Derrick Wood

Derrick Wood

Graduate Research Assistant
Department of Computer Science and Center for Bioinformatics and Computational Biology
University of Maryland, College Park

Center for Computational Biology
McKusick-Nathans Institute of Genetic Medicine
Johns Hopkins University School of Medicine

Contact

Email dwood@cs.umd.edu
Office 3104B Biomolecular Sciences Building (UMD)
463 Miller Research Building (JHU)

Research

Under the supervision of my advisor, Steven Salzberg, my research has focused on bioinformatics, and especially on microbial genomics. Through the use of machine learning techniques and sequence alignment, my work has found and proposed corrections to errors in public databases. I am also the developer of Kraken, an ultrafast taxonomic classification system for short DNA sequences obtained from metagenomic samples. In addition to Kraken's focus on speed, I've contributed work toward other bioinformatics pipelines that reduced runtimes from hours to minutes.

Outside of bioinformatics, I have an interest in artificial intelligence, especially as related to the use of automated agents developed using reinforcement learning; in particular, I would like to make an attempt at the Arimaa Challenge in the future.

Publications

Equal contributor.
  1. Kraken: ultrafast metagenomic sequence classification using exact alignments.
    Wood DE and Salzberg SL. Genome Biology 2014, 15:R46. Highly accessed.
  2. EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes.
    Magoc T, Wood D, Salzberg SL. Evolutionary Bioinformatics 2013, 9:127-136.
  3. Thousands of missed genes found in bacterial genomes and their analysis with COMBREX.
    Wood DE, Lin H, Levy-Moonshine A, Swaminathan R, Chang YC, Anton BP, Osmani L, Steffen M, Kasif S, Salzberg SL. Biology Direct 2012, 7:37. Highly accessed.

Presentations

  1. "Kraken: ultrafast metagenomic sequence classification using exact alignments." Poster presented at RECOMB 2014.
  2. "Kraken: metagenomic sample analysis in 30 minutes or less." Platform presentation at Genome Informatics 2013.

Teaching

I have taught one course as instructor, and assisted in the teaching of several more through presenting course material, grading, and syllabus and project preparation. These courses have generally covered the first three semesters of undergraduate computer science education, focusing on programming in Java, C, and assembly language.

Fall 2009: TA, CMSC 313, Intro. to Computer Systems
Summer 2009: Instructor, CMSC 212, Intro. to Low-Level Programming Concepts
Spring 2009: TA, development of CMSC 313, Intro. to Computer Systems (now named CMSC 216)
Fall 2008: TA, CMSC 212, Intro. to Low-Level Programming Concepts
Summer 2004: TA, UTSA CS 5063, Computers for Teachers
Fall 2001: TA, UTSA CS 1723, Data Structures
Summer 2001: TA, UTSA CS 1713, Intro. to Computer Science
Spring 2001: TA, UTSA CS 1713, Intro. to Computer Science

Education

Ph.D., Computer Science, University of Maryland (2014).
M.S., Computer Science, University of Maryland (2011).
B.S., Computer Science, University of Texas at San Antonio (2004).

Coursework

CMSC 634: Empirical Research Methods for Computer Science
CMSC 828N: Computational Gene Finding and Genome Assembly
CMSC 630: Theory of Programming Languages
CMSC 751: Parallel Algorithms
CMSC 660: Scientific Computing I
CMSC 828G: Bioinformatics for Metagenomics
CMSC 714: High Performance Computing Systems
CMSC 858W: Algorithms for Biosequence Analysis
CMSC 726: Machine Learning
CMSC 498T: Game Theory