NSF CAREER Project: Analysis, Construction and Visualization of 3D Genome Structures

[Research] [Education] [Outreach] [People]

Research

Journal Publications

1. M. Zhu, X. Deng, T. Joshi, D. Xu, G. Stacey, J. Cheng. Reconstructing Differentially Co-expressed Gene Modules and Regulatory Networks of Soybean Cells. BMC Genomics, 13:434, 2012. [at BMC Genomics web site].

2. Z. Wang, R. Cao, K. Taylor, A. Briley, C. Caldwell, J. Cheng. The Properties of Genome Conformation and Spatial Gene Interaction and Regulation Networks of Normal and Malignant Human Cell Types. PLoS ONE. 8(3):e58793, 2013 [at PLoS ONE's web site].

3. M. Zhu, J. Dahmen, G. Stacey, J. Cheng. Predicting Gene Regulatory Networks of Soybean Nodulation from RNA-Seq Transcriptome Data. Submitted.

4. K.H. Taylor, A. Briley, Z. Wang, J. Cheng, H. Shi, C.W. Caldwell. Aberrant Epigenetic Gene Regulation in Lymphoid Malignancies. Seminars in Hematology. 50(1):38-47, 2013. [at Elsevier's web site].

Abstracts and Posters

1. Z. Wang, R. Cao, K. Taylor, A. Briley, C. Caldwell, J. Cheng. The Properties of Human Genome Conformation and Spatial Gene Interaction and Regulation Networks . Pacific Symposium on Biocomputing , Hawaii, 2013.

2. T. Trieu, J. Cheng. Consructing Three-Dimensional Structures of Human Chromosomes from Chromosmal Contact Data. Submitted.

3. S. Ahmed, J. Cheng. Iterative Reconstruction of Three-Dimensinal Structures of Human Genome from Chromosomal Contact Data. Submitted.

4. C. He, A.O. Wells, J. Cheng. GMol: A Tool for 3D Genome Structure Visualization. Submitted.

Presentations

1. J. Cheng. Computational Construction, Analysis and Application of Biological Networks. Wayne State University, Nov., 2012.

Theses & Dissertations

1. Zheng Wang. Revealing the Conformation and Properties of Human Genome, Protein Molecules, and Protein Domain Co-Occurrence Network. PhD Dissertation. University of Missouri, Columbia, 2012.

Bioinformatics Software and Data

Education

Courses

Computational Modeling of Molecular Structures (Spring, 2013)

Videos and Gallery

The video of modeling a 3D human chromosome structure using a contact-driven gradient descent method. (Publically demonstrated first on March 14 to K1-12 students during the 2013 College of Enginering E-Week). The video was composed by Trieu Tuan, a PhD student in the Computer Science Department.

Outreach

1. The E-Week Lab Exhibit for Columbia K1-12 Students, Computational Modeling of Genome Strucutres, College of Engineering, University of Missouri, Columbia, March, 2013.
2. Training a high school student intern (Charles Shang) in the summer, 2012. His work in our group won semi-finalist in 2012 Siemens Science Talent Search and 2013 Intel Science Talent Search.
3. The video recording the first part of the genome project presentation given to K1-12 students on March 14 during the College of Engineering E-Week Exhibit. The speaker is Avery Wells, an undergraduate student in the Computer Science Department at the University of Missouri.