Publications

Recent BiC Publications (Listed in Chronological Order, BiC Members in Bold)

  1. Shaikh TH*, Gai X*, Perin JC, Glessner JT, Xie H, Murphy K, O'Hara R, Casalunovo T, Conlin LK, D'arcy M, Franckelton EC, Geiger EA, Haldeman-Englert C, Imielinski M, Kim CE, Medne L, Annaiah K, Bradfield J, 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 Jul 10. [Epub ahead of print] (* equal contribution; ** corresponding author)
  2. Elia J*, Gai X*, Xie H, Perin JC, Geiger E, Glessner JT, D’arcy M, deBeradinis R, Frackelton E, Kim C, Lantieri F, Muganga M, Wang L, Takeda T, Rappaport EF, Grant SFA, Berrettini W, Devoto M, Shaikh TH, Hakonarson H, Peter S. White. Rare Structural Variants found in Attention-Deficit Hyperactivity Disorder are Preferentially Associated with Neurodevelopmental Genes. Mol Psychiatry.2009 Jun 23. [Epub ahead of print] (* equal contribution, **corresponding author)
  3. Liu J, Zhang Z, Bando M, Itoh T, Deardorff MA, Clark D, Kaur M, Tandy S, Kondoh T, Rappaport E, Spinner NB, Vega H, Jackson LG, Shirahige K, Krantz ID. Transcriptional dysregulation in NIPBL and cohesin mutant human cells. PLoS Biol. 2009 May 5;7(5):e1000119. Epub 2009 May 26.
  4. An L, Xie H , Chin MH, Obradovic Z, Smith DJ, Megalooikonomou V. Analysis of multiplex gene expression maps obtained by voxelation. BMC Bioinformatics. 2009 Apr 29;10 Suppl 4:S10.
  5. 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.
  6. 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 single nucleotide polymorphism-based oligonucleotide arrays and multiplex ligation-dependent probe amplification provides a comprehensive analysis of INI1/SMARCB1 in malignant rhabdoid tumors. Clin Cancer Res. 2009 Mar 15;15(6):1923-30. Epub 2009 Mar 10.
  7. Heltzer ML, Coffin SE, Maurer K, Bagashev A, Zhang Z, Orange JS, Sullivan KE. Immune dysregulation in severe influenza. J Leukoc Biol. 2009 Mar 10.
  8. 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.
  9. Porter MW, Milley D, Oliveti K, Ladd A, O'Hara RJ, Desai BR, White PS. Balancing Entrepreneurship and Business Practices for e-Collaboration: Responsible Information Sharing in Academic Research. AMIA Annu Symp Proc, 2008. 1100.
  10. Xie H., Midic U., Vucetic S, Obradovic Z. (2008) "Algorithmic Methods for the Analysis of Gene Expression Data," chapter 4 in Handbook of Applied Algorithms: Solving Scientific, Engineering, and Practical Problems, Willey-IEEE Press, pp. 115-146.
  11. 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. 2008 Dec 13.
  12. 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. 2008 Oct 21.
  13. Okawa ER, Gotoh T, Manne J, Igarashi J, Fujita T, Silverman KA, Xhao H, Mosse YP, White PS, Brodeur GM. Expression and sequence analysis of candidates for the 1p36.31 tumor suppressor gene deleted in neuroblastomas. Oncogene. 2008 Jan 31;27(6):803-10. Epub 2007 Jul 30.
  14. 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 in press.
  15. Falk MJ, Zhang Z, Rosenjack JR, Nissim I, Daikhin E, Nissim I, Sedensky MM, Yudkoff M, Morgan PG.; Metabolic pathway profiling of mitochondrial respiratory chain mutants in C. elegans. Mol Genet Metab. 2008 in press
  16. Weiss JS, Kruth HS, Kuivaniemi H, Tromp G, Karkera J, Mahurkar S, Lisch W, Dupps WJ Jr, White PS, Winters RS, Kim C, Rapuano CJ, Sutphin J, Reidy J, Hu FR, Lu da W, Ebenezer N, Nickerson ML. Genetic analysis of 14 families with Schnyder crystalline corneal dystrophy reveals clues to UBIAD1 protein function. Am J Med Genet A. 2008 Feb 1;146(3):271-83.
  17. Desai BR, O'Hara RT, White PS. Use of an enterprise wiki as a research collaboration tool. AMIA Annu Symp Proc, 2007. 932.
  18. Krynetskaia N, Xie H, Vucetic S, Obradovic Z, Krynetskiy E. High mobility group protein B1 is an activator of apoptotic response to antimetabolite drugs. Mol Pharmacol. 2008 Jan;73(1):260-9. Epub 2007 Oct 19.
  19. Chen D, Zhang Z, Liu Z, Cheng X. An Ensemble Method of Discovering Sample Classes Using Gene Expression Profiling. Data Mining in Biomedicine, Series: Springer Optimization and Its Applications , Vol. 7, Pardalos, Panos M.; Boginski, Vladimir L.; Vazacopoulos, Alkis (Eds.), Springer, 2007, pp. 39-46.