Publications
2010. MetaPhyler: Taxonomic profiling for metagenomic sequences. 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
2008. Uncovering Genomic Reassortments among Influenza Strains by Enumerating Maximal Bicliques. IEEE International Conference on Bioinformatics and Biomedicine, 2008. BIBM '08.
2014. Developmental expression of chicken FOXN1 and putative target genes during feather development.. Int J Dev Biol. 58(1):57-64.
2010. The Alveolate Perkinsus marinus: biological insights from EST gene discovery.. BMC Genomics. 11:228.
2002. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.. Science. 298(5601):2157-67.
2006. Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic. BMC biologyBMC biology. 4
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
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
2012. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. The ISME journalThe ISME journal. 6
2012. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage.. ISME J. 6(6):1186-99.
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
2013. A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies). PLoS OnePLoS One. 8
2002. A new, expressed multigene family containing a hot spot for insertion of retroelements is associated with polymorphic subtelomeric regions of Trypanosoma brucei.. Eukaryot Cell. 1(1):137-51.
2011. ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process.. BMC Bioinformatics. 12:434.
2011. ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. BMC bioinformaticsBMC Bioinformatics. 12
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. 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
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.
2007. TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic acids researchNucleic Acids Research. 35