Chun Ye

 
 

I’m interested in developing and applying statistical methods that integrate data from high throughput technologies such as gene expression, genotyping and chIP-chip to understand how transcription regulatory networks can be perturbed to give rise to phenotypic differences.  Much of my work is interdisciplinary and as such I’m interested in both theoretical problems such as significance testing, statistical modeling, multiple hypothesis testing, causal inference and network reconstruction as well as their application to biological data.  Recently at the Broad, I have been actively participating not only on the development of new methodologies but also on the design and development of new biological experiments to generate informative primary data that we can learn structure from.

 

Mailing Address

Chun (Jimmie) Ye

7 Cambridge Center #6029

The Broad Institute

Cambridge, MA  02142


Email

yechun AT broadinstitute DOT org


Detailed CV

Bio Updates

Publications

  1. •Buhm Han, Chun Ye, Ted Choi, Eleazar Eskin.

  2. “Leveraging joint test status distribution for an optimal significance testing.”

  3. In Proceedings of NIPS 2009 Workshop on Machine Learning in Computational Biology.  Whistler, Canada:  December 11th, 2009.


  1. •Chun Ye, Simon Galbraith, James Liao, Eleazar Eskin.

  2. “Using Network Component Analysis to Dissect Regulatory Networks Mediated by Transcription Factors in Yeast.”

  3. PLoS Computation Biology.  5(3):e1000311, March 2009.

  4. •Eun Yong Kang, Hyun Min Kang, Chun Ye, Ilya Shpitser, Eleazar Eskin. 

  5. “Detecting the presence and absence of causal relationships between expression of yeast genes with very few samples.”

  6. In Proceedings of the Thirteenth Annual International Conference on Research in Computational Molecular Biology.  Tucson, Arizona:  May 18-21, 2009.

  7. •Eun Yong Kang, Hyun Min Kang, Chun Ye, Ilya Shpitser, Eleazar Eskin. 

  8. “Detecting the presence and absence of causal relationships between expression of yeast genes with very few samples.” 

  9. In Proceedings of NIPS 2008 Workshop on Machine Learning in Computational Biology.  Whistler, Canada:  December 12th, 2008.

  10. •Hyun Min Kang, Chun Ye, Eleazar Eskin. 

  11. “Accurate discovery of expression quantitative trait Loci under confounding from spurious and genuine regulatory hotspots.” 

  12. Genetics. 180(4):1909-25, 2008.

  13. •Chun Ye, Eleazar Eskin. 

  14. “Discovering tightly regulated and differentially expressed gene sets in whole genome expression data.” 

  15. Bioinformatics.  23(2):e84-90, 2007.

  16. •Chun Ye, Eleazar Eskin. 

  17. “Discovering tightly regulated and differentially expressed gene sets in whole genome expression data.” 

  18. In Proceedings of the 5th European Conference on Computaional Biology (ECCB-2006). Eilat, Israel: January 21st-24th, 2007.

  19. •Chun Ye, Matthew A. Zapala, Hyun Min Kang, Jennifer Wessel, Eleazar Eskin, Nicholas Schork. 

  20. “High-density QTL mapping to identify phenotypes and loci influencing gene expression patterns in entire biochemical pathways.” 

  21. In Proceedings of the Second RECOMB Satellite Workshop of Systems Biology.  San Diego, CA: December 1st-2nd, 2006.

  22. •Ali Bashir, Chun Ye, Alkes L. Price, Vineet Bafna. 

  23. “Orthologous repeats and mammalian phylogenetic inference.” 

  24. Genome Res.  2005 Jul;15(7):998-1006.

  25. •Martin Tompa, Nan Li, Timothy L. Bailey, George M. Church, Bart De Moor, Eleazar Eskin, Alexander V. Favorov, Martin C. Frith, Yutao Fu, W. James Kent, Vsevolod J. Makeev, Andrei A. Mironov, William Stafford Noble, Giulio Pavesi, Graziano Pesole, Mireille Regnier, Nicolas Simonis, Saurabh Sinha, Gert Thijs, Jacques van Helden, Mathias Vandenbogaert, Zhiping Weng, Christopher Workman, Chun Ye, Zhou Zhu.

  26. “Assessing computational tools for the discovery of transcription factor binding sites.”

  27. Nature Biotechnology. 23(1):137-44. 2005.

Hi!  I have recently started a post doctoral position at The Broad Institute in Dr. Aviv Regev’s lab.  I received my Ph.D. last December from the University of California, San Diego in the Bioinformatics and Systems Program.  My advisor was Dr. Eleazar Eskin, Assistant Professor in the Departments of Computer Science and Human Genetics at the University of California, Los Angeles.  Some of my previous collaborators include Dr. James C. Liao and Dr. Aldons “Jake” Lusis at UCLA, Dr. Nicholas Schork at The Scripps Research Institute, Dr. Ted Choi at Predictive Biology, Dr. Doug Fenger at Amylin Pharmaceuticals and Dr. Vineet Bafna at UCSD.

Research Interests