School of Medicine
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Sr. Software Developer, Health Research and Policy - Biostatistics
Current Role at Stanford Working within the School of Medicine, I am developing solutions for the Stanford Bone Marrow Transplant, Lymphoma, and Cancer Institute Research Databases
My Stanford Projects:
- Stanford Cancer Center Research Database (SCIRDB)
Developed a web-based platform to integrate data from the Stanford Cancer Institute (EPIC/Clarity), Stanford Tumor Registry, STRIDE (Tissue Bank & Pre-EPIC Data), and several other systems into a "one-stop shop" for data analysis and annotation by cancer researchers. This cohort-driven system allows users to focus on their patients of interest and provides free-text search of all their notes, reports and narratives as well as a timeline-based view of all events for a patient. Easy exports allow for data analysis in biostatistical tools and the system can perform complex analysis using the open-source R statistical software as a service.
- Lymphoma Program Project (LPP)
Rearchitected an existing legacy database system that tracks Stanford's Non-Hodgkins and Hodgkins Lymphoma cases back to the late 1960's. Enables clinicians to track diagnosis, courses of treatment, long-term follow-up, and clinical responses to the diseases.
- Bone Marrow Transplant Program
Developed replacement web-enabled database based on legacy system in place since 1980s that enhanced data capture abilities by leveraging data feeds from BMT Clinic and Stanford Hospital. Also enabled electronic form submission to national transplant databank via XML-based web-services.
- Transplant Arteriosclerosis, Viral and Host Mechanisms
Developed web-based application and reporting systems Gathered requirements, translated requirements into technical specifications, built reporting tools, designed table schemas, migrated database tables from Access to Oracle, normalizing and validating data in the process. Wrote all SQL scripts for automating data migration.
- Stanford Asian Pacific Program in Hypertension and Insulin Resistance (SAPPHIRe)
Provided on-going maintenance for the project by uploading data, generating reports for statistical analysis and modifying table schema to incorporate new measurements such as creatinine.
- GenePad Project
Developed a web-based tool for quality assurance of scanned form data that allows users to view scanned input and validate it before storing it into final database tables. The tool dynamically configures itself by examining the structure of the database.
Steven T. Woolson, MD
Clinical Professor, Orthopaedic Surgery
Current Research and Scholarly Interests Clinical Research in Total Joint Replacement
Postdoctoral Research fellow, Neurology and Neurological Sciences
Current Research and Scholarly Interests Stem cell fate determination and microenvironment dynamics
Postdoctoral Research fellow, Stem Cell Biology and Regenerative Medicine
Current Research and Scholarly Interests I am interested in the epigenetic reprogramming of DNA methylation during early mammalian preimplantation development. Early mammalian development is characterized by dramatic epigenetic changes. Upon fertilization of the oocyte with the sperm, the maternal and paternal genomes of the zygote are extensively reprogrammed to ensure the development of a totipotent potential. During this period of epigenetic reprogramming, DNA methylation (5-methyl-cytosine, 5mC) of paternal and maternal chromosomes is erased and reset during formation of the blastocyst. Interestingly, in mouse zygotes, the paternal genome becomes actively demethylated, as judged by immunofluorescence with antibodies against 5mC and bisulfite-sequencing data. Since the discovery of active DNA demethylation many scientists were trying to identify the putative “DNA demethylase” and a lot of candidate enzymes and pathways have been suggested and disproven. The identification of the enzymatic conversion of 5mC to 5-hydroxymethyl-cytosine (5hmC), 5-formyl-cytosine (5fC) and 5-carboxyl-cytosine (5caC) by Tet1-3 enzymes sheds new light on this process.
However, the analysis of epigenetic reprogramming in mammals is mainly focused on the mouse model and little is known about human embryonic development. Understanding the basic molecular mechanisms of human epigenetic reprogramming will impact human reproductive health and the generation of pluripotent stem cells