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Author Details

Brent S Pedersen
Center for Molecular Medicine, University Medical Center Utrecht
2001
65
35
PMIDPaper TitleJournal TitlePublished Year
36300617Echtvar: compressed variant representation for rapid annotation and filtering of SNPs and indels.Nucleic Acids Res2023
36376793Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies.BMC Bioinformatics2022
35639788A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar.PLoS Comput Biol2022
35396485Searching thousands of genomes to classify somatic and novel structural variants using STIX.Nat Methods2022
35618956Author Correction: Searching thousands of genomes to classify somatic and novel structural variants using STIX.Nat Methods2022
36477201Extensive Recombination-driven Coronavirus Diversification Expands the Pool of Potential Pandemic Pathogens.Genome Biol Evol2022
34146087Unfazed: parent-of-origin detection for large and small de novo variants.Bioinformatics2021
35936573Balancing efficient analysis and storage of quantitative genomics data with the D4 format and d4tools.Nat Comput Sci2021
33846313Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data.Nat Commun2021
33564759Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens.bioRxiv2021
33830997CaBagE: A Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing.PLoS One2021
34034781Samplot: a platform for structural variant visual validation and automated filtering.Genome Biol2021
30531870A map of constrained coding regions in the human genome.Nat Genet2019
31549960Large, three-generation human families reveal post-zygotic mosaicism and variability in germline mutation accumulation.Elife2019
31222198Duphold: scalable, depth-based annotation and curation of high-confidence structural variant calls.Gigascience2019
31019089Overlooked roles of DNA damage and maternal age in generating human germline mutations.Proc Natl Acad Sci U S A2019
29096012Mosdepth: quick coverage calculation for genomes and exomes.Bioinformatics2018
29860504SV-plaudit: A cloud-based framework for manually curating thousands of structural variants.Gigascience2018
30022098GOATOOLS: A Python library for Gene Ontology analyses.Sci Rep2018
30109124Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy.NPJ Genom Med2018
29718142hts-nim: scripting high-performance genomic analyses.Bioinformatics2018
29402882Publisher Correction: Combating subclonal evolution of resistant cancer phenotypes.Nat Commun2018
29431738Nanopore sequencing and assembly of a human genome with ultra-long reads.Nat Biotechnol2018
29309061GIGGLE: a search engine for large-scale integrated genome analysis.Nat Methods2018
29329322Methylene-tetrahydrofolate reductase contributes to allergic airway disease.PLoS One2018
27745942The nasal methylome and childhood atopic asthma.J Allergy Clin Immunol2017
28165109cyvcf2: fast, flexible variant analysis with Python.Bioinformatics2017
28190455Who's Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy.Am J Hum Genet2017
28272906Regulation of MUC5B Expression in Idiopathic Pulmonary Fibrosis.Am J Respir Cell Mol Biol2017
29048539Indexcov: fast coverage quality control for whole-genome sequencing.Gigascience2017
29093439Combating subclonal evolution of resistant cancer phenotypes.Nat Commun2017
27027970DNA Methylation Changes in Nasal Epithelia Are Associated with Allergic Asthma in the Inner City.Ann Am Thorac Soc2016
26669357Desmoplakin Variants Are Associated with Idiopathic Pulmonary Fibrosis.Am J Respir Crit Care Med2016
27356610Novel Innate Immune Genes Regulating the Macrophage Response to Gram Positive Bacteria.Genetics2016
27266705Genome-wide imputation study identifies novel HLA locus for pulmonary fibrosis and potential role for auto-immunity in fibrotic idiopathic interstitial pneumonia.BMC Genet2016
27250555Vcfanno: fast, flexible annotation of genetic variants.Genome Biol2016
25769910DNA methylation and childhood asthma in the inner city.J Allergy Clin Immunol2015
26546417Unique DNA Methylation Patterns in Offspring of Hypertensive Pregnancy.Clin Transl Sci2015
26642056In Utero Cigarette Smoke Affects Allergic Airway Disease But Does Not Alter the Lung Methylome.PLoS One2015
25934800Signatures of accelerated somatic evolution in gene promoters in multiple cancer types.Nucleic Acids Res2015
23956260The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment.Brief Bioinform2014
25333685Relationship of DNA methylation and gene expression in idiopathic pulmonary fibrosis.Am J Respir Crit Care Med2014
24307415Inhibition of peroxisome proliferator-activated receptor γ: a potential link between chronic maternal hypoxia and impaired fetal growth.FASEB J2014
23583980Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis.Nat Genet2013
24037212CruzDB: software for annotation of genomic intervals with UCSC genome-browser database.Bioinformatics2013
23874343Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses.Front Plant Sci2013
23716468Copy neutral loss of heterozygosity is more frequent in older ovarian cancer patients.Genes Chromosomes Cancer2013
23793816Loss of heterozygosity preferentially occurs in early replicating regions in cancer genomes.Nucleic Acids Res2013
22308264Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy.Genetics2012
22954632Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values.Bioinformatics2012
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Collaborators

University of Utah
Co-authored papers 27
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Boulder and BioFrontiers Institute, University of Colorado Boulder
Co-authored papers 10
Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University
Co-authored papers 5
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University of Pittsburgh
Co-authored papers 3
Columbia University Medical Center
Co-authored papers 3
USDA-ARS, Corn Insects and Crop Genetics Research Unit
Co-authored papers 3
Breathing Institute, Children's Hospital Colorado
Co-authored papers 3
University of Texas Southwestern Medical Center
Co-authored papers 3
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Boston University School of Medicine
Co-authored papers 3
National Institute of Allergy and Infectious Diseases, National Institutes of Health
Co-authored papers 3
University of Wisconsin School of Medicine and Public Health
Co-authored papers 3
University of Minnesota Genomics Center (UMNGC)
Co-authored papers 2
University of Arizona
Co-authored papers 2
National Institute of Allergy and Infectious Diseases
Co-authored papers 2
Oregon Health and Science University
Co-authored papers 2
Co-authored papers 2
Rho Inc.
Co-authored papers 2
University of Rochester Medical Center
Co-authored papers 2
Brigham Young University
Co-authored papers 2
Baylor College of Medicine
Co-authored papers 2
University of Utah School of Medicine
Co-authored papers 2
University of Utah School of Medicine
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Lineberger Cancer Center, University of North Carolina
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Oregon Health Sciences University
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Center for Translational Research.
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