Derrick Wood

Derrick Wood

Principal Bioinformatics Scientist
Personal Genome Diagnostics


Twitter @DerrickEWood


My research involves developing algorithms and writing software to solve problems that deal with DNA sequence data. Within the field of bioinformatics, I am especially interested in microbial genomics and microbiome analysis.

Through the use of machine learning techniques and sequence alignment, my work has found and proposed corrections to errors in public databases of microbial genomes. 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.

After earning my Ph.D. degree from the University of Maryland's Computer Science department, I moved to Johns Hopkins to work with Ben Langmead. My postdoctoral research is directed toward improving Kraken's performance and usability. I am also applying techniques from its development toward other areas of computational genomics, including sequence alignment.

As of November 2015, I am working at Personal Genome Diagnostics in Baltimore, MD, developing new software and algorithms for cancer diagnostic testing.


Equal contributor.
  1. Unexpected cross-species contamination in genome sequencing projects.
    Merchant S, Wood DE, Salzberg SL. PeerJ 2014, 2:e675. Selected as a Top Bioinformatics article in June 2015, and a Top Genomics article in October 2015.
  2. Kraken: ultrafast metagenomic sequence classification using exact alignments.
    Wood DE and Salzberg SL. Genome Biology 2014, 15:R46. Highly accessed.
  3. EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes.
    Magoc T, Wood D, Salzberg SL. Evolutionary Bioinformatics 2013, 9:127-136.
  4. 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.


  1. "Kraken 2: faster and more accurate taxonomic sequence classification." Poster presented at Genome Informatics 2015.
  2. "Kraken: ultrafast metagenomic sequence classification using exact alignments." Poster presented at RECOMB 2014.
  3. "Kraken: metagenomic sample analysis in 30 minutes or less." Platform presentation at Genome Informatics 2013.


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.

Courses at the University of Maryland, College Park

  1. CMSC 313: Intro. to Computer Systems (Spring 2009, development; Fall 2009, TA). A new third-semester course covering topics such as C, assembly language, systems programming, and multithreaded computing. Now offered permanently as CMSC 216.
  2. CMSC 212: Intro. to Low-Level Programming Concepts (Fall 2008, TA; Summer 2009, Instructor). A third-semester course covering topics such as C, memory management, and operating systems.

Courses at the University of Texas at San Antonio

  1. CS 5063: Computers for Teachers (Summer 2004, TA). This summer course introduced high school teachers to the material covered in the CS 1713 and CS 1723 courses.
  2. CS 1723: Data Structures (Fall 2001, TA). This second-semester course used Java to teach the use and implementation of data structures such as stacks, queues, hash tables, and trees.
  3. CS 1713: Intro. to Computer Science (Spring 2001, TA; Summer 2001, TA). This first-semester course used Java to teach introductory programming concepts as well as more advanced topics such as object-oriented programming.


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).