Publications

Siekierska A, Stamberger H, Deconinck T, Oprescu SN, Partoens M, Zhang Y, Sourbron J, Adriaenssens E, Mullen P, Wiencek P, Hardies K, Lee J-S, Giong H-K, Distelmaier F, Elpeleg O, Helbig KL, Hersh J, Isikay S, Jordan E, Karaca E, Kecskes A, Lupski JR, Kovacs-Nagy R, May P, Narayanan V, Pendziwiat M, Ramsey K, Rangasamy S, Shinde DN, Spiegel R, Timmerman V, von Spiczak S, Helbig I, Weckhuysen S, Francklyn C, Antonellis A, de Witte P, De Jonghe P. Biallelic VARS variants cause developmental encephalopathy with microcephaly that is recapitulated in vars knockout zebrafish. Nat Commun. 2019 ;10(1):708.

• PubMed
• DOI
• Google Scholar

Rogers J, Raveendran M, Harris RA, Mailund T, Leppälä K, Athanasiadis G, Schierup MHeide, Cheng J, Munch K, Walker JA, Konkel MK, Jordan V, Steely CJ, Beckstrom TO, Bergey C, Burrell A, Schrempf D, Noll A, Kothe M, Kopp GH, Liu Y, Murali S, Billis K, Martin FJ, Muffato M, Cox L, Else J, Disotell T, Muzny DM, Phillips-Conroy J, Aken B, Eichler EE, Marques-Bonet T, Kosiol C, Batzer MA, Hahn MW, Tung J, Zinner D, Roos C, Jolly CJ, Gibbs RA, Worley KC. The comparative genomics and complex population history of baboons. Sci Adv. 2019 ;5(1):eaau6947.

• PubMed
• DOI
• Google Scholar

Petersen M, Armisén D, Gibbs RA, Hering L, Khila A, Mayer G, Richards S, Niehuis O, Misof B. Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects. BMC Evol Biol. 2019 ;19(1):11.

• PubMed
• DOI
• Google Scholar

Vilgalys TP, Rogers J, Jolly CJ, Mukherjee S, Tung J. Evolution of DNA Methylation in Papio Baboons. Mol Biol Evol. 2019 ;36(3):527-540.

• PubMed
• DOI
• Google Scholar

Flannick J, Mercader JM, Fuchsberger C, Udler MS, Mahajan A, Wessel J, Teslovich TM, Caulkins L, Koesterer R, Barajas-Olmos F, Blackwell TW, Boerwinkle E, Brody JA, Centeno-Cruz F, Chen L, Chen S, Contreras-Cubas C, Córdova E, Correa A, Cortes M, DeFronzo RA, Dolan L, Drews KL, Elliott A, Floyd JS, Gabriel S, Garay-Sevilla MEugenia, García-Ortiz H, Gross M, Han S, Heard-Costa NL, Jackson AU, Jørgensen ME, Kang HMin, Kelsey M, Kim B-J, Koistinen HA, Kuusisto J, Leader JB, Linneberg A, Liu C-T, Liu J, Lyssenko V, Manning AK, Marcketta A, Malacara-Hernandez JManuel, Martínez-Hernández A, Matsuo K, Mayer-Davis E, Mendoza-Caamal E, Mohlke KL, Morrison AC, Ndungu A, C Y Ng M, O'Dushlaine C, Payne AJ, Pihoker C, Post WS, Preuss M, Psaty BM, Vasan RS, N Rayner W, Reiner AP, Revilla-Monsalve C, Robertson NR, Santoro N, Schurmann C, So WYee, Soberón X, Stringham HM, Strom TM, Tam CHT, Thameem F, Tomlinson B, Torres JM, Tracy RP, van Dam RM, Vujkovic M, Wang S, Welch RP, Witte DR, Wong T-Y, Atzmon G, Barzilai N, Blangero J, Bonnycastle LL, Bowden DW, Chambers JC, Chan E, Cheng C-Y, Cho YShin, Collins FS, de Vries PS, Duggirala R, Glaser B, Gonzalez C, Gonzalez MElena, Groop L, Kooner JSingh, Kwak SHeon, Laakso M, Lehman DM, Nilsson P, Spector TD, E Tai S, Tuomi T, Tuomilehto J, Wilson JG, Aguilar-Salinas CA, Bottinger E, Burke B, Carey DJ, Chan JCN, Dupuis J, Frossard P, Heckbert SR, Hwang MYeong, Kim YJin, H Kirchner L, Lee J-Y, Lee J, Loos RJF, Ma RCW, Morris AD, O'Donnell CJ, Palmer CNA, Pankow J, Park KSoo, Rasheed A, Saleheen D, Sim X, Small KS, Teo YYing, Haiman C, Hanis CL, Henderson BE, Orozco L, Tusie-Luna T, Dewey FE, Baras A, Gieger C, Meitinger T, Strauch K, Lange L, Grarup N, Hansen T, Pedersen O, Zeitler P, Dabelea D, Abecasis G, Bell GI, Cox NJ, Seielstad M, Sladek R, Meigs JB, Rich SS, Rotter JI, Altshuler D, Burtt NP, Scott LJ, Morris AP, Florez JC, McCarthy MI, Boehnke M. Exome sequencing of 20,791 cases of type 2 diabetes and 24,440 controls. Nature. 2019 ;570(7759):71-76.

• PubMed
• DOI
• Google Scholar

Oak N, Ghosh R, Huang K-L, Wheeler DA, Ding L, Plon SE. Framework for microRNA variant annotation and prioritization using human population and disease datasets. Hum Mutat. 2019 ;40(1):73-89.

• PubMed
• DOI
• Google Scholar

Zaneveld SAgrawal, Eblimit A, Liang Q, Bertrand R, Wu N, Liu H, Nguyen Q, Zaneveld J, Wang K, Li Y, Chen R. Gene Therapy Rescues Retinal Degeneration in Receptor Expression-Enhancing Protein 6 Mutant Mice. Hum Gene Ther. 2019 ;30(3):302-315.

• PubMed
• DOI
• Google Scholar

Li AH, Hanchard NA, Azamian M, D'Alessandro LCA, Coban-Akdemir Z, Lopez KN, Hall NJ, Dickerson H, Nicosia A, Fernbach S, Boone PM, Gambin T, Karaca E, Gu S, Yuan B, Jhangiani SN, Doddapaneni H, Hu J, Dinh H, Jayaseelan J, Muzny DM, Lalani S, Towbin J, Penny D, Fraser C, Martin J, Lupski JR, Gibbs RA, Boerwinkle E, Ware SM, Belmont JW. Genetic architecture of laterality defects revealed by whole exome sequencing. Eur J Hum Genet. 2019 ;27(4):563-573.

• PubMed
• DOI
• Google Scholar

Dennenmoser S, Sedlazeck FJ, Schatz MC, Altmüller J, Zytnicki M, Nolte AW. Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish. Mol Ecol. 2019 ;28(6):1491-1505.

• PubMed
• DOI
• Google Scholar

Rokita JLynne, Rathi KS, Cardenas MF, Upton KA, Jayaseelan J, Cross KL, Pfeil J, Egolf LE, Way GP, Farrel A, Kendsersky NM, Patel K, Gaonkar KS, Modi A, Berko ER, Lopez G, Vaksman Z, Mayoh C, Nance J, McCoy K, Haber M, Evans K, McCalmont H, Bendak K, Böhm JW, Marshall GM, Tyrrell V, Kalletla K, Braun FK, Qi L, Du Y, Zhang H, Lindsay HB, Zhao S, Shu J, Baxter P, Morton C, Kurmashev D, Zheng S, Chen Y, Bowen J, Bryan AC, Leraas KM, Coppens SE, Doddapaneni H, Momin Z, Zhang W, Sacks GI, Hart LS, Krytska K, Mosse YP, Gatto GJ, Sanchez Y, Greene CS, Diskin SJ, Vaske OMorozova, Haussler D, Gastier-Foster JM, E Kolb A, Gorlick R, Li X-N, C Reynolds P, Kurmasheva RT, Houghton PJ, Smith MA, Lock RB, Raman P, Wheeler DA, Maris JM. Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design. Cell Rep. 2019 ;29(6):1675-1689.e9.

• PubMed
• DOI
• Google Scholar

Fischer J, Higham JP, Alberts SC, Barrett L, Beehner JC, Bergman TJ, Carter AJ, Collins A, Elton S, Fagot J, da Silva MJoana Ferr, Hammerschmidt K, Henzi P, Jolly CJ, Knauf S, Kopp GH, Rogers J, Roos C, Ross C, Seyfarth RM, Silk J, Snyder-Mackler N, Staedele V, Swedell L, Wilson ML, Zinner D. Insights into the evolution of social systems and species from baboon studies. Elife. 2019 ;8.

• PubMed
• DOI
• Google Scholar

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.

• PubMed
• DOI
• Google Scholar

Panfilio KA, Jentzsch IMVargas, Benoit JB, Erezyilmaz D, Suzuki Y, Colella S, Robertson HM, Poelchau MF, Waterhouse RM, Ioannidis P, Weirauch MT, Hughes DST, Murali SC, Werren JH, Jacobs CGC, Duncan EJ, Armisén D, Vreede BMI, Baa-Puyoulet P, Berger CS, Chang C-C, Chao H, Chen M-JM, Chen Y-T, Childers CP, Chipman AD, Cridge AG, Crumière AJJ, Dearden PK, Didion EM, Dinh H, Doddapaneni H, Dolan A, Dugan S, Extavour CG, Febvay G, Friedrich M, Ginzburg N, Han Y, Heger P, Holmes CJ, Horn T, Hsiao Y-M, Jennings EC, J Johnston S, Jones TE, Jones JW, Khila A, Koelzer S, Kovacova V, Leask M, Lee SL, Lee C-Y, Lovegrove MR, Lu H-L, Lu Y, Moore PJ, Munoz-Torres MC, Muzny DM, Palli SR, Parisot N, Pick L, Porter ML, Qu J, Refki PN, Richter R, Rivera-Pomar R, Rosendale AJ, Roth S, Sachs L, M Santos E, Seibert J, Sghaier E, Shukla JN, Stancliffe RJ, Tidswell O, Traverso L, Van der Zee M, Viala S, Worley KC, Zdobnov EM, Gibbs RA, Richards S. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. Genome Biol. 2019 ;20(1):64.

• PubMed
• DOI
• Google Scholar

Link N, Chung H, Jolly A, Withers M, Tepe B, Arenkiel BR, Shah PS, Krogan NJ, Aydin H, Geckinli BB, Tos T, Isikay S, Tuysuz B, Mochida GH, Thomas AX, Clark RD, Mirzaa GM, Lupski JR, Bellen HJ. Mutations in ANKLE2, a ZIKA Virus Target, Disrupt an Asymmetric Cell Division Pathway in Drosophila Neuroblasts to Cause Microcephaly. Dev Cell. 2019 ;51(6):713-729.e6.

• PubMed
• DOI
• Google Scholar

Moshiri A, Chen R, Kim S, Harris RA, Li Y, Raveendran M, Davis S, Liang Q, Pomerantz O, Wang J, Garzel L, Cameron A, Yiu G, J Stout T, Huang Y, Murphy CJ, Roberts J, Gopalakrishna KN, Boyd K, Artemyev NO, Rogers J, Thomasy SM. A nonhuman primate model of inherited retinal disease. J Clin Invest. 2019 ;129(2):863-874.

• PubMed
• DOI
• Google Scholar

Lam MT, Coppola S, Krumbach OHF, Prencipe G, Insalaco A, Cifaldi C, Brigida I, Zara E, Scala S, Di Cesare S, Martinelli S, Di Rocco M, Pascarella A, Niceta M, Pantaleoni F, Ciolfi A, Netter P, Carisey AF, Diehl M, Akbarzadeh M, Conti F, Merli P, Pastore A, Mortera SLevi, Camerini S, Farina L, Buchholzer M, Pannone L, Cao TN, Coban-Akdemir ZH, Jhangiani SN, Muzny DM, Gibbs RA, Basso-Ricci L, Chiriaco M, Dvorsky R, Putignani L, Carsetti R, Janning P, Stray-Pedersen A, Erichsen HChristian, Horne AC, Bryceson YT, Torralba-Raga L, Ramme K, Rosti V, Bracaglia C, Messia V, Palma P, Finocchi A, Locatelli F, Chinn IK, Lupski JR, Mace EM, Cancrini C, Aiuti A, Ahmadian MR, Orange JS, De Benedetti F, Tartaglia M. A novel disorder involving dyshematopoiesis, inflammation, and HLH due to aberrant CDC42 function. J Exp Med. 2019 ;216(12):2778-2799.

• PubMed
• DOI
• Google Scholar

Justice AE, Karaderi T, Highland HM, Young KL, Graff M, Lu Y, Turcot V, Auer PL, Fine RS, Guo X, Schurmann C, Lempradl A, Marouli E, Mahajan A, Winkler TW, Locke AE, Medina-Gomez C, Esko T, Vedantam S, Giri A, Lo KSin, Alfred T, Mudgal P, C Y Ng M, Heard-Costa NL, Feitosa MF, Manning AK, Willems SM, Sivapalaratnam S, Abecasis G, Alam DS, Allison M, Amouyel P, Arzumanyan Z, Balkau B, Bastarache L, Bergmann S, Bielak LF, Blüher M, Boehnke M, Boeing H, Boerwinkle E, Böger CA, Bork-Jensen J, Bottinger EP, Bowden DW, Brandslund I, Broer L, Burt AA, Butterworth AS, Caulfield MJ, Cesana G, Chambers JC, Chasman DI, Chen Y-DIda, Chowdhury, iv R, Christensen C, Chu AY, Collins FS, Cook JP, Cox AJ, Crosslin DS, Danesh J, de Bakker PIW, de Denus S, de Mutsert R, Dedoussis G, Demerath EW, Dennis JG, Denny JC, Di Angelantonio E, Dörr M, Drenos F, Dube M-P, Dunning AM, Easton DF, Elliott P, Evangelou E, Farmaki A-E, Feng S, Ferrannini E, Ferrieres J, Florez JC, Fornage M, Fox CS, Franks PW, Friedrich N, Gan W, Gandin I, Gasparini P, Giedraitis V, Girotto G, Gorski M, Grallert H, Grarup N, Grove ML, Gustafsson S, Haessler J, Hansen T, Hattersley AT, Hayward C, Heid IM, Holmen OL, G Hovingh K, Howson JMM, Hu Y, Hung Y-J, Hveem K, M Ikram A, Ingelsson E, Jackson AU, Jarvik GP, Jia Y, Jørgensen T, Jousilahti P, Justesen JM, Kahali B, Karaleftheri M, Kardia SLR, Karpe F, Kee F, Kitajima H, Komulainen P, Kooner JS, Kovacs P, Krämer BK, Kuulasmaa K, Kuusisto J, Laakso M, Lakka TA, Lamparter D, Lange LA, Langenberg C, Larson EB, Lee NR, Lee W-J, Lehtimäki T, Lewis CE, Li H, Li J, Li-Gao R, Lin L-A, Lin X, Lind L, Lindström J, Linneberg A, Liu C-T, Liu DJ, Luan J'an, Lyytikäinen L-P, MacGregor S, Mägi R, Männistö S, Marenne G, Marten J, Masca NGD, McCarthy MI, Meidtner K, Mihailov E, Moilanen L, Moitry M, Mook-Kanamori DO, Morgan A, Morris AP, Müller-Nurasyid M, Munroe PB, Narisu N, Nelson CP, Neville M, Ntalla I, O'Connell JR, Owen KR, Pedersen O, Peloso GM, Pennell CE, Perola M, Perry JA, Perry JRB, Pers TH, Ewing A, Polasek O, Raitakari OT, Rasheed A, Raulerson CK, Rauramaa R, Reilly DF, Reiner AP, Ridker PM, Rivas MA, Robertson NR, Robino A, Rudan I, Ruth KS, Saleheen D, Salomaa V, Samani NJ, Schreiner PJ, Schulze MB, Scott RA, Segura-Lepe M, Sim X, Slater AJ, Small KS, Smith BH, Smith JA, Southam L, Spector TD, Speliotes EK, Stefansson K, Steinthorsdottir V, Stirrups KE, Strauch K, Stringham HM, Stumvoll M, Sun L, Surendran P, Swart KMA, Tardif J-C, Taylor KD, Teumer A, Thompson DJ, Thorleifsson G, Thorsteinsdottir U, Thuesen BH, Tonjes A, Torres M, Tsafantakis E, Tuomilehto J, Uitterlinden AG, Uusitupa M, van Duijn CM, Vanhala M, Varma R, Vermeulen SH, Vestergaard H, Vitart V, Vogt TF, Vuckovic D, Wagenknecht LE, Walker M, Wallentin L, Wang F, Wang CA, Wang S, Wareham NJ, Warren HR, Waterworth DM, Wessel J, White HD, Willer CJ, Wilson JG, Wood AR, Wu Y, Yaghootkar H, Yao J, Yerges-Armstrong LM, Young R, Zeggini E, Zhan X, Zhang W, Zhao JHua, Zhao W, Zheng H, Zhou W, M Zillikens C, Rivadeneira F, Borecki IB, J Pospisilik A, Deloukas P, Frayling TM, Lettre G, Mohlke KL, Rotter JI, Kutalik Z, Hirschhorn JN, L Cupples A, Loos RJF, North KE, Lindgren CM. Protein-coding variants implicate novel genes related to lipid homeostasis contributing to body-fat distribution. Nat Genet. 2019 ;51(3):452-469.

• PubMed
• DOI
• Google Scholar

Mahmoud M, Gobet N, Cruz-Dávalos DIvette, Mounier N, Dessimoz C, Sedlazeck FJ. Structural variant calling: the long and the short of it. Genome Biol. 2019 ;20(1):246.

• PubMed
• DOI
• Google Scholar

Liu J, Wu N, Yang N, Takeda K, Chen W, Li W, Du R, Liu S, Zhou Y, Zhang L, Liu Z, Zuo Y, Zhao S, Blank R, Pehlivan D, Dong S, Zhang J, Shen J, Si N, Wang Y, Liu G, Li S, Zhao Y, Zhao H, Chen Y, Zhao Y, Song X, Hu J, Lin M, Tian Y, Yuan B, Yu K, Niu Y, Yu B, Li X, Chen J, Yan Z, Zhu Q, Meng X, Chen X, Su J, Zhao X, Wang X, Ming Y, Li X, Raggio CL, Zhang B, Weng X, Zhang S, Zhang X, Watanabe K, Matsumoto M, Jin L, Shen Y, Sobreira NL, Posey JE, Giampietro PF, Valle D, Liu P, Wu Z, Ikegawa S, Lupski JR, Zhang F, Qiu G. TBX6-associated congenital scoliosis (TACS) as a clinically distinguishable subtype of congenital scoliosis: further evidence supporting the compound inheritance and TBX6 gene dosage model. Genet Med. 2019 ;21(7):1548-1558.

• PubMed
• DOI
• Google Scholar

Park YH, Snook JD, Ostrin EJ, Kim S, Chen R, Frankfort BJ. Transcriptomic profiles of retinal ganglion cells are defined by the magnitude of intraocular pressure elevation in adult mice. Sci Rep. 2019 ;9(1):2594.

• PubMed
• DOI
• Google Scholar

Yee SWah, Stecula A, Chien H-C, Zou L, Feofanova EV, van Borselen M, Cheung KWun Kathy, Yousri NA, Suhre K, Kinchen JM, Boerwinkle E, Irannejad R, Yu B, Giacomini KM. Unraveling the functional role of the orphan solute carrier, SLC22A24 in the transport of steroid conjugates through metabolomic and genome-wide association studies. PLoS Genet. 2019 ;15(9):e1008208.

• PubMed
• DOI
• Google Scholar

Rogers J. Adding resolution and dimensionality to comparative genomics: moving from reference genomes to clade genomics. Genome Biol. 2018 ;19(1):115.

• PubMed
• DOI
• Google Scholar

Joganic JL, Willmore KE, Richtsmeier JT, Weiss KM, Mahaney MC, Rogers J, Cheverud JM. Additive genetic variation in the craniofacial skeleton of baboons (genus Papio) and its relationship to body and cranial size. Am J Phys Anthropol. 2018 ;165(2):269-285.

• PubMed
• DOI
• Google Scholar

Rogers J. The behavioral genetics of nonhuman primates: Status and prospects. Am J Phys Anthropol. 2018 ;165 Suppl 65:23-36.

• PubMed
• DOI
• Google Scholar

Dinckan N, Du R, Akdemir ZC, Bayram Y, Jhangiani SN, Doddapaneni H, Hu J, Muzny DM, Guven Y, Aktoren O, Kayserili H, Boerwinkle E, Gibbs RA, Posey JE, Lupski JR, Uyguner ZO, Letra A. A biallelic ANTXR1 variant expands the anthrax toxin receptor associated phenotype to tooth agenesis. Am J Med Genet A. 2018 ;176(4):1015-1022.

• PubMed
• DOI
• Google Scholar