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Brent S. Pedersen, Ph.D. - Publications

Affiliations: 
2005 University of California, Berkeley, Berkeley, CA, United States 
Area:
Ecology Biology
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37 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Pedersen BS, Bhetariya PJ, Brown J, Kravitz SN, Marth G, Jensen RL, Bronner MP, Underhill HR, Quinlan AR. Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches. Genome Medicine. 12: 62. PMID 32664994 DOI: 10.1186/S13073-020-00761-2  0.34
2019 Pedersen BS, Quinlan AR. Duphold: scalable, depth-based annotation and curation of high-confidence structural variant calls. Gigascience. 8. PMID 31222198 DOI: 10.1093/Gigascience/Giz040  0.353
2019 Havrilla JM, Pedersen BS, Layer RM, Quinlan AR. A map of constrained coding regions in the human genome. Nature Genetics. 51: 88-95. PMID 30531870 DOI: 10.1038/S41588-018-0294-6  0.367
2018 Ostrander BEP, Butterfield RJ, Pedersen BS, Farrell AJ, Layer RM, Ward A, Miller C, DiSera T, Filloux FM, Candee MS, Newcomb T, Bonkowsky JL, Marth GT, Quinlan AR. Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy. Npj Genomic Medicine. 3: 22. PMID 30109124 DOI: 10.1038/S41525-018-0061-8  0.386
2018 Klopfenstein DV, Zhang L, Pedersen BS, Ramírez F, Warwick Vesztrocy A, Naldi A, Mungall CJ, Yunes JM, Botvinnik O, Weigel M, Dampier W, Dessimoz C, Flick P, Tang H. GOATOOLS: A Python library for Gene Ontology analyses. Scientific Reports. 8: 10872. PMID 30022098 DOI: 10.1038/S41598-018-28948-Z  0.335
2018 Pedersen BS, Quinlan AR. hts-nim: scripting high-performance genomic analyses. Bioinformatics (Oxford, England). PMID 29718142 DOI: 10.1093/Bioinformatics/Bty358  0.338
2018 Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT, Malla S, Marriott H, Nieto T, O'Grady J, Olsen HE, ... Pedersen BS, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nature Biotechnology. PMID 29431738 DOI: 10.1038/Nbt.4060  0.354
2018 Layer RM, Pedersen BS, DiSera T, Marth GT, Gertz J, Quinlan AR. GIGGLE: a search engine for large-scale integrated genome analysis. Nature Methods. PMID 29309061 DOI: 10.1038/Nmeth.4556  0.374
2017 Pedersen BS, Quinlan AR. mosdepth: quick coverage calculation for genomes and exomes. Bioinformatics (Oxford, England). PMID 29096012 DOI: 10.1093/Bioinformatics/Btx699  0.353
2017 Pedersen BS, Collins RL, Talkowski ME, Quinlan AR. Indexcov: fast coverage quality control for whole-genome sequencing. Gigascience. PMID 29048539 DOI: 10.1093/Gigascience/Gix090  0.401
2017 Pedersen BS, Quinlan AR. Who's Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy. American Journal of Human Genetics. PMID 28190455 DOI: 10.1016/J.Ajhg.2017.01.017  0.345
2017 Pedersen BS, Quinlan AR. cyvcf2: fast, flexible variant analysis with Python. Bioinformatics (Oxford, England). PMID 28165109 DOI: 10.1093/Bioinformatics/Btx057  0.348
2016 Fingerlin TE, Zhang W, Yang IV, Ainsworth HC, Russell PH, Blumhagen RZ, Schwarz MI, Brown KK, Steele MP, Loyd JE, Cosgrove GP, Lynch DA, Groshong S, Collard HR, Wolters PJ, ... ... Pedersen BS, et al. Genome-wide imputation study identifies novel HLA locus for pulmonary fibrosis and potential role for auto-immunity in fibrotic idiopathic interstitial pneumonia. Bmc Genetics. 17: 74. PMID 27266705 DOI: 10.1186/S12863-016-0377-2  0.34
2016 Pedersen BS, Layer RM, Quinlan AR. Vcfanno: fast, flexible annotation of genetic variants. Genome Biology. 17: 118. PMID 27250555 DOI: 10.1186/S13059-016-0973-5  0.389
2015 Mathai SK, Pedersen BS, Smith K, Russell P, Schwarz MI, Brown KK, Steele MP, Loyd JE, Crapo JD, Silverman EK, Nickerson D, Fingerlin TE, Yang IV, Schwartz DA. Desmoplakin (DSP) Variants are Associated with Idiopathic Pulmonary Fibrosis. American Journal of Respiratory and Critical Care Medicine. PMID 26669357 DOI: 10.1164/Rccm.201509-1863Oc  0.32
2015 Smith KS, Yadav VK, Pedersen BS, Shaknovich R, Geraci MW, Pollard KS, De S. Signatures of accelerated somatic evolution in gene promoters in multiple cancer types. Nucleic Acids Research. 43: 5307-17. PMID 25934800 DOI: 10.1093/Nar/Gkv419  0.345
2014 De S, Pedersen BS, Kechris K. The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment. Briefings in Bioinformatics. 15: 919-28. PMID 23956260 DOI: 10.1093/Bib/Bbt053  0.368
2013 Pedersen BS, Yang IV, De S. CruzDB: software for annotation of genomic intervals with UCSC genome-browser database. Bioinformatics (Oxford, England). 29: 3003-6. PMID 24037212 DOI: 10.1093/Bioinformatics/Btt534  0.386
2013 Turco G, Schnable JC, Pedersen B, Freeling M. Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses. Frontiers in Plant Science. 4: 170. PMID 23874343 DOI: 10.3389/Fpls.2013.00170  0.378
2013 Pedersen BS, De S. Loss of heterozygosity preferentially occurs in early replicating regions in cancer genomes. Nucleic Acids Research. 41: 7615-24. PMID 23793816 DOI: 10.1093/Nar/Gkt552  0.322
2013 Pedersen BS, Konstantinopoulos PA, Spillman MA, De S. Copy neutral loss of heterozygosity is more frequent in older ovarian cancer patients. Genes, Chromosomes & Cancer. 52: 794-801. PMID 23716468 DOI: 10.1002/Gcc.22075  0.31
2013 Fingerlin TE, Murphy E, Zhang W, Peljto AL, Brown KK, Steele MP, Loyd JE, Cosgrove GP, Lynch D, Groshong S, Collard HR, Wolters PJ, Bradford WZ, Kossen K, Seiwert SD, ... ... Pedersen BS, et al. Erratum: Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis Nature Genetics. 45: 1409-1409. DOI: 10.1038/Ng1113-1409A  0.344
2012 Tang H, Woodhouse MR, Cheng F, Schnable JC, Pedersen BS, Conant G, Wang X, Freeling M, Pires JC. Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy. Genetics. 190: 1563-74. PMID 22308264 DOI: 10.1534/Genetics.111.137349  0.373
2011 Schnable JC, Pedersen BS, Subramaniam S, Freeling M. Dose-sensitivity, conserved non-coding sequences, and duplicate gene retention through multiple tetraploidies in the grasses. Frontiers in Plant Science. 2: 2. PMID 22645525 DOI: 10.3389/Fpls.2011.00002  0.395
2011 Dale RK, Pedersen BS, Quinlan AR. Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Bioinformatics (Oxford, England). 27: 3423-4. PMID 21949271 DOI: 10.1093/Bioinformatics/Btr539  0.392
2011 Pedersen B, Hsieh TF, Ibarra C, Fischer RL. MethylCoder: Software pipeline for bisulte-treated sequences Bioinformatics. 27: 2435-2436. PMID 21724594 DOI: 10.1093/Bioinformatics/Btr394  0.305
2011 Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M. Screening synteny blocks in pairwise genome comparisons through integer programming. Bmc Bioinformatics. 12: 102. PMID 21501495 DOI: 10.1186/1471-2105-12-102  0.393
2011 Pedersen BS, Tang H, Freeling M. Gobe: an interactive, web-based tool for comparative genomic visualization. Bioinformatics (Oxford, England). 27: 1015-6. PMID 21296748 DOI: 10.1093/Bioinformatics/Btr056  0.367
2010 Woodhouse MR, Schnable JC, Pedersen BS, Lyons E, Lisch D, Subramaniam S, Freeling M. Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs. Plos Biology. 8: e1000409. PMID 20613864 DOI: 10.1371/Journal.Pbio.1000409  0.365
2010 Woodhouse MR, Pedersen B, Freeling M. Transposed genes in Arabidopsis are often associated with flanking repeats. Plos Genetics. 6: e1000949. PMID 20485521 DOI: 10.1371/Journal.Pgen.1000949  0.365
2008 Lyons E, Pedersen B, Kane J, Alam M, Ming R, Tang H, Wang X, Bowers J, Paterson A, Lisch D, Freeling M. Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiology. 148: 1772-81. PMID 18952863 DOI: 10.1104/Pp.108.124867  0.435
2008 Freeling M, Lyons E, Pedersen B, Alam M, Ming R, Lisch D. Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Research. 18: 1924-37. PMID 18836034 DOI: 10.1101/Gr.081026.108  0.336
2008 Lyons E, Pedersen B, Kane J, Freeling M. The Value of Nonmodel Genomes and an Example Using SynMap Within CoGe to Dissect the Hexaploidy that Predates the Rosids Tropical Plant Biology. 1: 181-190. DOI: 10.1007/S12042-008-9017-Y  0.399
2007 Freeling M, Rapaka L, Lyons E, Pedersen B, Thomas BC. G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis. The Plant Cell. 19: 1441-57. PMID 17496117 DOI: 10.1105/Tpc.107.050419  0.335
2007 Thomas BC, Rapaka L, Lyons E, Pedersen B, Freeling M. Arabidopsis intragenomic conserved noncoding sequence. Proceedings of the National Academy of Sciences of the United States of America. 104: 3348-53. PMID 17301222 DOI: 10.1073/Pnas.0611574104  0.38
2006 Thomas BC, Pedersen B, Freeling M. Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Research. 16: 934-46. PMID 16760422 DOI: 10.1101/Gr.4708406  0.348
2004 Pedersen BS, Mills NJ. Single vs. multiple introduction in biological control: The roles of parasitoid efficiency, antagonism and niche overlap Journal of Applied Ecology. 41: 973-984. DOI: 10.1111/J.0021-8901.2004.00953.X  0.469
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