| Research |
Cancer Genomics and Precision Medicine
Cancer is one of the leading causes of death and is the most costly disease. Using computational and integrative approaches, we aim to
understand better the heterogeneity of cancer and apply the understanding to precision medicine.
Selected publications in cancer health disparities:
- P A Stewart, J Luks, M D Roycik, Q A Sang, and J Zhang (2013)
Differentially Expressed Transcripts and Dysregulated Signaling Pathways and Networks in African American Breast Cancer.
PLoS One, 8(12): e82460.
- Kaixian Yu, Albert Steppi, Yun Xu, Ke Tang, Jinfeng Zhang. Differential DNA methylation and network analysis in African American breast cancer. In: Proceedings of the Eighth AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; Nov 13-16, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2016;25(3 Suppl):Abstract nr A04.
- Kaixian Yu, Yun Xu, Ke Tang, Albert Steppi, Jinfeng Zhang. Biological factors associated with cancer health disparity - a high-throughput approach using big data. In: Proceedings of the Eighth AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; Nov 13-16, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2016;25(3 Suppl):Abstract nr A05.
Selected publications in precision medicine:
- Kaixian Yu, Qingxiang Amy Sang, Winston Tan, Mayassa B Dargham, Ty Lively, Cedric Shefield, Jun S Liu, Jinfeng Zhang,
Personalized chemotherapy regimen selection for breast cancer. Proceedings of AACR 2016. Abstract # 2034.
Biological text mining and knowledge discovery
Traditionally, biomedical knowledge is stored in scientific publications. Reading published papers, reviews and books is the way
to grasp what has been discovered and known in a particular scientific field. As scientific publications are being accumulated at an
ever increasing speed, automatic extraction and effective organization of such information become critical for the integrative analysis of
existing knowledge and experimental data.
Selected publication and database/webserver:
Lindsey Bell, Rajesh Chowdhary, Jun S Liu, Xufeng Niu, Jinfeng Zhang. Integrated bio-entity network: a system
for biological knowledge discovery. PLoS ONE, 2011, 6(6): e21474, doi:10.1371/journal.pone.0021474.
R Chowdhary, J Zhang, JS Liu.
Bayesian Inference of Protein-protein Interactions from Biological Literature , Bioinformatics, 25(12), 1536-1542 (2009).
Protein-protein interaction extraction server: BioTextMiner.com
An integrated molecular interaction database:
| Understanding the sequence-structure-function relationship of proteins
Proteins, the machines of life, are involved in most biological processes.
Protein functions are determined by their structures, which is in turn determined by their sequences.
We aim to achieve a better understanding of the sequence-structure-function relationship of proteins through computational approaches.
In the past, we have worked on various problems from protein packing, energy functions for simplified models,
side chain packing and side chain entropy, protein interactions, protein folding, loop modeling, and structure prediction.
J Laborde, D Robinson, A Srivastava, E Klassen and J Zhang,
RNA global alignment in the joint sequence-structure space using Elastic Shape Analysis,
Nucl. Acids Res. (2013) 41 (11): e114. doi: 10.1093/nar/gkt187
W Liu, A Srivastava, J Zhang. A mathematical
framework for protein structure comparison. PLoS Computational Biology 7(2),
(2011): e1001075. doi:10.1371/journal.pcbi.1001075.
J Zhang, SC Kou, JS Liu.
Biopolymer structure simulation and optimization via fragment regrowth Monte Carlo. Journal of Chemical Physics, 126, 225101, (2007).
J Zhang, M Lin, R Chen, J Liang, JS Liu. Monte
Carlo sampling of near-native structures of proteins and applications, Proteins, 66, 61-68, (2007)
J Zhang, JS Liu. On
side-chain conformational entropy of proteins. PLoS Computational Biology, 2(12): e168. doi:10.1371/journal.pcbi.0020168, (2006)