Gardner PP - Search Results

1

A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes.

Wheeler NE, Barquist L, Kingsley RA, Gardner PP. Wheeler NE, et al. Among authors: gardner pp. Bioinformatics. 2016 Dec 1;32(23):3566-3574. doi: 10.1093/bioinformatics/btw518. Epub 2016 Aug 8. Bioinformatics. 2016. PMID: 27503221 Free PMC article.

2

A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.

Perkins TT, Kingsley RA, Fookes MC, Gardner PP, James KD, Yu L, Assefa SA, He M, Croucher NJ, Pickard DJ, Maskell DJ, Parkhill J, Choudhary J, Thomson NR, Dougan G. Perkins TT, et al. Among authors: gardner pp. PLoS Genet. 2009 Jul;5(7):e1000569. doi: 10.1371/journal.pgen.1000569. Epub 2009 Jul 17. PLoS Genet. 2009. PMID: 19609351 Free PMC article.

3

RNIE: genome-wide prediction of bacterial intrinsic terminators.

Gardner PP, Barquist L, Bateman A, Nawrocki EP, Weinberg Z. Gardner PP, et al. Nucleic Acids Res. 2011 Aug;39(14):5845-52. doi: 10.1093/nar/gkr168. Epub 2011 Apr 7. Nucleic Acids Res. 2011. PMID: 21478170 Free PMC article.

4

Rfam 11.0: 10 years of RNA families.

Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A. Burge SW, et al. Among authors: gardner pp. Nucleic Acids Res. 2013 Jan;41(Database issue):D226-32. doi: 10.1093/nar/gks1005. Epub 2012 Nov 3. Nucleic Acids Res. 2013. PMID: 23125362 Free PMC article.

5

A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium.

Barquist L, Langridge GC, Turner DJ, Phan MD, Turner AK, Bateman A, Parkhill J, Wain J, Gardner PP. Barquist L, et al. Among authors: gardner pp. Nucleic Acids Res. 2013 Apr;41(8):4549-64. doi: 10.1093/nar/gkt148. Epub 2013 Mar 6. Nucleic Acids Res. 2013. PMID: 23470992 Free PMC article.

6

Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar.

Kingsley RA, Kay S, Connor T, Barquist L, Sait L, Holt KE, Sivaraman K, Wileman T, Goulding D, Clare S, Hale C, Seshasayee A, Harris S, Thomson NR, Gardner P, Rabsch W, Wigley P, Humphrey T, Parkhill J, Dougan G. Kingsley RA, et al. mBio. 2013 Aug 27;4(5):e00565-13. doi: 10.1128/mBio.00565-13. mBio. 2013. PMID: 23982073 Free PMC article.

7

An introduction to RNA databases.

Hoeppner MP, Barquist LE, Gardner PP. Hoeppner MP, et al. Among authors: gardner pp. Methods Mol Biol. 2014;1097:107-23. doi: 10.1007/978-1-62703-709-9_6. Methods Mol Biol. 2014. PMID: 24639157 Review.

8

Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling.

Lindgreen S, Umu SU, Lai AS, Eldai H, Liu W, McGimpsey S, Wheeler NE, Biggs PJ, Thomson NR, Barquist L, Poole AM, Gardner PP. Lindgreen S, et al. Among authors: gardner pp. PLoS Comput Biol. 2014 Oct 30;10(10):e1003907. doi: 10.1371/journal.pcbi.1003907. eCollection 2014 Oct. PLoS Comput Biol. 2014. PMID: 25357249 Free PMC article.

9

Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families.

Barquist L, Burge SW, Gardner PP. Barquist L, et al. Among authors: gardner pp. Curr Protoc Bioinformatics. 2016 Jun 20;54:12.13.1-12.13.25. doi: 10.1002/cpbi.4. Curr Protoc Bioinformatics. 2016. PMID: 27322404 Free PMC article.

10

A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life.

Umu SU, Gardner PP. Umu SU, et al. Among authors: gardner pp. Bioinformatics. 2017 Apr 1;33(7):988-996. doi: 10.1093/bioinformatics/btw728. Bioinformatics. 2017. PMID: 27993777 Free PMC article.

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