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

[Research] [Software and Data] [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. BMC Bioinformatics. 14:278, 2013. [at BMC Bioinformatics' website].

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].

5. T. Trieu, J. Cheng. Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data. Nucleic Acids Research, accepted. [at NAR's website].

Conference Abstracts, Posters, and Presentations

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. (Poster presentation)

2. T. Trieu, J. Cheng. Consructing Three-Dimensional Structures of Human Chromosomes from Chromosmal Contact Data. Mid-South Computational Biology and Bioinformatics Conference, Columbia, MO, 2013. (Oral presentation).

3. S. Ahmed, J. Cheng. Iterative Reconstruction of Three-Dimensinal Structures of Human Genome from Chromosomal Contact Data. Mid-South Computational Biology and Bioinformatics Conference, Columbia, MO, 2013. (Poster presentation)

4. C. He, A.O. Wells, J. Cheng. GMol: A Tool for 3D Genome Structure Visualization. Mid-South Computational Biology and Bioinformatics Conference, Columbia, MO, 2013. (Poster presentation)

5. S. Ahmed, J. Cheng. Iterative Reconstruction of Three-Dimensinal Structures of Human Genome from Chromosomal Contact Data. Life Science Week Symposium, University of Missouri, Columbia, MO, 2013. (Poster presentation)

6. 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 . Mid-South Computational Biology and Bioinformatics Conference, Columbia, MO, 2013. (Oral presentation, won the first place award in the post-doctoral presentation category).

7. C. He, A.O. Wells, J. Cheng. GMol: A Tool for 3D Genome Structure Visualization. The Great Lake Bioinformatics Conference, Puttsburg, PA, 2013.(Poster presentation)

8. T. Trieu, J. Cheng. Consructing Three-Dimensional Structures of Human Chromosomes from Chromosmal Contact Data. Life Science Week, University of Missouri, Columbia, MO, 2013. (Poster presentation).

9. R. Cao, J. Cheng. Deciphering the Association between Gene Function and Spatial Gene-Gene Interactions in 3D Genome Conformation. The 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB). Berlin, Germany, 2013.

10. R. Cao, J. Cheng. Deciphering the Association between Gene Function and Spatial Gene-Gene Interactions in 3D Genome Conformation. The Automated Protein Function Annotation (AFA) SIG meeting of the 21st Annual International Conference on Intelligent Systems for Molecular Biology. Berlin, Germany, 2013.

Other Presentations of Genome Structure Modeling

4. J. Cheng. Analysis and Reconstruction of 3D Conformation of Human Genome. The Great Lake Bioinformatics Conference, Cincinati, OH, 2014.
3. J. Cheng. The Properties of 3D Human Genome. The ACM BCB Conference, Washington DC, Sept., 2013.
2. J. Cheng. Computational Modeling of 2D and 3D Human Genome Structure. Purdue University, April, 2013.
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.

Software and Data

  • The Hi-C data of three cells / cell lines (MHH-CALL4-CELL-LINE, Primary ALL B Cell, RL Cell Line published in Wang et al., PLoS ONE, 2013.
  • The 3D models of 23 pairs of chromosomes of healthy and luekemia B-cells constructed from Hi-C data published in Trieu and Cheng, Nucleic Acids Research, 2014.
  • Open source GMOL tool for visualizing 3D genome structures
  • Gene3D: an open source tool for reconstructing 3D genome structure from chromosomal conformation capturing (e.g. Hi-C) data.
  • 3D genome models of healthy and cancerous B-cells

  • Education

    Courses

  • Computational Modeling of Molecular Structures (Spring, 2013; Spring, 2014)

  • Computational Optimization Methods (Fall, 2013)

    • Videos and Gallery

  • The movie of folding / modeling Chromosome 11 of a human B-cell posted at YouTube.
  • 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.
    4. The video recording Avery Well's presentation to K12 students during 2014 College of Engineering's E-Week Exhibit at the University of Missouri, Columbia.

    News

  • Prof. Jianlin Cheng was honored as one of MU Chancellor's top achievers because of his work on this CAREEER project.
  • The research was featured in the Mizzou Alumni Magazine, 2013.
  • Cheng takes aim at genetic mysteries
  • Cheng receives NSF CAREER Award
  • Charles Shang Won Semi-Finalist of 2012 Simmens Science Talent Search
  • Charles Shang Won Semi-Finalist of 2013 Intel Science Talent Search

    • People

    Principle Investigator

    Dr. Jianlin Cheng

    Graduate Students

    Sharif Ahmed, Renzhi Cao, Chenfeng He, Tuan Anh Trieu, Dr. Zheng Wang (graduated in 2012), Lingfei Xu

    Undergraduate Students

    Avery Owen Wells, Jackson Nowotny, Sarah Kang, Hannah Wiedner, Nicholas Hunkins

    High School Students

    Charles Shang, Angela Zhang

    Contact

    Prof. Jianlin Jack Cheng

    Director of Bioinformatics, Data Mining and Machine Learning Laboratory

    Associate Professor
     Department of Computer Science
    Informatics Institute
    C. Bond Life Science Center
    College of Engineering
    University of Missouri, Columbia, MO 65211-2060

    Primary Office: EBW 109
    Secondary Office: LSC 271B
    Lab: EBN 304, 305, 307
    Phone: 573-882-7306
    Fax: 573-882-8318
    Email: chengji@missouri.edu