Postdoctoral Associates

  
Yujun Han
Atsushi Ishii
 
Atsushi received his PhD in Medical Science from Fukuoka University in March 2013 and joined CHGV in September 2013. While practicing as a pediatrician at Fukuoka University his research focused on the molecular genetics of child neurology with a particular interest in epilepsy. His postdoctoral work will focus on the genetic approach to the pathogenesis of child neurological disorder and the functional follow up of the mutations that CHGV has identified through Epi4K project.

 

Selected Publications 

  1. Sasaki M*., Ishii A*., Saito Y., Morisada N., Iijima K., Takada S., Araki A., Tanabe Y., Arai H., Yamashita S., Ohashi T., Oda Y., Ichiseki H., Hirabayashi S., Yasuhara A., Kawawaki H., Kimura S, Shimono M., Narumiya M., Suzuki M., Yoshida T., Oyazato Y., Tsuneishi S., Ozasa S., Yokochi K., Dejima S., Akiyama T., Kishi N., Kira R., Ikeda T., Oguni H, Zhang. B, Tsuji S., Hirose S. Genotype–Phenotype Correlations in Alternating Hemiplegia of Childhood. Neurology. 2013. In press (equal contributed)
  2. Sasaki M*., Ishii A*., Saito Y., Hirose S. Intermediate form between alternating hemiplegia of childhood and rapid-onset dystonia–parkinsonism. Mov Disord. 2013. In press (equal contributed)
  3. Ishii A., Shioda M., Okumura A., Kidokoro H., Sakauchi M., Shimada S., Shimizu T., Osawa M., Hirose S., Yamamoto T. A recurrent KCNT1 mutation in two sporadic cases with malignant migrating partial seizures in infancy. Gene. 2013. Epub 2013/09/14
  4. Ishii A., Saito Y., Mitsui J., Ishiura H., Yoshimura J., Arai H., Yamashita S., Kimura S., Oguni H., Morishita S., Tsuji S., Sasaki M., Hirose S. Identification of ATP1A3 mutations by exome sequencing as the cause of alternating hemiplegia of childhood in Japanese patients. PLOS ONE. 2013;8(2):e56120.
  5. Ishii A., Yasumoto S., Ihara Y., Inoue T., Fujita T., Nakamura N., Ohfu M., Yamashita Y., Takatsuka H., Taga T., Miyata R., Ito M., Tsuchiya H., Matsuoka T., Kitao T., Murakami K., Lee W. T., Kaneko S., Hirose S. Genetic analysis of PRRT2 for benign infantile epilepsy, infantile convulsions with choreoathetosis syndrome, and benign convulsions with mild gastroenteritis. Brain Dev. 2013;35(6):524-530.
  6. Ishii A., Miyajima T., Kurahashi H., Wang J. W., Yasumoto S., Kaneko S., Hirose S. KCNQ2 abnormality in BECTS: Benign childhood epilepsy with centrotemporal spikes following benign neonatal seizures resulting from a mutation of KCNQ2. Epilepsy Res. 2012;102(1-2):122-125.
  7. Shi X., Huang M. C., Ishii A., Yoshida S., Okada M., Morita K., Nagafuji H., Yasumoto S., Kaneko S., Kojima T., Hirose S. Mutational analysis of GABRG2 in a Japanese cohort with childhood epilepsies. J Hum Genet. 2010;55(6):375-378.
  8. Ishii A., Zhang B., Kaneko S., Hirose S. Positive association between benign familial infantile convulsions and LGI4. Brain Dev. 2010;32(7):538-543.
  9. Kurahashi H., Wang J. W., Ishii A., Kojima T., Wakai S., Kizawa T., Fujimoto Y., Kikkawa K., Yoshimura K., Inoue T., Yasumoto S., Ogawa A., Kaneko S., Hirose S. Deletions involving both KCNQ2 and CHRNA4 present with benign familial neonatal seizures. Neurology. 2009;73(15):1214-1217.
  10. Ishii A., Fukuma G., Uehara A., Miyajima T., Makita Y., Hamachi A., Yasukochi M., Inoue T., Yasumoto S., Okada M., Kaneko S., Mitsudome A., Hirose S. A de novo KCNQ2 mutation detected in non-familial benign neonatal convulsions. Brain Dev. 2009;31(1):27-33.
  11. Wang J. W., Kurahashi H., Ishii A., Kojima T., Ohfu M., Inoue T., Ogawa A., Yasumoto S., Oguni H., Kure S., Fujii T., Ito M., Okuno T., Shirasaka Y., Natsume J., Hasegawa A., Konagaya A., Kaneko S., Hirose S. Microchromosomal deletions involving SCN1A and adjacent genes in severe myoclonic epilepsy in infancy. Epilepsia. 2008;49(9):1528-1534.

 

Yujun Han
 Yujun Han
 
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.

Selected Publications
 
  1. MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences. Han Y and Wessler. S.R. Nucleic Acids Research. (2010)
  2. 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)
  3. 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)
  4. Applications of the double-barreled data in whole-genome shotgun sequence assembly and analysis.
  5. 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)
  6. RePS: A Sequence Assembler That Masks Exact Repeats Identified from the Shotgun Data.
  7. 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) 
 

 

Nanye Long
 
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.
 

Selected Publications

  1. 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
  2. Long N, Gianola D, Rosa GJM and Weigel KA (2011). Marker-assisted prediction of non-additive genetic values. Genetica, in press. PMID:21674154
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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 Petrovski

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.

 

 Selected Publications

  1. Petrovski S, Wang Q, Heinzen, EL, Allen AS, Goldstein DB. Genic Intolerance to Functional Variation and the Interpretation of Personal Genomes. PLOS Genetics 2013 (doi: 10.1371/journal.pgen.1003709).
  2. Epi4K Consortium. De novo mutation in epileptic encephalopathies. Nature 2013 (doi: doi:10.1038/nature12439).
  3. Goldstein DB, Allen A, Keebler J, Margulies E, Petrou S, Petrovski S, Sunyaev S. Sequencing studies in human genetics: design and interpretation. Nature Review Genetics  2013; 14,460–470; doi:10.1038/nrg3455
  4. Speed D*, Hoggart C*, Petrovski S*, Tachmazidou I*, Jorgensen A, De Iorio M, Todaro M, Coffey A, Smith D, Smith P, Jackson M, Cooper P, Kellett M, Howell S, Sills G, Chadwick D, Pirmohamed M, Bentley D, Scheffer I, Berkovic S, Balding D, Marson A, Palotie A, O’Brien TJ, Johnson MR. Genetic determinants for remission of seizures in newly treated epilepsy: a prospective cohort genome-wide association study. Human Molecular Genetics 2013 (in press).
  5. Bayly J, Carino J, Petrovski S, Smit M, Fernando DA, Vinton A, Yan B, Gubbi JR, Palaniswami MS, O'Brien TJ. Time-frequency mapping of the rhythmic limb movements distinguishes convulsive epileptic from psychogenic nonepileptic seizures. Epilepsia 2013 [doi: 10.1111/epi.12207].
  6. Petrovski S, Kwan P. Unravelling the genetics of common epilepsies: approaches, platforms, caveats. Epilepsy & Behaviour 2012 [doi: 10.1016/j.yebeh.2012.09.007].
  7. Hakami T, Todaro M, Petrovski S, MacGregor L, Velakoulis D, Tan M, Matkovic Z, Gorelik A, Liew D, Yerra R, O’Brien TJ. Substitution Monotherapy with Levetiracetam Versus Older AEDs: A RCT. Archives of Neurology 2012; Sep 3:1-9. [doi: 10.1001/archneurol.2012.2203]
  8. Zhu Q*, Ge D*, Maia J, Zhu M, Petrovski S, Dickson SP, Heinzen EL, Shianna KV, Goldstein DB. A genome-wide comparison of the functional properties of rare and common genetic variants in humans. AJHG 2011; 88(4): 458 – 468.
  9. Petrovski S*, Fellay J*, Shianna KV, Carpenetti N, Kumwenda J, Kamanga G, Kamwendo DD, Letvin NL, McMichael AJ, Haynes BF, Cohen MS, Goldstein DB. Common Human Genetic Variants and HIV-1 Susceptibility: A Genome-Wide Survey in a Homogeneous African Population. AIDS 2011; 24(4): 513-518.
  10. Petrovski S, Szoeke CEI, Jones NC, Salzberg MR, Sheffield LJ, Huggins RM, O’Brien TJ. Neuropsychiatric Symptomatology Predicts Seizure Recurrence In Newly Treated Patients. Neurology 2010; 75: 1015-1021.
  11. Miller H, Clarke S, Lane S, Lonie A, Lazaridis D, Petrovski S, Jones O. Predicting customer behaviour: The University of Melbourne's KDD Cup report. JMLR 2009; Volume 7 Workshop and Conference Proceedings: 45-55

 

 

Patrick Shea

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.

Selected Publications

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  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.
  7. 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.

 

Mingfu Zhu

Xiaodi Yao
 
 
Xiaodi received her Ph.D in Biochemistry, Cell and Developmental Biology at Emory University in 2012. She joined CHGV in July 2013. Her research focuses on functional analysis of variants associated with human diseases.
 

 Selected Publications

  1. Yao, X., Gross, C., Xing, L., and Bassell, G.J. miR-324-5p regulates the expression of A-type potassium channel Kv4.2. (manuscript in preparation)
  2. Xing, L., Yao, X., Williams, K.R., and Bassell, G.J. (2012). Negative regulation of RhoA translation and signaling by hnRNP-Q1 affects cellular morphogenesis. Mol Biol Cell 23, 1500-1509.
  3. Swanger, S.A., Yao, X., Gross, C., and Bassell, G.J. (2011). Automated 4D analysis of dendritic spine morphology: applications to stimulus-induced spine remodeling and pharmacological rescue in a disease model. Mol Brain 4, 38.
  4. Gross, C.*, Yao, X.*, Pong, D.L., Jeromin, A., and Bassell, G.J. (2011). Fragile x mental retardation protein regulates protein expression and mRNA translation of the potassium channel kv4.2. J Neurosci 31, 5693-5698. (*contributed equally to this work)
  5. Muddashetty, R.S., Nalavadi, V.C., Gross, C., Yao, X., Xing, L., Laur, O., Warren, S.T., and Bassell, G.J. (2011). Reversible inhibition of PSD-95 mRNA translation by miR-125a, FMRP phosphorylation, and mGluR signaling. Mol Cell 42, 673-688.
  6. Gross, C., Nakamoto, M.*, Yao, X.*, Chan, C.B., Yim, S.Y., Ye, K., Warren, S.T., and Bassell, G.J. (2010). Excess phosphoinositide 3-kinase subunit synthesis and activity as a novel therapeutic target in fragile X syndrome. J Neurosci 30, 10624-10638. (*contributed equally to this work)

 

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