Publications

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2016
Vetrini F, D'Alessandro LCA, Akdemir ZC, Braxton A, Azamian MS, Eldomery MK, Miller K, Kois C, Sack V, Shur N, Rijhsinghani A, Chandarana J, Ding Y, Holtzman J, Jhangiani SN, Muzny DM, Gibbs RA, Eng CM, Hanchard NA, Harel T, Rosenfeld JA, Belmont JW, Lupski JR, Yang Y. Bi-allelic Mutations in PKD1L1 Are Associated with Laterality Defects in Humans. Am J Hum Genet. 2016 ;99(4):886-893.
Chitsazzadeh V, Coarfa C, Drummond JA, Nguyen T, Joseph A, Chilukuri S, Charpiot E, Adelmann CH, Ching G, Nguyen TN, Nicholas C, Thomas VD, Migden M, MacFarlane D, Thompson E, Shen J, Takata Y, McNiece K, Polansky MA, Abbas HA, Rajapakshe K, Gower A, Spira A, Covington KR, Xiao W, Gunaratne P, Pickering C, Frederick M, Myers JN, Shen L, Yao H, Su X, Rapini RP, Wheeler DA, Hawk ET, Flores ER, Tsai KY. Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates. Nat Commun. 2016 ;7:12601.
Aken BL, Ayling S, Barrell D, Clarke L, Curwen V, Fairley S, Banet JFernandez, Billis K, Girón CGarcía, Hourlier T, Howe K, Kähäri A, Kokocinski F, Martin FJ, Murphy DN, Nag R, Ruffier M, Schuster M, Y Tang A, Vogel J-H, White S, Zadissa A, Flicek P, Searle SMJ. The Ensembl gene annotation system. Database (Oxford). 2016 ;2016.
Tsang YHuen, Dogruluk T, Tedeschi PM, Wardwell-Ozgo J, Lu H, Espitia M, Nair N, Minelli R, Chong Z, Chen F, Chang QEdward, Dennison JB, Dogruluk A, Li M, Ying H, Bertino JR, Gingras M-C, Ittmann M, Kerrigan J, Chen K, Creighton CJ, Eterovic K, Mills GB, Scott KL. Functional annotation of rare gene aberration drivers of pancreatic cancer. Nat Commun. 2016 ;7:10500.
Bailey P, Chang DK, Nones K, Johns AL, Patch A-M, Gingras M-C, Miller DK, Christ AN, Bruxner TJC, Quinn MC, Nourse C, L Murtaugh C, Harliwong I, Idrisoglu S, Manning S, Nourbakhsh E, Wani S, Fink L, Holmes O, Chin V, Anderson MJ, Kazakoff S, Leonard C, Newell F, Waddell N, Wood S, Xu Q, Wilson PJ, Cloonan N, Kassahn KS, Taylor D, Quek K, Robertson A, Pantano L, Mincarelli L, Sanchez LN, Evers L, Wu J, Pinese M, Cowley MJ, Jones MD, Colvin EK, Nagrial AM, Humphrey ES, Chantrill LA, Mawson A, Humphris J, Chou A, Pajic M, Scarlett CJ, Pinho AV, Giry-Laterriere M, Rooman I, Samra JS, Kench JG, Lovell JA, Merrett ND, Toon CW, Epari K, Nguyen NQ, Barbour A, Zeps N, Moran-Jones K, Jamieson NB, Graham JS, Duthie F, Oien K, Hair J, Grützmann R, Maitra A, Iacobuzio-Donahue CA, Wolfgang CL, Morgan RA, Lawlor RT, Corbo V, Bassi C, Rusev B, Capelli P, Salvia R, Tortora G, Mukhopadhyay D, Petersen GM, Munzy DM, Fisher WE, Karim SA, Eshleman JR, Hruban RH, Pilarsky C, Morton JP, Sansom OJ, Scarpa A, Musgrove EA, Bailey U-MHagbo, Hofmann O, Sutherland RL, Wheeler DA, Gill AJ, Gibbs RA, Pearson JV, Waddell N, Biankin AV, Grimmond SM. Genomic analyses identify molecular subtypes of pancreatic cancer. Nature. 2016 ;531(7592):47-52.
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.
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.
Xu M, Yamada T, Sun Z, Eblimit A, Lopez I, Wang F, Manya H, Xu S, Zhao L, Li Y, Kimchi A, Sharon D, Sui R, Endo T, Koenekoop RK, Chen R. Mutations in POMGNT1 cause non-syndromic retinitis pigmentosa. Hum Mol Genet. 2016 ;25(8):1479-88.
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.
Bissig-Choisat B, Kettlun-Leyton C, Legras XD, Zorman B, Barzi M, Chen LL, Amin MD, Huang Y-H, Pautler RG, Hampton OA, Prakash MM, Yang D, Borowiak M, Muzny DM, Doddapaneni H, Hu J, Shi Y, M Gaber W, M Hicks J, Thompson PA, Lu Y, Mills GB, Finegold M, Goss JA, D Parsons W, Vasudevan SA, Sumazin P, López-Terrada D, Bissig K-D. Novel patient-derived xenograft and cell line models for therapeutic testing of pediatric liver cancer. J Hepatol. 2016 ;65(2):325-33.
Zhang K, Gao M, Chong Z, Li Y, Han X, Chen R, Qin L. Single-cell isolation by a modular single-cell pipette for RNA-sequencing. Lab Chip. 2016 ;16(24):4742-4748.
2017
Chen Y, Bartanus J, Liang D, Zhu H, Breman AM, Smith JL, Wang H, Ren Z, Patel A, Stankiewicz P, Cram DS, Cheung SWai, Wu L, Yu F. Characterization of chromosomal abnormalities in pregnancy losses reveals critical genes and loci for human early development. Hum Mutat. 2017 ;38(6):669-677.
Lu H-C, Tan Q, Rousseaux MWC, Wang W, Kim J-Y, Richman R, Wan Y-W, Yeh S-Y, Patel JM, Liu X, Lin T, Lee Y, Fryer JD, Han J, Chahrour M, Finnell RH, Lei Y, Zurita-Jimenez ME, Ahimaz P, Anyane-Yeboa K, Van Maldergem L, Lehalle D, Jean-Marcais N, Mosca-Boidron A-L, Thevenon J, Cousin MA, Bro DE, Lanpher BC, Klee EW, Alexander N, Bainbridge MN, Orr HT, Sillitoe RV, M Ljungberg C, Liu Z, Schaaf CP, Zoghbi HY. Disruption of the ATXN1-CIC complex causes a spectrum of neurobehavioral phenotypes in mice and humans. Nat Genet. 2017 ;49(4):527-536.
Wang X, Charng W-L, Chen C-A, Rosenfeld JA, Shamsi AAl, Al-Gazali L, McGuire M, Mew NAh, Arnold GL, Qu C, Ding Y, Muzny DM, Gibbs RA, Eng CM, Walkiewicz M, Xia F, Plon SE, Lupski JR, Schaaf CP, Yang Y. Germline mutations in ABL1 cause an autosomal dominant syndrome characterized by congenital heart defects and skeletal malformations. Nat Genet. 2017 ;49(4):613-617.
Worley KC. A golden goat genome. Nat Genet. 2017 ;49(4):485-486.
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.
Xu M, Xie YAngela, Abouzeid H, Gordon CT, Fiorentino A, Sun Z, Lehman A, Osman IS, Dharmat R, Riveiro-Álvarez R, Bapst-Wicht L, Babino D, Arno G, Busetto V, Zhao L, Li H, Lopez-Martinez MA, Azevedo LF, Hubert L, Pontikos N, Eblimit A, Lorda-Sanchez I, Kheir V, Plagnol V, Oufadem M, Soens ZT, Yang L, Bole-Feysot C, Pfundt R, Allaman-Pillet N, Nitschké P, Cheetham ME, Lyonnet S, Agrawal SA, Li H, Pinton G, Michaelides M, Besmond C, Li Y, Yuan Z, von Lintig J, Webster AR, Le Hir H, Stoilov P, Amiel J, Hardcastle AJ, Ayuso C, Sui R, Chen R, Allikmets R, Schorderet DF. Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies. Am J Hum Genet. 2017 ;100(4):592-604.
Agrawal SA, Burgoyne T, Eblimit A, Bellingham J, Parfitt DA, Lane A, Nichols R, Asomugha C, Hayes MJ, Munro PM, Xu M, Wang K, Futter CE, Li Y, Chen R, Cheetham ME. REEP6 deficiency leads to retinal degeneration through disruption of ER homeostasis and protein trafficking. Hum Mol Genet. 2017 ;26(14):2667-2677.
Nargund AM, Pham CG, Dong Y, Wang PI, Osmangeyoglu HU, Xie Y, Aras O, Han S, Oyama T, Takeda S, Ray CE, Dong Z, Berge M, A Hakimi A, Monette S, Lekaye CL, Koutcher JA, Leslie CS, Creighton CJ, Weinhold N, Lee W, Tickoo SK, Wang Z, Cheng EH, Hsieh JJ. The SWI/SNF Protein PBRM1 Restrains VHL-Loss-Driven Clear Cell Renal Cell Carcinoma. Cell Rep. 2017 ;18(12):2893-2906.
2018
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.
Guo L, Akahori H, Harari E, Smith SL, Polavarapu R, Karmali V, Otsuka F, Gannon RL, Braumann RE, Dickinson MH, Gupta A, Jenkins AL, Lipinski MJ, Kim J, Chhour P, de Vries PS, Jinnouchi H, Kutys R, Mori H, Kutyna MD, Torii S, Sakamoto A, Choi CUng, Cheng Q, Grove ML, Sawan MA, Zhang Y, Cao Y, Kolodgie FD, Cormode DP, Arking DE, Boerwinkle E, Morrison AC, Erdmann J, Sotoodehnia N, Virmani R, Finn AV. CD163+ macrophages promote angiogenesis and vascular permeability accompanied by inflammation in atherosclerosis. J Clin Invest. 2018 ;128(3):1106-1124.
Eblimit A, Agrawal SAkshay, Thomas K, Anastassov IAssenov, Abulikemu T, Moayedi Y, Mardon G, Chen R. Conditional loss of Spata7 in photoreceptors causes progressive retinal degeneration in mice. Exp Eye Res. 2018 ;166:120-130.
Li L, Jiao X, D'Atri I, Ono F, Nelson R, Chan C-C, Nakaya N, Ma Z, Ma Y, Cai X, Zhang L, Lin S, Hameed A, Chioza BA, Hardy H, Arno G, Hull S, Khan MImran, Fasham J, Harlalka GV, Michaelides M, Moore AT, Akdemir ZHande Coba, Jhangiani S, Lupski JR, Cremers FPM, Qamar R, Salman A, Chilton J, Self J, Ayyagari R, Kabir F, Naeem MAsif, Ali M, Akram J, Sieving PA, Riazuddin S, Baple EL, S Riazuddin A, Crosby AH, J Hejtmancik F. Mutation in the intracellular chloride channel CLCC1 associated with autosomal recessive retinitis pigmentosa. PLoS Genet. 2018 ;14(8):e1007504.
Eblimit A, Zaneveld SAgrawal, Liu W, Thomas K, Wang K, Li Y, Mardon G, Chen R. NMNAT1 E257K variant, associated with Leber Congenital Amaurosis (LCA9), causes a mild retinal degeneration phenotype. Exp Eye Res. 2018 ;173:32-43.
McClard CK, Kochukov MY, Herman I, Liu Z, Eblimit A, Moayedi Y, Ortiz-Guzman J, Colchado D, Pekarek B, Panneerselvam S, Mardon G, Arenkiel BR. POU6f1 Mediates Neuropeptide-Dependent Plasticity in the Adult Brain. J Neurosci. 2018 ;38(6):1443-1461.