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A

Joseph SJ, Fernández-Robledo JA, Gardner MJ, El-Sayed NM, Kuo C-H, Schott EJ, Wang H, Kissinger JC, Vasta GR. 2010. The Alveolate Perkinsus marinus: biological insights from EST gene discovery.. BMC Genomics. 11:228.

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Hotopp JCDunning, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen JA, Eisen J, Seshadri R, Ren Q, Wu M et al.. 2006. Comparative genomics of emerging human ehrlichiosis agents. PLoS geneticsPLoS genetics. 2

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Darnell DK, Zhang LS, Hannenhalli S, Yaklichkin SY. 2014. Developmental expression of chicken FOXN1 and putative target genes during feather development.. Int J Dev Biol. 58(1):57-64.

Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM et al.. 2002. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.. Science. 298(5601):2157-67.

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Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN et al.. 2007. Evolution of genes and genomes on the Drosophila phylogeny.. Nature. 450(7167):203-18.

Haft DH, Paulsen IT, Ward N, Selengut J.. 2006. Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic. BMC biologyBMC biology. 4

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Cummings MP, Neel MC, Shaw KL. 2008. A GENEALOGICAL APPROACH TO QUANTIFYING LINEAGE DIVERGENCE. EvolutionEvolution. 62

Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, A. Durkin S et al.. 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

Methé B.A, Nelson K.E, Eisen J.A, Paulsen I.T, Nelson W., Heidelberg J.F, Wu D., Wu M., Ward N., Beanan M.J et al.. 2003. Genome of Geobacter sulfurreducens: metal reduction in subsurface environments. Science (New York, N.Y.)Science (New York, N.Y.). 302

Moran MAnn, Buchan A, González JM, Heidelberg JF, Whitman WB, Kiene RP, Henriksen JR, King GM, Belas R, Fuqua C et al.. 2004. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. NatureNature. 432

Dupont CL, Rusch DB, Yooseph S, Lombardo M-J, R Richter A, Valas R, Novotny M, Yee-Greenbaum J, Selengut JD, Haft DH et al.. 2012. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage.. ISME J. 6(6):1186-99.

Dupont CL, Rusch DB, Yooseph S, Lombardo M-J, R. Richter A, Valas R, Novotny M, Yee-Greenbaum J, Selengut J., Haft DH et al.. 2012. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. The ISME journalThe ISME journal. 6

Haft DH, Selengut J., Mongodin EF, Nelson KE. 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

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Regier JC, Mitter C, Zwick A, Bazinet AL, Cummings MP, Kawahara AY, Sohn J-C, Zwickl DJ, Cho S, Davis DR et al.. 2013. A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies). PLoS OnePLoS One. 8

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Liu B, Gibbons T., Ghodsi M., Pop M.. 2010. MetaPhyler: Taxonomic profiling for metagenomic sequences. 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

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Bringaud F, Biteau N, Melville SE, Hez S, El-Sayed NM, Leech V, Berriman M, Hall N, Donelson JE, Baltz T. 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.

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Basu MK, Selengut JD, Haft DH. 2011. ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process.. BMC Bioinformatics. 12:434.

Basu MK, Selengut J., Haft DH. 2011. ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. BMC bioinformaticsBMC Bioinformatics. 12

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Selengut JD, Rusch DB, Haft DH. 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.

Selengut J., Rusch DB, Haft DH. 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

Mount SM, Gotea V, Lin C-F, Hernandez K, Makalowski W. 2007. Spliceosomal small nuclear RNA genes in 11 insect genomes.. RNA. 13(1):5-14.

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Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J et al.. 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

Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J et al.. 2009. Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.. Appl Environ Microbiol. 75(7):2046-56.

Selengut J., Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, R. Richter A, White O. 2007. TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic acids researchNucleic Acids Research. 35

Haft DH, Selengut J., White O. 2003. The TIGRFAMs database of protein families. Nucleic acids researchNucleic Acids Research. 31

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