Welcome to the Computational and Analytical Molecular Evolution Lab at The Institute Formerly Known as CARB.

Publications

Posted Thu, 08/20/2009 - 12:21 by arlin

To find a paper in PubMed , click on the title. For supplementary data (where available), click on . To ask a question or request reprints, click on .

Extras Ask Complete Citation (click for link to PubMed)
NA Stoltzfus, A., and L. Y. Yampolsky. 2009. Climbing mount probable: mutation as a cause of nonrandomness in evolution. J Hered 100:637-647.
NA Prosdocimi, F., B. Chisham, E. Pontelli, J. D. Thompson, and A. Stoltzfus. 2009. Initial Implementation of a Comparative Data Analysis Ontology.Evolutionary Bioinformatics 5:47-66.
NA Stoltzfus, A. 2008. Evidence for a predominant role of oxidative damage in germline mutation in mammals.Mutat Res644:71-73
NA Yampolsky, L. Y., and A. Stoltzfus. 2008.Mutational Bias in Encyclopedia of Life Sciences(John Wiley & Sons, Chichester)
NA Stoltzfus, A., and L. Y. Yampolsky. 2007. Amino acid exchangeability and the adaptive code hypothesis. Journal of Molecular Evolution, 65:456-462
NA De Kee, D., V. Gopalan, and A. Stoltzfus. 2007. A sequence-based model accounts largely for the relationship of intron positions to protein structural features. Mol Biol Evol 24(10):2158-68.
Hladish, T., V. Gopalan, C. L. Liang, W. G. Qiu, P. J. Yang, and A. Stoltzfus. 2007. Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data. BMC Bioinformatics 8:191.
NA Stoltzfus, A. 2006. Mutation-Biased Adaptation in a Protein NK Model. Molecular Biology and Evolution 23:1852-1862.
Stoltzfus, A. 2006. Mutationism and the Dual Causation of Evolutionary Change. Evolution and Development 8: 304-317.
Gopalan V, Qiu WG, Chen MZ, Stoltzfus A. Nexplorer: phylogeny-based exploration of sequence family data. Bioinformatics. 2005 Nov 2.
Yampolsky LY, Stoltzfus A. The exchangeability of amino acids in proteins. Genetics. 2005 170 (4) 1459-72.
NA Yampolsky LY, Stoltzfus A. Untangling the effects of codon mutation and amino acid exchangeability. Pac Symp Biocomput. 2005 433-44.
Stoltzfus A. Molecular evolution: introns fall into place. Curr Biol. 2004 14 (9) R351-2.
Qiu WG, Schisler N, Stoltzfus A. The evolutionary gain of spliceosomal introns: sequence and phase preferences. Mol Biol Evol. 2004 21 (7) 1252-63.
NA Yampolsky LY, Stoltzfus A. Bias in the introduction of variation as an orienting factor in evolution. Evol Dev. 2001 3 (2) 73-83.
Stoltzfus A. On the possibility of constructive neutral evolution. J Mol Evol. 1999 49 (2) 169-81.
Logsdon JM Jr, Stoltzfus A, Doolittle WF. Molecular evolution: recent cases of spliceosomal intron gain? Curr Biol. 1998 8 (16) R560-3.
Stoltzfus A, Logsdon JM Jr, Palmer JD, Doolittle WF. Intron "sliding" and the diversity of intron positions. Proc Natl Acad Sci U S A. 1997 94 (20) 10739-44.

S. de Souza, W. Fischer, J.M. Logsdon, Jr., M. Long, W. Martin, and A. Stoltzfus. 1997. The great debate on the origin of introns. HMS Beagle.
Stoltzfus A, Spencer DF, Doolittle WF. Methods for evaluating exon-protein correspondences. Comput Appl Biosci. 1995 11 (5) 509-15.
Stoltzfus A, Spencer DF, Zuker M, Logsdon JM Jr, Doolittle WF. Testing the exon theory of genes: the evidence from protein structure. Science. 1994 265 (5169) 202-7.
NA Stoltzfus A. Origin of introns--early or late. Nature. 1994 369 526-7.
NA Stoltzfus A, Ford Doolittle W. Molecular evolution: slippery introns and globin gene evolution. Curr Biol. 1993 3 (4) 215-7.
NA Doolittle WF, Stoltzfus A. Molecular evolution. Genes-in-pieces revisited. Nature. 1993 361 403.
NA Milkman R, Stoltzfus A. Molecular evolution of the Escherichia coli chromosome. II. Clonal segments. Genetics. 1988 120 (2) 359-66.
NA Stoltzfus A, Leslie JF, Milkman R. Molecular evolution of the Escherichia coli chromosome. I. Analysis of structure and natural variation in a previously uncharacterized region between trp and tonB. Genetics. 1988 120 (2) 345-58.