Marine Biological Laboratory Workshop on Molecular Evolution  
Marine Biological Laboratory
HomePeopleScheduleSoftwareResources

Resources
File Formats
Glossary
Hardware
Quotations
References
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Substitution Models
The Amphioxus Song
UNIX Tutorial
Converting File Formats
Using a Laptop at the Workshop
Likelihood Ratio Test
Online Journals
Photo Gallery
Scientific Societies
Tree Formats
Course T-Shirts
Search


B

Bafna, V., S. Hannenhalli, K. Rice and L. Vawter. 2000. Ligand-receptor pairing via treecomparison. J. Comput. Biol. 7:59-70.

Bailey, T. L. and Elkan, C.1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, AAAI Press, Menlo PArk, California, U.S.A.: 28-36.

Bairoch, A. 1992. PROSITE: A Dictionary of Sites and Patterns in Proteins. Nucleic Acids Res. 20:2013-2018.

Ballard JW, Kreitman M. 1994. Unraveling selection in the mitochondrial genome of Drosophila. Genetics. 138(3):757-72.

Barrier M, Bustamante CD, Yu J, Purugganan MD. 2003. Selection on rapidly evolving proteins in the Arabidopsis genome.

Bayes, T. 1763. An essay towards solving a problem in the doctrine of chances. Phil. Trans. Roy. Soc. London 53:370-418.

Bayliss CD, Field D, and Moxon R (2001) The simple sequence contingency loci of Haemophilus influenzae and Neisseria meningitidis. J. Clin. Invest. 107: 657-662.

Bazin E, Glemin S and Galtier N. 2006. Population size does not influence mitochondrial genetic diversity in animals. Science 312(5773):570-2.

Beerli, P. 2004. Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations. Molecular Ecology 13:827-836.

Beerli, P. 2006. Comparison of Bayesian and maximum-likelihood inference of population genetic parameters. Bioinformatics 22:341-345.

Beerli, P. and J. Felsenstein. 1999. Maximum likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152:763-773.

Beerli, P. and J. Felsenstein. 2001. Maximum likelihood estimation of a migration matrix and effective populations sizes in n subpopulations by using a coalescent approach. Proc. Natl. Acad. Sci. USA 98:4563-4568.

Beier, B.-A., J. A. A. Nylander, M. W. Chase and M. Thulin. 2004. Phylogenetic relationships and biogeography of the plant genus Fagonia (Zygophyllaceae), inferred by parsimony and Bayesian model averaging. Mol. Phyl. Evol. 33:91-108

Begun DJ, Aquadro CF. 1992. Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature. 356(6369):519-20.

Bierne, P. and A. Eyre-Walker. 2003. The Problem of Counting Sites in the Estimation of the Synonymous and Nonsynonymous Substitution Rates: Implications for the Correlation Between the Synonymous Substitution Rate and Codon Usage Bias. Genetics 165:1587-1597.

Béjà, O., M. T. Suzuki, J. F. Heidelberg, W. C. Nelson, C. M. Preston, T. Hamada, J. A. Eisen, C. M. Fraser and E. F. DeLong. 2002. Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 415: 630-633.

Bernardi,G., G. D'Onofrio, S. Caccio, and G. Bernardi. 1993. Molecular phylogeny of bony fishes, based on amino acid sequence of the growth hormone. J. Mol. Evol. 37:644-649.

Berg, D. E. and M. M. Howe. 1989. Mobile DNA. American Society for Microbiology, Washington, DC.

Bielawski, J., K. Dunn and Z. Yang. 2000. Rates of nucleotide substitution and mammalian nuclear gene evolution: approximate and maximum-likelihood methods lead to different conclusions. Genetics 156:1299-1308.

Bielawski, J. P. and Z. Yang. 2001. The role of selection in the evolution of the DAZ gene family. Molecular Biology and Evolution, 18: 523-529.

Bielawski, J. P. and Z. Yang. 2003. Maximum likelihood methods for detecting adaptive evolution after gene duplication. Journal of Structural and Functional Genomics, 3:201-212.

Bielawski, J. and Z. Yang. 2004. In: Statistical methods in Molecular Evolution, Springer Verlag Series in Statistics in Health and Medicine. New York, New York. In Press.

Boeke, J. D., and S. E. Devine. 1998 Yeastretrotransposons: finding a nice quiet neighborhood. Cell. 93:1087-1089.

Boeke, J. D. and O. K. Pickeral. 1999. Retroshuffling the genomic deck. Nature 398:108-109, 111.

Boldrick, J. C., A. A. Alizadek, M. Diehn, S. Dudoit, C. I. Lui, C. E. Belcher, D. Botstein, L. M. Staudt, P. O. Brow, and D. A. Relman. 2002. Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc. Natl. Acad. Sci. USA 99:972-977.

Brandley, M. C., A. Schmitz, and T. W. Reeder. 2005. Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of Scincid lizards. Syst. Biol. 54:373-390.

Brauer MJ, Holder MT, Dries LA, Zwickl DJ, Lewis PO and Hillis DM. Mol. Biol. Evol. 19:1717-26.

Bremer, K. 1998. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution. 42:795-803.

Britt, A. B. and J. A. Eisen. 2000. DNA repair and recombination. In Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815.

Bromham, L., A. Rambaut, R. Fortey, A. Cooper, and D. Penny. 1998. Testing the Cambrian explosion hypothesis by using a molecular dating technique. Proc. Natl. Acad. Sci. USA 95:12386-12389.

Brumfield, R. T., P. Beerli, D. A. Nickerson, and S. V. Edwards. 2003. The utility of single nucleotide polymorphisms in inferences of population history. Trends in Ecology and Evolution 18:249-256.

Buckley, T. R., P. Arensburger, C. Simon and G. K. Chambers. 2002. Combined data, Bayesian phylogenetics, and the origin of the New Zealand cicada genera. Syst. Biol. 51:4-18.

Bull, J. J., Huelsenbeck, J. P., Cunningham, C. W., Swofford, D. L. 1993. Partitioning and combining data in phylogenetic analysis. Syst. Biol. 42:384-397.

Bureau, T. E., S. E. White, and S. R. Wessler. 1994. Transduction of a cellular gene by a plant retroelement. Cell 77:479-480.

K. P. Burnham and D. R. Anderson. 2002. Model Selection and Multimodel Inference: A Practical Information-theoretic Approach. Springer, New York, 2nd edition.

Bustamante CD, Nielsen R, Sawyer SA, Olsen KM, Purugganan MD, Hartl DL. 2002. The cost of inbreeding in Arabidopsis. Nature. 4;416(6880):531-4

.......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... ..........

Maintained by Adam Bazinet
Direct questions and comments to Michael Cummings
Maintained by Adam Bazinet
Direct questions and comments to Michael Cummings