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Items: 7

1.

Measuring evolutionary rates of proteins in a structural context.

Sydykova DK, Jack BR, Spielman SJ, Wilke CO.

Version 2. F1000Res. 2017 Oct 16 [revised 2018 Jan 1];6:1845. doi: 10.12688/f1000research.12874.2. eCollection 2017.

2.

Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates.

Sydykova DK, Wilke CO.

PeerJ. 2017 May 30;5:e3391. doi: 10.7717/peerj.3391. eCollection 2017.

3.

The E. coli molecular phenotype under different growth conditions.

Caglar MU, Houser JR, Barnhart CS, Boutz DR, Carroll SM, Dasgupta A, Lenoir WF, Smith BL, Sridhara V, Sydykova DK, Vander Wood D, Marx CJ, Marcotte EM, Barrick JE, Wilke CO.

Sci Rep. 2017 Apr 18;7:45303. doi: 10.1038/srep45303.

4.

Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation.

Houser JR, Barnhart C, Boutz DR, Carroll SM, Dasgupta A, Michener JK, Needham BD, Papoulas O, Sridhara V, Sydykova DK, Marx CJ, Trent MS, Barrick JE, Marcotte EM, Wilke CO.

PLoS Comput Biol. 2015 Aug 14;11(8):e1004400. doi: 10.1371/journal.pcbi.1004400. eCollection 2015 Aug.

5.

Predicting evolutionary site variability from structure in viral proteins: buriedness, packing, flexibility, and design.

Shahmoradi A, Sydykova DK, Spielman SJ, Jackson EL, Dawson ET, Meyer AG, Wilke CO.

J Mol Evol. 2014 Oct;79(3-4):130-42. doi: 10.1007/s00239-014-9644-x. Epub 2014 Sep 13.

6.

Maximum allowed solvent accessibilites of residues in proteins.

Tien MZ, Meyer AG, Sydykova DK, Spielman SJ, Wilke CO.

PLoS One. 2013 Nov 21;8(11):e80635. doi: 10.1371/journal.pone.0080635. eCollection 2013.

7.

PeptideBuilder: A simple Python library to generate model peptides.

Tien MZ, Sydykova DK, Meyer AG, Wilke CO.

PeerJ. 2013 May 21;1:e80. doi: 10.7717/peerj.80. Print 2013.

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