Publications

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2019
Berauer J-P, Mezina AI, Okou DT, Sabo A, Muzny DM, Gibbs RA, Hegde MR, Chopra P, Cutler DJ, Perlmutter DH, Bull LN, Thompson RJ, Loomes KM, Spinner NB, Rajagopalan R, Guthery SL, Moore B, Yandell M, Harpavat S, Magee JC, Kamath BM, Molleston JP, Bezerra JA, Murray KF, Alonso EM, Rosenthal P, Squires RH, Wang KS, Finegold MJ, Russo P, Sherker AH, Sokol RJ, Karpen SJ. Identification of PKD1L1 Gene Variants in Children with the Biliary Atresia Splenic Malformation Syndrome. Hepatology. 2019 ;.
Saha S, Hosmani PS, Villalobos-Ayala K, Miller S, Shippy T, Flores M, Rosendale A, Cordola C, Bell T, Mann H, DeAvila G, DeAvila D, Moore Z, Buller K, Ciolkevich K, Nandyal S, Mahoney R, Van Voorhis J, Dunlevy M, Farrow D, Hunter D, Morgan T, Shore K, Guzman V, Izsak A, Dixon DE, Cridge A, Cano L, Cao X, Jiang H, Leng N, Johnson S, Cantarel BL, Richards S, English A, Shatters RG, Childers C, Chen M-J, Hunter W, Cilia M, Mueller LA, Munoz-Torres M, Nelson D, Poelchau MF, Benoit JB, Wiersma-Koch H, D'Elia T, Brown SJ. Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community. Database (Oxford). 2019 ;2019.
Posey JE, O'Donnell-Luria AH, Chong JX, Harel T, Jhangiani SN, Akdemir ZHCoban, Buyske S, Pehlivan D, Carvalho CMB, Baxter S, Sobreira N, Liu P, Wu N, Rosenfeld JA, Kumar S, Avramopoulos D, White JJ, Doheny KF, P Witmer D, Boehm C, V Sutton R, Muzny DM, Boerwinkle E, Gunel M, Nickerson DA, Mane S, MacArthur DG, Gibbs RA, Hamosh A, Lifton RP, Matise TC, Rehm HL, Gerstein M, Bamshad MJ, Valle D, Lupski JR. Insights into genetics, human biology and disease gleaned from family based genomic studies. Genet Med. 2019 ;.
2018
Punetha J, Mackay-Loder L, Harel T, Coban-Akdemir Z, Jhangiani SN, Gibbs RA, Lee I, Terespolsky D, Lupski JR, Posey JE. Identification of a pathogenic PMP2 variant in a multi-generational family with CMT type 1: Clinical gene panels versus genome-wide approaches to molecular diagnosis. Mol Genet Metab. 2018 ;125(3):302-304.
Du R, Dinckan N, Song X, Coban-Akdemir Z, Jhangiani SN, Guven Y, Aktoren O, Kayserili H, Petty LE, Muzny DM, Below JE, Boerwinkle E, Wu N, Gibbs RA, Posey JE, Lupski JR, Letra A, Z Uyguner O. Identification of likely pathogenic and known variants in TSPEAR, LAMB3, BCOR, and WNT10A in four Turkish families with tooth agenesis. Hum Genet. 2018 ;137(9):689-703.
Coban-Akdemir Z, White JJ, Song X, Jhangiani SN, Fatih JM, Gambin T, Bayram Y, Chinn IK, Karaca E, Punetha J, Poli C, Boerwinkle E, Shaw CA, Orange JS, Gibbs RA, Lappalainen T, Lupski JR, Carvalho CMB. Identifying Genes Whose Mutant Transcripts Cause Dominant Disease Traits by Potential Gain-of-Function Alleles. Am J Hum Genet. 2018 ;103(2):171-187.
Shen H, Shih J, Hollern DP, Wang L, Bowlby R, Tickoo SK, Thorsson V, Mungall AJ, Newton Y, Hegde AM, Armenia J, Sánchez-Vega F, Pluta J, Pyle LC, Mehra R, Reuter VE, Godoy G, Jones J, Shelley CS, Feldman DR, Vidal DO, Lessel D, Kulis T, Cárcano FM, Leraas KM, Lichtenberg TM, Brooks D, Cherniack AD, Cho J, Heiman DI, Kasaian K, Liu M, Noble MS, Xi L, Zhang H, Zhou W, ZenKlusen JC, Hutter CM, Felau I, Zhang J, Schultz N, Getz G, Meyerson M, Stuart JM, Akbani R, Wheeler DA, Laird PW, Nathanson KL, Cortessis VK, Hoadley KA. Integrated Molecular Characterization of Testicular Germ Cell Tumors. Cell Rep. 2018 ;23(11):3392-3406.
Yeung K, Wang F, Li Y, Wang K, Mardon G, Chen R. Integrative genomic analysis reveals novel regulatory mechanisms of eyeless during Drosophila eye development. Nucleic Acids Res. 2018 ;46(22):11743-11758.
DuPont M, Jones EM, Xu M, Chen R. Investigating the disease association of USH2A p.C759F variant by leveraging large retinitis pigmentosa cohort data. Ophthalmic Genet. 2018 ;39(2):291-292.
2017
Bainbridge MNeil, Li L, Tan Y, Cheong BY, Marian AJ. Identification of established arrhythmogenic right ventricular cardiomyopathy mutation in a patient with the contrasting phenotype of hypertrophic cardiomyopathy. BMC Med Genet. 2017 ;18(1):24.
Dharmat R, Liu W, Ge Z, Sun Z, Yang L, Li Y, Wang K, Thomas K, Sui R, Chen R. IFT81 as a Candidate Gene for Nonsyndromic Retinal Degeneration. Invest Ophthalmol Vis Sci. 2017 ;58(5):2483-2490.
Saha S, Hosmani PS, Villalobos-Ayala K, Miller S, Shippy T, Flores M, Rosendale A, Cordola C, Bell T, Mann H, DeAvila G, DeAvila D, Moore Z, Buller K, Ciolkevich K, Nandyal S, Mahoney R, Van Voorhis J, Dunlevy M, Farrow D, Hunter D, Morgan T, Shore K, Guzman V, Izsak A, Dixon DE, Cridge A, Cano L, Cao X, Jiang H, Leng N, Johnson S, Cantarel BL, Richards S, English A, Shatters RG, Childers C, Chen M-J, Hunter W, Cilia M, Mueller LA, Munoz-Torres M, Nelson D, Poelchau MF, Benoit JB, Wiersma-Koch H, D'Elia T, Brown SJ. Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community. Database (Oxford). 2017 ;2017.
Prall TM, Graham ME, Karl JA, Wiseman RW, Ericsen AJ, Raveendran M, Harris RA, Muzny DM, Gibbs RA, Rogers J, O'Connor DH. Improved full-length killer cell immunoglobulin-like receptor transcript discovery in Mauritian cynomolgus macaques. Immunogenetics. 2017 ;69(5):325-339.
Bressler J, Knopman DS, A Sharrett R, Gottesman RF, Penman A, Chang PP, Rosamond WD, Boerwinkle E, Mosley TH. Incident Heart Failure and Cognitive Decline: The Atherosclerosis Risk in Communities Study. J Card Fail. 2017 ;23(1):47-55.
Farshidfar F, Zheng S, Gingras M-C, Newton Y, Shih J, A Robertson G, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu C-C, Shinbrot E, Stransky N, Hegde A, Yang JDong, Reznik E, Sadeghi S, Pedamallu CSekhar, Ojesina AI, Hess JM, J Auman T, Rhie SK, Bowlby R, Borad MJ, Zhu AX, Stuart JM, Sander C, Akbani R, Cherniack AD, Deshpande V, Mounajjed T, Foo WChin, Torbenson MS, Kleiner DE, Laird PW, Wheeler DA, McRee AJ, Bathe OF, Andersen JB, Bardeesy N, Roberts LR, Kwong LN. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles. Cell Rep. 2017 ;18(11):2780-2794.
Mamat N, Dou J, Lu X, Eblimit A, Akber AHaji. Isochlorogenic acid A promotes melanin synthesis in B16 cell through the β-catenin signal pathway. Acta Biochim Biophys Sin (Shanghai). 2017 ;49(9):800-807.
2016
Loviglio MNicla, Beck CR, White JJ, Leleu M, Harel T, Guex N, Niknejad A, Bi W, Chen ES, Crespo I, Yan J, Charng W-L, Gu S, Fang P, Coban-Akdemir Z, Shaw CA, Jhangiani SN, Muzny DM, Gibbs RA, Rougemont J, Xenarios I, Lupski JR, Reymond A. Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics, and 3D genomics. Genome Med. 2016 ;8(1):105.
Fieremans N, Van Esch H, Holvoet M, Van Goethem G, Devriendt K, Rosello M, Mayo S, Martinez F, Jhangiani S, Muzny DM, Gibbs RA, Lupski JR, Vermeesch JR, Marynen P, Froyen G. Identification of Intellectual Disability Genes in Female Patients with a Skewed X-Inactivation Pattern. Hum Mutat. 2016 ;37(8):804-11.
Jin M, Aibar S, Ge Z, Chen R, Aerts S, Mardon G. Identification of novel direct targets of Drosophila Sine oculis and Eyes absent by integration of genome-wide data sets. Dev Biol. 2016 ;415(1):157-67.
Yazdani A, Yazdani A, Liu X, Boerwinkle E. Identification of Rare Variants in Metabolites of the Carnitine Pathway by Whole Genome Sequencing Analysis. Genet Epidemiol. 2016 ;40(6):486-91.
Ogunwale AN, Morrison AC, Sun W, Dodge RC, Virani SS, Taylor A, Gottesman RF, Yang E, Wei P, McEvoy JW, Heiss G, Boerwinkle E, Ballantyne CM, Nambi V. The impact of multiple single day blood pressure readings on cardiovascular risk estimation: The Atherosclerosis Risk in Communities study. Eur J Prev Cardiol. 2016 ;23(14):1529-36.
A Hakimi A, Reznik E, Lee C-H, Creighton CJ, A Brannon R, Luna A, B Aksoy A, Liu EMinwei, Shen R, Lee W, Chen Y, Stirdivant SM, Russo P, Chen Y-B, Tickoo SK, Reuter VE, Cheng EH, Sander C, Hsieh JJ. An Integrated Metabolic Atlas of Clear Cell Renal Cell Carcinoma. Cancer Cell. 2016 ;29(1):104-16.
Lin FY, Bergstrom K, Person R, Bavle A, Ballester LY, Scollon S, Raesz-Martinez R, Jea A, Birchansky S, Wheeler DA, Berg SL, Chintagumpala MM, Adesina AM, Eng CM, Roy A, Plon SE, D Parsons W. Integrated tumor and germline whole-exome sequencing identifies mutations in MAPK and PI3K pathway genes in an adolescent with rosette-forming glioneuronal tumor of the fourth ventricle. Cold Spring Harb Mol Case Stud. 2016 ;2(5):a001057.
Zhao L, Chen Y, Bajaj AOnkar, Eblimit A, Xu M, Soens ZT, Wang F, Ge Z, Jung SYun, He F, Li Y, Wensel TG, Qin J, Chen R. Integrative subcellular proteomic analysis allows accurate prediction of human disease-causing genes. Genome Res. 2016 ;26(5):660-9.
Coppieters F, Ascari G, Dannhausen K, Nikopoulos K, Peelman F, Karlstetter M, Xu M, Brachet C, Meunier I, Tsilimbaris MK, Tsika C, Blazaki SV, Vergult S, Farinelli P, Van Laethem T, Bauwens M, De Bruyne M, Chen R, Langmann T, Sui R, Meire F, Rivolta C, Hamel CP, Leroy BP, De Baere E. Isolated and Syndromic Retinal Dystrophy Caused by Biallelic Mutations in RCBTB1, a Gene Implicated in Ubiquitination. Am J Hum Genet. 2016 ;99(2):470-80.