Shi, Mindy

Shi, Mindy

Assistant Professor

Bioinformatics and Genomics
Bioinformatics 271
704-687-8437
x.shi@uncc.edu

Personal website: http://shilab.uncc.edu/
Education: Ph.D., M.S. in Computer Science, University of Chicago, Chicago, IL, USA. M.Eng., B.Eng. in Computer Science, Beijing Institute of Technology, Beijing, China.

Biography:

Xinghua (Mindy) Shi is an assistant professor in the Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte. Before joining UNC Charlotte in January 2013, she was a postdoctoral research fellow at Brigham and Women’s Hospital and Harvard Medical School, a NIH T32 genetics training fellow at Harvard Medical school, a visiting research fellow in the Medical and Population Genetics program at Broad Institute, and an associate in the Quantitative Genetics Program at Harvard School of Public Health. She has received her Ph.D. and M.S. degrees in Computer Science from the University of Chicago, and M.Eng and B. Eng degrees in Computer Science from Beijing Institute of Technology, China. Her 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. She is currently focused on integrating large-scale "-omics" datasets to study how genetic architecture affects biological processes and complex phenotypes at the systems level. She is also interested in analyzing complex networks including computer networks, biological networks, and social networks.


Research Description:

Dr. Shi's 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. Her lab is currently focused on integrating large-scale "-omics" datasets to study how genetic architecture affects biological processes and complex phenotypes at the systems level. Dr. Shi is also interested in analyzing complex networks including computer networks, biological networks, and social networks.

Publications: 
  •  “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 RE, Lee C, and Xu J, In Proceedings of the 15thInternational Conference of Artificial Intelligence and Statistics (AISTATS) 2012, La Palma, Canary Islands, JMLR W&CP 22: 208-217, 2012.
  • “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).
  • “User Identification and Anonymization in 802.11 Wireless LANs”, Xu D, Wang Y, Shi X, and Yin X, Security and Communication Networks (Wiley), 2012. 5(1):15-27.
  • “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, Rigler D, Fitzgerald T, Lionel A, Thiruvahindrapuram B, MacDonald J, Mills R, Prasad A, Noonan K, Gribble S, Prigmore E, Donahoe P, Smith R, Park J.H, Hurles M, Carter N, Lee C, Scherer S, 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.
  • “Capacity of Data Collection in Randomly-Deployed Wireless Sensor Networks”, Chen S, Wang Y, Li X-Y, Shi X, ACM/Springer Wireless Networks (WINET), 2011. 17: 305-318.
  • “A Map of Human Genome Variation from Population Scale Sequencing”, The 1000 Genomes Project Consortium, Nature, 2010. 467: 1061-1073 (cover article).
  • “802.11 User Anonymization”, Xu D, Wang Y, Shi X, and Yin X, In Proc. of the IEEE Global Telecommunications Conference (GlobeCom 2010), 1-5, Miami, FL, December 2010.
  • “Order-Optimal Data Collection in Wireless Sensor Networks: Delay and Capacity”, Chen S, Wang Y, Li X-Y, and Shi X, In Proc. of the 6th Annual IEEE Communications Society Conference on Sensor, Mesh, and Ad Hoc Communications and Networks (SECON 2009), 1-9, Rome, Italy, June 2009.
  • “A Bayesian Approach to High-Throughput Biological Model Generation”, Shi X and Stevens R, In Proc. of the 1st Bioinformatics and Computational Biology Conference (BiCob 2009), Lecture Notes in Bioinformatics (Springer Verlag) 5462: 376-387, New Orleans, LA, April 2009.
  • “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), 1-6, 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), 2009. 3:19.1-19.21.
  • “SWARM: A Scientific Workflow for Supporting Bayesian Approaches to Improve Metabolic Models”, Shi X and Stevens R, In Proc. of The 6th ACM/IEEE International Workshop on Challenges of Large Applications in Distributed Environments (CLADE 2008), 25-34, Boston, MA, March, 2008.
  • “The National Microbial Pathogen Database Resource (NMPDR): A Genomics Platform Based on Subsystem Annotation”, McNeil L, Reich C, Aziz R, Bartels D, Cohoon M, Disz T, Edwards R, Gerdes S, Hwang K, Kubal M, Margaryan G, Meyer F, Mihalo W, Olsen G, Olson R, Osterman A, Paarmann D, Paczian T, Parrello B, Pusch G, Rodionov D, Shi X, Vassieva O, Vonstein V, Zagnitko O, Xia F, Zinner J, Overbeek R, Stevens R, Nucleic Acids Research, 2007.35:D347-D353.
  • “Efficient On-Demand Topology Control for Wireless Ad Hoc Networks”, Wang Y and Shi X, In Proc. of 14th IEEE International Conference on Computer Communications and Networks (ICCCN 2005), 159-164, San Diego, California, October 2005.