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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
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
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
Takala-Harrison S, Clark TG, Jacob CG, Cummings MP, Miotto O, Dondorp AM, Fukuda MM, Nosten F, Noedl H, Imwong M et al..  2013.  Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia. 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. 110
Takala-Harrison S, Clark TG, Jacob CG, Cummings MP, Miotto O, Dondorp AM, Fukuda MM, Nosten F, Noedl H, Imwong M et al..  2013.  Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia. 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. 110
Rohlfing A-K, Miteva Y, Hannenhalli S, Lamitina T.  2010.  Genetic and Physiological Activation of Osmosensitive Gene Expression Mimics Transcriptional Signatures of Pathogen Infection in C. elegans. PLoS ONEPLoS One. 5
Treangen T, Abraham A-L, Touchon M, Rocha EPC.  2009.  Genesis, effects and fates of repeats in prokaryotic genomes. FEMS microbiology reviews. 33:539–571.
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
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
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
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
Mazza A, Wagner A, Ruppin E, Sharan R.  2016.  Functional Alignment of Metabolic Networks.. J Comput Biol.
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.
Nagarajan N, Cook C, Di Bonaventura MPia, Ge H, Richards A, Bishop-Lilly KA, DeSalle R, Read TD, Pop M..  2010.  Finishing genomes with limited resources: lessons from an ensemble of microbial genomes. BMC GenomicsBMC Genomics. 11
Nagarajan N, Cook C, Di Bonaventura MPia, Ge H, Richards A, Bishop-Lilly KA, DeSalle R, Read TD, Pop M..  2010.  Finishing genomes with limited resources: lessons from an ensemble of microbial genomes. BMC GenomicsBMC Genomics. 11
White JRobert, Roberts M, Yorke JA, Pop M..  2008.  Figaro: A Novel Statistical Method for Vector Sequence Removal. BioinformaticsBioinformaticsBioinformaticsBioinformatics. 24
Nijkamp JF, Pop M., Reinders MJT, de Ridder D.  2013.  Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold. Bioinformatics (Oxford, England)Bioinformatics (Oxford, England). 29
Rangarajan N, Kulkarni P, Hannenhalli S.  2015.  Evolutionarily conserved network properties of intrinsically disordered proteins.. PLoS One. 10(5):e0126729.
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.
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. NatureNature. 450
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.
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. NatureNature. 450
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. NatureNature. 450
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.
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. NatureNature. 450

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