Gardner PP - Search Results

1

Essential guidelines for computational method benchmarking.

Weber LM, Saelens W, Cannoodt R, Soneson C, Hapfelmeier A, Gardner PP, Boulesteix AL, Saeys Y, Robinson MD. Weber LM, et al. Among authors: gardner pp. Genome Biol. 2019 Jun 20;20(1):125. doi: 10.1186/s13059-019-1738-8. Genome Biol. 2019. PMID: 31221194 Free PMC article. Review.

2

On the optimistic performance evaluation of newly introduced bioinformatic methods.

Buchka S, Hapfelmeier A, Gardner PP, Wilson R, Boulesteix AL. Buchka S, et al. Among authors: gardner pp. Genome Biol. 2021 May 11;22(1):152. doi: 10.1186/s13059-021-02365-4. Genome Biol. 2021. PMID: 33975646 Free PMC article.

3

Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software.

Gardner PP, Paterson JM, McGimpsey S, Ashari-Ghomi F, Umu SU, Pawlik A, Gavryushkin A, Black MA. Gardner PP, et al. Genome Biol. 2022 Feb 16;23(1):56. doi: 10.1186/s13059-022-02625-x. Genome Biol. 2022. PMID: 35172880 Free PMC article.

4

Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies.

Gardner PP, Watson RJ, Morgan XC, Draper JL, Finn RD, Morales SE, Stott MB. Gardner PP, et al. PeerJ. 2019 Jan 4;7:e6160. doi: 10.7717/peerj.6160. eCollection 2019. PeerJ. 2019. PMID: 30631651 Free PMC article.

5

Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites.

Bhandari BK, Lim CS, Remus DM, Chen A, van Dolleweerd C, Gardner PP. Bhandari BK, et al. Among authors: gardner pp. PLoS Comput Biol. 2021 Oct 5;17(10):e1009461. doi: 10.1371/journal.pcbi.1009461. eCollection 2021 Oct. PLoS Comput Biol. 2021. PMID: 34610008 Free PMC article.

6

Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA.

Freyhult EK, Bollback JP, Gardner PP. Freyhult EK, et al. Among authors: gardner pp. Genome Res. 2007 Jan;17(1):117-25. doi: 10.1101/gr.5890907. Epub 2006 Dec 6. Genome Res. 2007. PMID: 17151342 Free PMC article.

7

Solubility-Weighted Index: fast and accurate prediction of protein solubility.

Bhandari BK, Gardner PP, Lim CS. Bhandari BK, et al. Among authors: gardner pp. Bioinformatics. 2020 Sep 15;36(18):4691-4698. doi: 10.1093/bioinformatics/btaa578. Bioinformatics. 2020. PMID: 32559287 Free PMC article.

8

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.

9

The PitA protein contributes to colistin susceptibility in Pseudomonas aeruginosa.

Erdmann MB, Gardner PP, Lamont IL. Erdmann MB, et al. Among authors: gardner pp. PLoS One. 2023 Oct 12;18(10):e0292818. doi: 10.1371/journal.pone.0292818. eCollection 2023. PLoS One. 2023. PMID: 37824582 Free PMC article.

10

Complete Genome Sequences of Two Geographically Distinct Legionella micdadei Clinical Isolates.

Osborne AJ, Jose BR, Perry J, Smeele Z, Aitken J, Gardner PP, Slow S. Osborne AJ, et al. Among authors: gardner pp. Genome Announc. 2017 Jun 1;5(22):e00436-17. doi: 10.1128/genomeA.00436-17. Genome Announc. 2017. PMID: 28572318 Free PMC article.

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