Abstract

Developed an application for generation of phenotypic prototypes using simulated annealing (SAModk-prototypes). The application uses k-mode and k-means style clustering of categorical histopathology observations and numeric gene expression and clinical chemistry data respectively via simulated annealing optimization to cluster biological samples into groups which share phenotypic responses to stimuli. The clustering of the samples using SAModk-prototypes and all the data together performs better than clustering of the data using any one of the data domains separately or pairwise combinations of the data.? ? --------------------------------------------------------------------------------------------------? ? Developed a software for biclustering of gene expression data using phenotypic measurements to constraint the clustering of the genes or by unsupervised clustering. The biclusters are phenotypically anchored to the gene expression. Constraining the clusters by Gene Onology biological processes was investigated. ? ? --------------------------------------------------------------------------------------------------? ? Performed scanning of the rat genome to search for patterns of DNA sequence and motifs. The association of genome characteristics with differential expression of environmentally responsive genes was explored. ? ? --------------------------------------------------------------------------------------------------? ? Developed the MicroArray Project System (MAPS) database for more customized management of experimental information and data from microarray studies. ? ? --------------------------------------------------------------------------------------------------? ? Developed computational means to analyze the S. pombe (yeast) genome across multiple time series experiments and to find transcription factor-gene regulatory units. In addition, circle-circle regression modeling was performed on subsets of S. pombe cyclic genes to determine coherence between 10 time series experiments.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of Environmental Health Sciences (NIEHS)
Type
Intramural Research (Z01)
Project #
1Z01ES102345-02
Application #
7734565
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
2
Fiscal Year
2008
Total Cost
$1,155,605
Indirect Cost

  Institution

Name
National Institute of Environmental Health Sciences
Department
Type
DUNS #
City
State
Country
United States
Zip Code

  Publications

SEQC/MAQC-III Consortium (2014) A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat Biotechnol 32:903-14
Farnan, Laura; Ivanova, Anastasia; Peddada, Shyamal D (2014) Linear mixed effects models under inequality constraints with applications. PLoS One 9:e84778
Huang, Lingkang; Zhang, Hao Helen; Zeng, Zhao-Bang et al. (2013) Improved Sparse Multi-Class SVM and Its Application for Gene Selection in Cancer Classification. Cancer Inform 12:143-53
Lu, Jun; Bushel, Pierre R (2013) Dynamic expression of 3' UTRs revealed by Poisson hidden Markov modeling of RNA-Seq: implications in gene expression profiling. Gene 527:616-23
Davis, Barbara J; Risinger, John I; Chandramouli, Gadisetti V R et al. (2013) Gene expression in uterine leiomyoma from tumors likely to be growing (from black women over 35) and tumors likely to be non-growing (from white women over 35). PLoS One 8:e63909
Huda, Ahsan; Bushel, Pierre R (2013) Widespread Exonization of Transposable Elements in Human Coding Sequences is Associated with Epigenetic Regulation of Transcription. Transcr Open Access 1:
Williams-DeVane, Clarlynda R; Reif, David M; Hubal, Elaine Cohen et al. (2013) Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes. BMC Syst Biol 7:119
Zhang, Liwen; Simpson, Dennis A; Innes, Cynthia L et al. (2013) Gene expression signatures but not cell cycle checkpoint functions distinguish AT carriers from normal individuals. Physiol Genomics 45:907-16
Corton, J Christopher; Bushel, Pierre R; Fostel, Jennifer et al. (2012) Sources of variance in baseline gene expression in the rodent liver. Mutat Res 746:104-12
Zhang, Liwen; Bushel, Pierre R; Chou, Jeff et al. (2012) Identification of Identical Transcript Changes in Liver and Whole Blood during Acetaminophen Toxicity. Front Genet 3:162

Showing the most recent 10 out of 28 publications