Publications

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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.
Lin C-F, Mount SM, Jarmołowski A, Makałowski W.  2010.  Evolutionary dynamics of U12-type spliceosomal introns.. BMC Evol Biol. 10:47.
Lin C-F, Mount SM, Jarmołowski A, Makałowski W.  2010.  Evolutionary dynamics of U12-type spliceosomal introns.. BMC Evol Biol. 10:47.
Roe A., Weller S., Baixeras J., Brown J.W, Cummings MP, Davis D.R, Horak M., Kawahara A.Y, Mitter C., Parr C.S et al..  2010.  Evolutionary framework for Lepidoptera model systems. Genetics and Molecular Biology of LepidopteraGenetics and Molecular Biology of Lepidoptera.
Roe A., Weller S., Baixeras J., Brown J.W, Cummings MP, Davis D.R, Horak M., Kawahara A.Y, Mitter C., Parr C.S et al..  2010.  Evolutionary framework for Lepidoptera model systems. Genetics and Molecular Biology of LepidopteraGenetics and Molecular Biology of Lepidoptera.
Mount SM, Anderson P.  2000.  Expanding the definition of informational suppression.. Trends Genet. 16(4):157.
Myers D.S, Bazinet AL, Cummings MP.  2008.  Expanding the reach of Grid computing: combining Globus- and BOINC-based systems. Grids for Bioinformatics and Computational BiologyGrids for Bioinformatics and Computational Biology.
Ye C, Ma Z.S, Cannon C.H, Pop M., Yu D.W.  2012.  Exploiting sparseness in de novo genome assembly. BMC bioinformaticsBMC Bioinformatics. 13
F
Berman P, Hannenhalli S.  1996.  Fast sorting by reversal. Combinatorial Pattern MatchingCombinatorial Pattern Matching. 1075
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
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.
Methé B.A, Nelson K.E, Pop M., Creasy H.H, Giglio M.G, Huttenhower C., Gevers D., Petrosino J.F, Abubucker S., Badger J.H et al..  2012.  A framework for human microbiome research. NatureNature. 486
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.
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.
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.
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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
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
Mount S, Henikoff S.  1993.  Gene organization: nested genes take flight.. Curr Biol. 3(6):372-4.
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
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.
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.

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