Publications

Peer-reviewed

1. 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.


2. 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.


3. 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.


4. 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.


5. 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.


6. 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.


7. 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.


8. 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.


9. 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.


10. 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.


11. 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.


12. 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.


13. 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.


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


15. 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.


16. 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.


17. 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

1. 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.


2. 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.


3. 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.


4. 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.


5. Cunningham: a BLAST runtime estimator.
   White JR, Matalka M, Fricke WF, Angiuoli SV. Nature Precedings. doi: 10.1038/ npre.2011.5593.1, 2011 January.