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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.
Cummings MP.  1992.  Patterns and processes of sequence evolution: plant organelle genomes and copia-like retrotransposons.
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
Cummings MP.  1994.  Transmission patterns of eukaryotic transposable elements - arguments for and against horizontal transfer. Trends Ecol EvolTrends Ecol Evol. 9
Cummings MP, Huskamp J.C.  2005.  Grid computing. EDUCAUSE ReviewEDUCAUSE Review. 40
Cummings MP, Welschmeyer N.A.  1998.  Pigment composition of putatively achlorophyllous angiosperms. Plant Syst EvolPlant Syst Evol. 210
Cummings MP.  2004.  A book like its cover. HeredityHeredity. 93
Cummings MP, Nugent J.M, Olmstead R.G, Palmer J.D.  2003.  Phylogenetic analysis reveals five independent transfers of the chloroplast gene ıt rbcL to the mitochondrial genome in angiosperms. Curr GenetCurr Genet. 43
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.
Cummings MP.  1991.  Review of Fundamentals of Molecular Evolution, by Li. W.-H. and D. Graur. CladisticsCladistics. 7
Cummings MP, Otto S.P, Wakeley J..  1995.  Sampling properties of DNA sequence data in phylogenetic analysis. Mol Biol EvolMol Biol Evol. 12
Cummings MP.  2004.  PHYLIP (Phylogeny Inference Package).
Cummings MP, Neel MC, Shaw KL.  2008.  A GENEALOGICAL APPROACH TO QUANTIFYING LINEAGE DIVERGENCE. EvolutionEvolution. 62
Cummings MP, Handley S.A, Myers D.S, Reed D.L, Rokas A., Winka K..  2003.  Comparing bootstrap and posterior probability values in the four-taxon case. Syst BiolSyst Biol. 52
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.
D
DanČÍK V., Hannenhalli S, Muthukrishnan S..  1997.  Hardness of flip-cut problems from optical mapping. Journal of Computational BiologyJournal of Computational Biology. 4
Darling AE, Treangen T, Zhang L, Kuiken C, Messeguer X, Perna NT.  2006.  Procrastination Leads to Efficient Filtration for Local Multiple Alignment. 4175:126-137.
Darling AE, Treangen T, Messeguer X, Perna NT.  2007.  Analyzing patterns of microbial evolution using the mauve genome alignment system. Comparative Genomics. :135–152.
Darling AE, Treangen T, Zhang L, Kuiken C, Messeguer X, Perna NT.  2006.  Procrastination leads to efficient filtration for local multiple alignment. International Workshop on Algorithms in Bioinformatics.
Darnell DK, Zhang LS, Hannenhalli S, Yaklichkin SY.  2014.  Developmental expression of chicken FOXN1 and putative target genes during feather development.. Int J Dev Biol. 58(1):57-64.
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.
Davison M, Treangen T, Koren S, Pop M, Bhaya D.  2016.  Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers.. PLoS One. 11(9):e0160574.
G. de Magny C, Murtugudde R., Sapiano M.RP, Nizam A., Brown C.W, Busalacchi A.J, Yunus M., Nair G.B, Gil A.I, Lanata C.F et al..  2008.  Environmental signatures associated with cholera epidemics. Proceedings of the National Academy of SciencesProceedings of the National Academy of Sciences. 105
G. de Magny C, Long W., Brown C.W, Hood R.R, Huq A., Murtugudde R., Colwell RR.  2009.  Predicting the distribution of Vibrio spp. in the Chesapeake Bay: a Vibrio cholerae case study. EcoHealthEcoHealth. 6
De Magny GConstantin, Mozumder PK, Grim CJ, Hasan NA, M. Naser N, Alam M, R. Sack B, Huq A, Colwell RR.  2011.  Role of Zooplankton Diversity in Vibrio Cholerae Population Dynamics and in the Incidence of Cholera in the Bangladesh Sundarbans. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.. 77

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