Welcome to Our Lab

csbl_logo miniThe Computational Systems Biology Lab (CSBL) consists of scientists with highly diversified training background, ranging from biochemistry, computational chemistry, molecular biology, biophysics, physics to computer science, statistics and mathematics.

Our common interests are in development of computational tools for solving biological problems. Our work ranges from construction of mathematical/statistical models to development of algorithms to code implementation to applications of computational tools to solve various bio-data analysis and modeling problems.

Lab Accomplishments

$16 million - Value of Funded Projects
6900 - Google Scholar Citations
12 - Lab Grads in Tenure Track Positions

Our Focus

Cancer Research

  • Mechanisms of cancer initiation, progression, metastasis and post-metastasis development guided by large-scale omic data analyses of cancer tissue samples, statistical inference and computational modeling
  • Depiction of the internal stresses in cancer microenvironment and their corresponding responses
  • Development of diagnostic markers for cancer detection as well as the development of possible drug targets

Biofuels

  • Identification of key enzymes for converting (hemi)cellulose into ethanol in bacteria
  • Prediction of key metabolic pathways for (hemi)cellulose degradation
  • Identification of key enzymes for synthesis of (hemi)cellulose in plants
  • Prediction of key metabolic pathways for (hemi)cellulose synthesis

Publications

All Publications

Most Cited Paper

AD Williams, E Portelius, I Kheterpal, JT Guo, KD Cook, Y Xu, R Wetzel, Mapping Aβ amyloid fibril secondary structure using scanning proline mutagenesis, Journal of Molecular Biology, 335 (3), 833-842

Newest Paper on Software Tools

X Mao, Q Ma, C Zhou, X Chen, H Zhang, J Yang, F Mao, W Lai, Y Xu, DOOR 2.0: presenting operons and their functions through dynamic and integrated views, Nucleic Acids Research, 42 (D1), D654-D659

Newest Paper on Biofuels Research

Qin Ma, Hanyuan Zhang*, Xizeng Mao, Chuan Zhou, Bingqiang Liu, Xin Chen, Ying Xu, DMINDA: An integrated web server for DNA motif identification and analysis, Nucleic Acids Research, 2014, doi: 10.1093/nar/gku315

Newest Paper on Cancer Research

Chi Zhang, Sha Cao, Bryan P. Toole, and Ying Xu, Cancer may be a pathway to cell survival under persistent hypoxia and elevated ROS: A model for solid-cancer initiation and early development, International Journal of Cancer, 2014, doi: 10.1002/ijc.28975

Our collaborators

Current Projects

University of Connecticut
Jilin University
NIH
BESC
NSF

More on Our Research

Meet our lab members

Cancer Computational and Systems Biology

We are interested in developing integrated computational and omic techniques for (a) identification of biomarkers for a number of human cancers, detetable through analyses of serum/urine samples, and (b) understanding the relationships between molecular signatures and cancer formation & development. Our work involves microarray gene expression data generation and analyses, comparative genome analyses and analyses of other experimental data.

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Computational Study of Plant Cell-wall Synthesis Genes and Pathways

We are interested in developing computational prediction and analysis techniques for inference of genes involved in cell wall synthesis in plants and regulatory elements of these genes & their relevant biochemical pathways. Our work currently involves prediction and analyses of protein-protein interactins relevant to cell wall synthesis, prediction of Golgi-residing proteins, bi-clustering analyses of microarray gene expression data and co-evolutionary analyses of cell-wall synthesis genes.

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Principal Investigator

Ying Founder
Ying Xu, Ph.D.

Regents-GRA Eminent Scholar Chair and Professor Department of Biochemistry and Molecular Biology

Biofuels Research

Qin Square
Qin Ma, Ph.D.
Post Doctoral Research Associate
Xizeng Square
Xizeng Mao, Ph.D.
Assistant Research Scientist
Fei Square
Fei Ji
Graduate Student
Chunguo Square
Chunguo Wu, Ph.D.
Scholar in Residence

Cancer Research

Xizeng Square
Xizeng Mao, Ph.D.
Assistant Research Scientist
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Sha Cao
Graduate Student
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Chi Zhang
Graduate Student
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Chao Liu
Graduate Student
Xin Square
Xin Chen
Graduate Student
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Dorothy Hammond
Graduate Student
Hanyuan Square
Hanyuan Zhang
Graduate Student