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Items: 32

1.

Latent human traits in the language of social media: An open-vocabulary approach.

Kulkarni V, Kern ML, Stillwell D, Kosinski M, Matz S, Ungar L, Skiena S, Schwartz HA.

PLoS One. 2018 Nov 28;13(11):e0201703. doi: 10.1371/journal.pone.0201703. eCollection 2018.

2.

Prokaryotic coding regions have little if any specific depletion of Shine-Dalgarno motifs.

Yurovsky A, Amin MR, Gardin J, Chen Y, Skiena S, Futcher B.

PLoS One. 2018 Aug 23;13(8):e0202768. doi: 10.1371/journal.pone.0202768. eCollection 2018.

3.

Re-annotation of 12,495 prokaryotic 16S rRNA 3' ends and analysis of Shine-Dalgarno and anti-Shine-Dalgarno sequences.

Amin MR, Yurovsky A, Chen Y, Skiena S, Futcher B.

PLoS One. 2018 Aug 23;13(8):e0202767. doi: 10.1371/journal.pone.0202767. eCollection 2018.

4.

A codon-shuffling method to prevent reversion during production of replication-defective herpesvirus stocks: Implications for herpesvirus vaccines.

Li G, Ward C, Yeasmin R, Skiena S, Krug LT, Forrest JC.

Sci Rep. 2017 Mar 13;7:44404. doi: 10.1038/srep44404.

5.

Measurement of average decoding rates of the 61 sense codons in vivo.

Gardin J, Yeasmin R, Yurovsky A, Cai Y, Skiena S, Futcher B.

Elife. 2014 Oct 27;3. doi: 10.7554/eLife.03735.

6.

Deliberate reduction of hemagglutinin and neuraminidase expression of influenza virus leads to an ultraprotective live vaccine in mice.

Yang C, Skiena S, Futcher B, Mueller S, Wimmer E.

Proc Natl Acad Sci U S A. 2013 Jun 4;110(23):9481-6. doi: 10.1073/pnas.1307473110. Epub 2013 May 20.

7.

Identification of two functionally redundant RNA elements in the coding sequence of poliovirus using computer-generated design.

Song Y, Liu Y, Ward CB, Mueller S, Futcher B, Skiena S, Paul AV, Wimmer E.

Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14301-7. doi: 10.1073/pnas.1211484109. Epub 2012 Aug 10.

8.

Computationally designed adeno-associated virus (AAV) Rep 78 is efficiently maintained within an adenovirus vector.

Sitaraman V, Hearing P, Ward CB, Gnatenko DV, Wimmer E, Mueller S, Skiena S, Bahou WF.

Proc Natl Acad Sci U S A. 2011 Aug 23;108(34):14294-9. doi: 10.1073/pnas.1102883108. Epub 2011 Aug 15.

9.

Live attenuated influenza virus vaccines by computer-aided rational design.

Mueller S, Coleman JR, Papamichail D, Ward CB, Nimnual A, Futcher B, Skiena S, Wimmer E.

Nat Biotechnol. 2010 Jul;28(7):723-6. doi: 10.1038/nbt.1636. Epub 2010 Jun 13.

10.

Crystallizing short-read assemblies around seeds.

Hossain MS, Azimi N, Skiena S.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S16. doi: 10.1186/1471-2105-10-S1-S16.

11.

Virus attenuation by genome-scale changes in codon pair bias.

Coleman JR, Papamichail D, Skiena S, Futcher B, Wimmer E, Mueller S.

Science. 2008 Jun 27;320(5884):1784-7. doi: 10.1126/science.1155761.

12.

Elevated atmospheric CO2 affects soil microbial diversity associated with trembling aspen.

Lesaulnier C, Papamichail D, McCorkle S, Ollivier B, Skiena S, Taghavi S, Zak D, van der Lelie D.

Environ Microbiol. 2008 Apr;10(4):926-41. doi: 10.1111/j.1462-2920.2007.01512.x. Epub 2008 Jan 24.

13.

MultiPrimer: a system for microarray PCR primer design.

Fernandes R, Skiena S.

Methods Mol Biol. 2007;402:305-14. Review.

PMID:
17951802
14.

Spatial analysis of news sources.

Mehler A, Bao Y, Li X, Wang Y, Skiena S.

IEEE Trans Vis Comput Graph. 2006 Sep-Oct;12(5):765-71.

PMID:
17080798
16.

Meta-analysis based on control of false discovery rate: combining yeast ChIP-chip datasets.

Pyne S, Futcher B, Skiena S.

Bioinformatics. 2006 Oct 15;22(20):2516-22. Epub 2006 Aug 14.

PMID:
16908499
17.

The cell cycle-regulated genes of Schizosaccharomyces pombe.

Oliva A, Rosebrock A, Ferrezuelo F, Pyne S, Chen H, Skiena S, Futcher B, Leatherwood J.

PLoS Biol. 2005 Jul;3(7):e225. Epub 2005 Jun 28.

18.

Copy correction and concerted evolution in the conservation of yeast genes.

Pyne S, Skiena S, Futcher B.

Genetics. 2005 Aug;170(4):1501-13. Epub 2005 May 23.

19.

Genomic sorting with length-weighted reversals.

Pinter RY, Skiena S.

Genome Inform. 2002;13:103-11.

PMID:
14571379
20.

Deconvolving sequence variation in mixed DNA populations.

Wildenberg A, Skiena S, Sumazin P.

J Comput Biol. 2003;10(3-4):635-52.

PMID:
12935349
21.

Natural selection and algorithmic design of mRNA.

Cohen B, Skiena S.

J Comput Biol. 2003;10(3-4):419-32.

PMID:
12935336
22.

Microarray synthesis through multiple-use PCR primer design.

Fernandes RJ, Skiena SS.

Bioinformatics. 2002;18 Suppl 1:S128-35.

PMID:
12169540
23.

Analysis techniques for microarray time-series data.

Filkov V, Skiena S, Zhi J.

J Comput Biol. 2002;9(2):317-30.

PMID:
12015884
24.

Dealing with errors in interactive sequencing by hybridization.

Phan VT, Skiena SS.

Bioinformatics. 2001 Oct;17(10):862-70.

PMID:
11673230
25.

Designing better phages.

Skiena SS.

Bioinformatics. 2001;17 Suppl 1:S253-61.

PMID:
11473016
26.

A case study in genome-level fragment assembly.

Chen T, Skiena SS.

Bioinformatics. 2000 Jun;16(6):494-500.

PMID:
10980146
27.

Efficient split synthesis for targeted libraries.

Cohen B, Skiena S.

J Comb Chem. 2000 Jan-Feb;2(1):10-8.

PMID:
10750484
28.

Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model.

Agarwala R, Batzoglou S, DancĂ­k V, Decatur SE, Hannenhalli S, Farach M, Muthukrishnan S, Skiena S.

J Comput Biol. 1997 Fall;4(3):275-96.

PMID:
9278060
29.

Positional sequencing by hybridization.

Hannenhalli S, Feldman W, Lewis HF, Skiena SS, Pevzner PA.

Comput Appl Biosci. 1996 Feb;12(1):19-24.

PMID:
8670615
30.

Reconstructing strings from substrings.

Skiena SS, Sundaram G.

J Comput Biol. 1995 Summer;2(2):333-53.

PMID:
7497132
31.

A partial digest approach to restriction site mapping.

Skiena SS, Sundaram G.

Bull Math Biol. 1994 Mar;56(2):275-94.

PMID:
8186755
32.

A partial digest approach to restriction site mapping.

Skiena SS, Sundaram G.

Proc Int Conf Intell Syst Mol Biol. 1993;1:362-70.

PMID:
7584358

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