Alfonso Valencia Barcelona Supercomputing Center Biography Publications Institution JoVE Articles Alfonso Valencia has not added a biography. If you are Alfonso Valencia and would like to personalize this page please email our Author Liaison for assistance. 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 An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations (Video) | JoVE Llorenç Rovirosa*1, Laureano Tomás-Daza*1,2, Blanca Urmeneta1, Alfonso Valencia2,3, Biola M. Javierre1,4 1Josep Carreras Leukaemia Research Institute, 2Barcelona Supercomputing Center, 3Catalan Institution for Research and Advanced Studies (ICREA), 4Institute for Health Science Research Germans Trias i Pujol JoVE 65316 Genetica
An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations (Video) | JoVE Llorenç Rovirosa*1, Laureano Tomás-Daza*1,2, Blanca Urmeneta1, Alfonso Valencia2,3, Biola M. Javierre1,4 1Josep Carreras Leukaemia Research Institute, 2Barcelona Supercomputing Center, 3Catalan Institution for Research and Advanced Studies (ICREA), 4Institute for Health Science Research Germans Trias i Pujol JoVE 65316 Genetica