Yujun received his Ph.D from University of Georgia and he joined CHGV in September 2010. He focuses on the study of transposable elements and human genome variations.
- MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences. Han Y and Wessler. S.R. Nucleic Acids Research. (2010)
- TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences. Han, Y., Burnette, J.M. III and Wessler, S.R. Nucleic Acids Research. (2009)
- ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun. Li R, Ye J, Li S, Wang J, Han Y, Ye C, Wang J, Yang H, Yu J, Wong GK, Wang J. PLoS Comput Biol. (2005)
- Applications of the double-barreled data in whole-genome shotgun sequence assembly and analysis.
- Han Y, Ni P, Li H, Ye J, Hu J, Chen C, Huang X, Cong L, Li G, Wang J, Gu X, Yu J, Li S. Sci China C Life Sci. (2005)
- RePS: A Sequence Assembler That Masks Exact Repeats Identified from the Shotgun Data.
- Wang J, Wong GK, Ni P, Han Y, Huang X, Zhang J, Ye C, Zhang Y, Hu J, Zhang K, Xu X, Cong L, Lu H, Ren X, Ren X, He J, Tao L, Passey DA, Wang J, Yang H, Yu J, Li S. Genome Research. (2002)
Chul Joo Kang
CJ received his Ph.D. in Genetics from the University of Washington. His research focus is on the developing the statistical method for the association test for the rare variants.
- CJ Kang and P Marjoram Inference of population mutation rate and detection of segregating sites from next-generation sequence data. Genetics. 2011:189(2):595-605.
- F Yang*, CJ Kang* and P Marjoram Methods for detecting associations between phenotype and aggregations of rare variants. BMC Proc. 2011:5 Suppl 9:S51. (* equal contributors)
- CJ Kang and P Marjoram Exact coalescent simulation of new haplotype data from existing reference haplotypes. Bioinformatics. 2012:28(6)838-844.
Nanye received her PhD in Animal Science from the University of Wisconsin-Madison in May 2011. She joined CHGV in July 2011. Her postdoctoral work is primarily focused on pursuing statistical models for detecting variants associated with human diseases using next generation sequencing data.
- Long N, Gianola D, Rosa GJM and Weigel KA (2011). Application of support vector regression to genome-assisted prediction of quantitative traits. Theoretical and Applied Genetics, in press. PMID:21739137
- Long N, Gianola D, Rosa GJM and Weigel KA (2011). Marker-assisted prediction of non-additive genetic values. Genetica, in press. PMID:21674154
- Long N, Gianola D, Rosa GJM and Weigel KA (2011). Long-term impacts of genome-enabled selection. Journal of Applied Genetics, in press. PMID:21584728
- Long N, Gianola D, Rosa GJM and Weigel KA (2011). Dimension reduction and variable selection for genomic selection: application to predicting milk yield in Holsteins. Journal of Animal Breeding and Genetics, 128:247-257. PMID:21749471
- Long N, Gianola D, Rosa GJM, Weigel KA, Kranis A and Gonzalez-Recio O (2010). Radial basis function regression methods for predicting quantitative traits using SNP markers. Genetics Research, 92:209-225. PMID:20667165
- Long N, Gianola D, Rosa GJM, Weigel KA and Avendano S (2009). Comparison of classification methods for detecting associations between SNPs and chick mortality. Genetics Selection Evolution, 41:18. PMID:19284707
- Long N, Gianola D, Rosa GJM, Weigel KA and Avendano S (2008). Marker-assisted assessment of genotype by environment interaction: A case study of single nucleotide polymorphism-mortality association in broilers in two hygiene environments. Journal of Animal Science, 86:3358-3366. PMID:18765852
- Long N, Gianola D, Rosa GJM, Weigel KA and Avendano S (2007). Machine learning classification procedure for selecting SNPs in genomic selection: application to early mortality in broilers. Journal of Animal Breeding and Genetics, 124:377-389. PMID:18076475
Slavé received his PhD from University of Melbourne, Australia and he joined the CHGV for the second time in May 2012. He focuses on the study of population genetics and the role of genome variation in disease and treatment outcomes.
Patrick received his Ph.D. in human genetics from the University of Pittsburgh. He joined the Center for Human Genome Variation in 2011, following a two year fellowship in infectious disease. His research is focused on understanding how human genetic variation contributes to differences in infectious disease susceptibility and pathogenesis.
- Shea PR, Ewbank AL, Gonzalez-Lugo JH, Martagon-Rosado AJ, Martinez-Gutierrez JC, Rehman HA, Serrano-Gonzalez M, Fittipaldi N, Beres SB, Flores AR, Low DE, Willey BM, Musser JM. Group A Streptococcus emm Gene Types in Pharyngeal Isolates, Ontario, Canada, 2002-2010. Emerg Infect Dis. 2011 Nov;17(11):2010-7.
- Carroll RK, Shelburne SA 3rd, Olsen RJ, Suber B, Sahasrabhojane P, Kumaraswami M, Beres SB, Shea PR, Flores AR, Musser JM. Naturally occurring single amino acid replacements in a regulatory protein alter streptococcal gene expression and virulence in mice. J Clin Invest. 2011 May;121(5):1956-68.
- Shea PR, Beres SB, Flores AR, Ewbank AL, Gonzalez-Lugo JH, Martagon-Rosado AJ, Martinez-Gutierrez JC, Rehman HA, Serrano-Gonzalez M, Fittipaldi N, Ayers SD, Webb P, Willey BM, Low DE, Musser JM. Distinct signatures of diversifying selection revealed by genome analysis of respiratory tract and invasive bacterial populations. Proc Natl Acad Sci U S A. 2011 Mar 22;108(12):5039-44.
- Shea PR, Virtaneva K, Kupko JJ 3rd, Porcella SF, Barry WT, Wright FA, Kobayashi SD, Carmody A, Ireland RM, Sturdevant DE, Ricklefs SM, Babar I, Johnson CA, Graham MR, Gardner DJ, Bailey JR, Parnell MJ, Deleo FR, Musser JM. Interactome analysis of longitudinal pharyngeal infection of cynomolgus macaques by group A Streptococcus. Proc Natl Acad Sci U S A. 2010 Mar 9;107(10):4693-8.
- Beres SB, Carroll RK, Shea PR, Sitkiewicz I, Martinez-Gutierrez JC, Low DE, McGeer A, Willey BM, Green K, Tyrrell GJ, Goldman TD, Feldgarden M, Birren BW, Fofanov Y, Boos J, Wheaton WD, Honisch C, Musser JM. Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics. Proc Natl Acad Sci U S A. 2010 Mar 2;107(9):4371-6.
- Shea PR, Ishwad CS, Bunker CH, Patrick AL, Kuller LH, Ferrell RE. RNASEL and RNASEL-inhibitor variation and prostate cancer risk in Afro-Caribbeans. Prostate. 2008 Mar 1;68(4):354-9.
- Shea PR, Ferrell RE, Patrick AL, Kuller LH, Bunker CH. ELAC2 and prostate cancer risk in Afro-Caribbeans of Tobago. Hum Genet. 2002 Oct;111(4-5):398-400. Epub 2002 Aug 21.
Pingxing received her Ph.D. in genetics from Yale University, and joined CHGV in July 2012. Her research is focused on genetics of psychiatric disorders.
- Xie P, Kranzler HR, Farrer L, Gelernter J. Serotonin transporter 5-HTTLPR genotype moderates the effects of childhood adversity on posttraumatic stress disorder risk: A replication study. Am J Med Genet B Neuropsychiatr Genet. Jun 12 2012.
- Xie P, Kranzler HR, Zhang H, et al. Childhood adversity increases risk for nicotine dependence and interacts with alpha5 nicotinic acetylcholine receptor genotype specifically in males. Neuropsychopharmacology. Feb 2012;37(3):669-676.
- Chang SC, Xie P, Anton RF, et al. No association between ADCYAP1R1 and post-traumatic stress disorder in two independent samples. Mol Psychiatry. Mar 2012;17(3):239-241.
- Xie P, Kranzler HR, Krauthammer M, et al. Rare nonsynonymous variants in alpha-4 nicotinic acetylcholine receptor gene protect against nicotine dependence. Biol Psychiatry. Sep 15 2011;70(6):528-536.
- Xie P, Kranzler HR, Poling J, et al. Interaction of FKBP5 with childhood adversity on risk for post-traumatic stress disorder. Neuropsychopharmacology. Jul 2010;35(8):1684-1692.
- Xie P, Kranzler HR, Poling J, et al. Interactive effect of stressful life events and the serotonin transporter 5-HTTLPR genotype on posttraumatic stress disorder diagnosis in 2 independent populations. Arch Gen Psychiatry. Nov 2009;66(11):1201-1209.
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