Xinghua Mindy Shi
Postdoctoral Fellow in Computational Biology / Bioinformatics
One postdoctoral position in computational biology and bioinformatics is available in the Department of Bioinformatics and Genomics at the University of North Carolina at Charlotte. The appointee will support and complement ongoing projects in developing computational approaches/pipelines to integrate and analyze large-scale (epi)genomic, expression and interaction data sets for scientific discovery and validation.
Candidate must have or be close to obtaining a Ph.D. in quantitative fields (include but not limited to Bioinformatics, Computational Biology, Computer Science, Statistics, Mathematics, and Physics) and have demonstrated a high level of research productivity through publication in top peer-reviewed conferences and journals. Extensive experiences using scripting languages (e.g. Perl, Python) and statistical/mathematical toolkits (e.g. R, SAS, Matlab, Mathematica) are required. Proficiency with programming languages including C/C++/Java is desirable. Knowledge of machine/statistical learning and mathematical modeling techniques is also desirable. As a team player working closely with cross-institutional scientists with broad areas of expertise, strong interpersonal and communication skills are essential.
Applicants should email a single PDF file including cover letter, CV, brief research statement and list of 3 references to Dr. Mindy Shi (firstname.lastname@example.org).
I am seeking for highly motivated graduate students with undergraduate training in computer science, statistics, mathematics, chemistry, physics or biological sciences. Full assistantship will be provided upon admission. Please contact Dr. Mindy Shi (email@example.com) for details.
My research interest is in computational systems biology, particularly, the design and development of tools and algorithms to solve large-scale computational problems in biology and biomedical research. My current research is focused on integrating large-scale "-omics" datasets to study how genetic architecture affects biological processes and complex phenotypes at the systems level. I am also interested in analyzing complex networks including computer networks, biological networks, and social networks.
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
Assistant Professor, Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, (8/2013-)
Visiting Assistant Professor, Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, (1/2013-7/2013)
Postdoctoral Research Fellow, Brigham and Women's Hospital, Harvard Medical School,(8/2009-12/2012)
Visiting Research Fellow, Broad Institute of MIT and Harvard, (8/2009-12/2012)
Associate, Program in Quantitative Genomics , Harvard School of Public Health, (2/2011-12/2012)
NIH T32 Genetics Fellow, Harvard Medical School,(7/2010-6/2012)
Research Assistant, University of Chicago, Argonne National Laboratory, (6/2005-12/2008)
- System and Tools to Improving Large-Scale Metabolic Models
- NMPDR, Drug Targets Project
Research Assistant, University of Chicago, (7/2002-6/2005)
Research Assistant, Beijing Institute of Technology, (9/1998-3/2001)
Selected Publications(* These authors contribute equally to the work.)
- "An Integrated Map of Genetic Variation from 1,092 Human Genomes", The 1000 Genomes Project Consortium, Nature, 2012. 491: 56-65.
- "A Two-Graph Guided Multi-task Lasso Approach for eQTL Mapping", Chen X*, Shi X*, Xu X, Wang Z, Mills R, Lee C, Xu J, In Proceeding of the fifteenth international conference on Artificial Intelligence and Statistics (AISTATS 2012). JMLR W&CP, 2012. 22: 208-217.
- "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.
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