Yi-Chieh (Jessica) Wu

About Me | Teaching | Research | Software

Research Interests

I am interested in topics that apply EECS to biological problems. Currently, I work on phylogenetics. In particular, I develop evolutionary models and algorithms for reconstructing gene histories across multiple species, with a goal of discovering how genes form and function.

Publications

Find me on Google Scholar.
Undergraduate authors underlined. * Equal contribution. † Co-senior authors.

Journal Articles (in reverse chronological order)

  1. Jennifer Rogers, Andrew Fishberg, Nora Youngs, and Yi-Chieh Wu. “Reconciliation feasibility in the presence of gene duplication, loss, and coalescence with multiple individuals per species.” BMC Bioinformatics, 18:292-, Jun 2017. [doi]

  2. Mukul S. Bansal*, Yi-Chieh Wu*, Eric J. Alm, and Manolis Kellis. “Improved Gene Tree error Correction in the Presence of Horizontal Gene Transfer.” Bioinformatics, 31(8):1211-1218, Apr 2015. [doi]

  3. Roadmap Epigenomics Consortium (96 authors). “Integrative Analysis of 111 Reference Human Epigenomes.” Nature, 518(7539):317-330, Feb 2015. [doi]

  4. Michael C. Fontaine*, James B. Pease*, Aaron Steele, Robert M. Waterhouse, Daniel E. Neafsey, Igor V. Sharakhov, Xiaofang Jiang, Andrew B. Hall, Flaminia Catteruccia, Evdoxia Kakani, Sara N. Mitchell, Yi-Chieh Wu, Hilary A. Smith, R. Rebecca Love, Mara K. Lawniczak, Michel A. Slotman, Scott J. Emrich, Matthew W. Hahn, and Nora J. Besansky. “Extensive Introgression in a Malaria Vector Species Complex Revealed by Phylogenomics.” Science, Jan 2015. [doi]

  5. The Anopheles Genomes Cluster Consortium (120 authors). “Highly Evolvable Malaria Vectors: The Genomes of 16 Anopheles Mosquitoes.” Science, 347(6217), Jan 2015. [doi]

  6. The Mouse ENCODE Consortium (138 authors). “A Comparative Encyclopedia of DNA Elements in the Mouse Genome.” Nature, 515(7527):355-364, Nov 2014. [doi]

  7. Alan P. Boyle*, Carlos L. Araya*, Cathleen Brdlik, Philip Cayting, Chao Cheng, Yong Cheng, Kathryn Gardner, LaDeana W. Hillier, Judith Janette, Lixia Jiang, Dionna Kasper, Trupti Kawli, Pouya Kheradpour, Anshul Kundaje, Jingyi Jessica Li, Lijia Ma, Wei Niu, E. Jay Rehm, Joel Rozowsky, Matthew Slattery, Rebecca Spokony, Robert Terrell, Dionne Vafeados, Daifeng Wang, Peter Weisdepp, Yi-Chieh Wu, Dan Xie, KoonKiu Yan, Elise A. Feingold, Peter J. Good, Michael J. Pazin, Haiyan Huang, Peter J. Bickel, Steven E. Brenner, Valerie Reinke, Robert H. Waterston, Mark Gerstein, Kevin P. White†, Manolis Kellis†, and Michael Snyder†. “Comparative Analysis of Regulatory Information and Circuits across Distant Species.” Nature, 512(7515):453-456, Aug 2014. [doi]

  8. Yi-Chieh Wu, Matthew D. Rasmussen*, Mukul S. Bansal*, and Manolis Kellis. “Most Parsimonious Reconciliation in the Presence of Gene Duplication, Loss, and Deep Coalescence using Labeled Coalescent Trees.” Genome Research, 24(3):475-486, Mar 2014. [doi]

  9. Yi-Chieh Wu, Matthew D. Rasmussen, Mukul S. Bansal, and Manolis Kellis. “TreeFix: Statistically Informed Gene Tree Error Correction Using Species Trees.” Systematic Biology, 62(1):110-120, Jan 2013. [doi]

  10. Yi-Chieh Wu, Matthew D. Rasmussen, and Manolis Kellis. “Evolution at the Subgene Level: Domain Rearrangements in the Drosophila Phylogeny.” Molecular Biology and Evolution, 29(2):689-705, Feb 2012. [doi]

  11. Preston B. Landon, Jose Gutierrez, John P. Ferraris, Itzel Lucio Martinez, Rajiv Giridharagopal, Yi-Chieh Wu, Sergey Lee, Kunjal Parikh, Jessica Gillespie, Geoffrey Ussery, Behzad Karimi, Ray Baughman, Anvar Zakhidov, and R. Glosser. “Inverse Gold Photonic Crystals and Conjugated Polymer Coated Opals for Functional Materials.” Physica B: Condensed Matter, 338(1-4):165-170, Oct 2003. [doi]

Conference Proceedings (in reverse chronological order)

  1. Bo Zhang and Yi-Chieh Wu. “Coestimation of Gene Trees and Reconciliations under a Duplication-Loss-Coalescence Model.” In 13th International Symposium on Bioinformatics Research and Applications (ISBRA 2017), Honolulu, HI, May 29-Jun 1, 2017. [doi]

  2. Ran Libeskind-Hadas, Yi-Chieh Wu, Mukul S. Bansal, and Manolis Kellis. “Pareto-optimal Phylogenetic Tree Reconciliation.” In 22nd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2014), Boston, MA, Jul 11-15, 2014. Bioinformatics, 30 (12): i87-i95, Jun 2014. [doi]

Last updated 07/31/2017.