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Xinghua(Mindy) Shi
Department of Computer Science, |
Education
Ph.D. Department of Computer Science , University of Chicago, December 2008 Thesis: System and Tools to Support a Bayesian Approach to Improving Large-Scale Metabolic Models Advisor: Rick Stevens M.S. Department of Computer Science , University of Chicago, August 2003 Thesis: Extending Version Control to Track Sicentific Results Advisor: David Beazley M.Eng. Department of Computer Science and Technology, Beijing Institute of Technology, March 2001 B.Eng. Department of Computer Science and Technology, Beijing Institute of Technology, July 1998
Research Experiences
Genetics T32 Fellow, Harvard Medical School,(7/2010-present)
Postdoctoral Research Fellow, Harvard Medical School, Brigham and Women's Hospital, (8/2009-present)
Visiting Research Fellow, Broad Institute of MIT and Harvard, (8/2009-present)
Associate, Program in Quantitative Genomics, Harvard School of Public Health, (2/2011-present)Research Assistant, University of Chicago, Argonne National Laboratory, (6/2005-12/2008)
- System and Tools to Improving Large-Scale Metabolic Models
- Minimal-Organism Platform Project
- NMPDR, Drug Targets Project
Research Assistant, University of Chicago, (7/2002-6/2005)
Research Assistant, Beijing Institute of Technology, (9/1998-3/2001)
Teaching Experiences
Teaching Assistant, University of Chicago, (9/2001-5/2005)
- Graduate Courses: "Operating Systems","Advanced Operating Systems","Scientific Systems Programming",
"Unix Systems Programming","Networks and Distributed System","Cognetics: Humane Computer Interface",
"Object Oriented Architecture,Design, and Method", "Object Oriented Architecture: Patterns, Technologies, Implementations".- Undergraduate Courses: "Fundamentals of Computer Programming", "Programming with C++",
"Data Abstract and C++ Programming","Introduction to Programming for World Wide Web",
"Operating Systems","Networks and Distributed Systems".Teaching Assistant, Beijing Institute of Technology, (9/1998-3/2001)
- Graduate Course:“Software Engineering and Software Automation”.
- Undergraduate Course: “Compiling Theory”.
Selected Publications
(* These authors contributed equally to the work)
- "Extensive Genetic Diversity and Substructuring among Zebrafish Strains Revealed through Copy Number Variant Analysis", Brown KH*, Dobrinski KP*, Lee AS, Gokcumen O, Mills RE, Shi X, Chong W, Chen JY, Yoo P, David S, Petersond SM, Raj T, Choy KW, Stranger BE, Williamson RE, Zon LI, Freeman JL, and Lee C, Proceedings of the National Academy of Sciences of the USA (PNAS),2012. 109(2):529-534 (Cover Article).
- "Refinement of Primate CNV Hotspots Identifies Candidate Genomic Regions Evolving under Positive selection", Gokcumen O*, Babb PL*, Iskow RC, Zhu Q, Shi X, Mills RE, Ionita-Laza I, Vallender EJ, Clark A, Johnson WE, Lee C, Genome Biology,2011. 12:R52.
- "A Comprehensive Assessment of Array-Based Platforms and Calling Algorithms for Detection of Copy Number Variants", Pinto D*, Darvishi K*, Shi X, Rajan D, Rigler D, Fitzgerald T, Lionel A, Thiruvahindrapuram B, MacDonald JR, Mills R, Prasad A, Noonan K, Gribble S, Prigmore E, Donahoe PK, Smith R, Park JH, Hurles EM, Carter PN, Lee C, Scherer WS, Feuk L, Nature Biotechnology,2011. 29:512-520.
- "Mapping Copy Number Variation by Population-Scale Genome Sequencing" , Mills R*, Walter K*, Stewart C*, Handsaker R*, Chen K*, Alkan C*, Abyzov A*, Yoon S*, Ye K*, Cheetham R, Chinwalla A, Conrad D, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva L, Iqbal Z, Kang S, Kidd J, Konkel M, Korn J, Khurana E, Kural D, Lam H, Leng J, Li R, Li Y, Lin C, Luo R, Mu X, Nemesh J, Peckham H, Rausch T, Scally A, Shi X, Stromberg M, Stutz A, Urban A, Walker J, Wu J, Zhang Y, Zhang Z, Batzer M, Ding L, Marth G, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eicher E, Gerstein M, Hurles M, Lee C, McCarroll S, and Korbel J., and the 1000 Genomes Project, Nature, 2011. 470: 59-65.
- "A Map of Human Genome Variation from Population Scale Sequencing", The 1000 Genomes Project Consortium, Nature, 2010. 467: 1061-1073.
- "Enhanced Feature Selection and Generation for 802.11 User Identification", Xu D, Wang Y, and Shi X, In Proc. of The 18th International Conference on Computer Communications and Networks (ICCCN 2009), San Francisco, CA, August 2009.
- "Self-Organizing Fault Tolerant Topology Control in Large-Scale Three-Dimensional Wireless Networks", Wang Y, Cao L, Dahlberg T, Li F, and Shi X, ACM Transactions on Autonomous and Adaptive Systems (TAAS), Volume: 4, Issue: 3, Pages: 19:1-19:21, July 2009.
- "A Bayesian Approach to High-Throughput Biological Model Generation", Shi X, Stevens R, In Proc. of the 1st Bioinformatics and Computational Biology Conference (BiCob 2009), New Orleans, LA, April 2009.
- "SWARM: A Scientific Workflow for Supporting Bayesian Approaches to Improve Metabolic Models", Shi X, Stevens R, In Proc. of The 6th ACM/IEEE International Workshop on Challenges of Large Applications in Distributed Environments (CLADE 2008),in conjunction with the 17th International Symposium on High Performance Distributed Computing (HPDC 2008), Boston, MA, March, 2008.
- "The National Microbial Pathogen Database Resource (NMPDR): A Genomics Platform Based on Subsystem Annotation";, McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes S, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman A, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko O, Xia F, Zinner J, Overbeek R, Stevens R., Nucleic Acids Research, 2007. Vol. 35, D347-D353.
- "Efficient On-Demand Topology Control for Wireless Ad Hoc Networks", Wang Y, Shi X, In Proc. of 14th IEEE International Conference on Computer Communications and Networks (ICCCN 2005), San Diego, California, October 2005.
Miscellaneous
- In memory of Jef Raskin (1943-2005).
- Graduate Seminar, Fall 2004.
| shi@cs.uchicago.edu Last Modified: March 3, 2011 |