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Journal Articles
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
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.
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
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
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
Clayton C, Adams M, Almeida R, Baltz T, Barrett M, Bastien P, Belli S, Beverley S, Biteau N, Blackwell J et al..  1998.  Genetic nomenclature for Trypanosoma and Leishmania.. Mol Biochem Parasitol. 97(1-2):221-4.
Salzberg SL, Kingsford C, Cattoli G, Spiro DJ, Janies DA, Aly MMehrez, Brown IH, Couacy-Hymann E, De Mia GMario, Dung DHuu et al..  2007.  Genome Analysis Linking Recent European and African Influenza (H5N1) Viruses. Emerging Infectious DiseasesEmerg Infect DisEmerging Infectious DiseasesEmerg Infect Dis. 13
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
Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermolaeva MD, Allen JE, Selengut J., Koo HL et al..  2002.  Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. NatureNature. 419
Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermolaeva MD, Allen JE, Selengut J., Koo HL et al..  2002.  Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. NatureNature. 419
Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermolaeva MD, Allen JE, Selengut J., Koo HL et al..  2002.  Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. NatureNature. 419
Myers GSA, Parker D, Al-Hasani K, Kennan RM, Seemann T, Ren Q, Badger JH, Selengut JD, DeBoy RT, Tettelin H et al..  2007.  Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus.. Nat Biotechnol. 25(5):569-75.
Myers GSA, Parker D, Al-Hasani K, Kennan RM, Seemann T, Ren Q, Badger JH, Selengut J., DeBoy RT, Tettelin H et al..  2007.  Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus. Nature biotechnologyNature biotechnology. 25
Myers GSA, Parker D, Al-Hasani K, Kennan RM, Seemann T, Ren Q, Badger JH, Selengut JD, DeBoy RT, Tettelin H et al..  2007.  Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus.. Nat Biotechnol. 25(5):569-75.
Myers GSA, Parker D, Al-Hasani K, Kennan RM, Seemann T, Ren Q, Badger JH, Selengut J., DeBoy RT, Tettelin H et al..  2007.  Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus. Nature biotechnologyNature biotechnology. 25
Hannenhalli S, Chappey C., Koonin E.V, Pevzner P.A,.  1995.  Genome sequence comparison and scenarios for gene rearrangements: A test case. GenomicsGenomics. 30

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