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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.
Cummings MP, Neel MC, Shaw KL.  2008.  A GENEALOGICAL APPROACH TO QUANTIFYING LINEAGE DIVERGENCE. EvolutionEvolution. 62
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.
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
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.
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
Neel M.C, Cummings MP.  2003.  Genetic consequences of ecological reserve design guidelines: An empirical investigation. Conserv GenetConserv Genet. 4
Mount SM.  1997.  Genetic depletion reveals an essential role for an SR protein splicing factor in vertebrate cells.. Bioessays. 19(3):189-92.
Peng X, Mount SM.  1995.  Genetic enhancement of RNA-processing defects by a dominant mutation in B52, the Drosophila gene for an SR protein splicing factor.. Mol Cell Biol. 15(11):6273-82.
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
MacLeod A., Tweedie A., McLellan S., Taylor S., Hall N., Berriman M., El‐Sayed NM, Hope M., Turner C.MR, Tait A..  2005.  The genetic map and comparative analysis with the physical map of Trypanosoma brucei. Nucleic acids researchNucleic Acids Research. 33
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.
Bartholomeu D., Buck G., Teixeira S., El-Sayed N.M..  2010.  Genetics of Trypanosoma cruzi in American Trypanosomiasis: Chagas Disease One hundred Years of Research .
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

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