Qike Li
Statistical Informatics PhD and data scientist
Currently
I’m a Ph.D candidate at Statistics GIDP, University of Arizona.
Education
2012-present
PhD Candidate in Statistics–Statistical Informatics track University of Arizona
Statistics Graduate Interdisciplinary Program (GIDP),
Minor in Biostatistics
Advisors: Hao Helen Zhang (Statistics) & Yves A. Lussier (Bioinformatics)
Expected graduation date: August 2017
2006-2009
MS Molecular Biology Guizhou University
2001-2005
BS Biotechnology Zhengzhou University
Appointment
2014-present
Research Assistant Lussier Group, Center for Biomedical Informatics & Biostatistics, University of Arizona
Developing statistical informatics methodology for precision medicine. Engaging in interdisciplinary research: working with an expert team of statisticians, physicians, engineers, biologists, geneticists, and computer scientists. Responsibilities include original research, statistical support, grant writing, and software engineering.
2013-2014
Research Assistant Fionna McCarthy Group, University of Arizona
Developed statistical informatics methodology for RNA-Seq analysis.
2010-2012
Research Technician Rick Michod Group, University of Arizona
Studied the evolution of multicellularity by using bioinformatics, comparative genomics, phylogenetic analysis and molecular biology.g
Publications
[Google Scholar profile]
2017
Gardeux, Vincent, Joanne Berghout, Ikbel Achour, A. Grant Schissler, Qike Li, Colleen Kenost, Jianrong Li, Yuan Shang, Anthony Bosco, Saner Don, Marilyn J. Halonen, Daniel J. Jackson, Haiquan Li, Fernando D. Martinez, Yves A. Lussier. “A genome-by-environment interaction classifier for precision medicine: personal transcriptome response to rhinovirus identifies children prone to asthma exacerbations” Journal of the American Medical Informatics Association (in press)
2017
Li, Qike, A. Grant Schissler, Vincent Gardeux, Ikbel Achour, Colleen Kenost, Joanne Berghout, Haiquan Li, Hao Helen Zhang, and Yves A. Lussier. “N-of-1-pathways MixEnrich: advancing precision medicine via single-subject analysis in discovering dynamic changes of transcriptomes.” BMC medical genomics (2017) doi: DOI: 10.1186/s12920-017-0263-4 [link] [code]
2017
Li, Qike, A. Grant Schissler, Vincent Gardeux, Joanne Berghout, Ikbel Achour, Colleen Kenost, Haiquan Li, Hao Helen Zhang, and Yves A. Lussier. “kMEn: Analyzing noisy and bidirectional transcriptional pathway responses in single subjects.” Journal of biomedical informatics (2017) doi: 10.1016/j.jbi.2016.12.009 [link][code]
2016
Schissler, A. Grant*, Qike Li*, James L. Chen, Colleen Kenost, Ikbel Achour, D. Dean Billheimer, Haiquan Li, Walter W. Piegorsch, and Yves A. Lussier. “Analysis of aggregated cell–cell statistical distances within pathways unveils therapeutic-resistance mechanisms in circulating tumor cells.” Bioinformatics (2016) doi:https://doi.org/10.1093/bioinformatics/btw248 [link] (* joint first authorship)
2015
Schissler, A. Grant*, Vincent Gardeux*, Qike Li*, Ikbel Achour, Haiquan Li, Walter W. Piegorsch, and Yves A. Lussier. “Dynamic changes of RNA-sequencing expression for precision medicine: N-of-1-pathways Mahalanobis distance within pathways of single subjects predicts breast cancer survival.” Bioinformatics (2015), doi:10.1093/bioinformatics/btv253 [link] (* joint first authorship)
2015
Pookhao, Naruekamol, Michael B. Sohn, Qike Li, Isaac Jenkins, Ruofei Du, Hongmei Jiang, and Lingling An. “A two-stage statistical procedure for feature selection and comparison in functional analysis of metagenomes.” Bioinformatics (2015) doi:10.1093/bioinformatics/btu635 [link]
2015
Li, Haiquan, Nima Pouladi, Ikbel Achour, Vincent Gardeux, Jianrong Li, Qike Li, Hao Helen Zhang, Fernando D. Martinez, Joe G N Skip Garcia, Yves A. Lussier . “eQTL networks unveil enriched mRNA master
integrators downstream of complex disease-associated SNPs.” Journal of Biomedical Informatics (2015) doi:10.1016/j.jbi.2015.10.010 [link]
2015
Lussier, Yves a, Haiquan Li, Nima Pouladi, and Qike Li.“Accelerating precision biology and medicine with computational biology and bioinformatics.” Genome Biology (2014) doi:10.1186/s13059-014-0450-y [link]
2015
Sohn, Michael B, Lingling An, Naruekamol Pookhao, and Qike Li. “Accurate genome relative abundance estimation for closely related species in a metagenomic sample.” BMC Bioinformatics (2014) doi:10.1186/1471-2105-15-242 [link].
Presentations
Short Course
10/15/2016
Short Course: Computational methods for precision medicine and single subject studies with genomes and transcriptomes. (The 6th Annual Translational Bioinformatics Conference, Jeju, Korea)
Talks
7/302017
The 7th Annual Translational Bioinformatics Conference, (Los Angeles, USA) [slides]
7/30/2017
Joint Statistical Meetings (JSM) (Baltimore, USA) [slides]
6/27/2017
WNAR Annual Meeting (Santa Fe, USA) [slides]
10/16/2016
The 6th Annual Translational Bioinformatics Conference (Jeju, Korea) [slides]
Awards
June 2017
Distinguished Written Paper Award (WNAR)
Summer 2017
HE Carter Travel Award (Graduate Interdisciplinary Programs, University of Arizona)
Fall 2016
HE Carter Travel Award (Graduate Interdisciplinary Programs, University of Arizona)
Technical skills
- R
- Shell
- HTML and CSS
- Python
- Cluster computing
- Emacs and Elisp
- SQL
- Git and GitHub
- LaTex
- Adobe Illustrator
Links
References
Available upon request.