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Journal Articles

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

Bravo H.C, Lee K.E, Klein B.EK, Klein R., Iyengar S.K, Wahba G.. 2009. Examining the relative influence of familial, genetic, and environmental covariate information in flexible risk models. Proceedings of the National Academy of Sciences. 106(20):8128-8133.

Haft DH, Paulsen IT, Ward N, Selengut J.. 2006. Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic. BMC biologyBMC biology. 4

Dogan RIslamaj, Getoor L, W Wilbur J, Mount SM. 2007. Features generated for computational splice-site prediction correspond to functional elements.. BMC Bioinformatics. 8:410.

Dogan RIslamaj, Getoor L, W. Wilbur J, Mount SM. 2007. Features generated for computational splice-site prediction correspond to functional elements. BMC BioinformaticsBMC Bioinformatics. 8

White JRobert, Roberts M, Yorke JA, Pop M.. 2008. Figaro: A Novel Statistical Method for Vector Sequence Removal. BioinformaticsBioinformaticsBioinformaticsBioinformatics. 24

Navlakha S., White J.R, Nagarajan N., Pop M., Kingsford C. 2009. Finding Biologically Accurate Clusterings in Hierarchical Decompositions Using the Variation of Information. Lecture Notes in Computer Science: Research in Computational Molecular BiologyLecture Notes in Computer Science: Research in Computational Molecular Biology. 5541

Navlakha S, White J, Nagarajan N, Pop M., Kingsford C. 2010. Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information. Journal of Computational BiologyJournal of Computational Biology. 17

Mazza A, Wagner A, Ruppin E, Sharan R. 2016. Functional Alignment of Metabolic Networks.. J Comput Biol.

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

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

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

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.

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

Cummings MP, Otto S.P, Wakeley J.. 1999. Genes and other samples of DNA sequence data for phylogenetic inference. The Biological BulletinThe Biological Bulletin. 196

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

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

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

Brettin TS, Bruce DC, Challacombe JF, Detter JC, Han CS, Munik A.C, Chertkov O, Meincke L, Saunders E, Choi SY et al.. 2009. Genome assortment, not serogroup, defines Vibrio cholerae pandemic strains. NatureNature.

Methé B.A, Nelson K.E, Eisen J.A, Paulsen I.T, Nelson W., Heidelberg J.F, Wu D., Wu M., Ward N., Beanan M.J et al.. 2003. Genome of Geobacter sulfurreducens: metal reduction in subsurface environments. Science (New York, N.Y.)Science (New York, N.Y.). 302

Methé B.A, Nelson K.E, Eisen J.A, Paulsen I.T, Nelson W., Heidelberg J.F, Wu D., Wu M., Ward N., Beanan M.J et al.. 2003. Genome of Geobacter sulfurreducens: metal reduction in subsurface environments. Science (New York, N.Y.)Science (New York, N.Y.). 302

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