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.

Current Projects

  • Biological databases – LJ Wang and Stephen McGee
  • Biological knowledge discovery – LJ Wang
  • Developmentof computational tools for data integration and functional prediction of human genetic variants - Chin-Fu Chen
  • 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
  • Network Biology of micro RNAs in human autism spectrum disorders - Chin-Fu Chen
  • Next generation sequencing – Stephen McGee and Katharine Kubiak
  • Phelan-McDermid syndrome - Sara Sarasua and Chin-Fu Chen
  • SNP-based whole genome screening for disease genes - Sara Sarasua and Stephen McGee

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 Jul 133(7):847-859. read abstract
  • 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):318-328. read abstract
  • Alexander M, Steck SE, Burch JB, Chen C-F, Hurley TG, Cavicchia P, Ray M,Nitin Shivappa N, Guess J, Zhang H, Youngstedt SD, Creek KE, Lloyd SC, Yang X, Hebert JR. 2014. Case-Control Study of the PERIOD3 Clock Gene Length Polymorphism and Colorectal Adenoma Formation. Oncol Rep (In press).
  • Tabung FK, Steck SE, Burch JB, Chen C-F, Zhang H, Hurley TG, Cavicchia P, Alexander M, Nitin Shivappa N, Creek KE, Lloyd SC, Hebert JR. 2014. A Healthy Lifestyle Index is associated with reduced risk of colorectal adenomatous polyps among non-users of non-steroidal anti-inflammatory drugs. J Prim Prev (In press).
  • Lee, G, Chen, C-F. 2014. MICO: A meta-tool for prediction of the effects of non-synonymous mutations. Bioinformation 10 (7): 469-471. read article
  • Zhou P, Zhang G, Chen S, Jiang Z, Tang Y, Henrissat B, Yan Q, Yang S, Chen C-F, Zhang B, Du Z. 2014. Genome sequence and transcriptome analyses of the thermophilic zygomycete fungus Rhizomucor miehei. BMC Genomics 15:294.

2013 Publications

  • 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. read article
  • Xu Y, Chen C-F, Thomas TP, Azadi P, Diehl B, Tsai C.-J.,Brown N, Carlson JE, Tien M, Liang H. 2013. Wood chemistry analysis and expression profiling of a poplar clone expressing a tyrosine-rich peptide. Plant Cell Rep 32:1827-41.
  • Schwartz CE, Chen C-F. 2013. Progress in Detecting Genetic Alterations and Their Association with Human Disease. J Mol Biol 425: 3914–3918. read abstract

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. read article

2011 Publications

  • Cummins A, Eggert J, Pruitt R, Collins JS. (2011) Huntington's Disease: implications for practice. Nurse Pract, 36:41-47. read article
  • Collins JS, Marvelle AF, Stevenson RE (2011) Sibling recurrence in intellectual disability of unknow cause. Clin Genet, 79:498-500. read article
  • 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. read article
  • 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. read article
  • Rollins JD, Sarasua SM, Phelan MC, DuPont BR, Rogers RC, Collins JS. (2011) Growth in Phelan-McDermid syndrome. Amer J Med Genet, in press.
  • 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; In press.
  • 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. (2010) Sequence feature-based prediction of protein stability changes upon amino acid substitutions. BMC Genomics, in press.
  • Wang, L., Huang, C., Yang, M.Q. and Yang, J.Y. (2010) BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features. BMC Systems Biology, in press.
  • Wang, L., Srivastava, A.K. and Schwartz, C.E. (2010) Microarray data integration for genome-wide analysis of human tissue-selective gene expression. BMC Genomics, in press.

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

 

    Current/Recent Grant Standing

    Period: July 1, 2014 to June 30, 2015
    Agency:
    Self Regional Healthcare
    Principal Investigator:
    LJ Wang, Ph.D.
    Co-Principal Investigator:
    Anand Srivastava, Ph.D.
    "Genome-wide identification of autism associated long non-coding RNAs and circular RNAs"

    Period: July 1, 2014 to June 30, 2015
    Agency: Self Regional Healthcare
    Principal Investigator: Luigi Boccuto, M.D.
    Additional Investigators: Charles Schwartz, Ph.D., Chin-Fu Chen, Ph.D., Delphine Dean, Ph.D., Kevin Champaigne, Ph.D.
    "Investigation of aberrant tryptophan metabolism as a biochemical basis for autism spectrum disorders"

    Period: July 1, 2014 to June 30, 2015
    Agency: Self Regional Healthcare
    Principal Investigator: Anand Srivastava, Ph.D.
    Additional Investigators: Alka Chaubey, Ph.D., Tim Wood, Ph.D., Roger Stevesnon, M.D., Laura Pollard, Ph.D., LJ Wanf, Ph.D., Feng Luo, PhD.
    "Understanding contributions of transcriptome and metabolome to autism risk: Identification of long non-coding RNA (lncRNA) and metabolome biomarkers and therapeutic targets for ASDs"

    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"