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Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP et al..  2012.  BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics. Systematic BiologySyst BiolSystematic BiologySyst Biol. 61
Lee S.H, Kalejta R.F, Kerry J., Semmes O.J, O'Connor C.M, Khan Z., Garcia B.A, Shenk T., Murphy E..  2012.  BclAF1 restriction factor is neutralized by proteasomal degradation and microRNA repression during human cytomegalovirus infection. Proceedings of the National Academy of Sciences. 109(24):9575-9580.
Lee SHee, Kalejta RF, Kerry J, Semmes OJohn, O'Connor CM, Khan Z, Garcia BA, Shenk T, Murphy E.  2012.  BclAF1 restriction factor is neutralized by proteasomal degradation and microRNA repression during human cytomegalovirus infection.. Proc Natl Acad Sci U S A. 109(24):9575-80.
Lee S.H, Kalejta R.F, Kerry J., Semmes O.J, O'Connor C.M, Khan Z., Garcia B.A, Shenk T., Murphy E..  2012.  BclAF1 restriction factor is neutralized by proteasomal degradation and microRNA repression during human cytomegalovirus infection. Proceedings of the National Academy of Sciences. 109(24):9575-9580.
Das A, Morley M, Moravec CS, Tang W.HW, Hakonarson H, Ashley EA, Brandimarto J, Hu R, Li M, Li H et al..  2015.  Bayesian integration of genetics and epigenetics detects causal regulatory SNPs underlying expression variability. Nature Communications. 6:8555.
Koren S, Treangen T, Pop M..  2011.  Bambus 2: Scaffolding Metagenomes. Bioinformatics. 27
Cummings MP.  2004.  BAMBE, DnaSP, ENCprime/SeqCount, LAMARC, MacClade, MEGA, Modeltest, MrBayes, PAML, PAUP*, PHYLIP, r8s, readseq, Seq-Gen, Sites, TreeView. Dictionary of Bioinformatics. :39-40,123-124,146,288-289,305,318,337,352,388,392,398-399,455,457,502,522,568.
Hannenhalli S, Hayes WS, Hatzigeorgiou AG, Fickett JW.  1999.  Bacterial Start Site Prediction. Nucleic Acids ResearchNucl. Acids Res.Nucleic Acids ResearchNucl. Acids Res.. 27
Rasko D.A, Worsham P.L, Abshire T.G, Stanley S.T, Bannan J.D, Wilson M.R, Langham R.J, Decker R.S, Jiang L., Read T.D et al..  2011.  Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proceedings of the National Academy of SciencesProceedings of the National Academy of Sciences. 108
A
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.
Balch T, Khan Z, Veloso M.  2001.  Automatically tracking and analyzing the behavior of live insect colonies. the fifth international conferenceProceedings of the fifth international conference on Autonomous agents - AGENTS '01.
Koren S, Treangen T, Hill CM, Pop M, Phillippy AM.  2014.  Automated ensemble assembly and validation of microbial genomes.. BMC Bioinformatics. 15:126.
Acevedo MA, Corrada-Bravo CJ, Corrada-Bravo H, Villanueva-Rivera LJ, T. Aide M.  2009.  Automated classification of bird and amphibian calls using machine learning: A comparison of methods. Ecological Informatics. 4(4):206-214.
Mount SM.  1996.  AT-AC introns: an ATtACk on dogma.. Science. 271(5256):1690-2.
Rawlings TK, Ruiz GM, Colwell RR.  2007.  Association of Vibrio Cholerae O1 El Tor and O139 Bengal with the Copepods Acartia Tonsa and Eurytemora Affinis. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 73
Wetzel J., Kingsford C, Pop M..  2011.  Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. BMC bioinformaticsBMC Bioinformatics. 12
Marbach-Ad G., Briken V., El-Sayed N.M., Frauwirth K., Fredericksen B., Hutcheson S., Gao L.-Y., Joseph S., Lee V., McIver K.S. et al..  2009.  Assessing Student Understanding of Host Pathogen Interactions Using a Concept Inventory. J. Microbiol. Biol. Ed.. 10:43-50.
Kingsford C, Schatz M., Pop M..  2010.  Assembly complexity of prokaryotic genomes using short reads. BMC bioinformaticsBMC Bioinformatics. 11
Lerner MR, Boyle JA, Mount SM, Wolin SL, Steitz JA.  1980.  Are snRNPs involved in splicing? Nature. 283(5743):220-4.
Liu B., Pop M..  2009.  ARDB--Antibiotic Resistance Genes Database. Nucleic Acids ResearchNucleic Acids Research. 37
Haft DH, Payne SH, Selengut JD.  2012.  Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification.. J Bacteriol. 194(1):36-48.
Haft DH, Payne SH, Selengut J..  2012.  Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification. Journal of bacteriologyJournal of bacteriology. 194
Huq A., Grim C.J, Colwell RR.  2011.  Aquatic Realm and Cholera. Epidemiological and Molecular Aspects on CholeraEpidemiological and Molecular Aspects on Cholera.
Cummings MP, Myers D.S, Mangelson M..  2004.  Applying permutation tests to tree-based statistical models: extending the R package rpart. 2004-24
Colwell RR.  2003.  ANNUAL REVIEW & FORECAST REPORTS-THE OCEANS: TO PROTECT AND TO PLOW. Sea TechnologySea Technology. 44

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