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Items: 37

1.

Why we don't want another "Synthesis".

Stoltzfus A.

Biol Direct. 2017 Oct 2;12(1):23. doi: 10.1186/s13062-017-0194-1.

2.

Mutational Biases Influence Parallel Adaptation.

Stoltzfus A, McCandlish DM.

Mol Biol Evol. 2017 Sep 1;34(9):2163-2172. doi: 10.1093/molbev/msx180.

3.

On the Causes of Evolutionary Transition:Transversion Bias.

Stoltzfus A, Norris RW.

Mol Biol Evol. 2016 Mar;33(3):595-602. doi: 10.1093/molbev/msv274. Epub 2015 Nov 25.

PMID:
26609078
4.

Mutation-biased adaptation in Andean house wrens.

Stoltzfus A, McCandlish DM.

Proc Natl Acad Sci U S A. 2015 Nov 10;112(45):13753-4. doi: 10.1073/pnas.1518490112. Epub 2015 Oct 21. No abstract available.

5.

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
6.

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
7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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
13.

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.

14.

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.

PMID:
19625453
15.

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
16.

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
17.

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.

PMID:
17646255
18.

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.

19.

Mutation-biased adaptation in a protein NK model.

Stoltzfus A.

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

PMID:
16857856
20.

Mutationism and the dual causation of evolutionary change.

Stoltzfus A.

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

PMID:
16686641
21.

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.

22.

The exchangeability of amino acids in proteins.

Yampolsky LY, Stoltzfus A.

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

23.

Untangling the effects of codon mutation and amino acid exchangeability.

Yampolsky LY, Stoltzfus A.

Pac Symp Biocomput. 2005:433-44.

24.

Molecular evolution: introns fall into place.

Stoltzfus A.

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

25.

The evolutionary gain of spliceosomal introns: sequence and phase preferences.

Qiu WG, Schisler N, Stoltzfus A.

Mol Biol Evol. 2004 Jul;21(7):1252-63. Epub 2004 Mar 10. Erratum in: Mol Biol Evol. 2004 Sep;21(9):1812.

PMID:
15014153
26.

Bias in the introduction of variation as an orienting factor in evolution.

Yampolsky LY, Stoltzfus A.

Evol Dev. 2001 Mar-Apr;3(2):73-83.

PMID:
11341676
27.

On the possibility of constructive neutral evolution.

Stoltzfus A.

J Mol Evol. 1999 Aug;49(2):169-81.

PMID:
10441669
28.

Molecular evolution: recent cases of spliceosomal intron gain?

Logsdon JM Jr, Stoltzfus A, Doolittle WF.

Curr Biol. 1998 Jul 30-Aug 13;8(16):R560-3. Review.

29.

Intron "sliding" and the diversity of intron positions.

Stoltzfus A, Logsdon JM Jr, Palmer JD, Doolittle WF.

Proc Natl Acad Sci U S A. 1997 Sep 30;94(20):10739-44.

30.

Methods for evaluating exon-protein correspondences.

Stoltzfus A, Spencer DF, Doolittle WF.

Comput Appl Biosci. 1995 Oct;11(5):509-15.

PMID:
8590174
31.

Testing the exon theory of genes: the evidence from protein structure.

Stoltzfus A, Spencer DF, Zuker M, Logsdon JM Jr, Doolittle WF.

Science. 1994 Jul 8;265(5169):202-7.

PMID:
8023140
32.

Origin of introns--early or late.

Stoltzfus A.

Nature. 1994 Jun 16;369(6481):526-7; author reply 527-8. No abstract available.

PMID:
8202153
33.

High-level expression and purification of secreted forms of herpes simplex virus type 1 glycoprotein gD synthesized by baculovirus-infected insect cells.

Sisk WP, Bradley JD, Leipold RJ, Stoltzfus AM, Ponce de Leon M, Hilf M, Peng C, Cohen GH, Eisenberg RJ.

J Virol. 1994 Feb;68(2):766-75.

34.

Molecular evolution: slippery introns and globin gene evolution.

Stoltzfus A, Ford Doolittle W.

Curr Biol. 1993 Apr 1;3(4):215-7. No abstract available.

PMID:
15335770
35.

Molecular evolution. Genes-in-pieces revisited.

Doolittle WF, Stoltzfus A.

Nature. 1993 Feb 4;361(6411):403. No abstract available.

PMID:
8429878
36.

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