Dan Koboldt’s Publications
Bose R, Kavuri SM, Searleman AC, Shen W, Shen D, Koboldt DC, Monsey J, Goel N, Aronson AB, Li S, Ma CX, Ding L, Mardis ER, & Ellis MJ (2013).Activating HER2 mtations in HER2 gene amplification negative breast cancer. Cancer discovery PMID: 23220880
The 1000 Genomes Project Consortium (2012). An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56-65. DOI: 10.1038/nature11632
Cancer Genome Atlas Network (2012). Comprehensive molecular portraits of human breast tumours. Nature, 490 (7418), 61-70 PMID:23000897
Ellis MJ, Ding L, Shen D, Luo J, Suman VJ, Wallis JW, Van Tine BA, Hoog J, Goiffon RJ, Goldstein TC, Ng S, Lin L, Crowder R, Snider J, Ballman K, Weber J, Chen K, Koboldt DC, Kandoth C, Schierding WS, McMichael JF, Miller CA, Lu C, Harris CC, McLellan MD, Wendl MC, DeSchryver K, Allred DC, Esserman L, Unzeitig G, Margenthaler J, Babiera GV, Marcom PK, Guenther JM, Leitch M, Hunt K, Olson J, Tao Y, Maher CA, Fulton LL, Fulton RS, Harrison M, Oberkfell B, Du F, Demeter R, Vickery TL, Elhammali A, Piwnica-Worms H, McDonald S, Watson M, Dooling DJ, Ota D, Chang LW, Bose R, Ley TJ, Piwnica-Worms D, Stuart JM, Wilson RK, & Mardis ER (2012). Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature, 486 (7403), 353-60 PMID: 22722193
Welch JS, Ley TJ, Link DC, Miller CA, Larson DE, Koboldt DC, Wartman LD, Lamprecht TL, Liu F, Xia J, Kandoth C, Fulton RS, McLellan MD, Dooling DJ, Wallis JW, Chen K, Harris CC, Schmidt HK, Kalicki-Veizer JM, Lu C, Zhang Q, Lin L, O’Laughlin MD, McMichael JF, Delehaunty KD, Fulton LA, Magrini VJ, McGrath SD, Demeter RT, Vickery TL, Hundal J, Cook LL, Swift GW, Reed JP, Alldredge PA, Wylie TN, Walker JR, Watson MA, Heath SE, Shannon WD, Varghese N, Nagarajan R, Payton JE, Baty JD, Kulkarni S, Klco JM, Tomasson MH, Westervelt P, Walter MJ, Graubert TA, DiPersio JF, Ding L, Mardis ER, & Wilson RK (2012). The origin and evolution of mutations in acute myeloid leukemia. Cell, 150 (2), 264-78 PMID: 22817890
Cancer Genome Atlas Network (2012). Comprehensive molecular characterization of human colon and rectal cancer. Nature, 487(7407), 330-7 PMID: 22810696
Dees ND, Zhang Q, Kandoth C, Wendl MC, Schierding W, Koboldt DC, Mooney TB, Callaway MB, Dooling D, Mardis ER, Wilson RK, & Ding L (2012). MuSiC: identifying mutational significance in cancer genomes.Genome research, 22 (8), 1589-98 PMID: 22759861
Walter MJ, Shen D, Ding L, Shao J, Koboldt DC, Chen K, Larson DE, McLellan MD, Dooling D, Abbott R, Fulton R, Magrini V, Schmidt H, Kalicki-Veizer J, O’Laughlin M, Fan X, Grillot M, Witowski S, Heath S, Frater JL, Eades W, Tomasson M, Westervelt P, DiPersio JF, Link DC, Mardis ER, Ley TJ, Wilson RK, & Graubert TA (2012). Clonal architecture of secondary acute myeloid leukemia. The New England journal of medicine, 366(12), 1090-8 PMID: 22417201
Matsushita H, Vesely MD, Koboldt DC, Rickert CG, Uppaluri R, Magrini VJ, Arthur CD, White JM, Chen YS, Shea LK, Hundal J, Wendl MC, Demeter R, Wylie T, Allison JP, Smyth MJ, Old LJ, Mardis ER, & Schreiber RD (2012).Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting. Nature, 482 (7385), 400-4 PMID: 22318521
Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, & Wilson RK (2012). VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Research PMID: 22300766
Koboldt DC, Larson DE, Chen K, Ding L, & Wilson RK (2012). Massively parallel sequencing approaches for characterization of structural variation. Methods in molecular biology (Clifton, N.J.), 838, 369-84 PMID:22228022
Graubert TA, Shen D, Ding L, Okeyo-Owuor T, Lunn CL, Shao J, Krysiak K, Harris CC, Koboldt DC, Larson DE, McLellan MD, Dooling DJ, Abbott RM, Fulton RS, Schmidt H, Kalicki-Veizer J, O’Laughlin M, Grillot M, Baty J, Heath S, Frater JL, Nasim T, Link DC, Tomasson MH, Westervelt P, DiPersio JF, Mardis ER, Ley TJ, Wilson RK, & Walter MJ (2011). Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes. Nature genetics, 44 (1), 53-7 PMID: 22158538
Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, Ley TJ, Mardis ER, Wilson RK, & Ding L. (2011). SomaticSniper: Identification of Somatic Point Mutations in Whole Genome Sequencing Data.Bioinformatics, Online : doi: 10.1093/bioinformatics/btr665
Cancer Genome Atlas Research Network (2011). Integrated genomic analyses of ovarian carcinoma. Nature, 474 (7353), 609-15 PMID:21720365
Marth GT, Yu F, Indap AR, Garimella K, et al & the 1000 Genomes Project (2011). The functional spectrum of low-frequency coding variation.Genome biology, 12 (9) PMID: 21917140
Ross JA, Koboldt DC, Staisch JE, Chamberlin HM, Gupta BP, Miller RD, Baird SE, & Haag ES (2011). Caenorhabditis briggsae recombinant inbred line genotypes reveal inter-strain incompatibility and the evolution of recombination. PLoS genetics, 7 (7) PMID: 21779179
Bowne SJ, Humphries MM, Sullivan LS, Kenna PF, Tam LC, Kiang AS, Campbell M, Weinstock GM, Koboldt DC, Ding L, Fulton RS, Sodergren EJ, et al (2011). A dominant mutation in RPE65 identified by whole-exome sequencing causes retinitis pigmentosa with choroidal involvement. European journal of human genetics : EJHG, 19 (10) PMID:21938004
Link DC, Schuettpelz LG, Shen D, Wang J, Walter MJ, Kulkarni S, Payton JE, Ivanovich J, Goodfellow PJ, Le Beau M, Koboldt DC, Dooling DJ, Fulton RS, et al (2011). Identification of a novel TP53 cancer susceptibility mutation through whole-genome sequencing of a patient with therapy-related AML. JAMA : the journal of the American Medical Association, 305 (15), 1568-76 PMID: 21505135
Ley T, Ding L, Walter M, McLellan M, Lamprecht T, Larson D, Kandoth C, Payton J, Baty J, Welch J, Harris C, Lichti C, Townsend R, Fulton R, Dooling D, Koboldt D, et al. (2010). DNMT3A Mutations in Acute Myeloid Leukemia
New England Journal of Medicine DOI: 10.1056/NEJMoa1005143
Ding L, Wendl MC, Koboldt DC, & Mardis ER (2010). Analysis of next-generation genomic data in cancer: accomplishments and challenges. Human Molecular Genetics, 19 (R2):R188-96. PMID:20843826
Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, 1000 Genomes Project, & Eichler EE (2010). Diversity of human copy number variation and multicopy genes. Science (New York, N.Y.), 330 (6004), 641-6 PMID: 21030649
The 1000 Genomes Project Consortium (2010). A map of human genome variation from population-scale sequencing. Nature, 467(7319), 1061-1073 DOI: 10.1038/nature09534
Bowne SJ, Sullivan LS, Koboldt DC, Ding L, Fulton R, Abbott RM, Sodergren EJ, Birch DG, Wheaton DH, Heckenlively JR, Liu Q, Pierce EA, Weinstock GM, & Daiger SP (2010). Identification of Disease-Causing Mutations in Autosomal Dominant Retinitis Pigmentosa (adRP) Using Next-Generation DNA Sequencing. Investigative ophthalmology & visual science PMID: 20861475
Fehniger, T., Wylie, T., Germino, E., Leong, J., Magrini, V., Koul, S., Keppel, C., Schneider, S., Koboldt, D., Sullivan, R., Heinz, M., Crosby, S., Nagarajan, R., Ramsingh, G., Link, D., Ley, T., & Mardis, E. (2010). Next-generation sequencing identifies the natural killer cell microRNA transcriptome Genome Research DOI: 10.1101/gr.107995.110
Ramsingh G, Koboldt DC, Trissal M, Chiappinelli KB, Wylie T, Koul S, Chang LW, Nagarajan R, Fehniger TA, Goodfellow P, Magrini V, Wilson RK, Ding L, Ley TJ, Mardis ER, & Link DC (2010). Complete characterization of the microRNAome in a patient with acute myeloid leukemia. BloodPMID: 20876853
Koboldt DC, Ding L, Mardis ER & Wilson RK. (2010). Challenges of sequencing human genomes. Briefings in Bioinformatics DOI:10.1093/bib/bbq016
Ding L, Ellis MJ, Li S, Larson DE, Chen K, Wallis JW, Harris CC, McLellan MD, Fulton RS, Fulton LL, Abbott RM, Hoog J, Dooling DJ, Koboldt DC, et al. (2010). Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature, 464 (7291), 999-1005 PMID:20393555
Koboldt DC and Miller RD (2010). Identification of polymorphic markers for genetic mapping. Genomics: Essential Methods, In Press.
Koboldt DC, Staisch J, Thillainathan B, Haines K, Baird SE, Chamberlin HM, Haag ES, Miller RD, & Gupta BP (2010). A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae. BMC genomics, 11 (1) PMID: 20385026
Voora D, Koboldt DC, King CR, Lenzini PA, Eby CS, Porche-Sorbet R, Deych E, Crankshaw M, Milligan PE, McLeod HL, Patel SR, Cavallari LH, Ridker PM, Grice GR, Miller RD, & Gage BF (2010). A polymorphism in the VKORC1 regulator calumenin predicts higher warfarin dose requirements in African Americans. Clinical pharmacology and therapeutics, 87 (4), 445-51 PMID: 20200517
Zhang Q, Ding L, Larson DE, Koboldt DC, McLellan MD, Chen K, Shi X, Kraja A, et al (2009). CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data. Bioinformatics (Oxford, England) PMID: 20031968
Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, Koboldt DC, et al (2009). Recurring mutations found by sequencing an acute myeloid leukemia genome. The New England journal of medicine, 361(11), 1058-66 PMID: 19657110
Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, & Ding L (2009). VarScan: variant detection in massively parallel sequencing of individual and pooled samples.Bioinformatics (Oxford, England), 25 (17), 2283-5 PMID: 19542151
Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, Chen K, Dooling D, Dunford-Shore BH, McGrath S, Hickenbotham M, Cook L, Abbott R, Larson DE, Koboldt DC, et al (2008). DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature, 456 (7218), 66-72 PMID: 18987736
Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, et al (2008). Somatic mutations affect key pathways in lung adenocarcinoma. Nature, 455 (7216), 1069-75 PMID: 18948947
Cancer Genome Atlas Research Network (2008). Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455 (7216), 1061-8 PMID: 18772890
International HapMap Consortium (2007). A second generation human haplotype map of over 3.1 million SNPs. Nature, 449 (7164), 851-61 PMID: 17943122
Sabeti PC, Varilly P, Fry B, et al (2007). Genome-wide detection and characterization of positive selection in human populations. Nature, 449 (7164), 913-8 PMID: 17943131
Hillier LW, Miller RD, Baird SE, Chinwalla A, Fulton LA, Koboldt DC, & Waterston RH (2007). Comparison of C. elegans and C. briggsaegenome sequences reveals extensive conservation of chromosome organization and synteny. PLoS biology, 5 (7) PMID: 17608563
Stanley SL Jr, Frey SE, Taillon-Miller P, Guo J, Miller RD, Koboldt DC, Elashoff M, Christensen R, Saccone NL, & Belshe RB (2007). The immunogenetics of smallpox vaccination. The Journal of infectious diseases, 196 (2), 212-9 PMID: 17570108
Koboldt DC, Miller RD, & Kwok PY (2006). Distribution of human SNPs and its effect on high-throughput genotyping. Human mutation, 27(3), 249-54 PMID: 16425292
The International HapMap Consortium (2005). A haplotype map of the human genome. Nature, 437 (7063), 1299-1320 PMID: 16255080
Miller RD, Phillips MS, et al (2005). High-density single-nucleotide polymorphism maps of the human genome. Genomics, 86 (2), 117-26 PMID: 15961272
Other Writing by Dan Koboldt
Dan Koboldt is also the author of Get Your Baby to Sleep, a resource to help new parents whose baby won’t sleep with advice on establishing healthy baby sleep habits and handling baby sleep problems. He contributes to The Best of Twins and In Search of Whitetails blogs as well.
How would you like to start your own blog? See this guide to building a blog or website in 20 minutes. It walks you through setting up a site with open-source WordPress software, which happens to be what runs Massgenomics.
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