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B
Bloom JS, Khan Z, Kruglyak L, Singh M, Caudy AA.  2009.  Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays.. BMC Genomics. 10:221.
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.
Bringaud F, Müller M, Cerqueira GCoutinho, Smith M, Rochette A, el-Sayed NMA, Papadopoulou B, Ghedin E.  2007.  Members of a large retroposon family are determinants of post-transcriptional gene expression in Leishmania.. PLoS Pathog. 3(9):1291-307.
D
Dogan RIslamaj, Getoor L, W Wilbur J, Mount SM.  2007.  SplicePort--an interactive splice-site analysis tool.. Nucleic Acids Res. 35(Web Server issue):W285-91.
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.
H
Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD et al..  2003.  Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.. Nucleic Acids Res. 31(19):5654-66.
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
Haft DH, Selengut J., Richter RA, Harkins D, Basu MK, Beck E.  2013.  TIGRFAMs and Genome Properties in 2013. Nucleic acids researchNucleic Acids Research. 41
Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E.  2013.  TIGRFAMs and Genome Properties in 2013.. Nucleic Acids Res. 41(Database issue):D387-95.
Hannenhalli S, Russell RB.  2000.  Analysis and prediction of functional sub-types from protein sequence alignments. Journal of Molecular BiologyJournal of Molecular Biology. 303
K
Khan Z, Bloom JS, Kruglyak L, Singh M.  2009.  A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays.. Bioinformatics. 25(13):1609-16.
M
Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KLT et al..  2008.  The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).. Nature. 452(7190):991-6.
P
Peisach E, Selengut J., Dunaway-Mariano D, Allen KN.  2004.  X-ray crystal structure of the hypothetical phosphotyrosine phosphatase MDP-1 of the haloacid dehalogenase superfamily. BiochemistryBiochemistry. 43
R
Roberts M, Hayes W, Hunt BR, Mount SM, Yorke JA.  2004.  Reducing storage requirements for biological sequence comparison.. Bioinformatics. 20(18):3363-9.
S
Selengut J..  2001.  MDP-1 is a new and distinct member of the haloacid dehalogenase family of aspartate-dependent phosphohydrolases. BiochemistryBiochemistry. 40
T
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
Z
Zhang X-N, Mount SM.  2009.  Two alternatively spliced isoforms of the Arabidopsis SR45 protein have distinct roles during normal plant development.. Plant Physiol. 150(3):1450-8.

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