Bioinformatics and Epidemiology

Modern technologies in medical genetics often produce extremely large quantities of data that require new computational and statistical methods for insight and understanding of the underlying genetic and biological mechanisms. To better meet the challenges and to grasp the opportunities presented in the modern era of genomics, GGC has created the office of Bioinformatics and Epidemiology.

Publications

2014 Publications

  • Sarasua SM, Boccuto L, Sharp JL, Dwivedi A, Chen C-F, Rollins JD, Rogers RC, Phelan K, DuPont BR. Clinical and genomic evaluation of 201 patients with Phelan-McDermid syndrome. Human Genetics 2014 (in press).

2013 Publications

  • Sarasua SM, Dwivedi A, Boccuto L, Chen CF, Sharp JL, Rollins JD, Collins JS, Rogers RC, Phelan K, DuPont BR. 22q13.2q13.32 Genomic regions associated with severity of speech delay, developmental delay, and physical features in Phelan-McDermid syndrome. Genetics in Medicine. 2014 Apr;16(4):318-28. epub 2013
  • Boccuto L, Lauri M, Sarasua SM, Skinner CD, Buccella D, Dwivedi A, Orteschi D, Collins JS, Zollino M, Visconti P, DuPont B, Tiziano D, Schroer RJ, Neri G, Stevenson RE, Gurrieri F, Schwartz CE. Prevalence of SHANK3 variants in patients with different subtypes of autism spectrum disorders. European Journal of Human Genetics. 2013 Mar;21(3):310-6.

2012 Publications

  • Sarasua SM, Dwivedi A, Boccuto L, Rollins JD, Chen CF, Rogers RC, Phelan K, DuPont BR, Collins JS. Association between deletion size and important phenotypes expands the genomic region of interest in Phelan-McDermid syndrome (22q13 deletion syndrome).Journal of Medical Genetics 2011 Nov;48(11):761-6.

2011 Publications

  • Cummins A, Eggert J, Pruitt R, Collins JS. (2011) Huntington's Disease: implications for practice. Nurse Pract, 36:41-47.
  • Collins JS, Marvelle AF, Stevenson RE (2011) Sibling recurrence in intellectual disability of unknow cause. Clin Genet, 79:498-500.
  • Medina MT, Aguilar-Estrada RL, Alvarez A, Durón RM, Martínez L, Dubón S, Estrada AL, Zúniga C, Cartagena D, Thompson A, Ramirez E, Banegas L, Osorio JR, Delgado-Escueta AV, Collins JS, Holden KR. (2011) Community Interventions Reduce the Rate of Preventable Epilepsy from Neurocysticerosis: The Salamá Honduras Study. Epilepsia; 52:1177-1185.
  • Collins JS, Atkinson KK, Dean JH, Best RG, Stevenson RE. (2011) Long-term maintenance of neural tube defects prevention in a high prevalence state. J Pediatr; 159:143-149. PMCID: PMC3115395.
  • Rollins JD, Sarasua SM, Phelan MC, DuPont BR, Rogers RC, Collins JS. Growth in Phelan-McDermid syndrome. Amer J Med Genet. 2011 Sep;155A(9):2324-6.
  • Wang L, Huang C, Yang JY. (2011) Predicting siRNA potency with random forests and support vector machines. BMC Genomics, in press.


2010 Publications

  • Zhang Z, Teng S, Wang L, Schwartz CE, Alexov E. (2010) Computational analysis of missense mutations causing Snyder-Robinson Syndrome. Human Mutation, 31:1043-1049.
  • Rollins JD, Collins JS, Holden KR. (2010) United States head circumference growth reference charts: birth to 21 years. J Pediatr, 156:907-913.
  • Cheng C-H, Leung AY, Chen C-F. (2010) The effects of two different Ganoderma species (lingzhi) on gene expression in human monocytic THP-1 cells. Nutrition and Cancer, 62(5):1-11.
  • Li, D., Wang, L., Yang, X., Zhang, G. and Chen, L. (2010) Proteomic analysis of blue light-induced twining response in Cuscuta australis. Plant Molecular Biology, 72:205-213.
  • Parker SE, Mai CT, Canfield MA, Rickard R, Wang Y, Meyer RE, Anderson P, Mason CA, Collins JS, Kirby RS, Correa A. Updated National Birth Prevalence Estimates for Selected Birth Defects in the United States, 2004-2006. Birth Defects Research Part A Clin Mol Teratol 2010 Dec 88(12):1008-16.
  • Smith, C.M., Liu, X.M., Wang, L., Liu, X., Chen, M.S., Starkey, S. and Bai, G. (2010). Aphid feeding activates expression of a transcriptome of oxylipin-based defense signals in wheat involved in resistance to herbivory. Journal of Chemical Ecology, 36:260-276.
  • Teng, S., Srivastava, A.K. and Wang, L. Sequence feature-based prediction of protein stability changes upon amino acid substitutions. BMC Genomics. 2010 Nov 2; Suppl 2:S5.
  • Wang, L., Huang, C., Yang, M.Q. and Yang, J.Y.  BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features. BMC Systems Biology, 2010 May 28;4 Suppl 1:S3.
  • Wang, L., Srivastava, A.K. and Schwartz, C.E. Microarray data integration for genome-wide analysis of human tissue-selective gene expression. BMC Genomics. 2010 Nov 2; 11 Suppl 2:S15.

2009 Publications

  • Molinero MR, Holden KR, Rodriguez LC, Collins JS, Samra JA, Shinnar S. Pediatric convulsive status epilepticus in Honduras, Central America. Epilepsia 2009; 50:2314-2319.
  • Du Z, Li L, Chen C-F, Yu PS, Wang JZ. G-SESAME: web tools for GO-term-based gene similarity analysis and knowledge discovery. Nulceic Acids 2009: 37:W345-9.
  • Pawlowski P, Heringer-Walther S, Cheng C-H, Archie J, Chen C-F, Walther T, Srivastava A. Microarray Expression Profiling Identifies Differential Expression of Genes in the Developing Brain of Agtr2-/y Mice. Genomics 2009; 94:188-195.
  • Chen C-F, Cheng C-H. Regulation of cellular metabolism and cytokines by the medicinal herb feverfew in the human monocytic THP-1 cells. Evidence-based Complementart Alternative Med 2009; 61:91-98.
  • Collins JS, Canfield MA, Pearson K, Kirby RS, Case AP, Mai CT, Major J, Mulinare J. Public health projects for preventing the recurrence of neural tube defects in the United States. Birth Defects Res A Clin Mol Teratol 2009; 85:935-938.
  • Duron RM, Medina MT, Nicolás O, Varela FE, Battle S, Thompson A, Aguilar-Estrada RL, Pietsch-Escueta S, Collins JS, Holden KR. Adherence and complementary and alternative medicine use among Honduran people with epilepsy. Epilepsy Behav 2009; 14:645-650.
  • Hunter AGW, Collins JS, Deardorff MA, Krantz ID. Detailed assessment of the ear in Cornelia de Lange syndrome: comparison with a control sample using the new dysmorphology guidelines. Amer J Med Genet Part A 2009; 149A:2181-2192. PMCID: PMC2764032
  • Jackson PB, Luigi Boccuto L, Skinner C, Collins JS, Neri G, Gurrieri F, Schwartz CE. Further evidence that the rs1858830 C variant in the promoter region of the MET gene is associated with Autistic disorder. Autism Research 2009; 2:232-236.
  • Maghirang-Rodriguez R, Archie JG, Schwartz CE, Collins JS. The c.940G variant of the Microcephalin gene (MCPH1) is not associated with microcephaly or mental retardation. Amer J Med Genet Part A 2009; 149A:622-625.
  • Sarasua SM, Collins JS, Williamson D, Satten GA, Allen AS. Effect of population stratification on the identification of significant SNPs in genome wide association studies. BMC Proc 2009; 3:S13. PMCID: PMC2795903
  • Wang, L. (2009) Combining biochemical features and evolutionary information for predicting DNA-binding residues in protein sequences. In: Communications in Computer and Information Science, vol. 28, pp. 176-189. Springer.
  • Wang, L., Yang, M.Q. and Yang, J.Y. (2009) Prediction of DNA-binding residues from protein sequence information using random forests. BMC Genomics, 10:S1.

Bioinformatics Publications prior to 2009

Our Faculty & Staff

Clearing Div - do not delete (is not shown)

Current Projects

  • Abnormal gene methylation/expression – Chin-Fu Chen
  • Analysis of copy number variation - Chin-Fu Chen
  • Biological databases – LJ Wang, Chin-Fu Chen and Stephen McGee
  • Biological knowledge discovery – LJ Wang
  • Environmental epidemiology and nutritional genetics - Chin-Fu Chen and Sara Sarasua
  • Feature selection in genetic and genomic data - Chin-Fu Chen
  • Genomic data integration – LJ Wang and Ely Stein
  • Neural tube defect prevention
  • Next generation sequencing – Stephen McGee
  • Phelan-McDermid syndrome - Sara Sarasua and Chin-Fu Chen
  • SNP-based whole genome screening for disease genes - Sara Sarasua and Stephen McGee

Current Grant Standing

Type: Student Training Grant
Period:
January 1, 2010 to December 31, 2011
Agency: Phelan-McDermid Syndrome Foundation
Principal Investigator: Sara M. Sarasua, M.S.P.H.
“Genetic and epidemiologic characterization of 22q13 deletion syndrome”
The proposed research would bring together questionnaire and cytogenetic data on 22q13 deletion syndrome to investigate the role of individual deleted genes and environmental factors.

Type: Standard Grant #0960443
Period:
July 1, 2010 to June 30, 2013
Agency:
NSF
Principal Investigator: Philip Yu, Ph.D.
Co-Principal Investigator: Chin-Fu Chen, Ph.D.
“G-SESAME Cloud: A Dynamically Scalable Collaboration Community for Biological Knowledge Discovery”
The ultimate goal is to build a community-based scalable cloud computing infrastructure (G-SESAME Cloud) to help biological researchers disseminate their research results.

Type: R01
Period: April 1, 2011 to March 31, 2014
Agency: NIH NINDS
Principal Investigator: Charles E. Schwartz, Ph.D.
Co-Principal Investigator: Chin-Fu Chen, Ph.D.
"Identification of Novel X-linked Intellectual Disability Genes"