Welcome. If you can’t access something, let me know. There are a few glitches:

  • the citations links are via PubMed, which has about 5-fold less coverage than citations via Google Scholar
  • Some items are missing some links
  • The Altmetrics links are an experiment, handy for recent papers



  • Norris, R., C.L. Strope, D.L. McCandlish, and A. Stoltzfus. Bayesian priors for tree calibration: Evaluating two new approaches based on fossil intervals.  (available on bioarxiv)
  • A. Stoltzfus and D.L. McCandlish, 2015.  Mutation-biased adaptation in Andean house wrens.  PNAS 112 (45): 13753-13754.PubMed | Citations PDF
  • Stoltzfus, A. and R.W. Norris. 2015. On the causes of evolutionary transition:transversion bias PubMed | Citations PDF
  • Stoltzfus, A., and K. Cable. 2014. Mendelian-Mutationism: The Forgotten Evolutionary Synthesis. J Hist Biol. doi:10.1007/s10739-014-9383-2.  PubMed | Citations PDF
  • Stoltzfus, Arlin. 2014. In search of mutation-driven evolution. Evolution and Development 16 (1):57-59. doi:10.1111/ede.12062.   PubMed | PDF
  • McCandlish, D. M., and A. Stoltzfus. 2014. Modeling Evolution using the Probability of Fixation: History and Implications. Quarterly Review of Biology. PubMed | Citations  | PDF
  • Stoltzfus, A., H. Lapp, N. Matasci, H. Deus, B. Sidlauskas, C. M. Zmasek, G. Vaidya et al. 2013. Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. BMC Bioinformatics 14:158. doi:10.1186/1471-2105-14-158.   PubMed | Citations PDF
  • Yu, G., and A. Stoltzfus. 2012. Population diversity of ORFan genes in Escherichia coli. Genome Biology and Evolution 4 (11):1176-1187. doi:10.1093/gbe/evs081.   PubMed | Citations PDF
  • Vos, R. A., J. P. Balhoff, J. A. Caravas, M. T. Holder, H. Lapp, W. P. Maddison, P. E. Midford et al. 2012. NeXML: rich, extensible, and verifiable representation of comparative data and metadata. Systematic Biology 61 (4):675-689. doi:10.1093/sysbio/sys025.   PubMed | Citations PDF
  • Stoltzfus, A., B. O’Meara, J. Whitacre, R. Mounce, E. L. Gillespie, S. Kumar, D. F. Rosauer, and R. A. Vos. 2012. Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. BMC Research Notes 5:574. doi:10.1186/1756-0500-5-574.   PubMed | Citations PDF
  • Stoltzfus, A. 2012. Constructive neutral evolution: exploring evolutionary theory’s curious disconnect. Biol Direct 7 (1):35. doi:10.1186/1745-6150-7-35.   PubMed | Citations PDF
  • Panahiazar, M., A. Ranabahu, V. Taslimi, H. Yalamanchili, A. Stoltzfus, J. Leebens-Mack, and A.P. Sheth. 2012. PhylOnt: A Domain-Specific Ontology for Phylogeny Analysis. In IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2012). Philadelphia, PA.  abstract
  • Spiering, M. J., L. A. Urban, D. L. Nuss, V. Gopalan, A. Stoltzfus, and E. Eisenstein. 2011. Gene identification in black cohosh (Actaea racemosa L.): expressed sequence tag profiling and genetic screening yields candidate genes for production of bioactive secondary metabolites. Plant cell reports 30 (4):613-629. doi:10.1007/s00299-010-0979-5.   PubMed | Citations
  • Stoltzfus, A., and L. Y. Yampolsky. 2009. Climbing mount probable: mutation as a cause of nonrandomness in evolution. J Hered 100 (5):637-647.   PubMed | Citations
  • 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.   PubMed | Citations
  • Yampolsky, L. Y., and A. Stoltzfus. 2008. Mutational Bias. In Encyclopedia of Life Sciences. Chichester: John Wiley & Sons.   PDF
  • Stoltzfus, A. 2008. Evidence for a predominant role of oxidative damage in germline mutation in mammals. Mutat Res 644 (1-2):71-73.   PubMed | Citations
  • Stoltzfus, A., and L. Y. Yampolsky. 2007. Amino Acid Exchangeability and the Adaptive Code Hypothesis. J Mol Evol 65 (4):456-462.   PubMed | Citations
  • Lapp, H., S. Bala, J.P. Balhoff, A. Bouck, N. Goto, M. Holder, R. Hollan et al. 2007. The 2006 NESCent Phyloinformatics Hackathon: A field report. Evolutionary Bioinformatics 3:357-366.   PDF
  • Hladish, T., V. Gopalan, C. Liang, W. Qiu, P. Yang, and A. Stoltzfus. 2007. Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data. BMC Bioinformatics 8:191-201.   PubMed | Citations
  • De Kee, D. W., 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):2158-2168.   PubMed | Citations
  • Stoltzfus, A. 2006. Mutation-Biased Adaptation in a Protein NK Model. Mol Biol Evol 23 (10):1852-1862.   PubMed | Citations
  • Stoltzfus, A. 2006. Mutationism and the Dual Causation of Evolutionary Change. Evol Dev 8 (3):304-317.   PubMed | Citations
  • Gopalan, V., W. G. Qiu, M.Z. Chen, and A. Stoltzfus. 2006. Nexplorer: phylogeny-based exploration of sequence family data. Bioinformatics 22 (1):120-121.   PubMed | Citations
  • Yampolsky, L. Y., and A. Stoltzfus. 2005. Untangling the effects of codon mutation and amino acid exchangeability. Pac Symp Biocomput:433-444. PubMed | Citations
  • Yampolsky, L. Y., and A. Stoltzfus. 2005. The exchangeability of amino acids in proteins. Genetics 170 (4):1459-1472.   PubMed | Citations
  • Stoltzfus, A. 2004. Molecular evolution: introns fall into place. Curr Biol 14 (9):R351-352.   PubMed | Citations
  • Qiu, W. G., N. Schisler, and A. Stoltzfus. 2004. The evolutionary gain of spliceosomal introns: sequence and phase preferences. Mol Biol Evol 21 (7):1252-1263.    PubMed | Citations
  • Yampolsky, L. Y., and A. Stoltzfus. 2001. Bias in the introduction of variation as an orienting factor in evolution. Evol Dev 3 (2):73-83. PubMed | Citations
  • Stoltzfus, A. 2001. Introns and Exons. In The Encyclopaedia of Genetics, eds. S. Brenner, and J.H. Miller, 1052-1053. London: Academic Press.  PDF
  • Stoltzfus, A. 1999. On the possibility of constructive neutral evolution. J Mol Evol 49 (2):169-181. PubMed | Citations
  • Logsdon, J.M., Jr., A. Stoltzfus, and W.F. Doolittle. 1998. Molecular evolution: Recent cases of spliceosomal intron gain? Curr. Biol. 8:R560-R563. PubMed | Citations
  • Stoltzfus, A., J. M. Logsdon, Jr., J. D. Palmer, and W. F. Doolittle. 1997. Intron “sliding” and the diversity of intron positions. Proc Natl Acad Sci U S A 94 (20):10739-10744. PubMed | Citations
  • Doolittle, R., S. de Souza, W. Fischer, J.M. Logsdon, Jr., M. Long, W. Martin, and A. Stoltzfus. 1997. The origin and evolution of introns: A debate. HMS Beagle: The BioMedNet Magazine. Feb. 1    (this has disappeared without a trace)
  • Stoltzfus, A., D. F. Spencer, M. Zuker, J. M. Logsdon, Jr., and W.F. Doolittle. 1995. Introns and the origin of protein-coding genes (Response). Science 268:1367-1369.  PDF
  • Stoltzfus, A., D. Spencer, and W.F. Doolittle. 1995. Methods for Evaluating Exon-Protein Correspondences. CABIOS 11 (5):509-515. PubMed | Citations
  • Stoltzfus, A., D. F. Spencer, M. Zuker, J. M. Logsdon, Jr., and W. F. Doolittle. 1994. Testing the exon theory of genes: the evidence from protein structure [see comments]. Science 265 (5169):202-207.   PubMed | Citations
  • Stoltzfus, A. 1994. Origin of introns—early or late? Nature 369:526-527.   PubMed | Citations
  • Stoltzfus, A., and W. F. Doolittle. 1993. Slippery introns and globin gene evolution. Current Biology 3 (4):215-217.   PubMed | Citations
  • Doolittle, W. F., and A. Stoltzfus. 1993. Genes-in-pieces revisited. Nature 361:403.   PubMed | Citations
  • Stoltzfus, A., J. F. Leslie, and R. Milkman. 1988. Molecular evolution of the Escherichia coli chromosome. I. Analysis of structure and natural variation in a previously uncharacterized region between trp and tonB. Genetics 120 (2):345-358.   PubMed | Citations
  • Milkman, R., and A. Stoltzfus. 1988. Molecular evolution of the Escherichia coli chromosome. II. Clonal segments. Genetics 120 (2):359-366.   PubMed | Citations

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