Professional Experience
Research Associate, 2013 - present
Advisor: Dr.
Xian Chen
Department of Biochemistry and Biophysics
University of North Carolina, Chapel Hill,
NC
- Member of the informatics team for the University of North Carolina – Washington University Proteome Characterization Center (PCC) for the Clinical Proteomic Tumor Analysis Consortium (CPTAC) project. Analyzed proteogenomic mapping results produced from both basal-like and luminal types of breast cancer. Integrated genomic (SNPs, SNVs, CNVs) and transcriptomic (RNA-seq) data derived from the same samples, with our proteogenomic data. Worked with genomic, transcriptomic, and proteomic data tracks in the UCSC Genome Browser and the Integrative Genomics Viewer (IGV). Interpreted our CPTAC proteogenomic mapping results to identify biologically significant protein-coding regions in the human genome, as well as validating novel findings.
- Worked closely with the Assay Development team at Washington University to provide informatics support as it uses LC-MS/MS data to develop breast cancer assays, where peptides are quantified in tumor digests. Developed a series of R and Perl scripts to automate the determination of LOB and LOD, as well as plot calibration curves, for each peptide being considered for an assay.
- Developed a pipeline to process proteomic search results from LC-MS/MS data to identify alternative splicing of annotated genes at the protein level. Constructed a database to store and query the peptides spanning splice junctions. Produced mapping tracks in order to view the location of where the peptides map to the genome using the UCSC genome browser. This approached is being used to compare splicing differences among breast cancer subtypes.
- Member of CPTAC Assay Development Working Group and CPTAC Data Integration and Bioinformatics Working Group.
Research Associate, 2012 - 2014
Postdoctoral Research Associate, 2011
Advisor: Dr.
Morgan Giddings
College of Arts and Sciences
Boise State University, Boise,
ID
- Data Wrangler for large-scale proteomic data sets produced from ENCODE (ENCyclopedia Of DNA Elements) cell lines and the output results from an analysis of these data sets using our lab's Peppy proteogenomic mapping software.
- Ran the proteogenomic pipeline and produced BED tracks for submission to the ENCODE DCC. These BED tracks can be publicly viewed on the UCSC Genome Browser.
- Team member working in a collaboration with research groups from UNC and Washington University on the CPTAC (Clinical Proteomic Tumor Analysis Consortium) project. We are combining proteomics with genomics and transcriptomics to study breast cancer biology.
- Facilitated communication between bench scientists and computer programmers working on the proteogenomic mapping project.
Database Developer, 2009 - 2010
Advisor: Dr.
Morgan Giddings
Department of Microbiology and Immunology
University of North Carolina, Chapel Hill,
NC
- Worked on developing the Ultra-Structure database system to store data generated by the Genome Fingerprint Scanning (GFS) application for the ENCODE project.
- Worked on a MongoDB database system as an alternative method to store to GFS data.
Database Developer, 2006 - 2009
North Carolina Institute for Public Health (NCIPH)
University of North Carolina, Chapel Hill, NC
- Designed, implemented, and maintained a Microsoft Access application with an Oracle back-end database to store and query student records for programs offered by the Office of Executive Education at NCIPH.
- Worked with UNC Information Technology Services to merge my NCIPH executive education Oracle database with the new UNC-ALL campus registration system. Provided key guidance and recommendations to the Project Manager throughout the application development life cycle to ensure that my database application interfaced seamlessly with the new registration system.
- Designed, implemented, and maintained a Microsoft Access database application to store and query records of students enrolled in Certificate Education programs at NCIPH.
- Performed queries and generated summary reports for program directors, administrative assistants, registrars, and marketing staff members.
- Provided hands-on database training to administrative assistants to enable them to more effectively complete their assignments.
Research Associate, 2003 - 2006
Postdoctoral Research Associate, 1996
- 2003
Advisor: Dr.
Clyde A. Hutchison III
Department of Microbiology and Immunology
University of North Carolina, Chapel Hill,
NC
- Project leader for site-directed mutagenesis of recombinant HIV-1 reverse transcriptase used to define and characterize amino acid residues involved in protein stability and subunit dimerization of the HIV-1 reverse transcriptase. We now have a collection of over 600 single amino acid substitution mutants in the HIV-1 reverse transcriptase. In one study, our experimental data allowed us to identify hydrophobic cores and hydrogen bonding interactions critical for the protein stability of the HIV-1 reverse transcriptase (view interactive structural images) and to study the pattern of evolution of these critical residues in other retroviruses.
- Designed and maintained an Oracle database to store the genotype and phenotype data for 600 HIV-1 reverse transcriptase single amino acid substitution mutants generated in the Hutchison Lab. This database also contains data from analyses of HIV-1 sequences and protein structures.
- Worked on all aspects of the Oracle database design, implementation, and maintenance. Experience includes schema design of the database, creating relational tables to store biological data, using SQL*Loader to import data generated from bioinformatics applications, designing SQL queries to produce reports for other lab members, writing supporting PL/SQL code, and serving as DBA to administer the database.
- Developed an interactive web application using Java Servlets/JSP to allow researchers to query a database containing the Hutchison's lab reverse transcriptase mutant data.
- Constructed and analyzed structural models of reverse transcriptases related to HIV-1 to study the evolution of residues involved in protein stability and folding.
- Evalutated amino-acid substitutions
in the reverse transcriptase of clinical HIV-1 isolates using phenotype
data from a collection of HIV-1 reverse transcriptase mutants. This
analysis can serve as a method to predict if reported sequences of HIV-1
isolates are biologically functional. The mutational data can also
be used to aid in the understanding of drug resistant HIV-1 reverse transcriptase
mutants.
Graduate Student, 1988-96
Dissertation Advisor: Dr.
Clyde A. Hutchison III
Department of Microbiology and
Immunology
University of North Carolina,
Chapel Hill, NC
- High density saturation mutagenesis project of recombinant HIV-1 reverse transcriptase expressed in E. coli. The phenotype data generated from a collection of 366 different single amino acid substitutions in the HIV-1 reverse transcriptase provided a "genetic" means to identify amino acid residuess that are important for protein function or protein stability.
- Phenotype data from the mutant collection were combined with crystallographic data of several HIV-1 reverse transcriptase structures as well as the structure of the evolutionarily related Moloney murine leukemia virus reverse transcriptase to identify hydrogen bonding and hydrophobic interactions critical for the protein stability of this enzyme.
- Besides providing a better understanding of the HIV-1 reverse transcriptase in particular, this project demonstrated the utility of saturation mutagenesis to study the function and stability of proteins in general, especially for proteins for which no structural data are available.
Crystal Structure of the 66 kD subunit
of the HIV-1 Reverse Transcriptase
Teaching Assistant, 1989-90
University of North Carolina,
Chapel Hill, NC
Taught two semesters of Microbiology
55 Lab
(General Microbiology for nursing
students)
Graduate Student, 1987-88
Department of Microbiology and
Immunology
University of North Carolina,
Chapel Hill, NC
Four month rotation in Dr.
Jack Griffith's lab where I used electron microscopy to visualize the
binding of the tryptophan repressor protein (TrpR) to DNA.
Undergraduate Research Fellow,
1985-86
University
of Massachusetts Medical School, Worcester, MA
Research during the summers of 1985
and 1986 in Dr.
Carel Mulder's lab where I studied the molecular biology of herpesvirus
saimiri, an oncogenic member of the Herpesvirus family.
Undergraduate Research Student,
1985-86
College of the Holy Cross, Worcester,
MA
Three semesters of undergraduate
research in Dr.
George R. Hoffmann's lab where I studied the ability of various chemicals
to induce genetic duplications in Salmonella typhimurium.
COMPUTER SKILLS
Relational Database Management Systems: Oracle, MySQL, PostgreSQL, Microsoft Access, MongoDB
Programming Languages: Java (J2SE 5.0, Servlets, JSP, JDBC), Visual Basic, C++, PHP, Perl, R, PL/SQL, ASP.NET, VBA, JavaScript, HTML, XML
Developer Tools: Visual Studio, Eclipse, NetBeans, XML Spy, Toad for MySQL, Oracle SQL Developer
Cloud Computing: Amazon Web Services
Operating Systems: UNIX, Linux, Mac OS X, Windows XP/Vista/7
Data Analysis Programs: Microsoft Excel, Cricket Graph
Website Editing Programs: Adobe Dreamweaver, Adobe Flash
Word Processing Programs: Microsoft Word
Presentation/Drawing Programs: Microsoft PowerPoint, Microsoft Visio
Image Editing: Adobe Photoshop, Adobe Illustrator
Protein Crystal Structure Analysis Programs: Kinemage, RasMol, Protein Explorer, SwissPdbViewer, SYBYL, INSIGHT II, RIBBONS, MolScript, PyMOL
Protein/DNA Analysis Programs: GCG package, Vector NTI