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Author Details

John A Capra
Bakar Computational Health Sciences Institute, University of California san francisco
2003
111
31
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36824965Human gene regulatory evolution is driven by the divergence of regulatory element function in both <i>cis</i> and <i>trans</i>.bioRxiv2023
38095367Archaic Introgression Shaped Human Circadian Traits.Genome Biol Evol2023
38077057Associations with spontaneous and indicated preterm birth in a densely phenotyped EHR cohort.medRxiv2023
38076936Cell-Specific Transposable Element Gene Expression Analysis Identifies Associations with Systemic Lupus Erythematosus Phenotypes.bioRxiv2023
37961120Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees.bioRxiv2023
37609337Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates.bioRxiv2023
37440029Integrating Computational Approaches to Predict the Effect of Genetic Variants on Protein Stability in Retinal Degenerative Disease.Adv Exp Med Biol2023
37410590Cis-regulatory Landscape Size, Constraint, and Tissue Specificity Associate with Gene Function and Expression.Genome Biol Evol2023
37292728Comparing chromatin contact maps at scale: methods and insights.Res Sq2023
37162834High-throughput functional mapping of variants in an arrhythmia gene, <i>KCNE1</i>, reveals novel biology.bioRxiv2023
37142741Resurrecting the alternative splicing landscape of archaic hominins using machine learning.Nat Ecol Evol2023
37066196Comparing chromatin contact maps at scale: methods and insights.bioRxiv2023
37012456Genetic effects on the timing of parturition and links to fetal birth weight.Nat Genet2023
36875690Linking rare and common disease vocabularies by mapping between the human phenotype ontology and phecodes.JAMIA Open2023
36824965Human gene regulatory evolution is driven by the divergence of regulatory element function in both <i>cis</i> and <i>trans</i>.bioRxiv2023
36778254Archaic Introgression Shaped Human Circadian Traits.bioRxiv2023
36655767GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions.Bioinformatics2023
36516610Clinical characteristics and electrophysiologic properties of SCN5A variants in fever-induced Brugada syndrome.EBioMedicine2023
38077057Associations with spontaneous and indicated preterm birth in a densely phenotyped EHR cohort.medRxiv2023
38076936Cell-Specific Transposable Element Gene Expression Analysis Identifies Associations with Systemic Lupus Erythematosus Phenotypes.bioRxiv2023
37961120Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees.bioRxiv2023
37609337Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates.bioRxiv2023
38095367Archaic Introgression Shaped Human Circadian Traits.Genome Biol Evol2023
37292728Comparing chromatin contact maps at scale: methods and insights.Res Sq2023
37012456Genetic effects on the timing of parturition and links to fetal birth weight.Nat Genet2023
37410590Cis-regulatory Landscape Size, Constraint, and Tissue Specificity Associate with Gene Function and Expression.Genome Biol Evol2023
37142741Resurrecting the alternative splicing landscape of archaic hominins using machine learning.Nat Ecol Evol2023
37440029Integrating Computational Approaches to Predict the Effect of Genetic Variants on Protein Stability in Retinal Degenerative Disease.Adv Exp Med Biol2023
37066196Comparing chromatin contact maps at scale: methods and insights.bioRxiv2023
37162834High-throughput functional mapping of variants in an arrhythmia gene, <i>KCNE1</i>, reveals novel biology.bioRxiv2023
36655767GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions.Bioinformatics2023
36516610Clinical characteristics and electrophysiologic properties of SCN5A variants in fever-induced Brugada syndrome.EBioMedicine2023
36875690Linking rare and common disease vocabularies by mapping between the human phenotype ontology and phecodes.JAMIA Open2023
36778254Archaic Introgression Shaped Human Circadian Traits.bioRxiv2023
34314237Machine Learning Prediction of Kidney Stone Composition Using Electronic Health Record-Derived Features.J Endourol2022
36069078The immune deficiency and c-Jun N-terminal kinase pathways drive the functional integration of the immune and circulatory systems of mosquitoes.Open Biol2022
35853510Machine Learning Models to Predict 24 Hour Urinary Abnormalities for Kidney Stone Disease.Urology2022
35749358Microbiome-associated human genetic variants impact phenome-wide disease risk.Proc Natl Acad Sci U S A2022
35710621Genome-wide association study of musical beat synchronization demonstrates high polygenicity.Nat Hum Behav2022
35687855An Active Learning Framework Improves Tumor Variant Interpretation.Cancer Res2022
35672414The 3D mutational constraint on amino acid sites in the human proteome.Nat Commun2022
35609632R-loop Mapping and Characterization During Drosophila Embryogenesis Reveals Developmental Plasticity in R-loop Signatures.J Mol Biol2022
35606693Diverse functions associate with non-coding polymorphisms shared between humans and chimpanzees.BMC Ecol Evol2022
35560012Vascular alterations impede fragile tolerance to pregnancy in type 1 diabetes.F S Sci2022
35508071Integration of Protein Structure and Population-Scale DNA Sequence Data for Disease Gene Discovery and Variant Interpretation.Annu Rev Biomed Data Sci2022
35440148Predicting Archaic Hominin Phenotypes from Genomic Data.Annu Rev Genomics Hum Genet2022
35210353An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease-related patterns.Genome Res2022
34314237Machine Learning Prediction of Kidney Stone Composition Using Electronic Health Record-Derived Features.J Endourol2022
36351393Nucleoporins facilitate ORC loading onto chromatin.Cell Rep2022
36342969Mosaic patterns of selection in genomic regions associated with diverse human traits.PLoS Genet2022
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Collaborators

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Co-authored papers 16
Vanderbilt University
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Cleveland Institute for Computational Biology, Case Western Reserve University
Co-authored papers 9
Vanderbilt University Medical Center
Co-authored papers 5
University of California
Co-authored papers 5
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Gladstone Institutes of Cardiovascular Disease, Gladstone Institutes
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Duke University
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and Center for Structural Biology, Vanderbilt University
Co-authored papers 2
Gladstone Institute of Virology
Co-authored papers 2
Cleveland Institute for Computational Biology, Case Western Reserve University
Co-authored papers 2
Indiana University School of Medicine
Co-authored papers 2
Mayo Clinic
Co-authored papers 2
Invitae Corporation
Co-authored papers 2
Co-authored papers 2
Cleveland Institute for Computational Biology, Case Western Reserve University
Co-authored papers 2
Vanderbilt University
Co-authored papers 2
Duke Molecular Physiology Institute, Duke University School of Medicine
Co-authored papers 2
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Case Western Reserve University School of Medicine
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Northwestern University Feinberg School of Medicine
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Oslo University Hospital & Institute of Clinical Medicine, University of Oslo
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Institute for Systems Biology
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