Alfonso Valencia

Publications

• Engaging European Society at the Forefront of Cancer Research and Care
  Molecular Oncology. Mar, 2023  |   Pubmed ID: 36938773
• 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. Feb, 2023  |   Pubmed ID: 36798425
• Low Input Capture Hi-C (liCHi-C) Identifies Promoter-enhancer Interactions at High-resolution
  Nature Communications. Jan, 2023  |   Pubmed ID: 36650138
• Predicting the Evolution of COVID-19 Mortality Risk: A Recurrent Neural Network Approach
  Computer Methods and Programs in Biomedicine Update. 2023  |   Pubmed ID: 36593771
• Author Correction: Pathway and Network Analysis of More Than 2500 Whole Cancer Genomes
  Nature Communications. Dec, 2022  |   Pubmed ID: 36481610
• 3D Chromatin Connectivity Underlies Replication Origin Efficiency in Mouse Embryonic Stem Cells
  Nucleic Acids Research. Nov, 2022  |   Pubmed ID: 36453993
• A Structural Biology Community Assessment of AlphaFold2 Applications
  Nature Structural & Molecular Biology. Nov, 2022  |   Pubmed ID: 36344848
• ECCB2022: the 21st European Conference on Computational Biology
  Bioinformatics (Oxford, England). Sep, 2022  |   Pubmed ID: 36124809
• Look-alike Humans Identified by Facial Recognition Algorithms Show Genetic Similarities
  Cell Reports. Aug, 2022  |   Pubmed ID: 36001980
• Digital Biomarkers and Sex Impacts in Alzheimer's Disease Management - Potential Utility for Innovative 3P Medicine Approach
  The EPMA Journal. Jun, 2022  |   Pubmed ID: 35719134
• Evaluating the Policy of Closing Bars and Restaurants in Cataluña and Its Effects on Mobility and COVID19 Incidence
  Scientific Reports. Jun, 2022  |   Pubmed ID: 35672332
• Heterogeneous Infectivity and Pathogenesis of SARS-CoV-2 Variants Beta, Delta and Omicron in Transgenic K18-hACE2 and Wildtype Mice
  Frontiers in Microbiology. 2022  |   Pubmed ID: 35602059
• Detection of Oncogenic and Clinically Actionable Mutations in Cancer Genomes Critically Depends on Variant Calling Tools
  Bioinformatics (Oxford, England). Jun, 2022  |   Pubmed ID: 35512388
• Design and Methodological Characteristics of Studies Using Observational Routinely Collected Health Data for Investigating the Link Between Cancer and Neurodegenerative Diseases: Protocol for a Meta-research Study
  BMJ Open. Apr, 2022  |   Pubmed ID: 35487732
• Optimizing Dosage-Specific Treatments in a Multi-Scale Model of a Tumor Growth
  Frontiers in Molecular Biosciences. 2022  |   Pubmed ID: 35463947
• Clinical Course Impacts Early Kinetics,magnitude, and Amplitude of SARS-CoV-2 Neutralizing Antibodies Beyond 1 Year After Infection
  Cell Reports. Medicine. Feb, 2022  |   Pubmed ID: 35233547
• Patient-specific Boolean Models of Signalling Networks Guide Personalised Treatments
  ELife. Feb, 2022  |   Pubmed ID: 35164900
• Mortality in Persons With Autism Spectrum Disorder or Attention-Deficit/Hyperactivity Disorder: A Systematic Review and Meta-analysis
  JAMA Pediatrics. Apr, 2022  |   Pubmed ID: 35157020
• The Structural Coverage of the Human Proteome Before and After AlphaFold
  PLoS Computational Biology. Jan, 2022  |   Pubmed ID: 35073311
• ExTRI: Extraction of Transcription Regulation Interactions from Literature
  Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms. Jan, 2022  |   Pubmed ID: 34875418
• GA4GH: International Policies and Standards for Data Sharing Across Genomic Research and Healthcare
  Cell Genomics. Nov, 2021  |   Pubmed ID: 35072136
• COVID-19 Flow-Maps an Open Geographic Information System on COVID-19 and Human Mobility for Spain
  Scientific Data. Nov, 2021  |   Pubmed ID: 34848723
• Perspectives on Emerging Technologies, Personalised Medicine, and Clinical Research for Cancer Control in Latin America and the Caribbean
  The Lancet. Oncology. Nov, 2021  |   Pubmed ID: 34735818
• COVID19 Disease Map, a Computational Knowledge Repository of Virus-host Interaction Mechanisms
  Molecular Systems Biology. Oct, 2021  |   Pubmed ID: 34664389
• STAG2 Loss-of-function Affects Short-range Genomic Contacts and Modulates the Basal-luminal Transcriptional Program of Bladder Cancer Cells
  Nucleic Acids Research. Nov, 2021  |   Pubmed ID: 34648034
• Assessing the Accuracy of Contact and Distance Predictions in CASP14
  Proteins. Dec, 2021  |   Pubmed ID: 34595772
• Computational Analysis of Sense-antisense Chimeric Transcripts Reveals Their Potential Regulatory Features and the Landscape of Expression in Human Cells
  NAR Genomics and Bioinformatics. Sep, 2021  |   Pubmed ID: 34458728
• Transcriptomic and Genetic Associations Between Alzheimer's Disease, Parkinson's Disease, and Cancer
  Cancers. Jun, 2021  |   Pubmed ID: 34203763
• The Multilayer Community Structure of Medulloblastoma
  IScience. Apr, 2021  |   Pubmed ID: 33889829
• Identification of Plitidepsin As Potent Inhibitor of SARS-CoV-2-Induced Cytopathic Effect After a Drug Repurposing Screen
  Frontiers in Pharmacology. 2021  |   Pubmed ID: 33841165
• Protection Against Reinfection with D614- or G614-SARS-CoV-2 Isolates in Golden Syrian Hamster
  Emerging Microbes & Infections. Dec, 2021  |   Pubmed ID: 33825619
• The ETRANSAFE Project on Translational Safety Assessment Through Integrative Knowledge Management: Achievements and Perspectives
  Pharmaceuticals (Basel, Switzerland). Mar, 2021  |   Pubmed ID: 33800393
• Publisher Correction: LifeTime and Improving European Healthcare Through Cell-based Interceptive Medicine
  Nature. Apr, 2021  |   Pubmed ID: 33731935
• Artificial Intelligence-Aided Precision Medicine for COVID-19: Strategic Areas of Research and Development
  Journal of Medical Internet Research. Mar, 2021  |   Pubmed ID: 33560998
• Stable Neutralizing Antibody Levels 6 months After Mild and Severe COVID-19 Episodes
  Med (New York, N.Y.). Mar, 2021  |   Pubmed ID: 33554155
• Artificial Intelligence in Cancer Research: Learning at Different Levels of Data Granularity
  Molecular Oncology. Apr, 2021  |   Pubmed ID: 33533192
• SARS-CoV-2 Infection Elicits a Rapid Neutralizing Antibody Response That Correlates with Disease Severity
  Scientific Reports. Jan, 2021  |   Pubmed ID: 33510275
• Unraveling the Molecular Basis of Host Cell Receptor Usage in SARS-CoV-2 and Other Human Pathogenic β-CoVs
  Computational and Structural Biotechnology Journal. 2021  |   Pubmed ID: 33456724
• Simulating SARS-CoV-2 Epidemics by Region-specific Variables and Modeling Contact Tracing App Containment
  NPJ Digital Medicine. Jan, 2021  |   Pubmed ID: 33446891
• Pigs Are Not Susceptible to SARS-CoV-2 Infection but Are a Model for Viral Immunogenicity Studies
  Transboundary and Emerging Diseases. Jul, 2021  |   Pubmed ID: 33007154
• The ELIXIR Human Copy Number Variations Community: Building Bioinformatics Infrastructure for Research
  F1000Research. 2020  |   Pubmed ID: 34367618
• ECCB2020: the 19th European Conference on Computational Biology
  Bioinformatics (Oxford, England). Dec, 2020  |   Pubmed ID: 33381810
• 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. Oct, 2020  |   Pubmed ID: 32948692
• LifeTime and Improving European Healthcare Through Cell-based Interceptive Medicine
  Nature. 11, 2020  |   Pubmed ID: 32894860
• Author Correction: COVID-19 Disease Map, Building a Computational Repository of SARS-CoV-2 Virus-host Interaction Mechanisms
  Scientific Data. Jul, 2020  |   Pubmed ID: 32678106
• A User Guide for the Online Exploration and Visualization of PCAWG Data
  Nature Communications. Jul, 2020  |   Pubmed ID: 32636365
• Sex and Gender Differences and Biases in Artificial Intelligence for Biomedicine and Healthcare
  NPJ Digital Medicine. 2020  |   Pubmed ID: 32529043
• Interpreting Molecular Similarity Between Patients As a Determinant of Disease Comorbidity Relationships
  Nature Communications. Jun, 2020  |   Pubmed ID: 32504002
• COVID-19 Disease Map, Building a Computational Repository of SARS-CoV-2 Virus-host Interaction Mechanisms
  Scientific Data. May, 2020  |   Pubmed ID: 32371892
• Unveiling New Disease, Pathway, and Gene Associations Via Multi-scale Neural Network
  PloS One. 2020  |   Pubmed ID: 32251458
• Understanding Oncogenicity of Cancer Driver Genes and Mutations in the Cancer Genomics Era
  FEBS Letters. Dec, 2020  |   Pubmed ID: 32239503
• Pathway and Network Analysis of More Than 2500 Whole Cancer Genomes
  Nature Communications. Feb, 2020  |   Pubmed ID: 32024854
• On the Inconsistent Treatment of Gene-protein-reaction Rules in Context-specific Metabolic Models
  Bioinformatics (Oxford, England). Mar, 2020  |   Pubmed ID: 31722383
• Patient Dossier: Healthcare Queries over Distributed Resources
  PLoS Computational Biology. Oct, 2019  |   Pubmed ID: 31622330
• Molecular Inverse Comorbidity Between Alzheimer's Disease and Lung Cancer: New Insights from Matrix Factorization
  International Journal of Molecular Sciences. Jun, 2019  |   Pubmed ID: 31247897
• Association of Anorexia Nervosa With Risk of Cancer: A Systematic Review and Meta-analysis
  JAMA Network Open. Jun, 2019  |   Pubmed ID: 31173122
• Big Data Analytics for Personalized Medicine
  Current Opinion in Biotechnology. Aug, 2019  |   Pubmed ID: 30965188
• Reviewer-coerced Citation: Case Report, Update on Journal Policy and Suggestions for Future Prevention
  Bioinformatics (Oxford, England). Sep, 2019  |   Pubmed ID: 30698640
• Intronic CNVs and Gene Expression Variation in Human Populations
  PLoS Genetics. Jan, 2019  |   Pubmed ID: 30677042
• BIOLITMAP: a Web-based Geolocated, Temporal and Thematic Visualization of the Evolution of Bioinformatics Publications
  Bioinformatics (Oxford, England). Jul, 2019  |   Pubmed ID: 30521012
• Epigenetic and Transcriptional Variability Shape Phenotypic Plasticity
  BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology. Feb, 2018  |   Pubmed ID: 29251357
• Legacy Data Sharing to Improve Drug Safety Assessment: the ETOX Project
  Nature Reviews. Drug Discovery. Dec, 2017  |   Pubmed ID: 29026211
• 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 Systematic Review and Meta-analysis of Observational Studies
  Systematic Reviews. Sep, 2017  |   Pubmed ID: 28915839
• Anorexia Nervosa and Cancer: a Protocol for a Systematic Review and Meta-analysis of Observational Studies
  Systematic Reviews. Jul, 2017  |   Pubmed ID: 28693568
• A Molecular Hypothesis to Explain Direct and Inverse Co-morbidities Between Alzheimer's Disease, Glioblastoma and Lung Cancer
  Scientific Reports. Jun, 2017  |   Pubmed ID: 28667284
• LimTox: a Web Tool for Applied Text Mining of Adverse Event and Toxicity Associations of Compounds, Drugs and Genes
  Nucleic Acids Research. Jul, 2017  |   Pubmed ID: 28531339
• Most Alternative Isoforms Are Not Functionally Important
  Trends in Biochemical Sciences. Jun, 2017  |   Pubmed ID: 28483377
• Anna Tramontano 1957-2017
  Nature Structural & Molecular Biology. May, 2017  |   Pubmed ID: 28471426
• Cancer and Central Nervous System Disorders: Protocol for an Umbrella Review of Systematic Reviews and Updated Meta-analyses of Observational Studies
  Systematic Reviews. Apr, 2017  |   Pubmed ID: 28376926
• The BLUEPRINT Data Analysis Portal
  Cell Systems. Nov, 2016  |   Pubmed ID: 27863955
• Non-coding Recurrent Mutations in Chronic Lymphocytic Leukaemia
  Nature. Oct, 2015  |   Pubmed ID: 26200345
• Whole-genome Sequencing Identifies Recurrent Mutations in Chronic Lymphocytic Leukaemia
  Nature. Jul, 2011  |   Pubmed ID: 21642962
• Towards the Prediction of Protein Interaction Partners Using Physical Docking
  Molecular Systems Biology. Feb, 2011  |   Pubmed ID: 21326236