Publications
2002. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.. Science. 298(5601):2157-67.
2003. Genome of Geobacter sulfurreducens: metal reduction in subsurface environments. Science (New York, N.Y.)Science (New York, N.Y.). 302
2004. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. NatureNature. 432
2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proceedings of the National Academy of Sciences of the United States of AmericaProceedings of the National Academy of Sciences of the United States of America. 102
2005. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS computational biologyPLOS Computational Biology. 1
2007. TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic acids researchNucleic Acids Research. 35
2008. Uncovering Genomic Reassortments among Influenza Strains by Enumerating Maximal Bicliques. IEEE International Conference on Bioinformatics and Biomedicine, 2008. BIBM '08.
2009. Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Applied and environmental microbiologyApplied and environmental microbiology. 75
2009. Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.. Appl Environ Microbiol. 75(7):2046-56.
2010. The Alveolate Perkinsus marinus: biological insights from EST gene discovery.. BMC Genomics. 11:228.
2010. MetaPhyler: Taxonomic profiling for metagenomic sequences. 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
2010. Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function. BMC bioinformaticsBMC Bioinformatics. 11
2010. Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function.. BMC Bioinformatics. 11:52.
2010. Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria.. J Bacteriol. 192(21):5788-98.
2010. Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria. Journal of bacteriologyJournal of bacteriology. 192
2011. ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. BMC bioinformaticsBMC Bioinformatics. 12
2011. ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process.. BMC Bioinformatics. 12:434.