Research Scientist at UIUC 2015--2017
- Primarily responsible for the planning, design, organization, execution, and analysis of multiple complex epidemiological studies involving epigenomics, transcriptomics, and genomics of diseases of pregnancy and post-traumatic stress disorder.
- Published results in scientific publications and presented results orally at major scientific conferences.
- Wrote and completed grants, including budgeting, scientific direction, project management, and reporting.
- Mentored graduate students and collaborated with internal and external scientists.
- Performed literature review, training, and applied new techniques to maintain abreast of current scientific literature, principles of scientific research, and modern statistical methodology.
- Wrote software and designed relational databases using R, perl, C, SQL, make, and very large computational systems.
Postdoctoral Researcher at USC 2013--2015
- Primarily responsible for the design, execution, and analysis of an epidemiological study to identify genomic variants associated with systemic lupus erythematosus using targeted deep sequencing.
- Designed, budgeted, configured, maintained, and supported a secure linux analysis cluster (MPI/torque) with a shared filesystem (NFS over gluster) for statistical analyses.
- Wrote multiple pieces of software to reproducibly analyze and archive large datasets resulting from genomic sequencing.
- Coordinated with clinicians, molecular biologists, and biologists to produce analyses and major reports.
Postdoctoral Researcher at UCR 2010--2012
- Primarily responsible for the execution and analysis of an epidemiological study to identify genomic variants associated with systemic lupus erythematosus using prior information and array based approaches in a trio and cross sectional study of individuals from the Los Angeles and greater United States.
- Wrote and maintained multiple software components to reproducibly perform the analyses.
Debian Developer 2004--Present
- Maintained, managed configurations, and resolved issues in multiple packages written in R, perl, python, scheme, C++, and C.
- Resolved technical conflicts, developed technical standards, and provided leadership as the elected chair of the Technical Committee.
- Developer of Debbugs, a perl and SQL-based issue-tracker with ≥ 100 million entries with web, REST, and SOAP interfaces.
Independent Systems Administrator 2004--Present
- Researched, recommended, budgeted, designed, deployed, configured, operated, and monitored highly-available high-performance enterprise hardware and software for web applications, authentication, backup, email, and databases.
- Provided vendor-level support for complex systems integration issues on Debian GNU/Linux systems.
- Full life-cycle support of medium and small business networking infrastructure, including VPN, network security, wireless networks, routing, DNS, DHCP, and authentication.
- Doctor of Philosophy (PhD) in Cell, Molecular and Developmental Biology at UC Riverside
- Batchelor of Science (BS) in Biology at UC Riverside
- Reproducible, scalable analyses using R, perl, and python with workflows on cloud- and cluster-based systems on terabyte-scale datasets
- Experimental design and correction to overcome multiple testing, confounders, and batch effects using Bayesian and frequentist methods
- Design, development, and deployment of algorithms and data-driven products, including APIs, reports, and interactive web applications
- Statistical modeling (regression, inference, prediction/forecasting, time series, and machine learning in very large (> 1TB) datasets)
- Data mining, cleaning, processing and quality assurance of data sources and products using tidydata formalisms
- Visualization using R, ggplot, Shiny, and custom written routines.
- Languages: perl, R, C, C++, python, groovy, sh, make
- Collaborative Development: git, travis, continuous integration, automated testing
- Databases: Postgresql (PL/SQL), SQLite, Mysql, NoSQL
- Office Software: Gnumeric, Libreoffice, LaTeX, Word, Excel, Powerpoint
Genomics and Epigenomics
- NGS and array-based Genomics and Epigenomics of complex human diseases using RNA-seq, targeted DNA sequencing, RRBS, Illumina bead arrays, and Affymetrix microarrays from sample collection to publication.
- Reproducible, scalable bioinformatics analysis using make, nextflow, and cwl based workflows on cloud- and cluster-based systems on terabyte-scale datasets
- Alignment, annotation, and variant calling using existing and custom software, including GATK, bwa, STAR, and kallisto.
- Correcting for and experimental design to overcome multiple testing, confounders, and batch effects using Bayesian and frequentist methods approaches
- Using evolutionary genomics to identify causal human variants
- Statistical modeling (regression, inference, prediction, and learning in very large (> 1TB) datasets)
- Addressing confounders and batch effects
- Reproducible research
- Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure)
- Inter-process communication: MPI, OpenMP
- Filestorage: Gluster, CEFS, GPFS, Lustre
- Linux system administration
Genomics and Epigenomics
- Linkage and association-based mapping of complex phenotypes using next-generation sequencing and arrays
- Alignment, annotation, and variant calling using existing and custom software
Mentoring and Leadership
- Mentored graduate students and Outreachy and Google Summer of Code interns
- Former chair of Debian's Technical Committee
- Strong written communication skills as evidenced by publication record
- Strong verbal and presentation skills as evidenced by presentation and teaching record
- H3A Bionet: Generating workflows and cloud resources for H3 Africa
- Psychiatric Genomics Consortium: Identification of epigenetic variants which are correlated with PTSD.
- SLEGEN: System lupus erythematosus genetics consortium.
- Debbugs: Bug tracking software for the Debian GNU/Linux distribution. [https://bugs.debian.org]
- CairoHacks: Bookmarks and Raster images for large PDF plots in R.
- Function2Gene: Gene selection tool based on literature mining which enables Bayesian approaches to significance testing.
- Helical Wheel Projections: Web-based tool to draw helical wheel protein projections. [http://rzlab.ucr.edu/scripts/wheel]
Publications and Presentations
- 24 peer-reviewed publications cited over 1800 times: https://dla2.us/pubs
- H index of 11
- Numerous invited talks on EWAS of PTSD, genetics of SLE, and Open Source: https://dla2.us/pres
Funding and Awards
- 2017 R Consortium: Adding Linux Binary Builders to R-Hub Role: Co-PI
- 2015 Blue Waters Allocation Grant: Making ancestral trees using Bayesian inference to identify disease-causing genetic variants Role: Primary Investigator
- Tracking placenta and uterine funciton using urinary extracellular vesicles (R21 RFA-HD-16-037) Role: Key Personnel
- NIAMS R01-AR045650-04 Genetics of Childhood Onset SLE to Chaim O. Jacob. Role: Key Personnel
Scholarships and Fellowships
- 2001--2003: University of California, Riverside Doctoral Fellowship
- 1997--2001: Regents of the University of California Scholarship.
For my contact information or additional references, please e-mail email@example.com