 33800393	2021
Protection against reinfection with D614- or G614-SARS-CoV-2 isolates in golden Syrian hamster. Emerging microbes & infections\| PubMed ID: 33825619	2021
Identification of Plitidepsin as Potent Inhibitor of SARS-CoV-2-Induced Cytopathic Effect After a Drug Repurposing Screen. Frontiers in pharmacology\| PubMed ID: 33841165	2021
The multilayer community structure of medulloblastoma. iScience\| PubMed ID: 33889829	2021
Transcriptomic and Genetic Associations between Alzheimer's Disease, Parkinson's Disease, and Cancer. Cancers\| PubMed ID: 34203763	2021
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. F1000Research\| PubMed ID: 34367618	2020
Computational analysis of sense-antisense chimeric transcripts reveals their potential regulatory features and the landscape of expression in human cells. NAR genomics and bioinformatics\| PubMed ID: 34458728	2021
Assessing the accuracy of contact and distance predictions in CASP14. Proteins\| PubMed ID: 34595772	2021
STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells. Nucleic acids research\| PubMed ID: 34648034	2021
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Molecular systems biology\| PubMed ID: 34664389	2021
Perspectives on emerging technologies, personalised medicine, and clinical research for cancer control in Latin America and the Caribbean. The Lancet. Oncology\| PubMed ID: 34735818	2021
COVID-19 Flow-Maps an open geographic information system on COVID-19 and human mobility for Spain. Scientific data\| PubMed ID: 34848723	2021
ExTRI: Extraction of transcription regulation interactions from literature. Biochimica et biophysica acta. Gene regulatory mechanisms\| PubMed ID: 34875418	2022
GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell genomics\| PubMed ID: 35072136	2021
The structural coverage of the human proteome before and after AlphaFold. PLoS computational biology\| PubMed ID: 35073311	2022
Mortality in Persons With Autism Spectrum Disorder or Attention-Deficit/Hyperactivity Disorder: A Systematic Review and Meta-analysis. JAMA pediatrics\| PubMed ID: 35157020	2022
Patient-specific Boolean models of signalling networks guide personalised treatments. eLife\| PubMed ID: 35164900	2022
Clinical course impacts early kinetics,magnitude, and amplitude of SARS-CoV-2 neutralizing antibodies beyond 1 year after infection. Cell reports. Medicine\| PubMed ID: 35233547	2022
Optimizing Dosage-Specific Treatments in a Multi-Scale Model of a Tumor Growth. Frontiers in molecular biosciences\| PubMed ID: 35463947	2022
Design and methodological characteristics of studies using observational routinely collected health data for investigating the link between cancer and neurodegenerative diseases: protocol fo... BMJ open\| PubMed ID: 35487732	2022
Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools. Bioinformatics (Oxford, England)\| PubMed ID: 35512388	2022
Heterogeneous Infectivity and Pathogenesis of SARS-CoV-2 Variants Beta, Delta and Omicron in Transgenic K18-hACE2 and Wildtype Mice. Frontiers in microbiology\| PubMed ID: 35602059	2022
Evaluating the policy of closing bars and restaurants in Cataluña and its effects on mobility and COVID19 incidence. Scientific reports\| PubMed ID: 35672332	2022
Digital biomarkers and sex impacts in Alzheimer's disease management - potential utility for innovative 3P medicine approach. The EPMA journal\| PubMed ID: 35719134	2022
Look-alike humans identified by facial recognition algorithms show genetic similarities. Cell reports\| PubMed ID: 36001980	2022
ECCB2022: the 21st European Conference on Computational Biology. Bioinformatics (Oxford, England)\| PubMed ID: 36124809	2022
A structural biology community assessment of AlphaFold2 applications. Nature structural & molecular biology\| PubMed ID: 36344848	2022
3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells. Nucleic acids research\| PubMed ID: 36453993	2022
Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes. Nature communications\| PubMed ID: 36481610	2022
Predicting the evolution of COVID-19 mortality risk: A Recurrent Neural Network approach. Computer methods and programs in biomedicine update\| PubMed ID: 36593771	2023
Low input capture Hi-C (liCHi-C) identifies promoter-enhancer interactions at high-resolution. Nature communications\| PubMed ID: 36650138	2023
Analysis of electronic health records from three distinct and large populations reveals high prevalence and biases in the co-administration of drugs known to interact. medRxiv : the preprint server for health sciences\| PubMed ID: 36798425	2023
Engaging European society at the forefront of cancer research and care. Molecular oncology\| PubMed ID: 36938773	2023