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. ‡ Student authors listed alphabetically.

Journal Articles (in reverse chronological order)

  1. Sumaira Zaman*, Samuel Sledzieski*, Bonnie Berger, Yi-Chieh Wu, and Mukul S. Bansal. “virDTL: Viral Recombination Analysis through Phylogenetic Reconciliation and its Application to Sarbecoviruses and SARS-CoV-2.” Journal of Computational Biology, 30(1):3–20, Jan 2023. [doi]
  2. Matthew LeMay, Ran Libeskind-Hadas, and Yi-Chieh Wu. “A Polynomial-Time Algorithm for Minimizing the Deep Coalescence Cost for Level-1 Species Networks.” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 19(5):2642–2653, Sep 2022. [doi]

  3. Santi Santichaivekin, Qing Yang, Jingyi Liu, Ross Mawhorter, Justin Jiang, Trenton Wesley, Yi-Chieh Wu, and Ran Libeskind-Hadas. “eMPRess: A Systematic Cophylogeny Reconciliation Tool.” Bioinformatics, In press, Nov 2020. [doi]

  4. 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]

  5. 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]

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

  7. 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]

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

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

  10. 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]

  11. 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]

  12. 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]

  13. 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]

  14. 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. Matthew LeMay, Yi-Chieh Wu, and Ran Libeskind-Hadas. “The Most Parsimonious Reconciliation Problem in the Presence of Incomplete Lineage Sorting and Hybridization is NP-Hard.” In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021), Virtual due to COVID-19, August 2-4, 2021. [doi]

  2. Morgan Carothers‡, Joseph Gardi, Gianluca Gross, Tatsuki Kuze, Nuo Liu, Fiona Plunkett, Julia Qian, and Yi-Chieh Wu. “An Integer Linear Programming Solution for the Most Parsimonious Reconciliation Problem under the Duplication-Loss-Coalescence Model.” In 11th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB 2020), Virtual due to COVID-19, September 21-24, 2020. [doi]

  3. Ross Mawhorter, Nuo Liu, Ran Libeskind-Hadas, and Yi-Chieh Wu. “Inferring Pareto-Optimal Reconciliations across Multiple Event Costs under the Duplication-Loss-Coalescence Model.” In 17th Annual International Conference on Research in Computational Molecular Biology Comparative Genomics Satellite (RECOMB-CG2019), Montpellier, France, October 1-4, 2019. BMC Bioinformatics, 20:639, Dec 2019. [doi]

  4. Haoxing Du*, Yi Sheng Ong*, Marina Knittel, Ross Mawhorter, Nuo Liu, Gianluca Gross, Reiko Tojo, Ran Libeskind-Hadas, and Yi-Chieh Wu. “Multiple Optimal Reconciliations under the Duplication-Loss Coalescence Model.” In 17th Asia Pacific Bioinformatics Conference (APBC 2019), Wuhan, China, January 14-16, 2019. [doi]

  5. Ricson Cheng, Matt Dohlen*, Chen Pekker*, Gabriel Quiroz, Jincheng Wang, Ran Libeskind-Hadas, and Yi-Chieh Wu. “Reconciliation Feasibility of Non-Binary Gene Trees under a Duplication-Loss-Coalescence Model.” In 5th International Conference on Algorithms for Computational Biology (AlCoB 2018), Hong Kong, June 25-27, 2018. [doi]

  6. Jordan Haack, Eli Zupke, Andrew Ramirez, Yi-Chieh Wu, and Ran Libeskind-Hadas. “Computing the Diameter of the Space of Maximum Parsimony Reconciliations in the Duplication-Transfer-Loss Model.” In 16th Asia Pacific Bioinformatics Conference (APBC 2018), Yokoohama, Japan, January 15-17, 2018. Best student paper award. [doi]

  7. 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]

  8. 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 05/24/2024.