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A
Abel HJ, Larson DE, Regier AA, Chiang C, Das I, Kanchi KL, Layer RM, Neale BM, Salerno WJ, Reeves C, Buyske S, Matise TC, Muzny DM, Zody MC, Lander ES, Dutcher SK, Stitziel NO, Hall IM. Mapping and characterization of structural variation in 17,795 human genomes. Nature. 2020 ;583(7814):83-89.
Alonge M, Wang X, Benoit M, Soyk S, Pereira L, Zhang L, Suresh H, Ramakrishnan S, Maumus F, Ciren D, Levy Y, Harel THai, Shalev-Schlosser G, Amsellem Z, Razifard H, Caicedo AL, Tieman DM, Klee H, Kirsche M, Aganezov S, T Ranallo-Benavidez R, Lemmon ZH, Kim J, Robitaille G, Kramer M, Goodwin S, W McCombie R, Hutton S, Van Eck J, Gillis J, Eshed Y, Sedlazeck FJ, van der Knaap E, Schatz MC, Lippman ZB. Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato. Cell. 2020 ;182(1):145-161.e23.
Alonso A, Yu B, Qureshi WT, Grams ME, Selvin E, Soliman EZ, Loehr LR, Chen LY, Agarwal SK, Alexander D, Boerwinkle E. Metabolomics and Incidence of Atrial Fibrillation in African Americans: The Atherosclerosis Risk in Communities (ARIC) Study. PLoS One. 2015 ;10(11):e0142610.
Andersson B, Lu J, Edwards KE, Muzny DM, Gibbs RA. Method for 96-well M13 DNA template preparations for large-scale sequencing. Biotechniques. 1996 ;20(6):1022-7.
Arai E, Sakamoto H, Ichikawa H, Totsuka H, Chiku S, Gotoh M, Mori T, Nakatani T, Ohnami S, Nakagawa T, Fujimoto H, Wang L, Aburatani H, Yoshida T, Kanai Y. Multilayer-omics analysis of renal cell carcinoma, including the whole exome, methylome and transcriptome. Int J Cancer. 2014 ;135(6):1330-42.
Arno G, Agrawal SA, Eblimit A, Bellingham J, Xu M, Wang F, Chakarova C, Parfitt DA, Lane A, Burgoyne T, Hull S, Carss KJ, Fiorentino A, Hayes MJ, Munro PM, Nicols R, Pontikos N, Holder GE, Asomugha C, F Raymond L, Moore AT, Plagnol V, Michaelides M, Hardcastle AJ, Li Y, Cukras C, Webster AR, Cheetham ME, Chen R. Mutations in REEP6 Cause Autosomal-Recessive Retinitis Pigmentosa. Am J Hum Genet. 2016 ;99(6):1305-1315.
B
Beck CR, Carvalho CMB, Akdemir ZC, Sedlazeck FJ, Song X, Meng Q, Hu J, Doddapaneni H, Chong Z, Chen ES, Thornton PC, Liu P, Yuan B, Withers M, Jhangiani SN, Kalra D, Walker K, English AC, Han Y, Chen K, Muzny DM, Ira G, Shaw CA, Gibbs RA, Hastings PJ, Lupski JR. Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2. Cell. 2019 ;176(6):1310-1324.e10.
Bellott DW, Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Cho T-J, Koutseva N, Zaghlul S, Graves T, Rock S, Kremitzki C, Fulton RS, Dugan S, Ding Y, Morton D, Khan Z, Lewis L, Buhay C, Wang Q, Watt J, Holder M, Lee S, Nazareth L, Alföldi J, Rozen S, Muzny DM, Warren WC, Gibbs RA, Wilson RK, Page DC. Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Nature. 2014 ;508(7497):494-9.
Bentley AR, Sung YJ, Brown MR, Winkler TW, Kraja AT, Ntalla I, Schwander K, Chasman DI, Lim E, Deng X, Guo X, Liu J, Lu Y, Cheng C-Y, Sim X, Vojinovic D, Huffman JE, Musani SK, Li C, Feitosa MF, Richard MA, Noordam R, Baker J, Chen G, Aschard H, Bartz TM, Ding J, Dorajoo R, Manning AK, Rankinen T, Smith AV, Tajuddin SM, Zhao W, Graff M, Alver M, Boissel M, Chai JFang, Chen X, Divers J, Evangelou E, Gao C, Goel A, Hagemeijer Y, Harris SE, Hartwig FP, He M, Horimoto ARVR, Hsu F-C, Hung Y-J, Jackson AU, Kasturiratne A, Komulainen P, Kühnel B, Leander K, Lin K-H, Luan J'an, Lyytikäinen L-P, Matoba N, Nolte IM, Pietzner M, Prins B, Riaz M, Robino A, M Said A, Schupf N, Scott RA, Sofer T, Stančáková A, Takeuchi F, Tayo BO, van der Most PJ, Varga TV, Wang T-D, Wang Y, Ware EB, Wen W, Xiang Y-B, Yanek LR, Zhang W, Zhao JHua, Adeyemo A, Afaq S, Amin N, Amini M, Arking DE, Arzumanyan Z, Aung T, Ballantyne C, R Barr G, Bielak LF, Boerwinkle E, Bottinger EP, Broeckel U, Brown M, Cade BE, Campbell A, Canouil M, Charumathi S, Chen Y-DIda, Christensen K, Concas MPina, Connell JM, Fuentes Lde Las, H de Silva J, de Vries PS, Doumatey A, Duan Q, Eaton CB, Eppinga RN, Faul JD, Floyd JS, Forouhi NG, Forrester T, Friedlander Y, Gandin I, Gao H, Ghanbari M, Gharib SA, Gigante B, Giulianini F, Grabe HJ, C Gu C, Harris TB, Heikkinen S, Heng C-K, Hirata M, Hixson JE, M Ikram A, Jia Y, Joehanes R, Johnson C, Jonas JBruno, Justice AE, Katsuya T, Khor CChuen, Kilpeläinen TO, Koh W-P, Kolcic I, Kooperberg C, Krieger JE, Kritchevsky SB, Kubo M, Kuusisto J, Lakka TA, Langefeld CD, Langenberg C, Launer LJ, Lehne B, Lewis CE, Li Y, Liang J, Lin S, Liu C-T, Liu J, Liu K, Loh M, Lohman KK, Louie T, Luzzi A, Mägi R, Mahajan A, Manichaikul AW, McKenzie CA, Meitinger T, Metspalu A, Milaneschi Y, Milani L, Mohlke KL, Momozawa Y, Morris AP, Murray AD, Nalls MA, Nauck M, Nelson CP, North KE, O'Connell JR, Palmer ND, Papanicolau GJ, Pedersen NL, Peters A, Peyser PA, Polasek O, Poulter N, Raitakari OT, Reiner AP, Renstrom F, Rice TK, Rich SS, Robinson JG, Rose LM, Rosendaal FR, Rudan I, Schmidt CO, Schreiner PJ, Scott WR, Sever P, Shi Y, Sidney S, Sims M, Smith JA, Snieder H, Starr JM, Strauch K, Stringham HM, Tan NYQ, Tang H, Taylor KD, Teo YYing, Tham YChung, Tiemeier H, Turner ST, Uitterlinden AG, van Heemst D, Waldenberger M, Wang H, Wang L, Wang L, Bin Wei W, Williams CA, Wilson G, Wojczynski MK, Yao J, Young K, Yu C, Yuan J-M, Zhou J, Zonderman AB, Becker DM, Boehnke M, Bowden DW, Chambers JC, Cooper RS, de Faire U, Deary IJ, Elliott P, Esko T, Farrall M, Franks PW, Freedman BI, Froguel P, Gasparini P, Gieger C, Horta BL, Juang J-MJimmy, Kamatani Y, Kammerer CM, Kato N, Kooner JS, Laakso M, Laurie CC, Lee I-T, Lehtimäki T, Magnusson PKE, Oldehinkel AJ, Penninx BWJH, Pereira AC, Rauramaa R, Redline S, Samani NJ, Scott J, Shu X-O, van der Harst P, Wagenknecht LE, Wang J-S, Wang YXing, Wareham NJ, Watkins H, Weir DR, Wickremasinghe AR, Wu T, Zeggini E, Zheng W, Bouchard C, Evans MK, Gudnason V, Kardia SLR, Liu Y, Psaty BM, Ridker PM, van Dam RM, Mook-Kanamori DO, Fornage M, Province MA, Kelly TN, Fox ER, Hayward C, van Duijn CM, E Tai S, Wong TYin, Loos RJF, Franceschini N, Rotter JI, Zhu X, Bierut LJ, W Gauderman J, Rice K, Munroe PB, Morrison AC, Rao DC, Rotimi CN, L Cupples A. Multi-ancestry genome-wide gene-smoking interaction study of 387,272 individuals identifies new loci associated with serum lipids. Nat Genet. 2019 ;51(4):636-648.
Bernard L, Chen J, Kim H, Wong KE, Steffen LM, Yu B, Boerwinkle E, Rebholz CM. Metabolomics of Dietary Intake of Total, Animal, and Plant Protein: Results from the Atherosclerosis Risk in Communities (ARIC) Study. Curr Dev Nutr. 2023 ;7(4):100067.
Bonnen PE, Yarham JW, Besse A, Wu P, Faqeih EA, Al-Asmari AMohammad, Saleh MAM, Eyaid W, Hadeel A, He L, Smith F, Yau S, Simcox EM, Miwa S, Donti T, Abu-Amero KK, Wong L-J, Craigen WJ, Graham BH, Scott KL, McFarland R, Taylor RW. Mutations in FBXL4 cause mitochondrial encephalopathy and a disorder of mitochondrial DNA maintenance. Am J Hum Genet. 2013 ;93(3):471-81.
Brammer DW, Gillespie PJ, Tian M, Young D, Raveendran M, Williams LE, Gagea M, Benavides FJ, Perez CJ, Broaddus RR, Bernacky BJ, Barnhart KF, Alauddin MM, Bhutani MS, Gibbs RA, Sidman RL, Pasqualini R, Arap W, Rogers J, Abee CR, Gelovani JG. MLH1-rheMac hereditary nonpolyposis colorectal cancer syndrome in rhesus macaques. Proc Natl Acad Sci U S A. 2018 ;115(11):2806-2811.
Bressler J, Yu B, Mosley TH, Knopman DS, Gottesman RF, Alonso A, Sharrett AR, Wruck LM, Boerwinkle E. Metabolomics and cognition in African American adults in midlife: the atherosclerosis risk in communities study. Transl Psychiatry. 2017 ;7(7):e1173.
Bull-Otterson L, Feng W, Kirpich I, Wang Y, Qin X, Liu Y, Gobejishvili L, Joshi-Barve S, Ayvaz T, Petrosino J, Kong M, Barker D, McClain C, Barve S. Metagenomic analyses of alcohol induced pathogenic alterations in the intestinal microbiome and the effect of Lactobacillus rhamnosus GG treatment. PLoS One. 2013 ;8(1):e53028.
C
Calame DG, Guo T, Wang C, Garrett L, Jolly A, Dawood M, Kurolap A, Henig NZunz, Fatih JM, Herman I, Du H, Mitani T, Becker L, Rathkolb B, Gerlini R, Seisenberger C, Marschall S, Hunter JV, Gerard A, Heidlebaugh A, Challman T, Spillmann RC, Jhangiani SN, Coban-Akdemir Z, Lalani S, Liu L, Revah-Politi A, Iglesias A, Guzman E, Baugh E, Boddaert N, Rondeau S, Ormieres C, Barcia G, Tan QKG, Thiffault I, Pastinen T, Sheikh K, Biliciler S, Mei D, Melani F, Shashi V, Yaron Y, Steele M, Wakeling E, Østergaard E, Nazaryan-Petersen L, Millan F, Santiago-Sim T, Thevenon J, Bruel A-L, Thauvin-Robinet C, Popp D, Platzer K, Gawlinski P, Wiszniewski W, Marafi D, Pehlivan D, Posey JE, Gibbs RA, Gailus-Durner V, Guerrini R, Fuchs H, de Angelis MHrabě, Hölter SM, Cheung H-H, Gu S, Lupski JR. Monoallelic variation in DHX9, the gene encoding the DExH-box helicase DHX9, underlies neurodevelopment disorders and Charcot-Marie-Tooth disease. Am J Hum Genet. 2023 ;110(8):1394-1413.
Campbell IM, Gambin T, Jhangiani S, Grove ML, Veeraraghavan N, Muzny DM, Shaw CA, Gibbs RA, Boerwinkle E, Yu F, Lupski JR. Multiallelic Positions in the Human Genome: Challenges for Genetic Analyses. Hum Mutat. 2016 ;37(3):231-234.
Campeau PM, Kim JC, Lu JT, Schwartzentruber JA, Abdul-Rahman OA, Schlaubitz S, Murdock DM, Jiang M-M, Lammer EJ, Enns GM, Rhead WJ, Rowland J, Robertson SP, Cormier-Daire V, Bainbridge MN, Yang X-J, Gingras M-C, Gibbs RA, Rosenblatt DS, Majewski J, Lee BH. Mutations in KAT6B, encoding a histone acetyltransferase, cause Genitopatellar syndrome. Am J Hum Genet. 2012 ;90(2):282-9.
Carvalho CMB, Lupski JR. Mechanisms underlying structural variant formation in genomic disorders. Nat Rev Genet. 2016 ;17(4):224-38.
Caskey JR, Wiseman RW, Karl JA, Baker DA, Lee T, Maddox RJ, Raveendran M, Harris RA, Hu J, Muzny DM, Rogers J, O'Connor DH. MHC genotyping from rhesus macaque exome sequences. Immunogenetics. 2019 ;71(8-9):531-544.
Chakraborty R, Hampton OA, Shen X, Simko SJ, Shih A, Abhyankar H, Lim KPhaik Har, Covington KR, Treviño L, Dewal N, Muzny DM, Doddapaneni H, Hu J, Wang L, Lupo PJ, M Hicks J, Bonilla DL, Dwyer KC, Berres M-L, Poulikakos PI, Merad M, McClain KL, Wheeler DA, Allen CE, D Parsons W. Mutually exclusive recurrent somatic mutations in MAP2K1 and BRAF support a central role for ERK activation in LCH pathogenesis. Blood. 2014 ;124(19):3007-15.
Chen A, Tiosano D, Guran T, Baris HN, Bayram Y, Mory A, Shapiro-Kulnane L, Hodges CA, Akdemir ZC, Turan S, Jhangiani SN, van den Akker F, Hoppel CL, Salz HK, Lupski JR, Buchner DA. Mutations in the mitochondrial ribosomal protein MRPS22 lead to primary ovarian insufficiency. Hum Mol Genet. 2018 ;27(11):1913-1926.
Chen F, Zhang Y, Varambally S, Creighton CJ. Molecular Correlates of Metastasis by Systematic Pan-Cancer Analysis Across The Cancer Genome Atlas. Mol Cancer Res. 2019 ;17(2):476-487.
Chen F, Zhang Y, Sucgang R, Ramani S, Corry D, Kheradmand F, Creighton CJ. Meta-analysis of host transcriptional responses to SARS-CoV-2 infection reveals their manifestation in human tumors. Sci Rep. 2021 ;11(1):2459.
Chen F, Zhang Y, Şenbabaoğlu Y, Ciriello G, Yang L, Reznik E, Shuch B, Micevic G, De Velasco G, Shinbrot E, Noble MS, Lu Y, Covington KR, Xi L, Drummond JA, Muzny D, Kang H, Lee J, Tamboli P, Reuter V, Shelley CSimon, Kaipparettu BA, Bottaro DP, Godwin AK, Gibbs RA, Getz G, Kucherlapati R, Park PJ, Sander C, Henske EP, Zhou JH, Kwiatkowski DJ, Ho TH, Choueiri TK, Hsieh JJ, Akbani R, Mills GB, A Hakimi A, Wheeler DA, Creighton CJ. Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma. Cell Rep. 2016 ;14(10):2476-89.