Kelly Frazer

InstitutionUniversity of California San Diego
Address9500 Gilman Drive #0761
La Jolla CA 92093
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    Collapse Research 
    Collapse Research Activities and Funding
    Fine-mapping and functional analysis of T1D-associated variants
    NIH/NIDDK DP3DK112155Sep 30, 2016 - Jun 30, 2021
    Role: Principal Investigator
    Functional Analysis of T2D Associated Non-coding SNPs
    NIH/NIDDK U01DK105541May 1, 2015 - Apr 30, 2020
    Role: Principal Investigator
    Optimizing HaploSeq for whole-genome phased haplotypes in biomedical applications
    NIH/NHGRI R41HG008118Mar 1, 2015 - Jan 31, 2017
    Role: Principal Investigator
    NIH/NHLBI U01HL107442Jul 15, 2011 - Jun 30, 2017
    Role: Principal Investigator
    Biomarkers of Disease Progression in CLL
    NIH/NCI R21CA152613Jun 1, 2010 - May 31, 2012
    Role: Principal Investigator
    Large-Scale Low-Cost Genotyping for the Haplotype Map
    NIH/NHGRI U54HG003642Sep 20, 2004 - Aug 31, 2006
    Role: Principal Investigator
    Genetic Association in Austism Disorder
    NIH/NIMH R43MH072249Aug 6, 2004 - Jul 31, 2005
    Role: Principal Investigator
    Evolutionary Conserved Sequences in the Human Genome
    NIH/NHGRI R44HG002638Sep 30, 2002 - Dec 31, 2005
    Role: Principal Investigator
    NIH/NIGMS R01GM057482May 1, 1998 - Apr 30, 2003
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. D'Antonio M, Benaglio P, Jakubosky D, Greenwald WW, Matsui H, Donovan MKR, Li H, Smith EN, D'Antonio-Chronowska A, Frazer K. Insights into the Mutational Burden of Human Induced Pluripotent Stem Cells from an Integrative Multi-Omics Approach. Cell Rep. 2018 Jul 24; 24(4):883-894. PMID: 30044985.
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    2. Chekuri A, Guru AA, Biswas P, Branham K, Borooah S, Soto-Hermida A, Hicks M, Khan NW, Matsui H, Alapati A, Raghavendra PB, Roosing S, Sarangapani S, Mathavan S, Telenti A, Heckenlively JR, Riazuddin SA, Frazer K, Sieving PA, Ayyagari R. IFT88 mutations identified in individuals with non-syndromic recessive retinal degeneration result in abnormal ciliogenesis. Hum Genet. 2018 Jul 05. PMID: 29978320.
      View in: PubMed
    3. Benitez JA, Ma J, D'Antonio M, Boyer A, Camargo MF, Zanca C, Kelly S, Khodadadi-Jamayran A, Jameson NM, Andersen M, Miletic H, Saberi S, Frazer K, Cavenee WK, Furnari FB. Publisher Correction: PTEN regulates glioblastoma oncogenesis through chromatin-associated complexes of DAXX and histone H3.3. Nat Commun. 2018 May 25; 9:16217. PMID: 29799523.
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    4. Biswas P, Duncan JL, Ali M, Matsui H, Naeem MA, Raghavendra PB, Frazer K, Arts HH, Riazuddin S, Akram J, Hejtmancik JF, Riazuddin SA, Ayyagari R. A mutation in IFT43 causes non-syndromic recessive retinal degeneration. Hum Mol Genet. 2017 Dec 01; 26(23):4741-4751. PMID: 28973684.
      View in: PubMed
    5. Nariai N, Greenwald WW, DeBoever C, Li H, Frazer K. Efficient Prioritization of Multiple Causal eQTL Variants via Sparse Polygenic Modeling. Genetics. 2017 Dec; 207(4):1301-1312. PMID: 29074555.
      View in: PubMed
    6. Gustafson K, Duncan JL, Biswas P, Soto-Hermida A, Matsui H, Jakubosky D, Suk J, Telenti A, Frazer K, Ayyagari R. Correction: Gustafson et al., Whole Genome Sequencing Revealed Mutations in Two Independent Genes as the Underlying Cause of Retinal Degeneration in an Ashkenazi Jewish Pedigree. Genes 2017, 8, 210. Genes (Basel). 2017 Oct 23; 8(10). PMID: 29065517.
      View in: PubMed
    7. D Antonio M, Weghorn D, D Antonio-Chronowska A, Coulet F, Olson KM, DeBoever C, Drees F, Arias A, Alakus H, Richardson AL, Schwab RB, Farley EK, Sunyaev SR, Frazer K. Identifying DNase I hypersensitive sites as driver distal regulatory elements in breast cancer. Nat Commun. 2017 09 05; 8(1):436. PMID: 28874753.
      View in: PubMed
    8. Gustafson K, Duncan JL, Biswas P, Soto-Hermida A, Matsui H, Jakubosky D, Suk J, Telenti A, Frazer K, Ayyagari R. Whole Genome Sequencing Revealed Mutations in Two Independent Genes as the Underlying Cause of Retinal Degeneration in an Ashkenazi Jewish Pedigree. Genes (Basel). 2017 Aug 24; 8(9). PMID: 28837078.
      View in: PubMed
    9. Zanca C, Villa GR, Benitez JA, Thorne AH, Koga T, D'Antonio M, Ikegami S, Ma J, Boyer AD, Banisadr A, Jameson NM, Parisian AD, Eliseeva OV, Barnabe GF, Liu F, Wu S, Yang H, Wykosky J, Frazer K, Verkhusha VV, Isaguliants MG, Weiss WA, Gahman TC, Shiau AK, Chen CC, Mischel PS, Cavenee WK, Furnari FB. Glioblastoma cellular cross-talk converges on NF-?B to attenuate EGFR inhibitor sensitivity. Genes Dev. 2017 Jul 19. PMID: 28724615.
      View in: PubMed
    10. Benitez JA, Ma J, D'Antonio M, Boyer A, Camargo MF, Zanca C, Kelly S, Khodadadi-Jamayran A, Jameson NM, Andersen M, Miletic H, Saberi S, Frazer K, Cavenee WK, Furnari FB. PTEN regulates glioblastoma oncogenesis through chromatin-associated complexes of DAXX and histone H3.3. Nat Commun. 2017 May 12; 8:15223. PMID: 28497778.
      View in: PubMed
    11. D'Antonio M, Woodruff G, Nathanson JL, D'Antonio-Chronowska A, Arias A, Matsui H, Williams R, Herrera C, Reyna SM, Yeo GW, Goldstein LSB, Panopoulos AD, Frazer K. High-Throughput and Cost-Effective Characterization of Induced Pluripotent Stem Cells. Stem Cell Reports. 2017 04 11; 8(4):1101-1111. PMID: 28410643.
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    12. Panopoulos AD, D'Antonio M, Benaglio P, Williams R, Hashem SI, Schuldt BM, DeBoever C, Arias AD, Garcia M, Nelson BC, Harismendy O, Jakubosky DA, Donovan MKR, Greenwald WW, Farnam K, Cook M, Borja V, Miller CA, Grinstein JD, Drees F, Okubo J, Diffenderfer KE, Hishida Y, Modesto V, Dargitz CT, Feiring R, Zhao C, Aguirre A, McGarry TJ, Matsui H, Li H, Reyna J, Rao F, O'Connor DT, Yeo GW, Evans SM, Chi NC, Jepsen K, Nariai N, Müller FJ, Goldstein LSB, Izpisua Belmonte JC, Adler E, Loring JF, Berggren WT, D'Antonio-Chronowska A, Smith EN, Frazer K. iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types. Stem Cell Reports. 2017 04 11; 8(4):1086-1100. PMID: 28410642.
      View in: PubMed
    13. Greenwald WW, Li H, Smith EN, Benaglio P, Nariai N, Frazer K. Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data. BMC Bioinformatics. 2017 Apr 07; 18(1):207. PMID: 28388874.
      View in: PubMed
    14. DeBoever C, Li H, Jakubosky D, Benaglio P, Reyna J, Olson KM, Huang H, Biggs W, Sandoval E, D'Antonio M, Jepsen K, Matsui H, Arias A, Ren B, Nariai N, Smith EN, D'Antonio-Chronowska A, Farley EK, Frazer K. Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells. Cell Stem Cell. 2017 04 06; 20(4):533-546.e7. PMID: 28388430.
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    15. Panopoulos AD, Smith EN, Arias AD, Shepard PJ, Hishida Y, Modesto V, Diffenderfer KE, Conner C, Biggs W, Sandoval E, D'Antonio-Chronowska A, Berggren WT, Izpisua Belmonte JC, Frazer K. Aberrant DNA Methylation in Human iPSCs Associates with MYC-Binding Motifs in a Clone-Specific Manner Independent of Genetics. Cell Stem Cell. 2017 04 06; 20(4):505-517.e6. PMID: 28388429.
      View in: PubMed
    16. Kaneda MM, Messer KS, Ralainirina N, Li H, Leem CJ, Gorjestani S, Woo G, Nguyen AV, Figueiredo CC, Foubert P, Schmid MC, Pink M, Winkler DG, Rausch M, Palombella VJ, Kutok J, McGovern K, Frazer K, Wu X, Karin M, Sasik R, Cohen EE, Varner JA. Corrigendum: PI3K? is a molecular switch that controls immune suppression. Nature. 2017 02 02; 542(7639):124. PMID: 27974794.
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    17. Cui B, Ghia EM, Chen L, Rassenti LZ, DeBoever C, Widhopf GF, Yu J, Neuberg DS, Wierda WG, Rai KR, Kay NE, Brown JR, Jones JA, Gribben JG, Frazer K, Kipps TJ. High-level ROR1 associates with accelerated disease progression in chronic lymphocytic leukemia. Blood. 2016 12 22; 128(25):2931-2940. PMID: 27815263.
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    18. Branham K, Matsui H, Biswas P, Guru AA, Hicks M, Suk JJ, Li H, Jakubosky D, Long T, Telenti A, Nariai N, Heckenlively JR, Frazer K, Sieving PA, Ayyagari R. Establishing the involvement of the novel gene AGBL5 in retinitis pigmentosa by whole genome sequencing. Physiol Genomics. 2016 Dec 01; 48(12):922-927. PMID: 27764769.
      View in: PubMed
    19. Kaneda MM, Messer KS, Ralainirina N, Li H, Leem CJ, Gorjestani S, Woo G, Nguyen AV, Figueiredo CC, Foubert P, Schmid MC, Pink M, Winkler DG, Rausch M, Palombella VJ, Kutok J, McGovern K, Frazer K, Wu X, Karin M, Sasik R, Cohen EE, Varner JA. PI3K? is a molecular switch that controls immune suppression. Nature. 2016 11 17; 539(7629):437-442. PMID: 27642729.
      View in: PubMed
    20. D'Antonio M, Tamayo P, Mesirov JP, Frazer K. Kataegis Expression Signature in Breast Cancer Is Associated with Late Onset, Better Prognosis, and Higher HER2 Levels. Cell Rep. 2016 07 19; 16(3):672-83. PMID: 27373164; PMCID: PMC4972030.
    21. Solomon T, Smith EN, Matsui H, Braekkan SK. Associations Between Common and Rare Exonic Genetic Variants and Serum Levels of 20 Cardiovascular-Related Proteins: The Tromsø Study. Circ Cardiovasc Genet. 2016 Aug; 9(4):375-83. PMID: 27329291; PMCID: PMC4982757.
    22. Gran OV, Smith EN, Brækkan SK, Jensvoll H, Solomon T, Hindberg K, Wilsgaard T, Rosendaal FR, Frazer K, Hansen JB. Joint effects of cancer and variants in the factor 5 gene on the risk of venous thromboembolism. Haematologica. 2016 09; 101(9):1046-53. PMID: 27479824.
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    23. Zipeto MA, Court AC, Sadarangani A, Delos Santos NP, Balaian L, Chun HJ, Pineda G, Morris SR, Mason CN, Geron I, Barrett C, Goff DJ, Wall R, Pellecchia M, Minden M, Frazer K, Marra MA, Crews LA, Jiang Q, Jamieson CHM. ADAR1 Activation Drives Leukemia Stem Cell Self-Renewal by Impairing Let-7 Biogenesis. Cell Stem Cell. 2016 08 04; 19(2):177-191. PMID: 27292188.
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    24. Holm F, Hellqvist E, Mason CN, Ali SA, Delos-Santos N, Barrett CL, Chun HJ, Minden MD, Moore RA, Marra MA, Runza V, Frazer K, Sadarangani A, Jamieson CH. Reversion to an embryonic alternative splicing program enhances leukemia stem cell self-renewal. Proc Natl Acad Sci U S A. 2015 Dec 15; 112(50):15444-9. PMID: 26621726; PMCID: PMC4687548.
    25. Bao L, Messer K, Schwab R, Harismendy O, Pu M, Crain B, Yost S, Frazer K, Rana B, Hasteh F, Wallace A, Parker BA. Mutational Profiling Can Establish Clonal or Independent Origin in Synchronous Bilateral Breast and Other Tumors. PLoS One. 2015; 10(11):e0142487. PMID: 26554380; PMCID: PMC4640562.
    26. Barrett CL, DeBoever C, Jepsen K, Saenz CC, Carson DA, Frazer K. Systematic transcriptome analysis reveals tumor-specific isoforms for ovarian cancer diagnosis and therapy. Proc Natl Acad Sci U S A. 2015 Jun 09; 112(23):E3050-7. PMID: 26015570; PMCID: PMC4466751.
    27. Hashem SI, Perry CN, Bauer M, Han S, Clegg SD, Ouyang K, Deacon DC, Spinharney M, Panopoulos AD, Izpisua Belmonte JC, Frazer K, Chen J, Gong Q, Zhou Z, Chi NC, Adler ED. Brief Report: Oxidative Stress Mediates Cardiomyocyte Apoptosis in a Human Model of Danon Disease and Heart Failure. Stem Cells. 2015 Jul; 33(7):2343-50. PMID: 25826782; PMCID: PMC4651661.
    28. Alakus H, Yost SE, Woo B, French R, Lin GY, Jepsen K, Frazer K, Lowy AM, Harismendy O. BAP1 mutation is a frequent somatic event in peritoneal malignant mesothelioma. J Transl Med. 2015 Apr 16; 13:122. PMID: 25889843; PMCID: PMC4422481.
    29. DeBoever C, Ghia EM, Shepard PJ, Rassenti L, Barrett CL, Jepsen K, Jamieson CH, Carson D, Kipps TJ, Frazer K. Transcriptome sequencing reveals potential mechanism of cryptic 3' splice site selection in SF3B1-mutated cancers. PLoS Comput Biol. 2015 Mar; 11(3):e1004105. PMID: 25768983; PMCID: PMC4358997.
    30. Crews LA, Jiang Q, Zipeto MA, Lazzari E, Court AC, Ali S, Barrett CL, Frazer K, Jamieson CH. An RNA editing fingerprint of cancer stem cell reprogramming. J Transl Med. 2015 Feb 12; 13:52. PMID: 25889244; PMCID: PMC4341880.
    31. Shepard PJ, Barshop BA, Baumgartner MR, Hansen JB, Jepsen K, Smith EN, Frazer K. Consanguinity and rare mutations outside of MCCC genes underlie nonspecific phenotypes of MCCD. Genet Med. 2015 Aug; 17(8):660-7. PMID: 25356967; PMCID: PMC4422778.
    32. Smith EN, Jepsen K, Khosroheidari M, Rassenti LZ, D'Antonio M, Ghia EM, Carson DA, Jamieson CH, Kipps TJ, Frazer K. Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments. Genome Biol. 2014 Aug 07; 15(8):420. PMID: 25103687; PMCID: PMC4165357.
    33. Alakus H, Babicky ML, Ghosh P, Yost S, Jepsen K, Dai Y, Arias A, Samuels ML, Mose ES, Schwab RB, Peterson MR, Lowy AM, Frazer K, Harismendy O. Correction: Genome-wide mutational landscape of mucinous carcinomatosis peritonei of appendiceal origin. Genome Med. 2014; 6(7):53. PMID: 25228923; PMCID: PMC4165363.
    34. Cheng CP, Kuo IY, Alakus H, Frazer K, Harismendy O, Wang YC, Tseng VS. Network-based analysis identifies epigenetic biomarkers of esophageal squamous cell carcinoma progression. Bioinformatics. 2014 Nov 01; 30(21):3054-61. PMID: 25015989; PMCID: PMC4609006.
    35. Alakus H, Bollschweiler E, Hölscher AH, Warnecke-Eberz U, Frazer K, Harismendy O, Lowy AM, Mönig SP, Eberz PM, Maus M, Drebber U, Siffert W, Metzger R. Homozygous GNAS 393C-allele carriers with locally advanced esophageal cancer fail to benefit from platinum-based preoperative chemoradiotherapy. Ann Surg Oncol. 2014 Dec; 21(13):4375-82. PMID: 24986238.
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    36. Cheng CP, DeBoever C, Frazer K, Liu YC, Tseng VS. MiningABs: mining associated biomarkers across multi-connected gene expression datasets. BMC Bioinformatics. 2014 Jun 08; 15:173. PMID: 24909518; PMCID: PMC4068973.
    37. Alakus H, Babicky ML, Ghosh P, Yost S, Jepsen K, Dai Y, Arias A, Samuels ML, Mose ES, Schwab RB, Peterson MR, Lowy AM, Frazer K, Harismendy O. Genome-wide mutational landscape of mucinous carcinomatosis peritonei of appendiceal origin. Genome Med. 2014; 6(5):43. PMID: 24944587; PMCID: PMC4062050.
    38. Carson AR, Smith EN, Matsui H, Brækkan SK, Jepsen K, Hansen JB, Frazer K. Effective filtering strategies to improve data quality from population-based whole exome sequencing studies. BMC Bioinformatics. 2014 May 02; 15:125. PMID: 24884706; PMCID: PMC4098776.
    39. Mraz M, Chen L, Rassenti LZ, Ghia EM, Li H, Jepsen K, Smith EN, Messer K, Frazer K, Kipps TJ. miR-150 influences B-cell receptor signaling in chronic lymphocytic leukemia by regulating expression of GAB1 and FOXP1. Blood. 2014 Jul 03; 124(1):84-95. PMID: 24787006; PMCID: PMC4125356.
    40. Udpa N, Ronen R, Zhou D, Liang J, Stobdan T, Appenzeller O, Yin Y, Du Y, Guo L, Cao R, Wang Y, Jin X, Huang C, Jia W, Cao D, Guo G, Claydon VE, Hainsworth R, Gamboa JL, Zibenigus M, Zenebe G, Xue J, Liu S, Frazer K, Li Y, Bafna V, Haddad GG. Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes. Genome Biol. 2014 Feb 20; 15(2):R36. PMID: 24555826; PMCID: PMC4054780.
    41. Smith EN, Jepsen K, Arias AD, Shepard PJ, Chambers CD, Frazer K. Genetic ancestry of participants in the National Children's Study. Genome Biol. 2014 Feb 03; 15(2):R22. PMID: 24490717; PMCID: PMC4053981.
    42. Harismendy O, Schwab RB, Alakus H, Yost SE, Matsui H, Hasteh F, Wallace AM, Park HL, Madlensky L, Parker B, Carpenter PM, Jepsen K, Anton-Culver H, Frazer K. Evaluation of ultra-deep targeted sequencing for personalized breast cancer care. Breast Cancer Res. 2013 Dec 10; 15(6):R115. PMID: 24326041; PMCID: PMC3978701.
    43. He G, Dhar D, Nakagawa H, Font-Burgada J, Ogata H, Jiang Y, Shalapour S, Seki E, Yost SE, Jepsen K, Frazer K, Harismendy O, Hatziapostolou M, Iliopoulos D, Suetsugu A, Hoffman RM, Tateishi R, Koike K, Karin M. Identification of liver cancer progenitors whose malignant progression depends on autocrine IL-6 signaling. Cell. 2013 Oct 10; 155(2):384-96. PMID: 24120137; PMCID: PMC4015514.
    44. DeBoever C, Reid EG, Smith EN, Wang X, Dumaop W, Harismendy O, Carson D, Richman D, Masliah E, Frazer K. Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas. PLoS One. 2013; 8(9):e73956. PMID: 24023918; PMCID: PMC3762708.
    45. Zhou D, Udpa N, Ronen R, Stobdan T, Liang J, Appenzeller O, Zhao HW, Yin Y, Du Y, Guo L, Cao R, Wang Y, Jin X, Huang C, Jia W, Cao D, Guo G, Gamboa JL, Villafuerte F, Callacondo D, Xue J, Liu S, Frazer K, Li Y, Bafna V, Haddad GG. Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders. Am J Hum Genet. 2013 Sep 05; 93(3):452-62. PMID: 23954164; PMCID: PMC3769925.
    46. Yost SE, Alakus H, Matsui H, Schwab RB, Jepsen K, Frazer K, Harismendy O. Mutascope: sensitive detection of somatic mutations from deep amplicon sequencing. Bioinformatics. 2013 Aug 01; 29(15):1908-9. PMID: 23712659; PMCID: PMC3712217.
    47. Barrett CL, Schwab RB, Jung H, Crain B, Goff DJ, Jamieson CH, Thistlethwaite PA, Harismendy O, Carson DA, Frazer K. Transcriptome sequencing of tumor subpopulations reveals a spectrum of therapeutic options for squamous cell lung cancer. PLoS One. 2013; 8(3):e58714. PMID: 23527012; PMCID: PMC3604164.
    48. Yost SE, Pastorino S, Rozenzhak S, Smith EN, Chao YS, Jiang P, Kesari S, Frazer K, Harismendy O. High-resolution mutational profiling suggests the genetic validity of glioblastoma patient-derived pre-clinical models. PLoS One. 2013; 8(2):e56185. PMID: 23441165; PMCID: PMC3575368.
    49. Goff DJ, Court Recart A, Sadarangani A, Chun HJ, Barrett CL, Krajewska M, Leu H, Low-Marchelli J, Ma W, Shih AY, Wei J, Zhai D, Geron I, Pu M, Bao L, Chuang R, Balaian L, Gotlib J, Minden M, Martinelli G, Rusert J, Dao KH, Shazand K, Wentworth P, Smith KM, Jamieson CA, Morris SR, Messer K, Goldstein LS, Hudson TJ, Marra M, Frazer K, Pellecchia M, Reed JC, Jamieson CH. A Pan-BCL2 inhibitor renders bone-marrow-resident human leukemia stem cells sensitive to tyrosine kinase inhibition. Cell Stem Cell. 2013 Mar 07; 12(3):316-28. PMID: 23333150; PMCID: PMC3968867.
    50. Manolio TA, Chisholm RL, Ozenberger B, Roden DM, Williams MS, Wilson R, Bick D, Bottinger EP, Brilliant MH, Eng C, Frazer K, Korf B, Ledbetter DH, Lupski JR, Marsh C, Mrazek D, Murray MF, O'Donnell PH, Rader DJ, Relling MV, Shuldiner AR, Valle D, Weinshilboum R, Green ED, Ginsburg GS. Implementing genomic medicine in the clinic: the future is here. Genet Med. 2013 Apr; 15(4):258-67. PMID: 23306799; PMCID: PMC3835144.
    51. Jiang Q, Crews LA, Barrett CL, Chun HJ, Court AC, Isquith JM, Zipeto MA, Goff DJ, Minden M, Sadarangani A, Rusert JM, Dao KH, Morris SR, Goldstein LS, Marra MA, Frazer K, Jamieson CH. ADAR1 promotes malignant progenitor reprogramming in chronic myeloid leukemia. Proc Natl Acad Sci U S A. 2013 Jan 15; 110(3):1041-6. PMID: 23275297; PMCID: PMC3549099.
    52. Frazer K. Decoding the human genome. Genome Res. 2012 Sep; 22(9):1599-601. PMID: 22955971; PMCID: PMC3431476.
    53. Yost SE, Smith EN, Schwab RB, Bao L, Jung H, Wang X, Voest E, Pierce JP, Messer K, Parker BA, Harismendy O, Frazer K. Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens. Nucleic Acids Res. 2012 Aug; 40(14):e107. PMID: 22492626; PMCID: PMC3413110.
    54. Harismendy O, Schwab RB, Bao L, Olson J, Rozenzhak S, Kotsopoulos SK, Pond S, Crain B, Chee MS, Messer K, Link DR, Frazer K. Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing. Genome Biol. 2011 Dec 20; 12(12):R124. PMID: 22185227; PMCID: PMC3334619.
    55. Kinsella M, Harismendy O, Nakano M, Frazer K, Bafna V. Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics. 2011 Apr 15; 27(8):1068-75. PMID: 21330288; PMCID: PMC3072550.
    56. Harismendy O, Notani D, Song X, Rahim NG, Tanasa B, Heintzman N, Ren B, Fu XD, Topol EJ, Rosenfeld MG, Frazer K. 9p21 DNA variants associated with coronary artery disease impair interferon-? signalling response. Nature. 2011 Feb 10; 470(7333):264-8. PMID: 21307941; PMCID: PMC3079517.
    57. Zhou D, Udpa N, Gersten M, Visk DW, Bashir A, Xue J, Frazer K, Posakony JW, Subramaniam S, Bafna V, Haddad GG. Experimental selection of hypoxia-tolerant Drosophila melanogaster. Proc Natl Acad Sci U S A. 2011 Feb 08; 108(6):2349-54. PMID: 21262834; PMCID: PMC3038716.
    58. Harismendy O, Bansal V, Bhatia G, Nakano M, Scott M, Wang X, Dib C, Turlotte E, Sipe JC, Murray SS, Deleuze JF, Bafna V, Topol EJ, Frazer K. Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level. Genome Biol. 2010; 11(11):R118. PMID: 21118518; PMCID: PMC3156957.
    59. Bhatia G, Bansal V, Harismendy O, Schork NJ, Topol EJ, Frazer K, Bafna V. A covering method for detecting genetic associations between rare variants and common phenotypes. PLoS Comput Biol. 2010 Oct 14; 6(10):e1000954. PMID: 20976246.
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    60. Kirby A, Kang HM, Wade CM, Cotsapas C, Kostem E, Han B, Furlotte N, Kang EY, Rivas M, Bogue MA, Frazer K, Johnson FM, Beilharz EJ, Cox DR, Eskin E, Daly MJ. Fine mapping in 94 inbred mouse strains using a high-density haplotype resource. Genetics. 2010 Jul; 185(3):1081-95. PMID: 20439770; PMCID: PMC2907194.
    61. Bansal V, Harismendy O, Tewhey R, Murray SS, Schork NJ, Topol EJ, Frazer K. Accurate detection and genotyping of SNPs utilizing population sequencing data. Genome Res. 2010 Apr; 20(4):537-45. PMID: 20150320; PMCID: PMC2847757.
    62. Tewhey R, Warner JB, Nakano M, Libby B, Medkova M, David PH, Kotsopoulos SK, Samuels ML, Hutchison JB, Larson JW, Topol EJ, Weiner MP, Harismendy O, Olson J, Link DR, Frazer K. Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nat Biotechnol. 2009 Nov; 27(11):1025-31. PMID: 19881494; PMCID: PMC2779736.
    63. Tewhey R, Nakano M, Wang X, Pabón-Peña C, Novak B, Giuffre A, Lin E, Happe S, Roberts DN, LeProust EM, Topol EJ, Harismendy O, Frazer K. Enrichment of sequencing targets from the human genome by solution hybridization. Genome Biol. 2009; 10(10):R116. PMID: 19835619; PMCID: PMC2784331.
    64. Harismendy O, Frazer K. Elucidating the role of 8q24 in colorectal cancer. Nat Genet. 2009 Aug; 41(8):868-9. PMID: 19639026.
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    65. McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, Zeller G, Clark RM, Hoen DR, Bureau TE, Stokowski R, Ballinger DG, Frazer K, Cox DR, Padhukasahasram B, Bustamante CD, Weigel D, Mackill DJ, Bruskiewich RM, Rätsch G, Buell CR, Leung H, Leach JE. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci U S A. 2009 Jul 28; 106(30):12273-8. PMID: 19597147; PMCID: PMC2718348.
    66. Schork NJ, Murray SS, Frazer K, Topol EJ. Common vs. rare allele hypotheses for complex diseases. Curr Opin Genet Dev. 2009 Jun; 19(3):212-9. PMID: 19481926.
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