Publications | BCM-HGSC

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2020

Barish S, Barakat TStefan, Michel BC, Mashtalir N, Phillips JB, Valencia AM, Ugur B, Wegner J, Scott TM, Bostwick B, Murdock DR, Dai H, Perenthaler E, Nikoncuk A, van Slegtenhorst M, Brooks AS, Keren B, Nava C, Mignot C, Douglas J, Rodan L, Nowak C, Ellard S, Stals K, Lynch SAnn, Faoucher M, Lesca G, Edery P, Engleman KL, Zhou D, Thiffault I, Herriges J, Gass J, Louie RJ, Stolerman E, Washington C, Vetrini F, Otsubo A, Pratt VM, Conboy E, Treat K, Shannon N, Camacho J, Wakeling E, Yuan B, Chen C-A, Rosenfeld JA, Westerfield M, Wangler M, Yamamoto S, Kadoch C, Scott DA, Bellen HJ. BICRA, a SWI/SNF Complex Member, Is Associated with BAF-Disorder Related Phenotypes in Humans and Model Organisms. Am J Hum Genet. 2020 ;107(6):1096-1112.

2019

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.

2018

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.

2016

Kaiser TS, Poehn B, Szkiba D, Preussner M, Sedlazeck FJ, Zrim A, Neumann T, Nguyen L-T, Betancourt AJ, Hummel T, Vogel H, Dorner S, Heyd F, von Haeseler A, Tessmar-Raible K. The genomic basis of circadian and circalunar timing adaptations in a midge. Nature. 2016 ;540(7631):69-73.

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):157-167.

Jakobsdottir J, van der Lee SJ, Bis JC, Chouraki V, Li-Kroeger D, Yamamoto S, Grove ML, Naj A, Vronskaya M, Salazar JL, DeStefano AL, Brody JA, Smith AV, Amin N, Sims R, Ibrahim-Verbaas CA, Choi S-H, Satizabal CL, Lopez OL, Beiser A, M Ikram A, Garcia ME, Hayward C, Varga TV, Ripatti S, Franks PW, Hallmans G, Rolandsson O, Jansson J-H, Porteous DJ, Salomaa V, Eiriksdottir G, Rice KM, Bellen HJ, Levy D, Uitterlinden AG, Emilsson V, Rotter JI, Aspelund T, O'Donnell CJ, Fitzpatrick AL, Launer LJ, Hofman A, San Wang L-, Williams J, Schellenberg GD, Boerwinkle E, Psaty BM, Seshadri S, Shulman JM, Gudnason V, van Duijn CM. Rare Functional Variant in TM2D3 is Associated with Late-Onset Alzheimer's Disease. PLoS Genet. 2016 ;12(10):e1006327.

Harel T, Yoon WHee, Garone C, Gu S, Coban-Akdemir Z, Eldomery MK, Posey JE, Jhangiani SN, Rosenfeld JA, Cho MT, Fox S, Withers M, Brooks SM, Chiang T, Duraine L, Erdin S, Yuan B, Shao Y, Moussallem E, Lamperti C, Donati MA, Smith JD, McLaughlin HM, Eng CM, Walkiewicz M, Xia F, Pippucci T, Magini P, Seri M, Zeviani M, Hirano M, Hunter JV, Srour M, Zanigni S, Lewis RAlan, Muzny DM, Lotze TE, Boerwinkle E, Gibbs RA, Hickey SE, Graham BH, Yang Y, Buhas D, Martin DM, Potocki L, Graziano C, Bellen HJ, Lupski JR. Recurrent De Novo and Biallelic Variation of ATAD3A, Encoding a Mitochondrial Membrane Protein, Results in Distinct Neurological Syndromes. Am J Hum Genet. 2016 ;99(4):831-845.

2015

Wang F, Jiang L, Chen Y, Haelterman NA, Bellen HJ, Chen R. FlyVar: a database for genetic variation in Drosophila melanogaster. Database (Oxford). 2015 ;2015.

2014

Chen Z-X, Sturgill D, Qu J, Jiang H, Park S, Boley N, Suzuki AMaria, Fletcher AR, Plachetzki DC, FitzGerald PC, Artieri CG, Atallah J, Barmina O, Brown JB, Blankenburg KP, Clough E, Dasgupta A, Gubbala S, Han Y, Jayaseelan JC, Kalra D, Kim Y-A, Kovar CL, Lee SL, Li M, Malley JD, Malone JH, Mathew T, Mattiuzzo NR, Munidasa M, Muzny DM, Ongeri F, Perales L, Przytycka TM, Pu L-L, Robinson G, Thornton RL, Saada N, Scherer SE, Smith HE, Vinson C, Warner CB, Worley KC, Wu Y-Q, Zou X, Cherbas P, Kellis M, Eisen MB, Piano F, Kionte K, Fitch DH, Sternberg PW, Cutter AD, Duff MO, Hoskins RA, Graveley BR, Gibbs RA, Bickel PJ, Kopp A, Carninci P, Celniker SE, Oliver B, Richards S. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Res. 2014 ;24(7):1209-23.

Karandikar UC, Jin M, Jusiak B, Kwak SJ, Chen R, Mardon G. Drosophila eyes absent is required for normal cone and pigment cell development. PLoS One. 2014 ;9(7):e102143.

Yamamoto S, Jaiswal M, Charng W-L, Gambin T, Karaca E, Mirzaa G, Wiszniewski W, Sandoval H, Haelterman NA, Xiong B, Zhang K, Bayat V, David G, Li T, Chen K, Gala U, Harel T, Pehlivan D, Penney S, Vissers LELM, de Ligt J, Jhangiani SN, Xie Y, Tsang SH, Parman Y, Sivaci M, Battaloglu E, Muzny D, Wan Y-W, Liu Z, Lin-Moore AT, Clark RD, Curry CJ, Link N, Schulze KL, Boerwinkle E, Dobyns WB, Allikmets R, Gibbs RA, Chen R, Lupski JR, Wangler MF, Bellen HJ. A drosophila genetic resource of mutants to study mechanisms underlying human genetic diseases. Cell. 2014 ;159(1):200-214.

Ellis LL, Huang W, Quinn AM, Ahuja A, Alfrejd B, Gomez FE, Hjelmen CE, Moore KL, Mackay TFC, J Johnston S, Tarone AM. Intrapopulation genome size variation in D. melanogaster reflects life history variation and plasticity. PLoS Genet. 2014 ;10(7):e1004522.

Haelterman NA, Jiang L, Li Y, Bayat V, Sandoval H, Ugur B, Tan KLi, Zhang K, Bei D, Xiong B, Charng W-L, Busby T, Jawaid A, David G, Jaiswal M, Venken KJT, Yamamoto S, Chen R, Bellen HJ. Large-scale identification of chemically induced mutations in Drosophila melanogaster. Genome Res. 2014 ;24(10):1707-18.

Huang W, Massouras A, Inoue Y, Peiffer J, Ràmia M, Tarone AM, Turlapati L, Zichner T, Zhu D, Lyman RF, Magwire MM, Blankenburg K, Carbone MAnna, Chang K, Ellis LL, Fernandez S, Han Y, Highnam G, Hjelmen CE, Jack JR, Javaid M, Jayaseelan J, Kalra D, Lee S, Lewis L, Munidasa M, Ongeri F, Patel S, Perales L, Perez A, Pu LL, Rollmann SM, Ruth R, Saada N, Warner C, Williams A, Wu Y-Q, Yamamoto A, Zhang Y, Zhu Y, Anholt RRH, Korbel JO, Mittelman D, Muzny DM, Gibbs RA, Barbadilla A, J Johnston S, Stone EA, Richards S, Deplancke B, Mackay TFC. Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines. Genome Res. 2014 ;24(7):1193-208.

Jusiak B, Karandikar UC, Kwak S-J, Wang F, Wang H, Chen R, Mardon G. Regulation of Drosophila eye development by the transcription factor Sine oculis. PLoS One. 2014 ;9(2):e89695.

2012

Fondon JW, Martin A, Richards S, Gibbs RA, Mittelman D. Analysis of microsatellite variation in Drosophila melanogaster with population-scale genome sequencing. PLoS One. 2012 ;7(3):e33036.

Mackay TFC, Richards S, Stone EA, Barbadilla A, Ayroles JF, Zhu D, Casillas S, Han Y, Magwire MM, Cridland JM, Richardson MF, Anholt RRH, Barrón M, Bess C, Blankenburg KPetra, Carbone MAnna, Castellano D, Chaboub L, Duncan L, Harris Z, Javaid M, Jayaseelan JChristina, Jhangiani SN, Jordan KW, Lara F, Lawrence F, Lee SL, Librado P, Linheiro RS, Lyman RF, Mackey AJ, Munidasa M, Muzny DMarie, Nazareth L, Newsham I, Perales L, Pu L-L, Qu C, Ràmia M, Reid JG, Rollmann SM, Rozas J, Saada N, Turlapati L, Worley KC, Wu Y-Q, Yamamoto A, Zhu Y, Bergman CM, Thornton KR, Mittelman D, Gibbs RA. The Drosophila melanogaster Genetic Reference Panel. Nature. 2012 ;482(7384):173-8.

Huang W, Richards S, Carbone MAnna, Zhu D, Anholt RRH, Ayroles JF, Duncan L, Jordan KW, Lawrence F, Magwire MM, Warner CB, Blankenburg K, Han Y, Javaid M, Jayaseelan J, Jhangiani SN, Muzny D, Ongeri F, Perales L, Wu Y-Q, Zhang Y, Zou X, Stone EA, Gibbs RA, Mackay TFC. Epistasis dominates the genetic architecture of Drosophila quantitative traits. Proc Natl Acad Sci U S A. 2012 ;109(39):15553-9.

Hong X, Doddapaneni H, Comeron JM, Rodesch MJ, Halvensleben HA, Nien CY, Bolei F, Metpally R, Richmond TA, Albert TJ, Manak JR. Microarray-based capture of novel expressed cell type-specific transfrags (CoNECT) to annotate tissue-specific transcription in Drosophila melanogaster. G3 (Bethesda). 2012 ;2(8):873-82.

Ober U, Ayroles JF, Stone EA, Richards S, Zhu D, Gibbs RA, Stricker C, Gianola D, Schlather M, Mackay TFC, Simianer H. Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster. PLoS Genet. 2012 ;8(5):e1002685.

2011

Daines B, Wang H, Wang L, Li Y, Han Y, Emmert D, Gelbart W, Wang X, Li W, Gibbs R, Chen R. The Drosophila melanogaster transcriptome by paired-end RNA sequencing. Genome Res. 2011 ;21(2):315-24.

2010

Wang H, Chattopadhyay A, Li Z, Daines B, Li Y, Gao C, Gibbs R, Zhang K, Chen R. Rapid identification of heterozygous mutations in Drosophila melanogaster using genomic capture sequencing. Genome Res. 2010 ;20(7):981-8.

2009

Daines B, Wang H, Li Y, Han Y, Gibbs R, Chen R. High-throughput multiplex sequencing to discover copy number variants in Drosophila. Genetics. 2009 ;182(4):935-41.

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