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Items: 13

1.

N-Terminal Peptide Detection with Optimized Peptide-Spectrum Matching and Streamlined Sequence Libraries.

Lycette BE, Glickman JW, Roth SJ, Cram AE, Kim TH, Krizanc D, Weir MP.

J Proteome Res. 2016 Sep 2;15(9):2891-9. doi: 10.1021/acs.jproteome.5b00996. Epub 2016 Aug 23.

PMID:
27498768
2.

Accuracy and efficiency of algorithms for the demarcation of bacterial ecotypes from DNA sequence data.

Francisco JC, Cohan FM, Krizanc D.

Int J Bioinform Res Appl. 2014;10(4-5):409-25. doi: 10.1504/IJBRA.2014.062992.

PMID:
24989860
3.

Assessment of MS/MS search algorithms with parent-protein profiling.

Lin MS, Cherny JJ, Fournier CT, Roth SJ, Krizanc D, Weir MP.

J Proteome Res. 2014 Apr 4;13(4):1823-32. doi: 10.1021/pr401090d. Epub 2014 Mar 7.

4.

Asymptotic structural properties of quasi-random saturated structures of RNA.

Clote P, Kranakis E, Krizanc D.

Algorithms Mol Biol. 2013 Oct 25;8(1):24. doi: 10.1186/1748-7188-8-24.

5.

Asymptotic number of hairpins of saturated RNA secondary structures.

Clote P, Kranakis E, Krizanc D.

Bull Math Biol. 2013 Dec;75(12):2410-30. doi: 10.1007/s11538-013-9899-1. Epub 2013 Oct 19.

PMID:
24142625
6.

Speedy speciation in a bacterial microcosm: new species can arise as frequently as adaptations within a species.

Koeppel AF, Wertheim JO, Barone L, Gentile N, Krizanc D, Cohan FM.

ISME J. 2013 Jun;7(6):1080-91. doi: 10.1038/ismej.2013.3. Epub 2013 Jan 31.

7.

Amino termini of many yeast proteins map to downstream start codons.

Fournier CT, Cherny JJ, Truncali K, Robbins-Pianka A, Lin MS, Krizanc D, Weir MP.

J Proteome Res. 2012 Dec 7;11(12):5712-9. doi: 10.1021/pr300538f. Epub 2012 Nov 21.

8.

On the page number of RNA secondary structures with pseudoknots.

Clote P, Dobrev S, Dotu I, Kranakis E, Krizanc D, Urrutia J.

J Math Biol. 2012 Dec;65(6-7):1337-57. doi: 10.1007/s00285-011-0493-6. Epub 2011 Dec 10.

PMID:
22159642
9.

Ecology of speciation in the genus Bacillus.

Connor N, Sikorski J, Rooney AP, Kopac S, Koeppel AF, Burger A, Cole SG, Perry EB, Krizanc D, Field NC, Slaton M, Cohan FM.

Appl Environ Microbiol. 2010 Mar;76(5):1349-58. doi: 10.1128/AEM.01988-09. Epub 2010 Jan 4.

10.

Asymptotics of canonical and saturated RNA secondary structures.

Clote P, Kranakis E, Krizanc D, Salvy B.

J Bioinform Comput Biol. 2009 Oct;7(5):869-93.

PMID:
19785050
11.

Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics.

Koeppel A, Perry EB, Sikorski J, Krizanc D, Warner A, Ward DM, Rooney AP, Brambilla E, Connor N, Ratcliff RM, Nevo E, Cohan FM.

Proc Natl Acad Sci U S A. 2008 Feb 19;105(7):2504-9. doi: 10.1073/pnas.0712205105. Epub 2008 Feb 12.

12.

On realizing shapes in the theory of RNA neutral networks.

Clote P, Gasieniec L, Kolpakov R, Kranakis E, Krizanc D.

J Theor Biol. 2005 Sep 21;236(2):216-27.

PMID:
15878180
13.

Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency.

Clote P, Ferré F, Kranakis E, Krizanc D.

RNA. 2005 May;11(5):578-91.

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