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Results: 1 to 20 of 33

1.

Modeling evolution using the probability of fixation: history and implications.

McCandlish DM, Stoltzfus A.

Q Rev Biol. 2014 Sep;89(3):225-52. Review.

PMID:
25195318
2.

Mendelian-mutationism: the forgotten evolutionary synthesis.

Stoltzfus A, Cable K.

J Hist Biol. 2014 Winter;47(4):501-46. doi: 10.1007/s10739-014-9383-2.

PMID:
24811736
3.

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.

Stoltzfus A, Lapp H, Matasci N, Deus H, Sidlauskas B, Zmasek CM, Vaidya G, Pontelli E, Cranston K, Vos R, Webb CO, Harmon LJ, Pirrung M, O'Meara B, Pennell MW, Mirarab S, Rosenberg MS, Balhoff JP, Bik HM, Heath TA, Midford PE, Brown JW, McTavish EJ, Sukumaran J, Westneat M, Alfaro ME, Steele A, Jordan G.

BMC Bioinformatics. 2013 May 13;14:158. doi: 10.1186/1471-2105-14-158.

4.

Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis.

Stoltzfus A, O'Meara B, Whitacre J, Mounce R, Gillespie EL, Kumar S, Rosauer DF, Vos RA.

BMC Res Notes. 2012 Oct 22;5:574. doi: 10.1186/1756-0500-5-574.

5.

Constructive neutral evolution: exploring evolutionary theory's curious disconnect.

Stoltzfus A.

Biol Direct. 2012 Oct 13;7:35. doi: 10.1186/1745-6150-7-35. Review.

6.

Population diversity of ORFan genes in Escherichia coli.

Yu G, Stoltzfus A.

Genome Biol Evol. 2012;4(11):1176-87. doi: 10.1093/gbe/evs081.

7.

NeXML: rich, extensible, and verifiable representation of comparative data and metadata.

Vos RA, Balhoff JP, Caravas JA, Holder MT, Lapp H, Maddison WP, Midford PE, Priyam A, Sukumaran J, Xia X, Stoltzfus A.

Syst Biol. 2012 Jul;61(4):675-89. doi: 10.1093/sysbio/sys025. Epub 2012 Feb 22.

8.

Gene identification in black cohosh (Actaea racemosa L.): expressed sequence tag profiling and genetic screening yields candidate genes for production of bioactive secondary metabolites.

Spiering MJ, Urban LA, Nuss DL, Gopalan V, Stoltzfus A, Eisenstein E.

Plant Cell Rep. 2011 Apr;30(4):613-29. doi: 10.1007/s00299-010-0979-5. Epub 2010 Dec 28.

PMID:
21188383
9.

Initial implementation of a comparative data analysis ontology.

Prosdocimi F, Chisham B, Pontelli E, Thompson JD, Stoltzfus A.

Evol Bioinform Online. 2009 Jul 3;5:47-66.

10.

Climbing mount probable: mutation as a cause of nonrandomness in evolution.

Stoltzfus A, Yampolsky LY.

J Hered. 2009 Sep-Oct;100(5):637-47. doi: 10.1093/jhered/esp048. Epub 2009 Jul 22. Review.

11.

Evidence for a predominant role of oxidative damage in germline mutation in mammals.

Stoltzfus A.

Mutat Res. 2008 Sep 26;644(1-2):71-3. doi: 10.1016/j.mrfmmm.2008.05.003. Epub 2008 May 25.

PMID:
18597793
12.

Amino acid exchangeability and the adaptive code hypothesis.

Stoltzfus A, Yampolsky LY.

J Mol Evol. 2007 Oct;65(4):456-62. Epub 2007 Sep 26.

PMID:
17896070
13.

A sequence-based model accounts largely for the relationship of intron positions to protein structural features.

De Kee DW, Gopalan V, Stoltzfus A.

Mol Biol Evol. 2007 Oct;24(10):2158-68. Epub 2007 Jul 23.

14.

Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data.

Hladish T, Gopalan V, Liang C, Qiu W, Yang P, Stoltzfus A.

BMC Bioinformatics. 2007 Jun 8;8:191.

15.

Mutation-biased adaptation in a protein NK model.

Stoltzfus A.

Mol Biol Evol. 2006 Oct;23(10):1852-62. Epub 2006 Jul 20.

16.

Mutationism and the dual causation of evolutionary change.

Stoltzfus A.

Evol Dev. 2006 May-Jun;8(3):304-17. Review.

PMID:
16686641
17.

Nexplorer: phylogeny-based exploration of sequence family data.

Gopalan V, Qiu WG, Chen MZ, Stoltzfus A.

Bioinformatics. 2006 Jan 1;22(1):120-1. Epub 2005 Nov 2.

18.

The exchangeability of amino acids in proteins.

Yampolsky LY, Stoltzfus A.

Genetics. 2005 Aug;170(4):1459-72. Epub 2005 Jun 8.

19.

Untangling the effects of codon mutation and amino acid exchangeability.

Yampolsky LY, Stoltzfus A.

Pac Symp Biocomput. 2005:433-44.

20.

Molecular evolution: introns fall into place.

Stoltzfus A.

Curr Biol. 2004 May 4;14(9):R351-2. Review.

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