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    Hannah Carter

    TitleAssistant Professor
    SchoolUniversity of California, San Diego
    DepartmentMedicine
    Address9500 Gilman Drive #0688
    CA La Jolla 92093
    Phone858-822-4706
    vCardDownload vCard

      Collapse Biography 
      Collapse Education and Training
      University of Louisville, KentuckyMEng12/2004Electrical and Computer Engineering
      Johns Hopkins University, MarylandPhD02/2012Biomedical Engineering
      Collapse Awards and Honors
      Canadian Institute for Advanced Research (CIFAR)2017Azrieli Global Scholar
      Johns Hopkins University2015Johns Hopkins University Alumni Outstanding Recent Graduate Award
      NIH2013NIH Director's Early Independence Award
      Siebel Scholars Foundation2012Siebel Scholar

      Collapse Overview 
      Collapse Overview
      Dr. Hannah Carter’s research focuses on computationally modeling how DNA mutations in tumor genomes impact intracellular biological processes and cellular behaviors, and how these cellular level changes cause cancer.

      In 2013, Dr. Carter received a prestigious NIH Early Independence Award for her project, Network Approaches to Identify Cancer Drivers from High-Dimensional Tumor Data - Read UC San Diego Clinical and Translational Research Institute News Story


      Collapse Research 
      Collapse Research Activities and Funding
      (PQ3) Disruption of immune surveillance by aneuploidy and aberrant MHCII expression
      NIH/NCI R01CA220009Aug 17, 2017 - Jul 31, 2022
      Role: Co-Principal Investigator
      Network approaches to identify cancer drivers from high-dimensional tumor data
      NIH DP5OD017937Sep 24, 2013 - Aug 31, 2018
      Role: Principal Investigator

      Collapse ORNG Applications 
      Collapse Featured Publications
      Collapse Websites

      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.
      List All   |   Timeline
      1. Rachel Marty Saghar Kaabinejadian David Rossell Michael J. Slifker Joris van de Haar Hatice Billur Engin Nicola de Prisco Trey Ideker William H. Hildebrand Joan Font-Burgada Hannah Carter. MHC-I Genotype Restricts the Oncogenic Mutational Landscape. Cell. 2017.
      2. Wang T, Tsui B, Kreisberg JF, Robertson NA, Gross AM, Yu MK, Carter H, Brown-Borg HM, Adams PD, Ideker T. Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment. Genome Biol. 2017 Mar 28; 18(1):57. PMID: 28351423.
        View in: PubMed
      3. Carter H, Marty R, Hofree M, Gross AM, Jensen J, Fisch KM, Wu X, DeBoever C, Van Nostrand EL, Song Y, Wheeler E, Kreisberg JF, Lippman SM, Yeo GW, Gutkind JS, Ideker T. Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer. Cancer Discov. 2017 Apr; 7(4):410-423. PMID: 28188128.
        View in: PubMed
      4. Levy E, Marty R, Gárate Calderón V, Woo B, Dow M, Armisen R, Carter H, Harismendy O. Immune DNA signature of T-cell infiltration in breast tumor exomes. Sci Rep. 2016 Jul 25; 6:30064. PMID: 27452728; PMCID: PMC4958917.
      5. Hofree M, Carter H, Kreisberg JF, Bandyopadhyay S, Mischel PS, Friend S, Ideker T. Challenges in identifying cancer genes by analysis of exome sequencing data. Nat Commun. 2016 Jul 15; 7:12096. PMID: 27417679; PMCID: PMC4947162.
      6. Bromberg Y, Capriotti E, Carter H. VarI-SIG 2015: methods for personalized medicine - the role of variant interpretation in research and diagnostics. BMC Genomics. 2016 Jun 23; 17 Suppl 2:425. PMID: 27357578; PMCID: PMC4928159.
      7. Engin HB, Kreisberg JF, Carter H. Structure-Based Analysis Reveals Cancer Missense Mutations Target Protein Interaction Interfaces. PLoS One. 2016; 11(4):e0152929. PMID: 27043210; PMCID: PMC4820104.
      8. Font-Burgada J, Shalapour S, Ramaswamy S, Hsueh B, Rossell D, Umemura A, Taniguchi K, Nakagawa H, Valasek MA, Ye L, Kopp JL, Sander M, Carter H, Deisseroth K, Verma IM, Karin M. Hybrid Periportal Hepatocytes Regenerate the Injured Liver without Giving Rise to Cancer. Cell. 2015 Aug 13; 162(4):766-79. PMID: 26276631; PMCID: PMC4545590.
      9. Engin HB, Hofree M, Carter H. Identifying mutation specific cancer pathways using a structurally resolved protein interaction network. Pac Symp Biocomput. 2015; 84-95. PMID: 25592571; PMCID: PMC4299875.
      10. Chen YC, Douville C, Wang C, Niknafs N, Yeo G, Beleva-Guthrie V, Carter H, Stenson PD, Cooper DN, Li B, Mooney S, Karchin R. A probabilistic model to predict clinical phenotypic traits from genome sequencing. PLoS Comput Biol. 2014 Sep; 10(9):e1003825. PMID: 25188385; PMCID: PMC4154636.
      11. Gross AM, Orosco RK, Shen JP, Egloff AM, Carter H, Hofree M, Choueiri M, Coffey CS, Lippman SM, Hayes DN, Cohen EE, Grandis JR, Nguyen QT, Ideker T. Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss. Nat Genet. 2014 Sep; 46(9):939-43. PMID: 25086664; PMCID: PMC4146706.
      12. Carter H, Karchin R. Predicting the functional consequences of somatic missense mutations found in tumors. Methods Mol Biol. 2014; 1101:135-59. PMID: 24233781.
        View in: PubMed
      13. Carter H, Hofree M, Ideker T. Genotype to phenotype via network analysis. Curr Opin Genet Dev. 2013 Dec; 23(6):611-21. PMID: 24238873; PMCID: PMC3866044.
      14. Hofree M, Shen JP, Carter H, Gross A, Ideker T. Network-based stratification of tumor mutations. Nat Methods. 2013 Nov; 10(11):1108-15. PMID: 24037242; PMCID: PMC3866081.
      15. Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N. Computational approaches to identify functional genetic variants in cancer genomes. Nat Methods. 2013 Aug; 10(8):723-9. PMID: 23900255; PMCID: PMC3919555.
      16. Gartner JJ, Parker SC, Prickett TD, Dutton-Regester K, Stitzel ML, Lin JC, Davis S, Simhadri VL, Jha S, Katagiri N, Gotea V, Teer JK, Wei X, Morken MA, Bhanot UK, Chen G, Elnitski LL, Davies MA, Gershenwald JE, Carter H, Karchin R, Robinson W, Robinson S, Rosenberg SA, Collins FS, Parmigiani G, Komar AA, Kimchi-Sarfaty C, Hayward NK, Margulies EH, Samuels Y. Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proc Natl Acad Sci U S A. 2013 Aug 13; 110(33):13481-6. PMID: 23901115; PMCID: PMC3746936.
      17. Carter H, Douville C, Stenson PD, Cooper DN, Karchin R. Identifying Mendelian disease genes with the variant effect scoring tool. BMC Genomics. 2013; 14 Suppl 3:S3. PMID: 23819870; PMCID: PMC3665549.
      18. Chen YC, Carter H, Parla J, Kramer M, Goes FS, Pirooznia M, Zandi PP, McCombie WR, Potash JB, Karchin R. A hybrid likelihood model for sequence-based disease association studies. PLoS Genet. 2013; 9(1):e1003224. PMID: 23358228; PMCID: PMC3554549.
      19. Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R. CRAVAT: cancer-related analysis of variants toolkit. Bioinformatics. 2013 Mar 01; 29(5):647-8. PMID: 23325621; PMCID: PMC3582272.
      20. Liang H, Cheung LW, Li J, Ju Z, Yu S, Stemke-Hale K, Dogruluk T, Lu Y, Liu X, Gu C, Guo W, Scherer SE, Carter H, Westin SN, Dyer MD, Verhaak RG, Zhang F, Karchin R, Liu CG, Lu KH, Broaddus RR, Scott KL, Hennessy BT, Mills GB. Whole-exome sequencing combined with functional genomics reveals novel candidate driver cancer genes in endometrial cancer. Genome Res. 2012 Nov; 22(11):2120-9. PMID: 23028188; PMCID: PMC3483541.
      21. Jiao X, Wood LD, Lindman M, Jones S, Buckhaults P, Polyak K, Sukumar S, Carter H, Kim D, Karchin R, Sjöblom T. Somatic mutations in the Notch, NF-KB, PIK3CA, and Hedgehog pathways in human breast cancers. Genes Chromosomes Cancer. 2012 May; 51(5):480-9. PMID: 22302350; PMCID: PMC3302210.
      22. Wu J, Jiao Y, Dal Molin M, Maitra A, de Wilde RF, Wood LD, Eshleman JR, Goggins MG, Wolfgang CL, Canto MI, Schulick RD, Edil BH, Choti MA, Adsay V, Klimstra DS, Offerhaus GJ, Klein AP, Kopelovich L, Carter H, Karchin R, Allen PJ, Schmidt CM, Naito Y, Diaz LA, Kinzler KW, Papadopoulos N, Hruban RH, Vogelstein B. Whole-exome sequencing of neoplastic cysts of the pancreas reveals recurrent mutations in components of ubiquitin-dependent pathways. Proc Natl Acad Sci U S A. 2011 Dec 27; 108(52):21188-93. PMID: 22158988; PMCID: PMC3248495.
      23. Integrated genomic analyses of ovarian carcinoma. Nature. 2011 Jun 29; 474(7353):609-15. PMID: 21720365; PMCID: PMC3163504.
      24. Zhang X, Reis M, Khoriaty R, Li Y, Ouillette P, Samayoa J, Carter H, Karchin R, Li M, Diaz LA, Velculescu VE, Papadopoulos N, Kinzler KW, Vogelstein B, Malek SN. Sequence analysis of 515 kinase genes in chronic lymphocytic leukemia. Leukemia. 2011 Dec; 25(12):1908-10. PMID: 21701494; PMCID: PMC3523306.
      25. Wong WC, Kim D, Carter H, Diekhans M, Ryan MC, Karchin R. CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer. Bioinformatics. 2011 Aug 01; 27(15):2147-8. PMID: 21685053; PMCID: PMC3137226.
      26. Parsons DW, Li M, Zhang X, Jones S, Leary RJ, Lin JC, Boca SM, Carter H, Samayoa J, Bettegowda C, Gallia GL, Jallo GI, Binder ZA, Nikolsky Y, Hartigan J, Smith DR, Gerhard DS, Fults DW, VandenBerg S, Berger MS, Marie SK, Shinjo SM, Clara C, Phillips PC, Minturn JE, Biegel JA, Judkins AR, Resnick AC, Storm PB, Curran T, He Y, Rasheed BA, Friedman HS, Keir ST, McLendon R, Northcott PA, Taylor MD, Burger PC, Riggins GJ, Karchin R, Parmigiani G, Bigner DD, Yan H, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE. The genetic landscape of the childhood cancer medulloblastoma. Science. 2011 Jan 28; 331(6016):435-9. PMID: 21163964; PMCID: PMC3110744.
      27. Bozic I, Antal T, Ohtsuki H, Carter H, Kim D, Chen S, Karchin R, Kinzler KW, Vogelstein B, Nowak MA. Accumulation of driver and passenger mutations during tumor progression. Proc Natl Acad Sci U S A. 2010 Oct 26; 107(43):18545-50. PMID: 20876136; PMCID: PMC2972991.
      28. Carter H, Samayoa J, Hruban RH, Karchin R. Prioritization of driver mutations in pancreatic cancer using cancer-specific high-throughput annotation of somatic mutations (CHASM). Cancer Biol Ther. 2010 Sep 15; 10(6):582-7. PMID: 20581473; PMCID: PMC3040948.
      29. Carter H, Chen S, Isik L, Tyekucheva S, Velculescu VE, Kinzler KW, Vogelstein B, Karchin R. Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. Cancer Res. 2009 Aug 15; 69(16):6660-7. PMID: 19654296; PMCID: PMC2763410.
      30. Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan DT, Carter H, Mankoo P, Karchin R, Marti-Renom MA, Davis FP, Sali A. MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 2009 Jan; 37(Database issue):D347-54. PMID: 18948282; PMCID: PMC2686492.
      31. Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Kamiyama H, Jimeno A, Hong SM, Fu B, Lin MT, Calhoun ES, Kamiyama M, Walter K, Nikolskaya T, Nikolsky Y, Hartigan J, Smith DR, Hidalgo M, Leach SD, Klein AP, Jaffee EM, Goggins M, Maitra A, Iacobuzio-Donahue C, Eshleman JR, Kern SE, Hruban RH, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science. 2008 Sep 26; 321(5897):1801-6. PMID: 18772397; PMCID: PMC2848990.
      32. Parsons DW, Jones S, Zhang X, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Siu IM, Gallia GL, Olivi A, McLendon R, Rasheed BA, Keir S, Nikolskaya T, Nikolsky Y, Busam DA, Tekleab H, Diaz LA, Hartigan J, Smith DR, Strausberg RL, Marie SK, Shinjo SM, Yan H, Riggins GJ, Bigner DD, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW. An integrated genomic analysis of human glioblastoma multiforme. Science. 2008 Sep 26; 321(5897):1807-12. PMID: 18772396; PMCID: PMC2820389.