Biography

I am a Senior Associate Scientist at the Center for Cancer Research at the National Cancer Institute, part of the Intramural Research Program at the National Institutes of Health.

I received my B.S. in Mechanical and Aerospace Engineering from Princeton University, my M.D. and Ph.D. from the University of Pittsburgh in the Schools of Medicine and Public Health (thesis advisor, Dr. Daniel Weeks, Human Genetics), respectively. Childrens Hospital and Regional Medical Center was where I completed my residency in Pediatrics, followed by pediatric hematology/oncology training in the Johns Hopkins School of Medicine/National Cancer Institute joint fellowship.

Interests

  • Biomedical Informatics and Data Science
  • Software Development
  • Open Data
  • Reproducible Research
  • Education
  • Cloud and Distributed Computing

Education

  • MD, 1999

    University of Pittsburgh, Pittsburgh, PA

  • PhD, Human Genetics, 1997

    University of Pittsburgh, Pittsburgh, PA

  • BS, Mechanical and Aerospace Engineering, 1993

    Princeton University, Princeton, NJ

Experience

 
 
 
 
 

Senior Associate Scientist

National Cancer Institute, National Institutes of Health

January 2018 – Present Bethesda, MD
 
 
 
 
 

Staff Scientist

National Cancer Institute, National Institutes of Health

January 2008 – December 2017 Bethesda, MD
 
 
 
 
 

Clinical Fellow, Pediatric Hematology/Oncology

Johns Hopkins University & National Human Genome Research Institute, NIH

July 2002 – December 2007 Bethesda, MD
 
 
 
 
 

Resident, Pediatrics

Childrens Hospital and Regional Medical Center

July 1999 – June 2002 Seattle, WA

Recent Posts

Building R Binary Packages for Linux

Background One of the challenges of producing a performant build environment for linux, such as what might be used to have developers …

Experimenting with Github Actions

GitHub actions allow flexible and potentially complicated actions that comprise workflows that respond to events on Github. Continuous …

Elasticsearch Strings Runthrough

This little post is just a brain-dump post on elasticsearch testing and searching. I am writing it to allow easy testing of …

OmicIDX on BigQuery

Availability: This ipython notebook is available at https://github.com/seandavi/omicidx_examples. OmicIDX is a project to democratize …

Single cell packages and dependencies in Bioconductor using BiocPkgTools

The Bioconductor package ecosystem continues to grow at an exponential rate (check it–I am right). We have recently completed the …

Publications

Quickly discover relevant content by filtering publications.

restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor

Bioconductor’s SummarizedExperiment class unites numerical assay quantifications with sample- and experiment-level metadata. …

Orchestrating a community-developed computational workshop and accompanying training materials

The importance of bioinformatics, computational biology, and data science in biomedical research continues to grow, driving a need for …

Orchestrating a community-developed computational workshop and accompanying training materials

The importance of bioinformatics, computational biology, and data science in biomedical research continues to grow, driving a need for …

Recent & Upcoming Talks

Howard County Community College STEM Career Panel

This is a career panel for students interested in STEM fields.

Bioconductor: Tools for interpreting high-throughput biological data

In this talk, I give a high-level overview of the Bioconductor project.

ATAC-Seq workshop

This workshop introduces ATAC-Seq, quality control approaches, isolating nucleosome compartments, and profile plots and heatmaps.

Statistical Methods in Functional Genomics

In a series of talks and exercises, I cover introduction to R, Bioconductor, genomic ranges, container classes, annotation of genes and …

Public Data Resources and Bioconductor

The goal of this workshop is to introduce Bioconductor packages for finding, accessing, and using large-scale public data resources …

Contact