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Results: 1 to 20 of 53

1.

Protein domain hierarchy Gibbs sampling strategies.

Neuwald AF.

Stat Appl Genet Mol Biol. 2014 Aug;13(4):497-517. doi: 10.1515/sagmb-2014-0008.

PMID:
24988248
2.

Evaluating, comparing, and interpreting protein domain hierarchies.

Neuwald AF.

J Comput Biol. 2014 Apr;21(4):287-302. doi: 10.1089/cmb.2013.0098. Epub 2014 Feb 21.

3.

A Bayesian sampler for optimization of protein domain hierarchies.

Neuwald AF.

J Comput Biol. 2014 Mar;21(3):269-86. doi: 10.1089/cmb.2013.0099. Epub 2014 Feb 4.

4.

Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures.

Neuwald AF, Lanczycki CJ, Marchler-Bauer A.

BMC Bioinformatics. 2012 Jun 22;13:144. doi: 10.1186/1471-2105-13-144.

5.

Surveying the manifold divergence of an entire protein class for statistical clues to underlying biochemical mechanisms.

Neuwald AF.

Stat Appl Genet Mol Biol. 2011;10:Article 36. doi: 10.2202/1544-6115.1666. Epub 2011 Aug 4.

6.
7.

Natural mutagenesis of human genomes by endogenous retrotransposons.

Iskow RC, McCabe MT, Mills RE, Torene S, Pittard WS, Neuwald AF, Van Meir EG, Vertino PM, Devine SE.

Cell. 2010 Jun 25;141(7):1253-61. doi: 10.1016/j.cell.2010.05.020.

8.

A typhus group-specific protease defies reductive evolution in rickettsiae.

Ammerman NC, Gillespie JJ, Neuwald AF, Sobral BW, Azad AF.

J Bacteriol. 2009 Dec;191(24):7609-13. doi: 10.1128/JB.01077-09. Epub 2009 Oct 9.

9.

Rapid detection, classification and accurate alignment of up to a million or more related protein sequences.

Neuwald AF.

Bioinformatics. 2009 Aug 1;25(15):1869-75. doi: 10.1093/bioinformatics/btp342. Epub 2009 Jun 8. Erratum in: Bioinformatics. 2009 Nov 15;25(22):3047.

10.

The charge-dipole pocket: a defining feature of signaling pathway GTPase on/off switches.

Neuwald AF.

J Mol Biol. 2009 Jul 3;390(1):142-53. doi: 10.1016/j.jmb.2009.05.001. Epub 2009 May 7.

11.
12.

Evolution of allostery in the cyclic nucleotide binding module.

Kannan N, Wu J, Anand GS, Yooseph S, Neuwald AF, Venter JC, Taylor SS.

Genome Biol. 2007;8(12):R264.

13.

Analogous regulatory sites within the alphaC-beta4 loop regions of ZAP-70 tyrosine kinase and AGC kinases.

Kannan N, Neuwald AF, Taylor SS.

Biochim Biophys Acta. 2008 Jan;1784(1):27-32. Epub 2007 Sep 29. Review.

15.

The CHAIN program: forging evolutionary links to underlying mechanisms.

Neuwald AF.

Trends Biochem Sci. 2007 Nov;32(11):487-93. Epub 2007 Oct 24.

PMID:
17962021
16.

The hallmark of AGC kinase functional divergence is its C-terminal tail, a cis-acting regulatory module.

Kannan N, Haste N, Taylor SS, Neuwald AF.

Proc Natl Acad Sci U S A. 2007 Jan 23;104(4):1272-7. Epub 2007 Jan 16. Erratum in: Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):9130.

18.

Bayesian shadows of molecular mechanisms cast in the light of evolution.

Neuwald AF.

Trends Biochem Sci. 2006 Jul;31(7):374-82.

PMID:
16766187
20.
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