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2012
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S et al..  2012.  InterPro in 2011: new developments in the family and domain prediction database.. Nucleic Acids Res. 40(Database issue):D306-12.
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S et al..  2012.  InterPro in 2011: new developments in the family and domain prediction database. Nucleic acids researchNucleic Acids Research. 40
Phillippy A, Treangen T.  2012.  Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone. Genome Biology. 13
Regier JC, Brown JW, Mitter C, Baixeras J, Cho S, Cummings MP, Zwick A.  2012.  A molecular phylogeny for the leaf-roller moths (Lepidoptera: Tortricidae) and its implications for classification and life history evolution.. PloS one. 7:e35574.
Regier JC, Mitter C, M. SOLIS ALMA, HAYDEN JAMESE, LANDRY BERNARD, NUSS MATTHIAS, Simonsen TJ, Yen S-H, Zwick A, Cummings MP.  2012.  A molecular phylogeny for the pyraloid moths (Lepidoptera: Pyraloidea) and its implications for higher-level classification. Systematic Entomology. 37(4):635-656.
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.
Li J, Nina B, Lan C, Mary C, Hannenhalli S, Xiaohong Z, P. Thomas C, Parmacek MS.  2012.  Myocardin-like Protein (MKL)-2 Regulates TGF-beta Signaling. Embryonic Stem Cells and the Developing Vasculature DevelopmentEmbryonic Stem Cells and the Developing Vasculature Development.
Mozumder P.K, Banu M.A, Naser M.N, Ali M.S, Alam M., Sack R.B, Colwell RR, Huq A..  2012.  Occurrence of protozoans & their limnological relationships in some ponds of Mathbaria, Bangladesh. University Journal of Zoology, Rajshahi UniversityUniversity Journal of Zoology, Rajshahi University. 29
Shi W, Wahba G, Irizarry RA, Bravo HCorrada, Wright SJ.  2012.  The partitioned LASSO-patternsearch algorithm with application to gene expression data. BMC bioinformaticsBMC Bioinformatics. 13
Waisberg M, Cerqueira GC, Yager SB, Francischetti IMB, Lu J, Gera N, Srinivasan P, Miura K, Rada B, Lukszo J et al..  2012.  Plasmodium falciparum merozoite surface protein 1 blocks the proinflammatory protein S100P.. Proc Natl Acad Sci U S A. 109(14):5429-34.
Khan Z, Bloom JS, Amini S, Singh M, Perlman DH, Caudy AA, Kruglyak L.  2012.  Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.. Mol Syst Biol. 8:602.
Khan Z, Bloom JS, Amini S, Singh M, Perlman DH, Caudy AA, Kruglyak L.  2012.  Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS. Molecular Systems Biology. 8
Nahar S, Sultana M, M. Naser N, Nair GB, Watanabe H, Ohnishi M, Yamamoto S, Endtz H, Cravioto A, R. Sack B et al..  2012.  Role of Shrimp Chitin in the Ecology of Toxigenic Vibrio cholerae and Cholera Transmission. Frontiers in MicrobiologyFront MicrobiolFrontiers in MicrobiologyFront Microbiol. 2
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.
Huttenhower C., Gevers D., Knight R., Abubucker S., Badger J.H, Chinwalla A.T, Creasy H.H, Earl A.M, Fitzgerald M.G, Fulton R.S et al..  2012.  Structure, function and diversity of the healthy human microbiome. NatureNature. 486
Consortium HMicrobiome, Treangen T.  2012.  Structure, function and diversity of the healthy human microbiome. Nature. 486:207–214.
Banakar V., G. de Magny C, Jacobs J., Murtugudde R., Huq A., Wood R.J, Colwell RR.  2012.  Temporal and Spatial Variability in the Distribution of Vibrio vulnificus in the Chesapeake Bay: A Hindcast Study. EcoHealthEcoHealth.
Savage AF, Cerqueira GC, Regmi S, Wu Y, Sayed NMEl, Aksoy S.  2012.  Transcript expression analysis of putative Trypanosoma brucei GPI-anchored surface proteins during development in the tsetse and mammalian hosts.. PLoS Negl Trop Dis. 6(6):e1708.
Alam M, M. Islam T, Rashed SManzur, Johura F-T, Bhuiyan NA, Delgado G, Morales R, Mendez JLuis, Navarro A, Watanabe H et al..  2012.  Vibrio Cholerae Classical Biotype Strains Reveal Distinct Signatures in Mexico. Journal of Clinical MicrobiologyJ. Clin. Microbiol.Journal of Clinical MicrobiologyJ. Clin. Microbiol..
Pop M..  2012.  We are what we eat: how the diet of infants affects their gut microbiome. Genome BiologyGenome Biology. 13
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.
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
Carl JTrgovcich, Hannenhalli S.  2012.  Widespread evidence of viral miRNAs targeting host pathways. BMC GenomicsBMC Genomics.
2013
Cummings MP.  2013.  AWTY, BAMBE, BEAGLE, BEAST, BEAUti, Bio++, DataMonkey, DendroPy, DnaSP, ENCprime/SeqCount, FigTree, GARLI, genealogical sorting index (gsi), HyPhy, IMa2, jModelTest, JELLYFISH, LAMARC, MacClade, MEGA, Mesquite. Dictionary of Bioinformatics.
Bazinet AL, Cummings MP, Mitter KT, Mitter CW.  2013.  Can RNA-Seq resolve the rapid radiation of advanced moths and butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An exploratory study PLoS One. 8

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