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Reports
Wagner J, Paulson JN, Wang X-S, Bhattacharjee B, Bravo HCorrada.  2015.  Privacy-Preserving Microbiome Analysis Using Secure Computation.
Wagner J, Paulson JN, Wang X-S, Bhattacharjee B, Bravo HCorrada.  2015.  Privacy-Preserving Microbiome Analysis Using Secure Computation.
Bravo HCorrada, Eng K.H, Keles S., Wahba G., Wright S..  2008.  Estimating Tree-Structured Covariance Matrices via Mixed-Integer Programming with an Application to Phylogenetic Analysis of Gene Expression. 1142
Bravo HCorrada, Eng K.H, Keles S., Wahba G., Wright S..  2008.  Estimating Tree-Structured Covariance Matrices via Mixed-Integer Programming with an Application to Phylogenetic Analysis of Gene Expression. 1142
Miscellaneous
Pop M, Touzet H.  2015.  Algorithms in Bioinformatics: 15th International Workshop, WABI 2015. Lecture Notes in Bioinformatics. :328.
Journal Articles
Istrail S., Sutton G.G, Florea L., Halpern A.L, Mobarry C.M, Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R et al..  2004.  Whole-genome shotgun assembly and comparison of human genome assemblies. 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. 101
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
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
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
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.
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
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..
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
Westenberger S, Cerqueira G, El‐Sayed NM, Zingales B, Campbell D, Sturm N.  2006.  Trypanosoma cruzi mitochondrial maxicircles display species- and strain-specific variation and a conserved element in the non-coding region. BMC GenomicsBMC Genomics. 7
Westenberger SJ, Cerqueira GC, El-Sayed NM, Zingales B, Campbell DA, Sturm NR.  2006.  Trypanosoma cruzi mitochondrial maxicircles display species- and strain-specific variation and a conserved element in the non-coding region.. BMC Genomics. 7:60.
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
Boonyaratanakornkit BB, Simpson AJ, Whitehead TA, Fraser CM, El‐Sayed NM, Clark DS.  2005.  Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non‐lethal cold shock. Environmental MicrobiologyEnvironmental Microbiology. 7
Boonyaratanakornkit BB, Simpson AJ, Whitehead TA, Fraser CM, el-Sayed NMA, Clark DS.  2005.  Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non-lethal cold shock.. Environ Microbiol. 7(6):789-97.
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
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
Nguyen N-phuong, Mirarab S, Liu B, Pop M, Warnow T.  2014.  TIPP:Taxonomic Identification and Phylogenetic Profiling. BioinformaticsBioinformatics.
Haft DH, Selengut J., White O.  2003.  The TIGRFAMs database of protein families. Nucleic acids researchNucleic Acids Research. 31
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
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.

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