2012 Publications

  1. Abyzov A, Mariani J, Palejev D, Zhang Y, Haney MS, Tomasini L, Ferrandino AF, Belmaker LAR, Szekely A, Wilson M, Kocabas A, Calixto NE, Grigorenko EL, Huttner A, Chawarska K, Weissman S, Urban AE, Gerstein M, Vaccarino FM. (2012) Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells. Nature 492: 438-442.
  2. Bamshad MJ, Shendure JA, Valle D, Hamosh A, Lupski JR, Gibbs RA, Boerwinkle E, Lifton RP, Gerstein M, Gunel M, Mane S, Nickerson DA. (2012) The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions. Am. J. Med. Genet. A. 158A: 1523-1525.
  3. Bandyopadhyay U, Cotney J, Nagy M, Oh S, Leng J, Mahajan M, Mane S, Fenton WA, Noonan JP, Horwich AL. (2012) RNA-Seq Profiling of Spinal Cord Motor Neurons from a Presymptomatic SOD1 ALS Mouse. Plos One 8: e53575.
  4. Beech RD, Qu J, Leffert JJ, Lin A, Hong KA, Hansen J, Umlauf S, Mane S, Zhao H, Sinha R. (2012) Altered expression of cytokine signaling pathway genes in peripheral blood cells of alcohol dependent subjects: preliminary findings. Alcohol. Clin. Exp. Res. 36: 1487-1496.
  5. Boyden LM, Choi M, Choate KA, Nelson-Williams CJ, Farhi A, Toka HR, Tikhonova IR, Bjornson R, Mane SM, Colussi G, Lebel M, Gordon RD, Semmekrot BA, Poujol A, Valimaki MJ, De Ferrari ME, Sanjad SA, Gutkin M, Karet FE, Tucci JR, Stockigt JR, Keppler-Noreuil KM, Porter CC, Anand SK, Whiteford ML, Davis ID, Dewar SB, Bettinelli A, Fadrowski JJ, Belsha CW, Hunley TE, Nelson RD, Trachtman H, Cole TRP, Pinsk M, Bockenhauer D, Shenoy M, Vaidyanathan P, Foreman JW, Rasoulpour M, Thameem F, Al-Shahrouri HZ, Radhakrishnan J, Gharavi AG, Goilav B, Lifton RP. (2012) Mutations in kelch-like 3 and cullin 3 cause hypertension and electrolyte abnormalities. Nature 482: 98-102.
  6. Cromer MK, Starker LF, Choi M, Udelsman R, Nelson-Williams C, Lifton RP, Carling T. (2012) Identification of Somatic Mutations in Parathyroid Tumors Using Whole-Exome Sequencing. J. Clin. Endocrinol. Metab. 97: E1774-E1781.
  7. del Viso F, Bhattacharya D, Kong Y, Gilchrist MJ, Khokha MK. (2012) Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing. BMC Genomics 13: 649.
  8. DeWan AT, Egan KB, Hellenbrand K, Sorrentino K, Pizzoferrato N, Walsh KM, Bracken MB. (2012) Whole-exome sequencing of a pedigree segregating asthma. BMC Med. Genet.13: 95.
  9. Fernandez TV, Sanders SJ, Yurkiewicz IR, Ercan-Sencicek AG, Kim YS, Fishman DO, Raubeson MJ, Song Y, Yasuno K, Ho WS, Bilguvar K, Glessner J, Chu SH, Leckman JF, King RA, Gilbert DL, Heiman GA, Tischfield JA, Hoekstra PJ, Devlin B, Hakonarson H, Mane SM, Günel M, State MW. (2012) Rare Copy Number Variants in Tourette Syndrome Disrupt Genes in Histaminergic Pathways and Overlap with Autism. Biol. Psychiatry. 7: 392-402.
  10. Fonseca AL, Kugelberg J, Starker LF, Scholl U, Choi M, Hellman P, Akerstrom G, Westin G, Lifton RP, Bjorklund P, Carling T. (2012) Comprehensive DNA methylation analysis of benign and malignant adrenocortical tumors. Genes Chromosomes Cancer 51: 949-960.
  11. Gathungu G, Zhang CK, Zhang W, Cho JH. (2012) A two-marker haplotype in the IRF5 gene is associated with inflammatory bowel disease in a North American cohort. Genes Immun. 13: 351-355.
  12. Huang X, Narayanaswamy R, Fenn K, Szpakowski S, Sasaki C, Costa J, Blancafort P, Lizardi PM. (2012) Sequence-specific biosensors report drug-induced changes in epigenetic silencing in living cells. DNA Cell Biol. 31 Suppl 1: S2-10.
  13. Jun HJ, Acquaviva J, Chi D, Lessard J, Zhu H, Woolfenden S, Bronson RT, Pfannl R, White F, Housman DE, Iyer L, Whittaker CA, Boskovitz A, Raval A, Charest A. (2012) Acquired MET expression confers resistance to EGFR inhibition in a mouse model of glioblastoma multiforme. Oncogene. 31: 3039-3050.
  14. Kang DD, Sibille E, Kaminski N, Tseng GC. (2012) MetaQC: objective quality control and inclusion/exclusion criteria for genomic meta-analysis. Nucleic Acids Res. 40: e15.
  15. Keller PJ, Arendt LM, Skibinski A, Logvinenko T, Klebba I, Dong S, Smith AE, Prat A, Perou CM, Gilmore H, Schnitt S, Naber SP, Garlick JA, Kuperwasser C. (2012) Defining the cellular precursors to human breast cancer. Proc. Natl. Acad. Sci. U.S.A. 109: 2772-2777.
  16. Kenny EE, Pe'er I, Karban A, Ozelius L, Mitchell AA, Ng SM, Erazo M, Ostrer H, Abraham C, Abreu MT, Atzmon G, Barzilai N, Brant SR, Bressman S, Burns ER, Chowers Y, Clark LN, Darvasi A, Doheny D, Duerr RH, Eliakim R, Giladi N, Gregersen PK, Hakonarson H, Jones MR, Marder K, McGovern DP, Mulle J, Orr-Urtreger A, Proctor DD, Pulver A, Rotter JI, Silverberg MS, Ullman T, Warren ST, Waterman M, Zhang W, Bergman A, Mayer L, Katz S, Desnick RJ, Cho JH, Peter I. (2012) A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci. PLoS Genet. 8: e1002559.
  17. Klei L, Sanders SJ, Murtha MT, Hus V, Lowe JK, Willsey AJ, Moreno-De-Luca D, Yu TW, Fombonne E, Geschwind D, Grice DE, Ledbetter DH, Lord C, Mane SM, Martin CL, Martin DM, Morrow EM, Walsh CA, Melhem NM, Chaste P, Sutcliffe JS, State MW, Cook EH, Jr., Roeder K, Devlin B. (2012) Common genetic variants, acting additively, are a major source of risk for autism. Mol. Autism 3: 9.
  18. Krauthammer M, Kong Y, Ha BH, Evans P, Bacchiocchi A, McCusker JP, Cheng E, Davis MJ, Goh G, Choi M, Ariyan S, Narayan D, Dutton-Regester K, Capatana A, Holman EC, Bosenberg M, Sznol M, Kluger HM, Brash DE, Stern DF, Materin MA, Lo RS, Mane S, Ma S, Kidd KK, Hayward NK, Lifton RP, Schlessinger J, Boggon TJ, Halaban R. (2012) Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma. Nat. Genet. 44: 1006-1014.
  19. Lin WM, Lewis JM, Filler RB, Modi BG, Carlson KR, Reddy S, Thornberg A, Saksena G, Umlauf S, Oberholzer PA, Karpova M, Getz G, Mane S, Garraway LA, Dummer R, Berger CL, Edelson RL, Girardi M.(2012) Characterization of the DNA copy-number genome in the blood of cutaneous T-cell lymphoma patients. J. Invest. Dermatol. 132: 188-197.
  20. Liu W, Singh R, Choi CS, Hui-Young L, Keramati AR, Samuel VT, Lifton RP, Shulman GI, Mani A. (2012) Low density lipoprotein (LDL) receptor-related protein 6 (LRP6) regulates body fat and glucose homeostasis by modulating nutrient sensing pathways and mitochondrial energy expenditure. J. Biol. Chem. 287: 7213-7223.
  21. Lo SM, Choi M, Liu J, Jain D, Boot RG, Kallemeijn WW, Aerts JM, Pashankar F, Kupfer GM, Mane S, Lifton RP, Mistry PK. (2012) Phenotype diversity in type 1 Gaucher disease: discovering the genetic basis of Gaucher disease/hematologic malignancy phenotype by individual genome analysis. Blood 119: 4731-4740.
  22. Lohmann E, Koroglu C, Hanagasi HA, Dursun B, Tasan E, Tolun A (2012) A homozygous frameshift mutation of sepiapterin reductase gene causing parkinsonism with onset in childhood. Parkinsonism Relat. Disord. 18: 191-193.
  23. Lowthert L, Leffert J, Lin A, Umlauf S, Maloney K, Muralidharan A, Lorberg B, Mane S, Zhao H, Sinha R, Bhagwagar Z, Beech R. (2012) Increased ratio of anti-apoptotic to pro-apoptotic Bcl2 gene-family members in lithium-responders one month after treatment initiation. Biol. Mood Anxiety Disord. 2: 15.
  24. Modi BG, Neustadter J, Binda E, Lewis J, Filler RB, Roberts SJ, Kwong BY, Reddy S, Overton JD, Galan A, Tigelaar R, Cai L, Fu P, Shlomchik M, Kaplan DH, Hayday A, Girardi M. (2012) Langerhans cells facilitate epithelial DNA damage and squamous cell carcinoma. Science 335: 104-108.
  25. Narayan A, Carriero NJ, Gettinger SN, Kluytenaar J, Kozak KR, Yock TI, Muscato NE, Ugarelli P, Decker RH, Patel AA. (2012) Ultrasensitive Measurement of Hotspot Mutations in Tumor DNA in Blood Using Error-Suppressed Multiplexed Deep Sequencing. Cancer Res. 72: 3492-3498.
  26. Naumova OY, Palejev D, Vlasova NV, Lee M, Rychkov SY, Babich ON, Vaccarino FM, Grigorenko EL. (2012) Age-related changes of gene expression in the neocortex: Preliminary data on RNA-Seq of the transcriptome in three functionally distinct cortical areas. Dev. Psychopathol. 24: 1427-1442.
  27. Ponomarev I, Wang S, Zhang L, Harris RA, Mayfield RD. (2012) Gene coexpression networks in human brain identify epigenetic modifications in alcohol dependence. J. Neurosci. 32: 1884-1897.
  28. Rompolas P, Deschene ER, Zito G, Gonzalez DG, Saotome I, Haberman AM, Greco V. (2012) Live imaging of stem cell and progeny behaviour in physiological hair-follicle regeneration. Nature 487: 496-499.
  29. Sanders SJ, Murtha MT, Gupta AR, Murdoch JD, Raubeson MJ, Willsey AJ, Ercan-Sencicek AG, DiLullo NM, Parikshak NN, Stein JL, Walker MF, Ober GT, Teran NA, Song Y, El-Fishawy P, Murtha RC, Choi M, Overton JD, Bjornson RD, Carriero NJ, Meyer KA, Bilguvar K, Mane SM, Sestan N, Lifton RP, Gunel M, Roeder K, Geschwind DH, Devlin B, State MW. (2012) De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature 485: 237-241.
  30. Sanna-Cherchi S, Kiryluk K, Burgess KE, Bodria M, Sampson MG, Hadley D, Nees SN, Verbitsky M, Perry BJ, Sterken R, Lozanovski VJ, Materna-Kiryluk A, Barlassina C, Kini A, Corbani V, Carrea A, Somenzi D, Murtas C, Ristoska-Bojkovska N, Izzi C, Bianco B, Zaniew M, Flogelova H, Weng PL, Kacak N, Giberti S, Gigante M, Arapovic A, Drnasin K, Caridi G, Curioni S, Allegri F, Ammenti A, Ferretti S, Goj V, Bernardo L, Jobanputra V, Chung WK, Lifton RP, Sanders S, State M, Clark LN, Saraga M, Padmanabhan S, Dominiczak AF, Foroud T, Gesualdo L, Gucev Z, Allegri L, Latos-Bielenska A, Cusi D, Scolari F, Tasic V, Hakonarson H, Ghiggeri GM, Gharavi AG. (2012) Copy-number disorders are a common cause of congenital kidney malformations. Am. J. Hum. Genet. 91: 987-997.
  31. Santoro N, Savoye M, Kim G, Marotto K, Shaw MM, Pierpont B, Caprio S. (2012) Hepatic Fat Accumulation Is Modulated by the Interaction between the rs738409 Variant in the PNPLA3 Gene and the Dietary Omega6/Omega3 PUFA Intake. Plos One 7: e37827.
  32. Santoro N, Zhang CK, Zhao H, Pakstis AJ, Kim G, Kursawe R, Dykas DJ, Bale AE, Giannini C, Pierpont B, Shaw MM, Groop L, Caprio S. (2012) Variant in the glucokinase regulatory protein (GCKR) gene is associated with fatty liver in obese children and adolescents. Hepatology 55:7 81-789.
  33. Sherwin R, Slayman C, Rockwell S, Herold K, Williams K, Carson R, Mane S, Seow H, Max J, Johnson T. (2012) Yale Center for Clinical Investigation: Leveraging Industry Partnerships and Research Cores. Clin. Transl. Sci. 5: 435-436.
  34. Wagner GP, Kin K, Lynch VJ. (2012) Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory Biosci. 131: 281-285.
  35. Zarychanski R, Schulz VP, Houston BL, Maksimova Y, Houston DS, Smith B, Rinehart J, Gallagher PG. (2012) Mutations in the mechanotransduction protein PIEZO1 are associated with hereditary xerocytosis. Blood 120: 1908-1915.
  36. Zhao BY, Lu JG, Yin JK, Liu HQ, Guo X, Yang YF, Ge NJ, Zhu Y, Zhang HX, Xing JL. (2012) A functional polymorphism in PER3 gene is associated with prognosis in hepatocellular carcinoma. Liver Int. 32: 1451-1459.
  37. Zhao LL, Triche EW, Walsh KM, Bracken MB, Saftlas AF, Hoh J, Dewan AT. (2012) Genome-wide association study identifies a maternal copy-number deletion in PSG11 enriched among preeclampsia patients. BMC Pregnancy Childbirth 12: 61.