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User profile
Qingyu Wang
[Direct message]An innovative computational biologist with the focus on sequencing data analysis. A creative self-starter as evidenced by independently developed methods and algorithms in analyzing various genomics data sets (including whole genome/exome sequencing data, RNA-seq data, ChIP-seq data, multiple sequence alignments, and SNPs data). Currently looking for a Bioinformatics Researcher position in both academic and industrial setting.
Current address
422 Thomas Building
State College, PA
United States
Education
the Pennsylvania State University
2008 — 2015
Purdue University
2006 — 2008
Tsinghua University
2000 — 2003
Experience
the Pennsylvania State University
2008 — Pres
Purdue University
2006 — 2008
Red Hat
2005 — 2006
Skills
- Programming languages: C/C++ (OpenCV library), Java, R (Bioconductor), MATLAB, QT, AWK, Shell script, PHP, JavaScript, and SQL
- Computing: 10 years of programming experience under Linux environment, 5 years of experience on distributed file system (AFS) and high-performance clustered file system (GPFS), and owner of 3 open source projects
- Pattern recognition: capable of developing/improving/implementing machine learning algorithms to identify specific patterns in genomic data
- Large-scale genomic data analysis: 5 years of experience on NGS data (whole exome/genome sequencing, RNA-Seq, ChIP-Seq data) analysis, genetic variants calling, annotation, and association study, sequences alignment, and statistical analysis
- Presentation and consulting: teaching, lecturing, and troubleshooting skills and 5 years of experience on supporting various biological projects with different types of genomic/genetic data
Activities
- Conference organizer: annual Bioinformatics and Genomics Retreat (one and a half days conference), the Penn State University, 2012
- Committee co-chair: Graduate Women in Science (GWIS), the Penn State University, 2012 -- 2015
- Teaching assistant of courses in Cold Spring Harbor: Statistical Analysis of Genome Scale Data (2-weeks courses), Cold Spring Harbor Lab, NY, 2010-2011
- Membership: International Society for Computational Biology (ISCB), 2016
References
Iyer, J.*, Wang, Q.*, Le, T.*, Pizzo, et al. Quantitative assessment of phenotypes for functional genetic studies using Drosophila melanogaster. 2016. G3: Genes| Genomes| Genetics. 6(5), 1427-1437 (*these authors contributed equally to this work)
Wang, Q., Shashikant, C.S., Altman, N.S., and Girirajan, S., Novel metrics to measure coverage in Whole Exome Sequencing (WES) datasets reveal local and global non-uniformity. 2016. Scientific reports (submitted: in review)
Wang, Q., Girirajan, S., and Altman, N.S., Rescuer: a local assembly based program for recovering discarded reads from Whole Exome Sequencing (WES) datasets (in preparation)
Schuster, S.C., Miller, W., Ratan A., ..., Wang, Q., et al. Complete Khoisan and Bantu genomes from southern Africa. 2010. Nature. 463, 943 -- 947
Miller, W., Hayes, V.M., Ratan, A., ..., Wang, Q., et al. Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). 2011. Proc Natl Acad Sci. 108.30, 12348-12353
Other
Open source project: ExomeCQA (http://exomecqa.sourceforge.net/), a quality assessment tool for cohort exome sequencing data (C/C++)
Open source project: Flynotyper (http://flynotyper.sourceforge.net/), an image processing software to quantify phenotypic variations in Drosophila eye (Java, C/C++)
Open source project: Chinese Linux Standard Interface (https://sourceforge.net/projects/clsi/),an input method engine interface (API) library (C/C++)
Web application developed: Coding SNPs (http://coding-snps.bx.psu.edu/), a web server presenting SNPs and alignment in coding regions (PHP, Javascript, C, AWK)