YI-CHIEH (JESSICA) WU
yjw@mit.edu
http://www.mit.edu/~yjw
MIT EECS Dept.
77 Massachusetts Avenue, 32-D510
Cambridge, MA 02139 USA
Office: (617) 253-3434, Cell: (832) 483-0499
EDUCATION
Massachusetts Institute of Technology
Cambridge, MA
Ph.D. in Electrical Engineering and Computer Science
Expected Feb 2014
Proposed Thesis: Models and Algorithms for Phylogenetic Inference: Incorporating SubGene Evolution, Statistical Uncertainty, and Population Genetics
Research Advisor: Manolis Kellis
Thesis Committee: Constantinos Daskalakis, Eric Alm, Daniel Hartl
GPA: 5.0/5.0
S.M. in Electrical Engineering and Computer Science
June 2009
Thesis: Deciphering the Neural Code for Retinal Ganglion Cells through Statistical Inference
Research Advisor: John L. Wyatt
GPA: 5.0/5.0
Rice University
Houston, TX
B.S.E.E. (Electrical Engineering), specialization in Systems
May 2007
GPA: 4.05/4.33. Honors: Summa Cum Laude; President’s Honor Roll, All Semesters
Hong Kong University of Science and Technology
Kowloon, Hong Kong
Rice University Study Abroad, School of Electrical and Electronic Engineering
Spring 2006
GPA: 11.63/12. Honors: Dean’s List
PUBLICATIONS
Journal Articles
[J1]
Yi-Chieh Wu, Matthew D. Rasmussen, Mukul S. Bansal, Manolis Kellis. “TreeFix:
Statistically Informed Gene Tree Error Correction using Species Trees.” Systematic
Biology, 62 (1): 110-120, Jan. 2013.
[J2]
Yi-Chieh Wu, Matthew D. Rasmussen, Manolis Kellis. “Evolution at the Sub-gene Level:
Domain Rearrangements in the Drosophila Phylogeny.” Molecular Biology and Evolution,
29 (2): 689-705, Feb. 2012.
[J3]
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, 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.
Journal Articles in Preparation/Submitted
[J4]
Yi-Chieh Wu, Matthew D. Rasmussen*, Mukul S. Bansal*, Manolis Kellis. “Most
Parsimonious Reconciliation in the Presence of Gene Duplication, Loss, and Deep
Coalescence using Labeled Coalescent Trees.” Revise and resubmit.
[J5]
Mukul S. Bansal*, Yi-Chieh Wu*, Eric J. Alm, Manolis Kellis. “Improved Gene Tree
Reconstruction for Deciphering Microbial Evolution.” Under review.
[J6]
Yi-Chieh Wu, Mukul S. Bansal, Matthew D. Rasmussen, Javier Herrero, Manolis Kellis.
“Phylogenetic Identification and Functional Characterization of Orthologous and
Paralogous Genes across Human, Mouse, Fly, Worm and Yeast.” In prep.
[J7]
The Mouse ENCODE Consortium. “An Integrated and Comparative Encyclopedia of DNA
Elements in the Mouse Genome.” Under review.
[J8]
Alan P. Boyle*, Carlos L. Araya*, Cathleen Brdlik, Philip Cayting, Chao Cheng, Yong
Cheng, Kathryn Gardner, LaDeana Hillier, Judith Janette, Lixia Jiang, Dionna Kasper,
Trupti Kawli, Pouya Kheradpour, Anshul Kundaje, 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, Koon-Kiu Yan, Elise A. Feingold,
Peter J. Good, Michael J. Pazin, Valerie Reinke, Robert H. Waterston, Mark Gerstein,
Kevin P. White†, Manolis Kellis†, Michael Snyder†, the modENCODE and ENCODE
Consortia. “Comparative Analysis of Regulatory Information and Circuits across Diverse
Species.” In prep.
[J9]
Yi-Chieh Wu, Steven F. Stasheff, Ofer Ziv, John L. Wyatt. “Deciphering Retinal Ganglion
Cell Output through Maximum Likelihood.” In prep.
[J10] Yi-Chieh Wu, John L. Wyatt. “Closed-Form Calculation of the Response of Retinal
Ganglion Cell Models to a Class of Moving Visual Inputs.” In prep.
Conference Posters
[P1] Yi-Chieh Wu, Matthew D. Rasmussen, Mukul S. Bansal, Manolis Kellis. “Inferring Gene
Duplications and Losses in the Presence of Incomplete Lineage Sorting.” SMBE 2013,
July 7-11, 2013. Chicago, IL.
[P2] Mukul S. Bansal, Yi-Chieh Wu, Eric J. Alm, Manolis Kellis. “Understanding Gene Family
Evolution by Gene Duplication, Horizontal Transfer, and Loss.” Broad Retreat 2012, Nov
12-13, 2012. Boston, MA.
[P3] Yi-Chieh Wu, Matthew D. Rasmussen, Manolis Kellis. “Evolution at the Sub-gene Level:
Domain Rearrangements in the Drosophila Phylogeny.” 16th Evolutionary Biology
Meeting. Sep 18-21, 2012. Marseilles, France.
[P4] Yi-Chieh Wu, Matthew D. Rasmussen, Mukul S. Bansal, Manolis Kellis. “TreeFix:
Statistically Informed Gene Tree Error Correction using Species Trees.” Broad Retreat
2011, Nov 7-8, 2011. Boston, MA.
[P5] Yi-Chieh Wu, Matthew D. Rasmussen, Manolis Kellis. “Evolution at the Sub-gene Level:
Domain Rearrangements in Drosophila.” CRA-W Grad Cohort 2010, Apr 23-24, 2010.
Seattle, WA.
[P6] Yi-Chieh Wu, Steven F. Stasheff, Ofer Ziv, John L. Wyatt. “Deciphering the Retinal Neural
Code through Statistical Inference.” MIT EECS MasterWorks 2009, May 5, 2009.
Cambridge, MA.
*
†
Equal contribution.
Co-senior authors.
[P7] John L. Wyatt, Jr, Stavros Valavanis, Yi-Chieh Wu, Shamim Nemati, Adam Eisenman,
Shelley Fried, Steven Stasheff, Joseph F. Rizzo. “A Likelihood Method for Estimating
Visual Motion Parameters from Retinal Ganglion Cell Responses.” ARVO Annual
Meeting, Apr 27-May 1, 2008. Fort Lauderdale, FL.
[P8] Yi-Chieh Wu, Amarda Shehu, Lydia Kavraki. “Modeling Protein Flexibility with Spatial and
Energetic Constraints.” Rice University Computer Science Corporate Affiliates Meeting.
Dec 5, 2005. Poster competition, first place winner. Houston, TX.
TALKS
Conferences and Workshops
[T1] “Most Parsimonious Reconciliation in the Presence of Gene Duplication, Loss, and Deep
Coalescence using Labeled Coalescent Trees.” Boston Evolutionary Genomics
Supergroup Retreat. August 30, 2013. Cambridge, MA.
[T2] “ENCODE/modENCODE Ortholog Resource.” Encode AWG/PI Meeting. May 22-23,
2012. Cambridge, MA.
[T3] “Accounting for sub-gene evolution and statistical uncertainty in phylogenetic
reconstruction.” NIMBioS Working Group: Gene Tree Reconciliation. Aug 11, 2011.
Knoxville, TN.
[T4] “Deciphering the Retinal Neural Code through Statistical Inference.” MIT 14th Annual
LIDS Student Conference. Jan 29-30, 2009. Cambridge, MA.
RESEARCH EXPERIENCE
Computational Biology Group, Computer Science and Artificial
Cambridge, MA
Intelligence Laboratory, MIT
Jun. 2009 - present
Research Assistant
Supervisor: Dr. Manolis Kellis
Studied principles underlying gene and genome evolution through phylogenetics and
comparative genomics. Developed algorithms for (1) inferring evolutionary domains and
reconstructing their most parsimonious history, (2) accounting for topological uncertainty in gene
trees by combining sequence data and gene tree-species tree reconciliation in a statistical
framework and (3) inferring gene duplications and losses in the presence of incomplete lineage
sorting through maximum parsimony. Analyzed fly, worm, human, and mouse genomes.
Retinal Implant Research Group, Research Laboratory of
Cambridge, MA
Electronics, MIT
Sep. 2007 - Jun. 2009
Research Assistant
Supervisor: Dr. John L. Wyatt
Developed neural models and information coding algorithms to analyze retinal ganglion cell
spike trains. Incorporated receptive field models into a statistical inference framework to
estimate visual stimuli parameters. Focused on population recordings and reconstruction of
global motion parameters and natural images.
Physical and Biological Computing Group, Rice University
Houston, TX
Research Assistant
Supervisor: Dr. Lydia Kavraki
Jan. 2005 - Aug. 2005
Developed computational models of protein structure and function. Worked on project to predict
protein function through geometric structural comparison. Modeled protein flexibility at the
binding site by generating physical conformations along its principal components.
Nanophysics for Devices Group, University of Texas at Dallas
Richardson, TX
Research Intern
Supervisor: Dr. Anvar Zakhidov
Jun. 2002 - Jul. 2002
Part of Welch Summer Scholar Program. Synthesized colloids and analyzed their structures
and characteristics. Focused on engineering conjugated polymer coated silica and yeast cells
for use as photonic crystals.
RESEARCH INTERESTS
Phylogenetics and comparative genomics.
Applications of EECS to biological problems, in particular in the fields of computational biology,
neuroscience, and representations of natural signals.
TEACHING EXPERIENCE
MIT, Women’s Technology Program
Cambridge, MA
Computer Science Instructor
Supervisor: Cynthia Skier
Summer 2012
WTP is a rigorous four-week summer academic and residential program in which female high
school students explore engineering through hands-on classes, labs, and team-based projects.
Taught forty rising seniors how to think computationally and program in Python. Also developed
curriculum, including planning daily class lectures, labs, and projects, selecting readings, and
creating homework assignments, and supervised and mentored three tutors.
Science Club for Girls
Cambridge, MA
Mentor Scientist
Supervisor: Karen O’Neill
Spring 2010
SCFG works to build the self-confidence and science literacy of girls grades K-12 belonging to
underrepresented groups in the science through free, after-school based experiential learning,
mentorship, and leadership opportunities. Worked with two co-mentors at Cambridgeport
Elementary School, leading ~10 second grade students in making maps and models of the
human body.
MIT, Dept of Electrical and Computer Engineering
Cambridge, MA
As a co-instructor, taught classes of twenty to forty students. Held biweekly lectures and weekly
office hours. Prepared lecture materials, problem sets, and solutions; graded problem sets;
assigned grades; and maintained course webpage. As a teaching assistant, taught three
weekly tutorial sections of up to ten students, conducted exam reviews, and held weekly office
hours. Prepared handouts, problem sets, exams, and solutions. Graded exams and assigned
grades in cooperation with the entire teaching staff. As a grader, graded weekly problem sets.
Grader, Introduction to Inference (6.S080)
Grader, Digital Image Processing (6.344)
Tutor, Signals and Systems (6.003) through MIT HKN
Co-Instructor, Review of Signals and Systems (6.097)
Grader, Discrete-Time Signal Processing (6.341)
Co-Instructor, Linear Algebra and Differential Equations Review (6.913)
Teaching Assistant, Probabilistic Systems Analysis (6.041)
Fall 2012
Spring 2011
Spring 2009
Winter 2009,
Winter 2010
Fall 2008, Fall 2009,
Fall 2010, Fall 2011
Winter 2008
Fall 2007
Rice University, Dept of Electrical Engineering, Dept of Computer
Houston, TX
Science, Dept of Computational and Applied Mathematics
As a course assistant in CS, assisted students in designing, implementing, and delivering a
product to an academic or industrial customer. Evaluated technical aspects of project and nontechnical aspects of class management, graded weekly progress reports and biweekly
deliverables, and evaluated the final product and presentation. As a course assistant in EE, led
weekly two-hour discussion sessions with up to 35 students, conducted exam reviews, and
evaluated semester projects. As a lab assistant, conducted weekly lab lectures or assisted in
weekly lab sessions, held office hours, and graded problem sets.
Course Assistant, Real-World Software Engineering (COMP 415)
Course Assistant, Software Construction Methodology (COMP 410)
Course Assistant, Signals and Systems (ELEC 301)
Course Assistant, Fundamentals of Electrical Engineering (ELEC 241)
Lab Assistant, Fundamentals of Computer Engineering (ELEC 220)
Lab Assistant, Introduction to Engineering Computation (CAAM 201)
Scholastic Tutors
Tutor, Algebra II
Spring 2007
Fall 2006
Fall 2006
Fall 2005
Spring 2005
Fall 2004, Fall 2005
Houston, TX
Aug. 2002 - May 2003
INDUSTRY EXPERIENCE
National Instruments
Austin, TX
Software Engineer Intern - High-Frequency Measurements Group
May 2007 - Aug. 2007
Added PM/PSK functionality to a RF signal generator. Developed an IVI-compliant driver for a
USB power sensor. Programming language: C/C++. Manager: Mr. Evan Cone.
Microsoft Corporation
Redmond, WA
Software Design Engineer in Test Intern - Unified Communications Group May 2006 - Aug. 2006
Developed an automated solution to service deployment of Microsoft Communicator for use in
testing and preproduction. Programming language: C#. Manager: Mr. Achal Shah.
AWARDS AND HONORS
MIT/Whitehead/Broad Computational Genetics Training Program Fellowship, awarded Oct. 2012
Kambourides Graduate Fellowship in Computational Engineering, awarded Jan. 2011
National Science Foundation Graduate Research Fellowship, awarded Jun. 2007
Sid Richardson Residential College Athena Award, May 2007
Google Anita Borg Memorial Scholarship Finalist, Mar. 2007, Recipient, Apr. 2009
Texas Society of Professional Engineers’ Outstanding Senior ECE Engineering Student, Feb.
2007
Rice Engineering Alumni Outstanding Junior Award, Apr. 2006, Senior Merit Award, Apr. 2007
Computing Research Association (Committee on the Status of Women in Computing Research)
Distributed Mentor Program Participant, Summer 2005
ExxonMobil and Teagle Foundation Scholarship, Fall 2004 - Spring 2008
Louis J. Walsh Scholarship in Engineering, Aug. 2004, Aug. 2005, Aug. 2006
George S. Cohen Memorial Scholarship, Aug. 2003, Aug. 2005
Emma S. McGree Scholarship, Aug. 2003, Aug. 2005
National Merit Scholar, Spring 2003
Presidential Scholar Program Semifinalist, Spring 2003
National Honor Society Scholarship, Spring 2003
TestMasters SAT Perfect Score Scholarship, Spring 2003
PROFESSIONAL ACTIVITIES
Phi Beta Kappa, inducted Spring 2007
Tau Beta Pi, inducted Spring 2007
Eta Kappa Nu, inducted Spring 2006
Institute of Electrical and Electronic Engineers (IEEE), joined Fall 2003
UNIVERSITY SERVICE
MIT
EECS Departmental Blogger, Mar. 2008 - May 2012
EECS Graduate Student Association, Aug. 2007 - present
Academic Committee Co-Chair, Jan. 2010 - Jan. 2011
Treasurer, Jan. 2009 - Jan. 2010
Orientation Committee Co-Chair, Jan. 2008 - Jan. 2009
GW6 (MIT Society for Graduate Women in EECS), Aug. 07 - present
Rice University
Rice IEEE, Jan. 2003 - May 2007
Internal Vice-President, Mar. 2006 - Mar. 2007
CSters (Rice Society for Women in CS), Jan. 2004 - May 2007
Drew Academy Visit Day at Rice University, Volunteer, Nov. 2006
Sally Ride Science Festival, Exhibitor, “Mobile Wireless Service Projects”, Oct. 2006
Sid Richardson Residential College
Fellow, Apr. 2005 - May 2007; Head Fellow, Apr. 2006 - May 2007
Peer Academic Advisor (Academic Advising Office), Apr. 2004 - May 2007
Off-Campus Representative, Aug. 2004 - May 2005
Academics Committee, Aug. 2004 - May 2007
Associates Committee, Aug. 2004 - May 2007
Rice Marching Owl Band, Aug. 2003 - May 2007
Clarinet Section Leader, Aug. 2004 - May 2007
Rice Fencing Club, Aug. 2003 - Dec. 2004
Vice-President, Jan. 2004 - Dec. 2004
SOFTWARE DEVELOPED
DLCpar (Duplication-Loss-Coalescence through Parsimony)
Phylogenetic software for reconciling gene trees to species trees by inferring gene duplications,
losses, and coalescence (accounting for incomplete lineage sorting).
http://compbio.mit.edu/dlcpar
TreeFix-DTL (TreeFix – Duplication/Transfer/Loss)
Phylogenetic software for correcting topological errors in prokaryotic gene tree reconstructions.
http://compbio.mit.edu/treefix-dtl
TreeFix
Phylogenetic software for correcting topological errors in eukaryotic gene tree reconstructions.
http://compbio.mit.edu/treefix
STAR-MP (Species Tree informed Architecture Reconstruction – Maximum Parsimony)
Phylogenetic software for reconstructing domain architecture evolution.
http://compbio.mit.edu/starmp