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T
Hannenhalli S, Levy S.  2003.  Transcriptional regulation of protein complexes and biological pathways. Mammalian GenomeMammalian Genome. 14
Everett LJ, Jensen ST, Hannenhalli S.  2011.  Transcriptional Regulation Via TF-Modifying Enzymes: An Integrative Model-Based Analysis. Nucleic Acids ResearchNucl. Acids Res.Nucleic Acids ResearchNucl. Acids Res.. 39
Dillon LAL, Okrah K, V Hughitt K, Suresh R, Li Y, Fernandes MCecilia, A Belew T, Bravo HCorrada, Mosser DM, El-Sayed NM.  2015.  Transcriptomic profiling of gene expression and RNA processing during Leishmania major differentiation.. Nucleic Acids Res. 43(14):6799-813.
Hannenhalli S, Pevzner P.  1995.  Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. Proceedings of the twenty-seventh annual ACM symposium on Theory of computing.
Hannenhalli S, Pevzner PA.  1999.  Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. J. ACMJ. ACM. 46
Hannenhalli S.  1995.  Transforming men into mice (a computational theory of genome rearrangements).
Hannenhalli S, Pevzner P.A.  1995.  Transforming men into mice (polynomial algorithm for genomic distance problem). Foundations of Computer Science, Annual IEEE Symposium on.
Singh L.N, Wang L.S, Hannenhalli S.  2007.  TREMOR—a tool for retrieving transcriptional modules by incorporating motif covariance. Nucleic acids researchNucleic Acids Research. 35
Tilghman S., Astin H.S, Brinkley W., Chilton M.D, Cummings MP, Ehrenberg R.G, Fox M.F, Glenn K., Green P.J, Hans S. et al..  1998.  Trends in the early careers of life scientists - Preface and executive summary. Mol Biol CellMol Biol Cell. 9
Sethupathy P, Hannenhalli S.  2008.  A Tutorial of the Poisson Random Field Model in Population Genetics. Advances in BioinformaticsAdvances in Bioinformatics. 2008
U
Mount SM, Pettersson I, Hinterberger M, Karmas A, Steitz JA.  1983.  The U1 small nuclear RNA-protein complex selectively binds a 5' splice site in vitro.. Cell. 33(2):509-18.
Chaiyanan S, Chaiyanan S, Grim C, Maugel T, Huq A, Colwell RR.  2007.  Ultrastructure of coccoid viable but non‐culturable Vibrio cholerae. Environmental MicrobiologyEnvironmental Microbiology. 9
Selengut J., Haft DH.  2010.  Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria. Journal of bacteriologyJournal of bacteriology. 192
Selengut JD, Haft DH.  2010.  Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria.. J Bacteriol. 192(21):5788-98.
V
Minkah N, Hwang Y, Perry K, Van Duyne GD, Hendrickson R, Lefkowitz EJ, Hannenhalli S, Bushman FD.  2007.  Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes. VirologyVirology. 365
Minkah N, Hwang Y, Perry K, Van Duyne GD, Hendrickson R, Lefkowitz EJ, Hannenhalli S, Bushman FD.  2007.  Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes. VirologyVirology. 365
Minkah N, Hwang Y, Perry K, Van Duyne GD, Hendrickson R, Lefkowitz EJ, Hannenhalli S, Bushman FD.  2007.  Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes. VirologyVirology. 365
Alam M., Sultana M., Nair G.B, Siddique A.K, Hasan N.A, Sack R.B, Sack D.A, Ahmed K.U, Sadique A., Watanabe H. et al..  2007.  Viable but nonculturable Vibrio cholerae O1 in biofilms in the aquatic environment and their role in cholera transmission. Proceedings of the National Academy of SciencesProceedings of the National Academy of Sciences. 104
Binsztein N, Costagliola MC, Pichel M, Jurquiza V, Ramírez FC, Akselman R, Vacchino M, Huq A, Colwell RR.  2004.  Viable but Nonculturable Vibrio Cholerae O1 in the Aquatic Environment of Argentina. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 70
Alam M, M. Islam T, Rashed SManzur, Johura F-T, Bhuiyan NA, Delgado G, Morales R, Mendez JLuis, Navarro A, Watanabe H et al..  2012.  Vibrio Cholerae Classical Biotype Strains Reveal Distinct Signatures in Mexico. Journal of Clinical MicrobiologyJ. Clin. Microbiol.Journal of Clinical MicrobiologyJ. Clin. Microbiol..
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Barry JD, Marcello L, Morrison LJ, Read AF, Lythgoe K, Jones N, Carrington M, Blandin G, Böhme U, Caler E et al..  2005.  What the genome sequence is revealing about trypanosome antigenic variation.. Biochem Soc Trans. 33(Pt 5):986-9.
Ricaldi JN, Fouts DE, Selengut J., Harkins DM, Patra KP, Moreno A, Lehmann JS, Purushe J, Sanka R, Torres M et al..  2012.  Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity. PLoS neglected tropical diseasesPLoS neglected tropical diseases. 6
Ricaldi JN, Fouts DE, Selengut JD, Harkins DM, Patra KP, Moreno A, Lehmann JS, Purushe J, Sanka R, Torres M et al..  2012.  Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity.. PLoS Negl Trop Dis. 6(10):e1853.
Nelson KE, Fouts DE, Mongodin EF, Ravel J, DeBoy RT, Kolonay JF, Rasko DA, Angiuoli SV, Gill SR, Paulsen IT et al..  2004.  Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species. Nucleic acids researchNucleic Acids Research. 32
Joardar V, Lindeberg M, Jackson RW, Selengut J., Dodson R, Brinkac LM, Daugherty SC, Deboy R, A. Durkin S, Giglio MGwinn et al..  2005.  Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition. Journal of bacteriologyJournal of bacteriology. 187

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