Publications

Xie HM, Perin JC, Schurr TG, Dulik MC, Zhadanov SI, Baur JA, King MP, Place E, Clarke C, Grauer M, Schug J, Santani A, Albano A, Kim C, Hakonarson H, Gai X*, Falk MJ*. Mitochondrial Genome Sequence Analysis: A Custom Bioinformatics Pipeline Substantially Improves Affymetrix MitoChip v2.0 Call Rate and Accuracy. BMC Bioinformatics 2011, 12:402 (* Corresponding author)
Goldmuntz E, Paluru P, Glessner J, Hakonarson H, Biegel JA, White PS, Gai X, Shaikh TH. Microdeletions and Microduplications in Patients with Congenital Heart Disease and Multiple Congenital Anomalies. Congenit Heart Dis. 2011 Oct 20. doi: 10.1111/j.1747-0803.2011.00582.x. [Epub ahead of print]
Rosenfeld AB. Suppression of cellular transformation by poly (A) binding protein interacting protein 2 (Paip2). PLoS One 2011: 6 e25116.
Gai X, Xie H, Perin JC, Murphy K, Wenocur AS, D’Arcy M, O’Hara RJ, Goldmuntz E, Grice DD, Shaikh TH, Devoto M, Hakonarson H, Buxbaum JD, Elia J, White PS. Rare Structural Variation of Synapse and Neurotransmission Genes in Autism. Mol Psychiatry. 2011 Mar 1. [Epub ahead of print].
Jaramillo M, Gomez MA, Larsson O, Shio MT, Topisirovic I, Contreras I, Luxenburg R, Rosenfeld AB, Colina R, McMaster RW, Olivier M, Costa-Mattioli M, Sonenberg N. Leishmania repression of host translation through mTOR cleavage is required for parasite survival and infection. Cell Host and Microbe. 2011: 9 331-341.
Elia J, Gai X, Hakonarson H, White PS. Structural variations in attention-deficit hyperactivity disorder. Lancet. 2011 Jan 29;377(9763):377-8.
Dougherty MJ, Wilmoth DM, Tooke LS, Shaikh TH, Gai X, Hakonarson H, Biegel JA. Implementation of high resolution single nucleotide polymorphism array analysis as a clinical test for patients with hematologic malignancies. Cancer Genet. 2011 Jan;204(1):26-38.
Lind C, Ferriola D, Mackiewicz K, Heron S, Rogers M, Slavich L, Walker R, Hsiao T, McLaughlin L, D'Arcy M, Gai X, Goodridge D, Sayer D, Monos D. Next-generation sequencing: the solution for high-resolution, unambiguous human leukocyte antigen typing. Hum Immunol. 2010 Oct;71(10):1033-42. Epub 2010 Aug 5.
Gai X, Perin JC, Murphy K, O'Hara R, D'arcy M, Wenocur A, Xie HM, Rappaport EF, Shaikh TH, White PS. CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics. BMC Bioinformatics. 2010 Feb 4;11:74.
Rosenfeld AB and Racaniello VR. Components of the multifactor complex needed for internal initiation by the IRES of hepatitis C virus. RNA Biology 2010: 7 596-605.
Rosenfeld AB and Racaniello VR. Components of the multifactor complex needed for internal initiation by the IRES of hepatitis C virus. RNA Biology 2010: 7 596-605.
Leyva-Vega M, Gerfen J, Thiel BD, Jurkiewicz D, Rand EB,  Pawlowska J, Kaminska D, Russo P, Gai X, Krantz ID, Kamath BM, Hakonarson H, Haber BA, Spinner NB.  Genomic Alterations in Biliary Atresia Suggests Region of Potential Disease Susceptibility in 2q37.3.  Am J Med Genet A. 2010 Apr;152A(4):886-95.
Shaikh TH*, Gai X*, Perin JC, Glessner JT, Xie H, Murphy K, O'Hara R, Casalunovo T, Conlin LK, D'Arcy M, Frackelton EC, Geiger EA, Haldeman-Englert C, Imielinski M, Kim CE, Medne L, Annaiah K, Bradfield JP, Dabaghyan E, Eckert A, Onyiah CC, Ostapenko S, Otieno FG, Santa E, Shaner JL, Skraban R, Smith RM, Elia J, Goldmuntz E, Spinner NB, Zackai EH, Chiavacci RM, Grundmeier R, Rappaport EF, Grant SF, White PS, Hakonarson H.  High-resolution mapping and analysis of copy number variations in the human genome: A data resource for clinical and research applications. Genome Res. 2009 Sep;19(9):1682-90. (* Equal contribution)
Elia J*, Gai X*, Xie HM, Perin JC, Geiger E, Glessner JT, D'arcy M, Deberardinis R, Frackelton E, Kim C, Lantieri F, Muganga BM, Wang L, Takeda T, Rappaport EF, Grant SF, Berrettini W, Devoto M, Shaikh TH, Hakonarson H, White PS.  Rare structural variants found in attention-deficit hyperactivity disorder are preferentially associated with neurodevelopmental genes. Mol Psychiatry. 2010 Jun;15(6):637-46. Epub 2009 Jun 23. (* Equal contribution)
Kamath BM, Thiel BD, Gai X, Conlin LK, Munoz PS, Glessner J, Clark D, Warthen DM, Shaikh TH, Mihci E, Piccoli DA, Grant SF, Hakonarson H, Krantz ID, Spinner NB.  SNP array mapping of chromosome 20p deletions: genotypes, phenotypes, and copy number variation. Hum Mutat. 2009 Mar;30(3):371-8.
Jackson EM, Sievert AJ, Gai X, Hakonarson H, Judkins AR, Tooke L, Perin JC, Xie H, Shaikh TH, Biegel JA. Genomic analysis using high density SNP based oligonucleotide arrays and MLPA provides a comprehensive analysis of INI1/SMARCB1 in malignant rhabdoid tumors. Clin Cancer Res. 2009 Mar 15;15(6):1923-30.
Elling AA, Mitreva M, Gai X, Martin J, Recknor J, Davis EL, Hussey RS, Nettleton D, McCarter JP, Baum TJ. Sequence mining and transcript profiling to explore cyst nematode parasitism. BMC Genomics. 2009 Jan 30;10:58.
Haldeman-Englert CR, Gai X, Perin JC, Ciano M, Halbach SS, Geiger EA, McDonald-McGinn DM, Hakonarson H, Zackai EH, Shaikh TH. A 3.1-Mb microdeletion of 3p21.31 associated with cortical blindness, cleft lip, CNS abnormalities, and developmental delay. Eur J Med Genet. 2009 Jul-Aug;52(4):265-8.
Keating BJ, Tischfield S, Murray SS, Bhangale T, Price TS, Glessner JT, Galver L, Barrett JC, Grant SF, Farlow DN, Chandrupatla HR, Hansen M, Ajmal S, Papanicolaou GJ, Guo Y, Li M, Derohannessian S, de Bakker PI, Bailey SD, Montpetit A, Edmondson AC, Taylor K, Gai X, Wang SS, Fornage M, Shaikh T, Groop L, Boehnke M, Hall AS, Hattersley AT, Frackelton E, Patterson N, Chiang CW, Kim CE, Fabsitz RR, Ouwehand W, Price AL, Munroe P, Caulfield M, Drake T, Boerwinkle E, Reich D, Whitehead AS, Cappola TP, Samani NJ, Lusis AJ, Schadt E, Wilson JG, Koenig W, McCarthy MI, Kathiresan S, Gabriel SB, Hakonarson H, Anand SS, Reilly M, Engert JC, Nickerson DA, Rader DJ, Hirschhorn JN, Fitzgerald GA.  Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies. PLoS One. 2008;3(10):e3583.
Sievert AJ, Jackson EM, Gai X, Hakonarson H, Judkins AR, Resnick AC, Sutton LN, Storm PB, Shaikh TH, Biegel JA. Duplication of 7q34 in Pediatric Low-Grade Astrocytomas Detected by High-Density Single-Nucleotide Polymorphism-Based Genotype Arrays Results in a Novel BRAF Fusion Gene. Brain Pathol. Brain Pathol. 2009 Jul;19(3):449-58.
Dore LC, Amigo JD, Dos Santos CO, Zhang Z, Gai X, Tobias JW, Yu D, Klein AM, Dorman C, Wu W, Hardison RC, Paw BH, Weiss MJ. A GATA-1-regulated microRNA locus essential for erythropoiesis. Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3333-8.
Elling AA, Mitreva M, Recknor J, Gai X, Martin J, Maier TR, McDermott JP, Hewezi T, McKBird D, Davis EL, Hussey RS, Nettleton D, McCarter JP, Baum TJ. Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines. Genome Biol. 2007;8(10):R211.
Rosenfeld AB and Racaniello VR. Hepatitis C virus internal ribosome entry site-dependent translation in Saccharomyces cerevisiae is independent of polypyrimidine tract-binding protein, poly (rC)-binding protein 2 and La protein. Journal of Virology 20005: 79 10126-10137.
Gao X, Rowley DJ, Gai X, Voytas DF. Ty5 gag mutations increase retrotransposition and suggest a role for hydrogen bonding in the function of the nucleocapsid zinc finger. J Virol. 2002 Apr;76(7):3240-7.
Shoemaker R, Keim P, Vodkin L, Retzel E, Clifton SW, Waterston R, Smoller D, Coryell V, Khanna A, Erpelding J, Gai X, Brendel V, Raph-Schmidt C, Shoop EG, Vielweber CJ, Schmatz M, Pape D, Bowers Y, Theising B, Martin J, Dante M, Wylie T, Granger C. A compilation of soybean ESTs: generation and analysis. Genome. 2002 Apr;45(2):329-38.
Fernandes J, Brendel V, Gai X, Lal S, Chandler VL, Elumalai RP, Galbraith DW, Pierson EA, Walbot V. Comparison of RNA expression profiles based on maize expressed sequence tag frequency analysis and micro-array hybridization. Plant Physiol. 2002 Mar;128(3):896-910.
Xie W*, Gai X*, Zhu Y, Zappulla DC, Sternglanz R, Voytas DF. Targeting of the yeast Ty5 retrotransposon to silent chromatin is mediated by interactions between integrase and Sir4p. Mol Cell Biol. 2001 Oct;21(19):6606-14. (*Equal contribution).
Gonzalez S, Rosenfeld AB, Szeto D and Wetmur JG. The ruv proteins of Thermotoga maritima: branch migration and resolution of Holliday junctions. Biochim Biophys Acta. 2000: 494 217-225.
Gai X, Lal S, Xing L, Brendel V, Walbot V. Gene discovery using maize genome database ZmDB. Nucleic Acids Res. 2000 Jan 1;28(1):94-6.
Gai X. and Voytas DF. A single amino acid change identifies a Ty5 retrotransposon domain that targets integration to silent chromatin. Mol Cell. 1998 Jun;1(7):1051-5. (Review: Yeast retrotransposons: finding a nice quiet neighborhood. Boeke JD and Devine SE. Cell 93, 1087-1089)
Rao HG, Rosenfeld AB and Wetmur JG. Methanococcus jannaschii flap endonucleases: expression, purification and substrate requirements. Journal of Bacteriology. 1998: 180 5406-5412