Jiping Wang, leader of the NU-PSOC Bioinformatics Core, will speak on Modeling causalities of mixed features in TCGA data using Bayesian network analysis at the 1st Annual ICBP/PSOC Mathematical and computational modeling meeting entitled, Modeling Cancer: Integrating Scales, Disciplines and Programs on February 25th in Tampa, FL. The three day meeting is sponsored by NCI¹s Integrative Cancer Biology Program (ICBP) & Physical Sciences in Oncology programs. The limited attendance format will enable participants to discuss theoretical tools and approaches in greater depth than is usually possible in larger program meetings with the goal of building a community resource in this topic area.
Wang is an associate professor and director of graduate studies in the department of physics. His NU-PSOC-funded research has deployed bioinformatics and computational biology aims to develop complex statistical methods for analysis of high throughput genomic and genetic data. His current projects include Expressed Sequence Tag (EST) data analysis, nucleosome sequence alignment and positioning prediction, human brain mapping, DNA methylation differentiation and tRNA inter-positional association. He has developed multiple software tools to support these efforts that he freely shares, including: ESTstat (EST), NuPoP (nucleosome) and SPECIES (species number estimation). Sample publications associated with his role in the NU-PSOC include:
1. Popovic, R., Martinez-Garcia, E., Giannopoulou, E., Zhang, Q., Ezponda, T., Shah, M.Y., Zheng, Y., Will, C.M., Small, E.C., Hua, Y., Bulic, M., Jiang, Y., Carrara, M., Calogero, R.A., Kath, W.L., Kelleher, N.L., Wang, J.-P., Elemento, O. and Licht, J.D., Histone methyltransferase MMSET/NSD2 alters EZH2 binding and reprograms the myeloma epigenome through global and focal changes in H3K36 and H3K27 methylation, PLoS Genetics 2014,10(9): e1004566, doi: 10.1371/journal.pgen.1004566 .
2. Small, E.C., Xi, L., Wang, J.-P., Widom, J., and Licht, J.D., Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity. PNAS 2014,111(24):E2462-71,doi: 10.1073/pnas. 1400517111.
3. Henikoff, S., Ramachandran, S., Krassovsky, K., Bryson, E.D., Codomo, C.A., Brogaard, K., Widom, J., Wang, J.-P., Henikoff, J.G., The budding yeast centromere DNA element II wraps a stable Cse4 hemisome in either orientation in vivo, eLife, 2014, 3:e01861.
4. Xi, L., Brogaard,K., Zhang, Q., Lindsay, B.G., Widom, J., and Wang, J.-P., A locally convoluted cluster model for nucleosome positioning signals in chemical map, Journal of American Statistical Association 2014, 109 (505):48-62, DOI:10.1080/01621459.2013.862169
5. Moyle-Heyrman, G., Zaichuk, T., Xi, L., Zhang, Q., Uhlenbeck, O.C., Holmgren, R., Widom, J. and Wang, J.-P., Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning. PNAS 2013,110(50),20158-20163 pdf; Supplementary materials
6. McCallum, K.J. and Wang, J.-P., Quantifying copy number variations using a hidden Markov model with inhomogeneous emission distributions. Biostatistics 2013, Jul;14(3):600-11. doi: 10.1093/ biostatistics/kxt003
7. Nalabothula,N., Xi,L., Bhattacharyya,S., Widom,J., Wang, J.-P., Reeve,NJ, Santangelo, JT, Fondufe-Mittendorf, NY, Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs. BMC Genomics 2013, 14:391 PDF
8. Yigit, E., Zhang, Q., Xi, L., Grilley, D., Widom, J., Wang, J.-P., Rao, A. and Pipkin, M.E. High-resolution nucleosome mapping of targeted regions using BAC-based enrichment. Nucleic Acids Res. 2013;doi: 10.1093/ nar/gkt081 PDF;Supplementary materials
9. Brogaard, K., Xi, L., Wang, J.-P., and Widom, J., A chemical approach to mapping nucleosomes at base pair resolution. Methods Enzymol. 2012;513:315-34
10. Brogaard, K., Xi, L., Wang, J.-P., and Widom, J., A map of nucleosome positions in yeast at base-pair resolution Nature, 2012, 486: 496501. Online Supplementary Methods; Other supplementary materials