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Consortium HMicrobiome, Treangen T.  2012.  A framework for human microbiome research. Nature. 486:215–221.
Bravo HCorrada, Page D., Ramakrishnan R., Shavlik J., Costa V.S.  2005.  A framework for set-oriented computation in inductive logic programming and its application in generalizing inverse entailment. Inductive Logic ProgrammingInductive Logic Programming.
Colwell RR, Faruque S.M, Nair G.B.  2004.  Free-Living to Freewheeling: The Evolution of Vibrio cholerae from Innocence to Infamy. Infectious Disease and Host-Pathogen EvolutionInfectious Disease and Host-Pathogen Evolution.
Colwell RR.  2003.  From terabytes to insights. Communications of the ACMCommunications of the ACM. 46
Valdes KM, Sundar GS, Vega LA, Belew AT, Islam E, Binet R, El-Sayed NM, Le Breton Y, McIver KS.  2016.  The fruRBA operon is necessary for Group A Streptococcal growth in fructose and for resistance to neutrophil killing during growth in whole human blood.. Infect Immun.
Colwell RR.  2002.  Fulfilling the promise of marine biotechnology. Marine biotechnology in the twenty-first century: problems, promise, and productsMarine biotechnology in the twenty-first century: problems, promise, and products.
Zheng L, Cardaci S, Jerby L, MacKenzie ED, Sciacovelli M, T Johnson I, Gaude E, King A, Leach JDG, Edrada-Ebel RA et al..  2015.  Fumarate induces redox-dependent senescence by modifying glutathione metabolism.. Nat Commun. 6:6001.
Mazza A, Wagner A, Ruppin E, Sharan R.  2016.  Functional Alignment of Metabolic Networks.. J Comput Biol.
Ross DA, Hannenhalli S, Tobias JW, Cooch N, Shiekhattar R, Kadesch T.  2006.  Functional Analysis of Hes-1 in Preadipocytes. Molecular EndocrinologyMolecular EndocrinologyMolecular EndocrinologyMolecular Endocrinology. 20
Khaladkar M, Hannenhalli S.  2012.  Functional Divergence of Gene Duplicates a Domain-centric view. BMC Evolutionary BiologyBMC Evolutionary Biology.
Singh LN, Hannenhalli S.  2008.  Functional Diversification of Paralogous Transcription Factors via Divergence in DNA Binding Site Motif and in Expression. PLoS ONEPLoS ONEPLoS ONEPLoS ONE. 3
Choi J, El-Sayed NM.  2012.  Functional genomics of trypanosomatids.. Parasite Immunol. 34(2-3):72-9.
Salzberg S.L, Phillippy A.M, Zimin A., Puiu D., Magoc T., Koren S., Treangen T, Schatz M.C, Delcher A.L, Roberts M. et al..  2012.  GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome researchGenome Research. 22
Zhang Y, Rath N, Hannenhalli S, Wang Z, Cappola T, Kimura S, Atochina-Vasserman E, Lu MMin, Beers MF, Morrisey EE.  2007.  GATA and Nkx factors synergistically regulate tissue-specific gene expression and development in vivo. DevelopmentDevelopment. 134
Bazinet AL, Zwickl DJ, Cummings MP.  2014.  A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0. Syst Biol.
Dewey F.E, Perez M.V, Wheeler M.T, Watt C., Spin J., Langfelder P., Horvath S., Hannenhalli S, Cappola T.P, Ashley E.A.  2011.  Gene Coexpression Network Topology of Cardiac Development, Hypertrophy, and FailureClinical Perspective. Circulation: cardiovascular geneticsCirculation: Cardiovascular Genetics. 4
Bravo HCorrada, Pihur V, McCall M, Irizarry RA, Leek JT.  2012.  Gene expression anti-profiles as a basis for accurate universal cancer signatures. BMC bioinformaticsBMC Bioinformatics. 13
Dinalankara W, Bravo HCorrada.  2015.  Gene Expression Signatures Based on Variability can Robustly Predict Tumor Progression and Prognosis.. Cancer Inform. 14:71-81.
Mount S, Henikoff S.  1993.  Gene organization: nested genes take flight.. Curr Biol. 3(6):372-4.
Kelley DR, Liu B, Delcher AL, Pop M., Salzberg SL.  2012.  Gene Prediction with Glimmer for Metagenomic Sequences Augmented by Classification and Clustering. Nucleic Acids ResearchNucl. Acids Res.Nucleic Acids ResearchNucl. Acids Res.. 40
Shah R, Lu Y, Hinkle CC, McGillicuddy FC, Kim R, Hannenhalli S, Cappola TP, Heffron S, Wang XM, Mehta NN et al..  2009.  Gene Profiling of Human Adipose Tissue During Evoked Inflammation In Vivo. DiabetesDiabetesDiabetesDiabetes. 58
Ghedin E, Bringaud F, Peterson J, Myler P, Berriman M, Ivens A, Andersson B, Bontempi E, Eisen J, Angiuoli S et al..  2004.  Gene synteny and evolution of genome architecture in trypanosomatids.. Mol Biochem Parasitol. 134(2):183-91.
Wang J, Hannenhalli S.  2005.  Generalizations of Markov model to characterize biological sequences. BMC BioinformaticsBMC Bioinformatics. 6
Fleming BD, Chandrasekaran P, Dillon LAL, Dalby E, Suresh R, Sarkar A, El-Sayed NM, Mosser DM.  2015.  The generation of macrophages with anti-inflammatory activity in the absence of STAT6 signaling.. J Leukoc Biol. 98(3):395-407.