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Journal Articles
Vishnoi A, Kryazhimskiy S, Bazykin GA, Hannenhalli S, Plotkin JB.  2010.  Young Proteins Experience More Variable Selection Pressures Than Old Proteins. Genome ResearchGenome Res.Genome ResearchGenome Res.. 20
Nelson KE, Fouts DE, Mongodin EF, Ravel J, DeBoy RT, Kolonay JF, Rasko DA, Angiuoli SV, Gill SR, Paulsen IT et al..  2004.  Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species. Nucleic acids researchNucleic Acids Research. 32
Ricaldi JN, Fouts DE, Selengut J., Harkins DM, Patra KP, Moreno A, Lehmann JS, Purushe J, Sanka R, Torres M et al..  2012.  Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity. PLoS neglected tropical diseasesPLoS neglected tropical diseases. 6
Ricaldi JN, Fouts DE, Selengut JD, Harkins DM, Patra KP, Moreno A, Lehmann JS, Purushe J, Sanka R, Torres M et al..  2012.  Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity.. PLoS Negl Trop Dis. 6(10):e1853.
Binsztein N, Costagliola MC, Pichel M, Jurquiza V, Ramírez FC, Akselman R, Vacchino M, Huq A, Colwell RR.  2004.  Viable but Nonculturable Vibrio Cholerae O1 in the Aquatic Environment of Argentina. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 70
Minkah N, Hwang Y, Perry K, Van Duyne GD, Hendrickson R, Lefkowitz EJ, Hannenhalli S, Bushman FD.  2007.  Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes. VirologyVirology. 365
Cunningham CE, Li S, Vizeacoumar FS, Bhanumathy KKalyanasun, Lee JSang, Parameswaran S, Furber L, Abuhussein O, Paul JM, McDonald M et al..  2016.  Therapeutic relevance of the protein phosphatase 2A in cancer. Oncotarget.com.
Cunningham CE, Li S, Vizeacoumar FS, Bhanumathy KKalyanasun, Lee JSang, Parameswaran S, Furber L, Abuhussein O, Paul JM, McDonald M et al..  2016.  Therapeutic relevance of the protein phosphatase 2A in cancer. Oncotarget.com.
Goodheart J, Camacho-García Y, Padula V, Schrödl M, Cervera JL, Gosliner TM, Valdés Á.  2015.  Systematics and biogeography of Pleurobranchus  Cuvier, 1804, sea slugs (Heterobranchia: Nudipleura: Pleurobranchidae). Zoological Journal of the Linnean Society. :n/a-n/a.
Konieczny A., Voytas D.F, Cummings MP, Ausubel F.M.  1991.  A superfamily of ıt Arabidopsis thaliana retrotransposons. GeneticsGenetics. 127
Voytas D.F, Konieczny A., Cummings MP, Ausubel F.M.  1990.  The structure, distribution and evolution of the ıt Ta1 retrotransposable element family of ıt Arabidopsis thaliana. GeneticsGenetics. 126
Patro R., Dickerson J.P, Bista S., Gupta S.K, Varshney A.  2012.  Speeding Up Particle Trajectory Simulations under Moving Force Fields using GPUs. Journal of Computing and Information Science in EngineeringJournal of Computing and Information Science in Engineering.
Patro R., Ip CYiu, Bista S., Varshney A.  2011.  Social Snapshot: A System for Temporally Coupled Social Photography. Computer Graphics and Applications, IEEEComputer Graphics and Applications, IEEE. 31
Gardner MJ, Shallom SJ, Carlton JM, Salzberg SL, Nene V, Shoaibi A, Ciecko A, Lynn J, Rizzo M, Weaver B et al..  2002.  Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14. NatureNature. 419
el-Sayed NMA, Ghedin E, Song J, MacLeod A, Bringaud F, Larkin C, Wanless D, Peterson J, Hou L, Taylor S et al..  2003.  The sequence and analysis of Trypanosoma brucei chromosome II.. Nucleic Acids Res. 31(16):4856-63.
Patro R., Ip C.Y, Varshney A, Hagen H..  2010.  Saliency Guided Summarization of Molecular Dynamics Simulations. Scientific Visualization: Advanced ConceptsScientific Visualization: Advanced Concepts. 1
Maximo A., Patro R., Varshney A, Farias R..  2011.  A robust and rotationally invariant local surface descriptor with applications to non-local mesh processing. Graphical ModelsGraphical Models. 73
Goodheart J, Valdés Á.  2013.  Re-evaluation of the Doriopsilla areolata Bergh, 1880 (Mollusca: Opisthobranchia) subspecies complex in the eastern Atlantic Ocean and its relationship to South African Doriopsilla miniata (Alder & Hancock, 1864) based on molecular data. Marine Biodiversity. 43(2):113-120.
Everett L., Vo A., Hannenhalli S.  2009.  PTM-Switchboard—a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes. Nucleic acids researchNucleic Acids Research. 37
Vardhanabhuti S, Wang J, Hannenhalli S.  2007.  Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. Nucleic Acids ResearchNucleic Acids Research. 35
Yizhak K, Gaude E, Le Dévédec S, Waldman YY, Stein GY, van de Water B, Frezza C, Ruppin E.  2014.  Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer.. Elife. 3
Hadley D., Murphy T., Valladares O., Hannenhalli S, Ungar L., Kim J., Bucan M.,.  2006.  Patterns of sequence conservation in presynaptic neural genes. Genome BiolGenome Biol. 7
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R et al..  2007.  New developments in the InterPro database.. Nucleic Acids Res. 35(Database issue):D224-8.
Ronquist F., Teslenko M., van der Mark P., Ayres D.L, Darling A., Hohna S., Larget B., Liu L., Suchard M.A, Huelsenbeck J.P.  2012.  MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space. Systematic Biology. 61:539-542.
Regier JC, Mitter C, KRISTENSEN NIELSP, Davis DR, VAN NIEUKERKEN ERIKJ, ROTA JADRANKA, Simonsen TJ, Mitter KT, Kawahara AY, Yen S-H et al..  2015.  A molecular phylogeny for the oldest (nonditrysian) lineages of extant Lepidoptera, with implications for classification, comparative morphology and life-history evolution. Systematic Entomology. :n/a-n/a.

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