James Robert White

Research

• comparative metagenomics: applications to medicine and biotechnology.
• advisor: Mihai Pop.

Relevant Prior Work

• comparative metagenomics of subseafloor ocean sediment. (09')
• comparative metagenomic analysis of cockroach and human guts. (08')
• methods for neural decoding of prosthetic limb movements. Johns Hopkins Applied Physics Lab (APL), (08')
• analyzing the phyllosphere of apple trees. (07'-08'), collaborator: Andrea Ottesen
• Figaro: novel statistical vector trimming. (07'-08')
• detection of lateral gene transfer events in Pyrococcus furiosus (07'), advisor: Jocelyne DiRuggiero.
• CRISPR (clustered regularly interspaced palindromic repeats) analysis in metagenomic data (07'), course professor: Chuck Delwiche.
• algorithms for automated heterozygous indel determination (06'-07'), J. Craig Venter Institute. advisor: Tim Stockwell.
• comparative bioinformatics to prioritize gene knockout experiments in M. tuberculosis (06'), course professor: Mihai Pop.
• protein folding using homotopy methods (06'), course professor: Dianne O'leary.
• algorithms for genome assembly (05'-06'), advisor: Jim Yorke.

Publications

   Peer-reviewed articles

1. The impact of organic and conventional management on the phyllosphere microbial ecology of an apple crop.
   Ottesen A, White JR, Skaltsas DN, Newell MJ, Walsh CS. Journal of Food Protection. v. 72, no. 11, 2009 Nov.


2. Computational complexity versus accuracy in classification of cortical neural signals.
   Tenore F, Aggarwal V, White JR, Schieber MH, Thakor NV. Proc IEEE Eng Med Biol Soc on Neural Eng. 2009.


3. Statistical methods for detecting differentially abundant features in clinical metagenomic samples.
   White JR, Nagarajan N, Pop M. PLoS Computational Biology. 2009 April.


4. Finding Biologically Accurate Clusterings in Hierarchical Decompositions Using Variation of Information.
   Navlakha S, White JR, Nagarajan N, Pop M, Kingsford C. Proceedings of RECOMB. 2009 May.


5. Extensive Genome Rearrangements and Multiple Horizontal Gene Transfers in a Population of Pyrococcus Isolates from Vulcano Island, Italy.
   White JR, Escobar-Paramo P, Mongodin E, Nelson K, DiRuggiero J. Applied and Environmental Microbiology. 2008 Oct.


6. Improving Phrap-based assembly of the rat using reliable overlaps.
   Roberts M, Zimin A, Hayes W, Hunt BR, Ustun C, White JR, Havlak P, Yorke JA. PLoS ONE. 2008 March.


7. Figaro: a novel statistical method for vector sequence removal.
   White JR, Roberts M, Yorke JA, Pop M. Bioinformatics. 2008 Jan.

   Educational

1. Protein folding using homotopy methods.
   White JR. Supplementary case study for Scientific Computing with Case Studies. O'leary DP. 2008 Dec.

Posters & Presentations

1. "Statistical methods for microbial community comparison." AMSC Applied Statistics Ten Minute Madness seminar, May 2009.
2. "Microbial dynamics of human obesity." University of Maryland - Graduate Research Interaction Day, (Awarded 1st place in Health theme), April 2009.
3. "Novel approaches to metagenomic analysis." CBCB seminar, April 2009.
4. "Detecting differentially abundant features in metagenomic samples." Metagenomics 2008 - UCSD, November 2008.
5. "Comparative metagenomics of organic and conventional apple tree microflora." Biology of Genomes 2008 - Cold Spring Harbor Laboratory, May 2008.
6. "Statistical methods for microbial community comparison." CBCB seminar, April 2008.
7. "Statistical methods for detecting differentially abundant taxa in metagenomic samples." University of Maryland - Graduate Research Interaction Day, (Awarded 1st place in Environmental Science theme), April 2008.
8. "Figaro: a statistical vector trimmer." 15th Annual international conference on microbial genomics, 2007.
9. "Improving genome assemblies with reliable overlaps." Cold Spring Harbor, 2006.
10. "Triangle tessellations of the hyperbolic plane." Mary Washington undergraduate mathematics conference, 2005, and American Mathematical Society sectional meeting at University of Delaware, 2005.

Teaching

• Fall 2008 - TA for CMSC828N - Computational Gene Finding and Genome Assembly (Prof. Steven Salzberg).

Education

• Ph.D. Applied Mathematics and Scientific Computation, University of Maryland - College Park. In progress.
• B.S. Summa Cum Laude, Mathematics, University of Maryland - College Park. May 2006.

Ph.D. Coursework

• Scientific computation I,II: Monte Carlo simulation, numerical linear algebra and sparse matrices, nonlinear systems, optimization, numerical methods for ordinary and partial differential equations, finite element methods.
• Mathematical methods for signal and image processing
• Algorithms for biosequence analysis
• Computational gene finding and genome assembly
• Comparative bioinformatics
• Metagenomic sequencing and analysis
• Biostatistics
• Computer science for scientific computation

Contact

Biomolecular Sciences Building #296
3rd Floor, Lab 3104B
University of Maryland
College Park, MD 20742

Email: whitej [at] umd.edu
Phone: 301.405.3234
Fax: 301.314.1341