Hannah Carter • UCSD Profiles (original) (raw)

  1. Discovery of novel ancestry specific genes for androgens and hypogonadism in Million Veteran Program Men. Nat Commun. 2025 May 02; 16(1):4104. Pagadala MS, Teerlink CC, Jasuja GK, Palnati M, Anglin-Foote T, Chang NN, Deka R, Lee KM, Agiri FY, Amariuta T, Seibert TM, Rose BS, Pridgen KM, Lynch JA, Carter HK, Panizzon MS, Hauger RL. PMID: 40316537; PMCID: PMC12048691.
    View in: PubMed Mentions: 1 Fields:
    Translation:Humans
  2. Session Introduction: Precision Medicine: Multi-modal and multi-scale methods to promote mechanistic understanding of disease. Pac Symp Biocomput. 2025; 30:377-381. Carter H, Brenner S, Bromberg Y. PMID: 39670383.
    View in: PubMed Mentions: Fields:
    Translation:Humans
  3. Estimating the Uninsured Cancer Rate: Unraveling the Indelible Link Between Insurance, Age, and the Accessibility of Cancer Treatment. Prev Oncol Epidemiol. 2024; 2(1). Carter HK, Keighley J, Pepper S, Ratnayake I, Chollet Hinton L, Van Goethem K, Krebill H, Mudaranthakam DP. PMID: 39564543; PMCID: PMC11575479.
    View in: PubMed Mentions:
  4. Agent orange exposure and prostate cancer risk in the million veteran program. Acta Oncol. 2024 May 23; 63:373-378. Pagadala MS, Lui AJ, Zhong AY, Lynch JA, Karunamuni R, Lee KM, Plym A, Rose BS, Carter HK, Kibel AS, DuVall SL, Gaziano JM, Panizzon MS, Hauger RL, Seibert TM. PMID: 38779869; PMCID: PMC11332552.
    View in: PubMed Mentions: 4 Fields:
    Translation:Humans
  5. Predictive analyses of regulatory sequences with EUGENe. Nat Comput Sci. 2023 11; 3(11):946-956. Klie A, Laub D, Talwar JV, Stites H, Jores T, Solvason JJ, Farley EK, Carter H. PMID: 38177592; PMCID: PMC10768637.
    View in: PubMed Mentions: 10 Fields:
  6. IRE1α and IGF signaling predict resistance to an endoplasmic reticulum stress-inducing drug in glioblastoma cells. Sci Rep. 2020 05 20; 10(1):8348. Rodvold JJ, Xian S, Nussbacher J, Tsui B, Cameron Waller T, Searles SC, Lew A, Jiang P, Babic I, Nomura N, Lin JH, Kesari S, Carter H, Zanetti M. PMID: 32433555; PMCID: PMC7239929.
    View in: PubMed Mentions: 12 Fields:
    Translation:HumansCells
  7. Non-viral reprogramming and induced pluripotent stem cells for cardiovascular therapy. Differentiation. 2020 Mar - Apr; 112:58-66. Panda A, Gurusamy N, Rajasingh S, Carter HK, Thomas EL, Rajasingh J. PMID: 31954271; PMCID: PMC7138699.
    View in: PubMed Mentions: 4 Fields:
    Translation:HumansCells
  8. Elevated neoantigen levels in tumors with somatic mutations in the HLA-A, HLA-B, HLA-C and B2M genes. BMC Med Genomics. 2019 07 25; 12(Suppl 6):107. Castro A, Ozturk K, Pyke RM, Xian S, Zanetti M, Carter H. PMID: 31345234; PMCID: PMC6657029.
    View in: PubMed Mentions: 53 Fields:
    Translation:HumansCells
  9. VarI-COSI 2018: a forum for research advances in variant interpretation and diagnostics. BMC Genomics. 2019 Jul 16; 20(Suppl 8):550. Bromberg Y, Capriotti E, Carter H. PMID: 31307380; PMCID: PMC6631439.
    View in: PubMed Mentions: 1 Fields:
  10. Mutation hotspots may not be drug targets. Science. 2019 06 28; 364(6447):1228-1229. Carter H. PMID: 31249043.
    View in: PubMed Mentions: 2 Fields:
    Translation:Humans
  11. Identifying Driver Interfaces Enriched for Somatic Missense Mutations in Tumors. Methods Mol Biol. 2019; 1907:51-72. Ozturk K, Carter H. PMID: 30542990.
    View in: PubMed Mentions: Fields:
    Translation:HumansCells
  12. Integrative genomic analysis of mouse and human hepatocellular carcinoma. Proc Natl Acad Sci U S A. 2018 10 16; 115(42):E9879-E9888. Dow M, Pyke RM, Tsui BY, Alexandrov LB, Nakagawa H, Taniguchi K, Seki E, Harismendy O, Shalapour S, Karin M, Carter H, Font-Burgada J. PMID: 30287485; PMCID: PMC6196518.
    View in: PubMed Mentions: 51 Fields:
    Translation:HumansAnimalsCells
  13. Evolutionary Pressure against MHC Class II Binding Cancer Mutations. Cell. 2018 10 04; 175(2):416-428.e13. Marty Pyke R, Thompson WK, Salem RM, Font-Burgada J, Zanetti M, Carter H. PMID: 30245014; PMCID: PMC6482006.
    View in: PubMed Mentions: 108 Fields:
    Translation:HumansAnimalsCells
  14. The Emerging Potential for Network Analysis to Inform Precision Cancer Medicine. J Mol Biol. 2018 09 14; 430(18 Pt A):2875-2899. Ozturk K, Dow M, Carlin DE, Bejar R, Carter H. PMID: 29908887; PMCID: PMC6097914.
    View in: PubMed Mentions: 38 Fields:
    Translation:Humans
  15. MHC-I Genotype Restricts the Oncogenic Mutational Landscape. Cell. 2017. 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. .
  16. Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment. Genome Biol. 2017 03 28; 18(1):57. Wang T, Tsui B, Kreisberg JF, Robertson NA, Gross AM, Yu MK, Carter H, Brown-Borg HM, Adams PD, Ideker T. PMID: 28351423; PMCID: PMC5371228.
    View in: PubMed Mentions: 173 Fields:
    Translation:HumansAnimalsCells
  17. Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer. Cancer Discov. 2017 04; 7(4):410-423. 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. PMID: 28188128; PMCID: PMC5460679.
    View in: PubMed Mentions: 86 Fields:
    Translation:HumansCells
  18. Immune DNA signature of T-cell infiltration in breast tumor exomes. Sci Rep. 2016 07 25; 6:30064. Levy E, Marty R, Gárate Calderón V, Woo B, Dow M, Armisen R, Carter H, Harismendy O. PMID: 27452728; PMCID: PMC4958917.
    View in: PubMed Mentions: 13 Fields:
    Translation:HumansCells
  19. Challenges in identifying cancer genes by analysis of exome sequencing data. Nat Commun. 2016 07 15; 7:12096. Hofree M, Carter H, Kreisberg JF, Bandyopadhyay S, Mischel PS, Friend S, Ideker T. PMID: 27417679; PMCID: PMC4947162.
    View in: PubMed Mentions: 24 Fields:
    Translation:Humans
  20. VarI-SIG 2015: methods for personalized medicine - the role of variant interpretation in research and diagnostics. BMC Genomics. 2016 06 23; 17 Suppl 2:425. Bromberg Y, Capriotti E, Carter H. PMID: 27357578; PMCID: PMC4928159.
    View in: PubMed Mentions: 2 Fields:
    Translation:HumansCells
  21. Structure-Based Analysis Reveals Cancer Missense Mutations Target Protein Interaction Interfaces. PLoS One. 2016; 11(4):e0152929. Engin HB, Kreisberg JF, Carter H. PMID: 27043210; PMCID: PMC4820104.
    View in: PubMed Mentions: 48 Fields:
    Translation:HumansCells
  22. Hybrid Periportal Hepatocytes Regenerate the Injured Liver without Giving Rise to Cancer. Cell. 2015 Aug 13; 162(4):766-79. 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. PMID: 26276631; PMCID: PMC4545590.
    View in: PubMed Mentions: 273 Fields:
    Translation:AnimalsCells
  23. Identifying mutation specific cancer pathways using a structurally resolved protein interaction network. Pac Symp Biocomput. 2015; 84-95. Engin HB, Hofree M, Carter H. PMID: 25592571; PMCID: PMC4299875.
    View in: PubMed Mentions: 8 Fields:
    Translation:Humans
  24. A probabilistic model to predict clinical phenotypic traits from genome sequencing. PLoS Comput Biol. 2014 Sep; 10(9):e1003825. 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. PMID: 25188385; PMCID: PMC4154636.
    View in: PubMed Mentions: 7 Fields:
    Translation:Humans
  25. Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss. Nat Genet. 2014 Sep; 46(9):939-43. 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. PMID: 25086664; PMCID: PMC4146706.
    View in: PubMed Mentions: 76 Fields:
    Translation:HumansCells
  26. Predicting the functional consequences of somatic missense mutations found in tumors. Methods Mol Biol. 2014; 1101:135-59. Carter H, Karchin R. PMID: 24233781.
    View in: PubMed Mentions: 7 Fields:
    Translation:Humans
  27. Genotype to phenotype via network analysis. Curr Opin Genet Dev. 2013 Dec; 23(6):611-21. Carter H, Hofree M, Ideker T. PMID: 24238873; PMCID: PMC3866044.
    View in: PubMed Mentions: 68 Fields:
    Translation:Humans
  28. Network-based stratification of tumor mutations. Nat Methods. 2013 Nov; 10(11):1108-15. Hofree M, Shen JP, Carter H, Gross A, Ideker T. PMID: 24037242; PMCID: PMC3866081.
    View in: PubMed Mentions: 417 Fields:
    Translation:Humans
  29. Computational approaches to identify functional genetic variants in cancer genomes. Nat Methods. 2013 Aug; 10(8):723-9. 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, International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinforma. PMID: 23900255; PMCID: PMC3919555.
    View in: PubMed Mentions: 97 Fields:
    Translation:Humans
  30. 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. 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, NISC Comparative Sequencing Program, 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. PMID: 23901115; PMCID: PMC3746936.
    View in: PubMed Mentions: 101 Fields:
    Translation:HumansCells
  31. Identifying Mendelian disease genes with the variant effect scoring tool. BMC Genomics. 2013; 14 Suppl 3:S3. Carter H, Douville C, Stenson PD, Cooper DN, Karchin R. PMID: 23819870; PMCID: PMC3665549.
    View in: PubMed Mentions: 320 Fields:
    Translation:Humans
  32. A hybrid likelihood model for sequence-based disease association studies. PLoS Genet. 2013; 9(1):e1003224. Chen YC, Carter H, Parla J, Kramer M, Goes FS, Pirooznia M, Zandi PP, McCombie WR, Potash JB, Karchin R. PMID: 23358228; PMCID: PMC3554549.
    View in: PubMed Mentions: 15 Fields:
    Translation:HumansCells
  33. CRAVAT: cancer-related analysis of variants toolkit. Bioinformatics. 2013 Mar 01; 29(5):647-8. Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R. PMID: 23325621; PMCID: PMC3582272.
    View in: PubMed Mentions: 79 Fields:
    Translation:Humans
  34. Whole-exome sequencing combined with functional genomics reveals novel candidate driver cancer genes in endometrial cancer. Genome Res. 2012 Nov; 22(11):2120-9. 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. PMID: 23028188; PMCID: PMC3483541.
    View in: PubMed Mentions: 148 Fields:
    Translation:HumansCells
  35. Somatic mutations in the Notch, NF-KB, PIK3CA, and Hedgehog pathways in human breast cancers. Genes Chromosomes Cancer. 2012 May; 51(5):480-9. Jiao X, Wood LD, Lindman M, Jones S, Buckhaults P, Polyak K, Sukumar S, Carter H, Kim D, Karchin R, Sjöblom T. PMID: 22302350; PMCID: PMC3302210.
    View in: PubMed Mentions: 43 Fields:
    Translation:HumansCells
  36. 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. 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. PMID: 22158988; PMCID: PMC3248495.
    View in: PubMed Mentions: 278 Fields:
    Translation:HumansCells
  37. Integrated genomic analyses of ovarian carcinoma. Nature. 2011 Jun 29; 474(7353):609-15. Cancer Genome Atlas Research Network. PMID: 21720365; PMCID: PMC3163504.
    View in: PubMed Mentions: 4323 Fields:
    Translation:HumansCells
  38. Sequence analysis of 515 kinase genes in chronic lymphocytic leukemia. Leukemia. 2011 Dec; 25(12):1908-10. 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. PMID: 21701494; PMCID: PMC3523306.
    View in: PubMed Mentions: 11 Fields:
    Translation:Humans
  39. CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer. Bioinformatics. 2011 Aug 01; 27(15):2147-8. Wong WC, Kim D, Carter H, Diekhans M, Ryan MC, Karchin R. PMID: 21685053; PMCID: PMC3137226.
    View in: PubMed Mentions: 67 Fields:
    Translation:HumansCells
  40. The genetic landscape of the childhood cancer medulloblastoma. Science. 2011 Jan 28; 331(6016):435-9. 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. PMID: 21163964; PMCID: PMC3110744.
    View in: PubMed Mentions: 441 Fields:
    Translation:HumansCells
  41. Accumulation of driver and passenger mutations during tumor progression. Proc Natl Acad Sci U S A. 2010 Oct 26; 107(43):18545-50. Bozic I, Antal T, Ohtsuki H, Carter H, Kim D, Chen S, Karchin R, Kinzler KW, Vogelstein B, Nowak MA. PMID: 20876136; PMCID: PMC2972991.
    View in: PubMed Mentions: 411 Fields:
    Translation:Humans
  42. 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. Carter H, Samayoa J, Hruban RH, Karchin R. PMID: 20581473; PMCID: PMC3040948.
    View in: PubMed Mentions: 53 Fields:
    Translation:Humans
  43. Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. Cancer Res. 2009 Aug 15; 69(16):6660-7. Carter H, Chen S, Isik L, Tyekucheva S, Velculescu VE, Kinzler KW, Vogelstein B, Karchin R. PMID: 19654296; PMCID: PMC2763410.
    View in: PubMed Mentions: 261 Fields:
    Translation:Humans
  44. MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 2009 Jan; 37(Database issue):D347-54. 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. PMID: 18948282; PMCID: PMC2686492.
    View in: PubMed Mentions: 78 Fields:
    Translation:HumansCells
  45. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science. 2008 Sep 26; 321(5897):1801-6. 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. PMID: 18772397; PMCID: PMC2848990.
    View in: PubMed Mentions: 2137 Fields:
    Translation:HumansCells
  46. An integrated genomic analysis of human glioblastoma multiforme. Science. 2008 Sep 26; 321(5897):1807-12. 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. PMID: 18772396; PMCID: PMC2820389.
    View in: PubMed Mentions: 3026 Fields:
    Translation:HumansCells

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