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Huttenhower C., Gevers D., Knight R., Abubucker S., Badger J.H, Chinwalla A.T, Creasy H.H, Earl A.M, Fitzgerald M.G, Fulton R.S et al..  2012.  Structure, function and diversity of the healthy human microbiome. NatureNature. 486
Oberhardt MA, Zarecki R, Reshef L, Xia F, Duran-Frigola M, Schreiber R, Henry CS, Ben-Tal N, Dwyer DJ, Gophna U et al..  2016.  Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E. coli.. PLoS Comput Biol. 12(1):e1004705.
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Kimes NE, Grim CJ, Johnson WR, Hasan NA, Tall BD, Kothary MH, Kiss H, A. Munk C, Tapia R, Green L et al..  2011.  Temperature regulation of virulence factors in the pathogen Vibrio coralliilyticus. The ISME JournalThe ISME journal. 6
Banakar V., G. de Magny C, Jacobs J., Murtugudde R., Huq A., Wood R.J, Colwell RR.  2012.  Temporal and Spatial Variability in the Distribution of Vibrio vulnificus in the Chesapeake Bay: A Hindcast Study. EcoHealthEcoHealth.
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. 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. 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.
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.
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.
Choi S.S, Hannenhalli S.  2013.  Three independent determinants of protein evolutionary rate. J Mol EvolJ Mol EvolJ Mol Evol. 76:98-111.
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 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.
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.
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
Hannenhalli S, Pevzner P.  1996.  To cut… or not to cut (applications of comparative physical maps in molecular evolution). Proceedings of the seventh annual ACM-SIAM symposium on Discrete algorithms.
Wang H, Duggal G, Patro R, Girvan M, Hannenhalli S, Kingsford C.  2013.  Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin. Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics. :306-315.
Regier J.C, Zwick A., Cummings MP, Kawahara A.Y, Cho S., Weller S., Roe A., Baixeras J., Brown J.W, Parr C. et al..  2009.  Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study. BMC Evol BiolBMC Evol Biol. 9
Regier J.C, Zwick A., Cummings MP, Kawahara A.Y, Cho S., Weller S., Roe A., Baixeras J., Brown J.W, Parr C. et al..  2009.  Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study. BMC Evol BiolBMC Evol Biol. 9
Hannenhalli S, Pevzner P.  1995.  Towards a computational theory of genome rearrangements. Computer Science TodayComputer Science Today. 1000
Alam M, Sultana M, G. Nair B, R. Sack B, Sack DA, Siddique A.K, Ali A, Huq A, Colwell RR.  2006.  Toxigenic Vibrio Cholerae in the Aquatic Environment of Mathbaria, Bangladesh. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 72
Dingermann T, Sharp S, Appel B, DeFranco D, Mount S, Heiermann R, Pongs O, Söll D.  1981.  Transcription of cloned tRNA and 5S RNA genes in a Drosophila cell free extract.. Nucleic Acids Res. 9(16):3907-18.
Hannenhalli S, Putt ME, Gilmore JM, Wang J, Parmacek MS, Epstein JA, Morrisey EE, Margulies KB, Cappola TP.  2006.  Transcriptional Genomics Associates FOX Transcription Factors With Human Heart Failure. CirculationCirculation. 114

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