I am an independent research specialist providing expertise in computational biology and statistical analysis. The purpose of my work is to develop and apply state-of-the-art methods to highly complex datasets in order to help scientists, doctors and researchers gain insight into the phenomena that shape our world. My clients include groups within academia, government and the private sector. Feel free to contact me to discuss potential projects.

  • Metagenomic analysis (e.g. human microbiome studies)
  • 16S rRNA/18S rRNA/ITS amplicon microbial diversity analysis
  • HIV quasi-species analysis
  • Microbial genome assembly, gene-finding & annotation
Statistical analysis
  • Data mining of high-dimensional datasets
  • Biomarker discovery & validation
  • Power analysis
  • Statistical modeling & prediction

I've been fortunate to work on cutting-edge research with scientists & doctors from a variety of leading institutions:

  • National Institutes of Health
  • Johns Hopkins University - Sidney Kimmel Comprehensive Cancer Center
  • Johns Hopkins University - Bloomberg School of Public Health
  • U.S. Food and Drug Administration
  • University of Maryland - School of Medicine
  • University of Maryland - College Park
  • University of Delaware
  • Childrens Hospital of Pittsburgh
  • Nova Southeastern University
  • American Urological Association
  • Johns Hopkins University - Applied Physics Laboratory
  • J. Craig Venter Institute
  • PhD Applied Mathematics & Scientific Computation - University of Maryland College Park - 2010
  • BSc Mathematics - University of Maryland College Park - 2006
  • Perl
  • Python
  • R
  • C/C++
  • HTML, PHP & Javascript
Open source software
  • CloVR - automated sequence analysis from your desktop
  • Cunningham - BLAST runtime estimation
  • Metastats - statistical comparison of metagenomic data
  • Figaro - statistical vector trimming
  1. Anticoagulation and Antiplatelet Therapy in Urologic Practices: ICUD/AUA Review Paper.
    Culkin DJ, Exaire, EJ, Green D, Soloway M, Gross A, Desai M, White JR, Lightner DJ. J Urology. v. 192, 2014 October.
  2. Medical Management of Kidney Stones: AUA Guideline.
    Pearle MS, Goldfarb DS, Assimos DG, Curhan G, Denu-Ciocca CJ, Matlaga B, Monga M, Penniston K, Preminger G, Turk T, White JR. J Urology. v. 192, 2014 August.
  3. The potential role of lung microbiota in lung cancer attributed to household coal burning exposures.
    Hosgood HD, Sapkota AR, Rothman N, Rohan T, Hu W, Xu J, Vermeulen R, He X, White JR, Wu G, Wei F, Mongodin E, Lan Q. Environmental and Molecular Mutagenesis. doi:10.1002/em.21878, 2014 June.
  4. Extensively duplicated and transcriptionally active recent lateral gene transfer from a bacterial Wolbachia endosymbiont to its host filarial nematode Brugia malayi.
    Ioannidis P, Johnston KL, Riley DR, Kumar N, White JR, Olarte KT, Ott S, Tallon LJ, Foster JM, Taylor MJ, Dunning Hotopp JC. BMC Genomics. v. 14, no. 639, 2013 September.
  5. Bacteria-Human somatic cell lateral gene transfer is enriched in cancer samples.
    Riley DR, Sieber KB, Robinson KM, White JR, Ganesan A, Nourbakhsh S, Dunning Hotopp JC. PLoS Comp Biol. v. 9, no. 6, 2013 June.
  6. Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato).
    Ottesen AR, Gonzalez-Pena A, White JR, Pettengill JB, Li C, Allard S, Rideout S, Allard M, Hill T, Evans P, Strain E, Musser S, Knight R, Brown E. BMC Microbiology. v. 13, no. 114, 2013 June.
  7. Immune status, antibiotic medication and pH are associated with changes in the stomach fluid microbiota.
    von Rosenvinge EC, Song Y, White JR, Maddox C, Blanchard T, Fricke WF. ISME J. doi:10.1038 / ismej.2013.33, 2013 March.
  8. CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota.
    White JR, Maddox C, White O, Angiuoli SV, Fricke WF. Microbiome. v. 1, no. 6, 2013 February.
  9. Characterization of microflora in Latin-style cheeses by next- generation sequencing technology.
    Lusk T, Ottesen A, White JR, Allard M, Brown E, Kase J. BMC Microbiology. v. 12, no. 254, 2012 November.
  10. Using metagenomic analyses to estimate the consequences of enrichment bias for pathogen detection.
    Pettengill JB, McAvoy E, White JR, Allard M, Brown E, Ottesen A. BMC Research Notes. doi:10.1186 / 1756-0500-5-378, 2012 July.
  11. Structure, function and diversity of the healthy human microbiome.
    The Human Microbiome Consortium. Nature. v. 486, 2012 June.
  12. A framework for human microbiome research.
    The Human Microbiome Consortium. Nature. v. 486, 2012 June.
  13. Pyrosequencing of bacterial symbionts within Axinella corrugata sponges: diversity and seasonal variability.
    White JR, Patel J, Ottesen A, Arce G, Blackwelder P, Lopez JV. PLoS One. v. 7, no. 6, 2012 June.
  14. Proof of Concept of Microbiome-Metabolome Analysis and Delayed Gluten Exposure on Celiac Disease Autoimmunity in Genetically At-Risk Infants.
    Sellitto M, Bai G, Serena G, Fricke WF, Sturgeon C, Gajer P, White JR, Koenig SK, Sakamoto J, Boothe D, Gicquelais R, Kryszak D, Puppa E, Catassi C, Ravel J, Fasano A. PLoS One. v. 7, no. 3, 2012 March.
  15. Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis.
    Donia MS, Fricke WF, Partensky F, Cox J, Elshahawi SI, White JR, Phillippy AM, Schatz MC, Piel J, Haygood MG, Ravel J, Schmidt EW Proc Natl Acad Sci USA. doi:10.1073 / pnas.1111712108, 2011 November.
  16. Resources and costs for microbial sequence analysis evaluated using virtual machines and cloud computing.
    Angiuoli SV, White JR, Matalka M, White O, Fricke WF. PLoS One. v. 6, no. 10, 2011 October.
  17. CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing.
    Angiuoli SV, Matalka M, Gussman A, Galens K, Vangala M, Riley D, Arze C, White JR, White O, Fricke WF. BMC Bioinformatics. v. 12, no. 356, 2011 September.
  18. Bacterial community diversity and variation in spray water sources and the tomato fruit surface.
    Telias A, White JR, Pahl DM, Ottesen AR, Walsh CS. BMC Microbiology. v. 11, no. 81, 2011 April.
  19. Metagenomics of the subsurface Brazos-Trinity Basin (IODP site 1320): comparison with other sediment and pyrosequenced metagenomes.
    Biddle JF, White JR, Teske AP, House CH. ISME J. doi:10.1038/ismej.2010.199, 2011 January.
  20. Gut Microbial Gene Expression in Mother-Fed and Formula-Fed Piglets.
    Poroyko V, White JR, Wang M, Donovan S, Alverdy J, Liu DC, Morowitz MJ. PLoS One. v. 5, no. 8, 2010 August.
  21. Alignment and clustering of phylogenetic markers - implications for microbial diversity studies.
    White JR, Navlakha S, Nagarajan N, Ghodsi MR, Kingsford C, Pop M. BMC Bioinformatics. v. 11, no. 152, 2010 March.
  22. Real-time decision fusion for multimodal neural prosthetic devices.
    White JR, Levy T, Bishop W, Beaty JD. PLoS One. v. 5, no. 3, 2010 March.
  23. 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.
  24. 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 June.
  25. Statistical methods for detecting differentially abundant features in clinical metagenomic samples.
    White JR, Nagarajan N, Pop M. PLoS Computational Biology. v. 5, no. 4, 2009 April.
  26. Finding Biologically Accurate Clusterings in Hierarchical Decompositions Using Variation of Information.
    Navlakha S, White JR, Nagarajan N, Pop M, Kingsford C. Proceedings of RECOMB, Lecture Notes in Computer Science. 5541, 2009 May.
  27. Protein folding using homotopy methods.
    White JR. Supplementary case study for Scientific Computing with Case Studies. O'leary DP. 2008 December.
  28. 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. v. 74, no. 20, 2008 October.
  29. 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. v. 3, no. 3, 2008 March.
  30. Figaro: a novel statistical method for vector sequence removal.
    White JR, Roberts M, Yorke JA, Pop M. Bioinformatics. v. 24, no. 4, 2008 January.
White papers, technical reports & book chapters
  1. CloVR-ITS: Automated ITS amplicon sequence analysis pipeline for fungal microbiota analysis– standard operating procedure, version 1.0
    White JR, Fricke WF. Protocol Exchange. doi:10.1038/protex.2013.017, February 2013.
  2. Microbial genomics in foodborne pathogens.
    Fricke WF, White JR. In: Foley SL, editor. Molecular Typing Methods for Tracking Foodborne Micoorganisms. Hauppauge, NY: Nova Science Publishers, 2012.
  3. CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing – standard operating procedure, version 1.1.
    White JR, Arze C, Matalka M, The CloVR Team, Angiuoli S, Fricke WF. Nature Precedings. doi:10.1038 / npre.2011.6287.1, August 2011.
  4. CloVR-Metagenomics: Functional and taxonomic microbial community characterization from metagenomic whole-genome shotgun (WGS) sequences – standard operating procedure, version 1.0.
    White JR, Arze C, Matalka M, The CloVR Team, Angiuoli S, Fricke WF. Nature Precedings. doi:10.1038 / npre.2011.5886.1, April 2011.
  5. CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing – standard operating procedure, version 1.0.
    White JR, Arze C, Matalka M, The CloVR Team, Angiuoli S, Fricke WF. Nature Precedings. doi:10.1038 / npre.2011.5888.1, April 2011.
  6. CloVR-Microbe: Assembly, gene finding and functional annotation of raw sequence data from single microbial genome projects – standard operating procedure, version 1.0.
    Galens K, White JR, Arze C, Matalka M, Gwinn Giglio M, The CloVR Team, Angiuoli S, Fricke WF. Nature Precedings. doi:10.1038 / npre.2011.5887.1, April 2011.
  7. Cunningham: a BLAST runtime estimator.
    White JR, Matalka M, Fricke WF, Angiuoli SV. Nature Precedings. doi: 10.1038 / npre.2011.5593.1, 2011 January.
Recent presentations

  1. "CloVR-ITS: Automated ITS amplicon sequence analysis pipeline for the characterization of fungal microbiota." Joint Conference: The Microbiome / Innate Immunity, Keystone, CO, March 2012.
  2. "CloVR: A cloud-ready platform for bioinformatics analysis." NIH Bioinformatics and Computational Biosciences Festival, Bethesda, MD, February 2012.
  3. "CloVR: Utility and cost of automated sequence analysis on the cloud." University of Maryland - School of Medicine, November 2011.
  4. "CloVR: Automated sequence analysis from your desktop using virtual machines and clouds." Bio-IT Cloud Summit, La Jolla, CA, September 2011.
  5. "Novel approaches for comparative metagenomics." University of Colorado Boulder, November 2010.
  6. "Microbial interaction web inference using metagenomic data." Bauer Forum Seminar - Harvard University, April 2010; Johns Hopkins University, April 2010; RECOMB Regulatory Genomics & Systems Biology, MIT-Harvard, December 2009.