Research
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.
Publications
† Equal contributor.
-
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.
-
Kraken:
ultrafast metagenomic sequence classification using exact
alignments.
Wood DE and Salzberg SL.
Genome Biology 2014, 15:R46.
Highly accessed.
-
EDGE-pro:
Estimated Degree of Gene Expression in Prokaryotic Genomes.
Magoc T, Wood D, Salzberg SL.
Evolutionary Bioinformatics 2013, 9:127-136.
-
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
- "Kraken 2: faster and more accurate taxonomic sequence
classification." Poster presented at Genome Informatics 2015.
- "Kraken: ultrafast metagenomic sequence classification using
exact alignments." Poster presented at RECOMB 2014.
- "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.
Courses at the University of Maryland, College Park
- 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.
- 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
- 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.
- 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.
- 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.
