	Computational and Analytical Molecular Evolution Lab at CARB						Nexplorer
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Publications

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NA		Stoltzfus, A., and L. Y. Yampolsky. 2007. Amino acid exchangeability and the adaptive code hypothesis. Journal of Molecular Evolution, in press
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.