Publications

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Journal Article
Atkinson EG, Rogers J, Mahaney MC, Cox LA, Cheverud JM. Cortical Folding of the Primate Brain: An Interdisciplinary Examination of the Genetic Architecture, Modularity, and Evolvability of a Significant Neurological Trait in Pedigreed Baboons (Genus Papio). Genetics. 2015 ;200(2):651-65.
Eblimit A, Agrawal SA, Thomas K, Anastassov IA, Abulikemu T, Moayedi Y, Mardon G, Chen R. Corrigendum to "Conditional loss of Spata7 in photoreceptors causes progressive retinal degeneration in mice" [Exp. Eye Res. 166 (2018) 120-130]. Exp Eye Res. 2018 ;171:119.
Chen N, Caruso C, Alonso A, Derebail VK, Kshirsagar AV, A Sharrett R, Key NS, Gottesman RF, Grove ML, Bressler J, Boerwinkle E, B Windham G, Mosley TH, Hyacinth HI. Corrigendum to 'Association of sickle cell trait with measures of cognitive function and dementia in African Americans' Vol. 16 (2019), 100,201. eNeurologicalSci. 2020 ;21:100281.
Bis JC, Jian X, Kunkle BW, Chen Y, Hamilton-Nelson KL, Bush WS, Salerno WJ, Lancour D, Ma Y, Renton AE, Marcora E, Farrell JJ, Zhao Y, Qu L, Ahmad S, Amin N, Amouyel P, Beecham GW, Below JE, Campion D, Cantwell L, Charbonnier C, Chung J, Crane PK, Cruchaga C, L Cupples A, Dartigues J-F, Debette S, Deleuze J-F, Fulton L, Gabriel SB, Genin E, Gibbs RA, Goate A, Grenier-Boley B, Gupta N, Haines JL, Havulinna AS, Helisalmi S, Hiltunen M, Howrigan DP, M Ikram A, Kaprio J, Konrad J, Kuzma A, Lander ES, Lathrop M, Lehtimäki T, Lin H, Mattila K, Mayeux R, Muzny DM, Nasser W, Neale B, Nho K, Nicolas G, Patel D, Pericak-Vance MA, Perola M, Psaty BM, Quenez O, Rajabli F, Redon R, Reitz C, Remes AM, Salomaa V, Sarnowski C, Schmidt H, Schmidt M, Schmidt R, Soininen H, Thornton TA, Tosto G, Tzourio C, van der Lee SJ, van Duijn CM, Valladares O, Vardarajan B, San Wang L-, Wang W, Wijsman E, Wilson RK, Witten D, Worley KC, Zhang X, Bellenguez C, Lambert J-C, Kurki MI, Palotie A, Daly M, Boerwinkle E, Lunetta KL, DeStefano AL, Dupuis J, Martin ER, Schellenberg GD, Seshadri S, Naj AC, Fornage M, Farrer LA. Correction: Whole exome sequencing study identifies novel rare and common Alzheimer's-Associated variants involved in immune response and transcriptional regulation. Mol Psychiatry. 2020 ;25(8):1901-1903.
Rotenberg D, Baumann AA, Ben-Mahmoud S, Christiaens O, Dermauw W, Ioannidis P, Jacobs CGC, Jentzsch IMVargas, Oliver JE, Poelchau MF, Rajarapu SPriya, Schneweis DJ, Snoeck S, Taning CNT, Wei D, Gamage SMKWidana, Hughes DST, Murali SC, Bailey ST, Bejerman NE, Holmes CJ, Jennings EC, Rosendale AJ, Rosselot A, Hervey K, Schneweis BA, Cheng S, Childers C, Simão FA, Dietzgen RG, Chao H, Dinh H, Doddapaneni H, Dugan S, Han Y, Lee SL, Muzny DM, Qu J, Worley KC, Benoit JB, Friedrich M, Jones JW, Panfilio KA, Park Y, Robertson HM, Smagghe G, Ullman DE, Van der Zee M, Van Leeuwen T, Veenstra JA, Waterhouse RM, Weirauch MT, Werren JH, Whitfield AE, Zdobnov EM, Gibbs RA, Richards S. Correction to: Genome-enabled insights into the biology of thrips as crop pests. BMC Biol. 2020 ;18(1):169.
Petersen M, Armisén D, Gibbs RA, Hering L, Khila A, Mayer G, Richards S, Niehuis O, Misof B. Correction to: Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects. BMC Ecol Evol. 2021 ;21(1):146.
Vetrini F, McKee S, Rosenfeld JA, Suri M, Lewis AM, Nugent KMargaret, Roeder E, Littlejohn RO, Holder S, Zhu W, Alaimo JT, Graham B, Harris JM, Gibson JB, Pastore M, McBride KL, Komara M, Al-Gazali L, Shamsi AAl, Fanning EA, Wierenga KJ, Scott DA, Ben-Neriah Z, Meiner V, Cassuto H, Elpeleg O, J Holder L, Burrage LC, Seaver LH, Van Maldergem L, Mahida S, Soul JS, Marlatt M, Matyakhina L, Vogt J, Gold J-A, Park S-M, Varghese V, Lampe AK, Kumar A, Lees M, Holder-Espinasse M, McConnell V, Bernhard B, Blair E, Harrison V, Muzny DM, Gibbs RA, Elsea SH, Posey JE, Bi W, Lalani S, Xia F, Yang Y, Eng CM, Lupski JR, Liu P. Correction to: De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith-Magenis syndrome. Genome Med. 2019 ;11(1):16.
Bozkurt-Yozgatli T, Pehlivan D, Gibbs RA, Sezerman U, Posey JE, Lupski JR, Coban-Akdemir Z. Correction: Multilocus pathogenic variants contribute to intrafamilial clinical heterogeneity: a retrospective study of sibling pairs with neurodevelopmental disorders. BMC Med Genomics. 2024 ;17(1):201.
Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, Singh S, Thevasagayam NM, Prakki SRama Srida, Purushothaman K, Saju JM, Jiang J, Mbandi SKimbung, Jonas M, Tong AHin Yan, Mwangi S, Lau D, Ngoh SYan, Liew WChang, Shen X, Hon LS, Drake JP, Boitano M, Hall R, Chin C-S, Lachumanan R, Korlach J, Trifonov V, Kabilov M, Tupikin A, Green D, Moxon S, Garvin T, Sedlazeck FJ, Vurture GW, Gopalapillai G, Katneni VKumar, Noble TH, Scaria V, Sivasubbu S, Jerry DR, O'Brien SJ, Schatz MC, Dalmay T, Turner SW, Lok S, Christoffels A, Orbán L. Correction: Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genet. 2016 ;12(12):e1006500.
Bressler J, Davies G, Smith AV, Saba Y, Bis JC, Jian X, Hayward C, Yanek L, Smith JA, Mirza SS, Wang R, Adams HHH, Becker D, Boerwinkle E, Campbell A, Cox SR, Eiriksdottir G, Fawns-Ritchie C, Gottesman RF, Grove ML, Guo X, Hofer E, Kardia SLR, Knol MJ, Koini M, Lopez OL, Marioni RE, Nyquist P, Pattie A, Polasek O, Porteous DJ, Rudan I, Satizabal CL, Schmidt H, Schmidt R, Sidney S, Simino J, Smith BH, Turner ST, van der Lee SJ, Ware EB, Whitmer RA, Yaffe K, Yang Q, Zhao W, Gudnason V, Launer LJ, Fitzpatrick AL, Psaty BM, Fornage M, M Ikram A, van Duijn CM, Seshadri S, Mosley TH, Deary IJ. Correction: Association of low-frequency and rare coding variants with information processing speed. Transl Psychiatry. 2022 ;12(1):88.
Polfus LM, Gibbs RA, Boerwinkle E. Coronary heart disease and genetic variants with low phospholipase A2 activity. N Engl J Med. 2015 ;372(3):295-6.
Machol K, Jain M, Almannai M, Orand T, Lu JT, Tran A, Chen Y, Schlesinger A, Gibbs RA, Bonafe L, Campos-Xavier ABelinda, Unger S, Superti-Furga A, Lee BH, Campeau PM, Burrage LC. Corner fracture type spondylometaphyseal dysplasia: Overlap with type II collagenopathies. Am J Med Genet A. 2017 ;173(3):733-739.
Feng X, Ye Y, Zhang J, Zhang Y, Zhao S, Mak JCW, Otomo N, Zhao Z, Niu Y, Yonezawa Y, Li G, Lin M, Li X, Cheung PWing Hang, Xu K, Takeda K, Wang S, Xie J, Kotani T, Choi VNT, Song Y-Q, Yang Y, Luk KDip Kei, Lee KShing, Li Z, Li PShan, Leung CYH, Lin X, Wang X, Qiu G, Watanabe K, Wu Z, Posey JE, Ikegawa S, Lupski JR, Cheung JPui Yin, Zhang TJianguo, Gao B, Wu N. Core planar cell polarity genes and in predisposition to congenital vertebral malformations. Proc Natl Acad Sci U S A. 2024 ;121(18):e2310283121.
Lindstrand A, Frangakis S, Carvalho CMB, Richardson EB, McFadden KA, Willer JR, Pehlivan D, Liu P, Pediaditakis IL, Sabo A, Lewis RAlan, Banin E, Lupski JR, Davis EE, Katsanis N. Copy-Number Variation Contributes to the Mutational Load of Bardet-Biedl Syndrome. Am J Hum Genet. 2016 ;99(2):318-36.
Degenhardt JD, de Candia P, Chabot A, Schwartz S, Henderson L, Ling B, Hunter M, Jiang Z, Palermo RE, Katze M, Eichler EE, Ventura M, Rogers J, Marx P, Gilad Y, Bustamante CD. Copy number variation of CCL3-like genes affects rate of progression to simian-AIDS in Rhesus Macaques (Macaca mulatta). PLoS Genet. 2009 ;5(1):e1000346.
Xi R, Hadjipanayis AG, Luquette LJ, Kim T-M, Lee E, Zhang J, Johnson MD, Muzny DM, Wheeler DA, Gibbs RA, Kucherlapati R, Park PJ. Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. Proc Natl Acad Sci U S A. 2011 ;108(46):E1128-36.
Brasó-Vives M, Povolotskaya IS, Hartasánchez DA, Farré X, Fernandez-Callejo M, Raveendran M, Harris RA, Rosene DL, Lorente-Galdos B, Navarro A, Marques-Bonet T, Rogers J, Juan D. Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta). PLoS Genet. 2020 ;16(5):e1008742.
Dharmadhikari AV, Ghosh R, Yuan B, Liu P, Dai H, Masri SAl, Scull J, Posey JE, Jiang AH, He W, Vetrini F, Braxton AA, Ward P, Chiang T, Qu C, Gu S, Shaw CA, Smith JL, Lalani S, Stankiewicz P, Cheung S-W, Bacino CA, Patel A, Breman AM, Wang X, Meng L, Xiao R, Xia F, Muzny DM, Gibbs RA, Beaudet AL, Eng CM, Lupski JR, Yang Y, Bi W. Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases. Genome Med. 2019 ;11(1):30.
Dennenmoser S, Sedlazeck FJ, Iwaszkiewicz E, Li X-Y, Altmüller J, Nolte AW. Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin. Mol Ecol. 2017 ;26(18):4712-4724.
Yuan B, Liu P, Rogers J, Lupski JR. Copy number analysis of the low-copy repeats at the primate NPHP1 locus by array comparative genomic hybridization. Genom Data. 2016 ;8:106-9.
Marom R, Burrage LC, Venditti R, Clément A, Blanco-Sánchez B, Jain M, Scott DA, Rosenfeld JA, V Sutton R, Shinawi M, Mirzaa G, DeVile C, Roberts R, Calder AD, Allgrove J, Grafe I, Lanza DG, Li X, Joeng KSang, Lee Y-C, Song I-W, Sliepka JM, Batkovskyte D, Washington M, Dawson BC, Jin Z, Jiang M-M, Chen S, Chen Y, Tran AA, Emrick LT, Murdock DR, Hanchard NA, Zapata GE, Mehta NR, Weis MAnn, Scott AA, Tremp BA, Phillips JB, Wegner J, Taylor-Miller T, Gibbs RA, Muzny DM, Jhangiani SN, Hicks J, Stottmann RW, Dickinson ME, Seavitt JR, Heaney JD, Eyre DR, Westerfield M, De Matteis MAntonietta, Lee B. COPB2 loss of function causes a coatopathy with osteoporosis and developmental delay. Am J Hum Genet. 2021 ;108(9):1710-1724.
Watkin LB, Jessen B, Wiszniewski W, Vece TJ, Jan M, Sha Y, Thamsen M, Santos-Cortez RLP, Lee K, Gambin T, Forbes LR, Law CS, Stray-Pedersen A, Cheng MH, Mace EM, Anderson MS, Liu D, Tang LFung, Nicholas SK, Nahmod K, Makedonas G, Canter DL, Kwok P-Y, Hicks J, Jones KD, Penney S, Jhangiani SN, Rosenblum MD, Dell SD, Waterfield MR, Papa FR, Muzny DM, Zaitlen N, Leal SM, Gonzaga-Jauregui C, Boerwinkle E, N Eissa T, Gibbs RA, Lupski JR, Orange JS, Shum AK. COPA mutations impair ER-Golgi transport and cause hereditary autoimmune-mediated lung disease and arthritis. Nat Genet. 2015 ;47(6):654-60.
Foote AD, Liu Y, Thomas GWC, Vinar T, Alföldi J, Deng J, Dugan S, van Elk CE, Hunter ME, Joshi V, Khan Z, Kovar C, Lee SL, Lindblad-Toh K, Mancia A, Nielsen R, Qin X, Qu J, Raney BJ, Vijay N, Wolf JBW, Hahn MW, Muzny DM, Worley KC, M Gilbert TP, Gibbs RA. Convergent evolution of the genomes of marine mammals. Nat Genet. 2015 ;47(3):272-5.
Nandakumar P, Morrison AC, Grove ML, Boerwinkle E, Chakravarti A. Contributions of rare coding variants in hypotension syndrome genes to population blood pressure variation. Medicine (Baltimore). 2018 ;97(33):e11865.
Wang L, Liu P, Bi W, Sim T, Wang X, Walkiewicz M, Leduc MSophie, Meng L, Xia F, Eng CM, Yang Y, Yuan B, Dai H. Contribution of uniparental disomy in a clinical trio exome cohort of 2675 patients. Mol Genet Genomic Med. 2021 ;9(11):e1792.