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Items: 1 to 20 of 63


Essential guidelines for computational method benchmarking.

Weber LM, Saelens W, Cannoodt R, Soneson C, Hapfelmeier A, Gardner PP, Boulesteix AL, Saeys Y, Robinson MD.

Genome Biol. 2019 Jun 20;20(1):125. doi: 10.1186/s13059-019-1738-8. Review.


Convergent regulatory evolution and loss of flight in paleognathous birds.

Sackton TB, Grayson P, Cloutier A, Hu Z, Liu JS, Wheeler NE, Gardner PP, Clarke JA, Baker AJ, Clamp M, Edwards SV.

Science. 2019 Apr 5;364(6435):74-78. doi: 10.1126/science.aat7244.


Transcriptional noise and exaptation as sources for bacterial sRNAs.

Jose BR, Gardner PP, Barquist L.

Biochem Soc Trans. 2019 Apr 30;47(2):527-539. doi: 10.1042/BST20180171. Epub 2019 Mar 5. Review.


Genomic correlates of extraintestinal infection are linked with changes in cell morphology in Campylobacter jejuni.

Wheeler NE, Blackmore T, Reynolds AD, Midwinter AC, Marshall J, French NP, Savoian MS, Gardner PP, Biggs PJ.

Microb Genom. 2019 Feb;5(2). doi: 10.1099/mgen.0.000251. Epub 2019 Feb 19.


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.

PeerJ. 2019 Jan 4;7:e6160. doi: 10.7717/peerj.6160. eCollection 2019.


Towards robust and repeatable sampling methods in eDNA-based studies.

Dickie IA, Boyer S, Buckley HL, Duncan RP, Gardner PP, Hogg ID, Holdaway RJ, Lear G, Makiola A, Morales SE, Powell JR, Weaver L.

Mol Ecol Resour. 2018 May 26. doi: 10.1111/1755-0998.12907. [Epub ahead of print] Review.


Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica.

Wheeler NE, Gardner PP, Barquist L.

PLoS Genet. 2018 May 8;14(5):e1007333. doi: 10.1371/journal.pgen.1007333. eCollection 2018 May.


An Evaluation of Function of Multicopy Noncoding RNAs in Mammals Using ENCODE/FANTOM Data and Comparative Genomics.

Hoeppner MP, Denisenko E, Gardner PP, Schmeier S, Poole AM.

Mol Biol Evol. 2018 Jun 1;35(6):1451-1462. doi: 10.1093/molbev/msy046.


Genomic, Transcriptomic, and Phenotypic Analyses of Neisseria meningitidis Isolates from Disease Patients and Their Household Contacts.

Ren X, Eccles DA, Greig GA, Clapham J, Wheeler NE, Lindgreen S, Gardner PP, MacKichan JK.

mSystems. 2017 Nov 14;2(6). pii: e00127-17. doi: 10.1128/mSystems.00127-17. eCollection 2017 Nov-Dec.


Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution.

Wu C, Jordan MD, Newcomb RD, Gemmell NJ, Bank S, Meusemann K, Dearden PK, Duncan EJ, Grosser S, Rutherford K, Gardner PP, Crowhurst RN, Steinwender B, Tooman LK, Stevens MI, Buckley TR.

BMC Genomics. 2017 Oct 17;18(1):795. doi: 10.1186/s12864-017-4197-1.


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.

Genome Announc. 2017 Jun 1;5(22). pii: e00436-17. doi: 10.1128/genomeA.00436-17.


Transposon insertion libraries for the characterization of mutants from the kiwifruit pathogen Pseudomonas syringae pv. actinidiae.

Mesarich CH, Rees-George J, Gardner PP, Ghomi FA, Gerth ML, Andersen MT, Rikkerink EH, Fineran PC, Templeton MD.

PLoS One. 2017 Mar 1;12(3):e0172790. doi: 10.1371/journal.pone.0172790. eCollection 2017.


Why so narrow: Distribution of anti-sense regulated, type I toxin-antitoxin systems compared with type II and type III systems.

Coray DS, Wheeler NE, Heinemann JA, Gardner PP.

RNA Biol. 2017 Mar 4;14(3):275-280. doi: 10.1080/15476286.2016.1272747. Epub 2017 Jan 9. Review.


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

Umu SU, Gardner PP.

Bioinformatics. 2017 Apr 1;33(7):988-996. doi: 10.1093/bioinformatics/btw728.


Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea.

Umu SU, Poole AM, Dobson RC, Gardner PP.

Elife. 2016 Sep 20;5. pii: e13479. doi: 10.7554/eLife.13479.


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

Wheeler NE, Barquist L, Kingsley RA, Gardner PP.

Bioinformatics. 2016 Dec 1;32(23):3566-3574. doi: 10.1093/bioinformatics/btw518. Epub 2016 Aug 8.


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

Barquist L, Burge SW, Gardner PP.

Curr Protoc Bioinformatics. 2016 Jun 20;54:12.13.1-12.13.25. doi: 10.1002/cpbi.4.


An evaluation of the accuracy and speed of metagenome analysis tools.

Lindgreen S, Adair KL, Gardner PP.

Sci Rep. 2016 Jan 18;6:19233. doi: 10.1038/srep19233.


Third Report on Chicken Genes and Chromosomes 2015.

Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RP, Damas J, Davis RV, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MA, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JM, Wragg D, Zhou H.

Cytogenet Genome Res. 2015;145(2):78-179. doi: 10.1159/000430927. Epub 2015 Jul 14. No abstract available.


Conservation and losses of non-coding RNAs in avian genomes.

Gardner PP, Fasold M, Burge SW, Ninova M, Hertel J, Kehr S, Steeves TE, Griffiths-Jones S, Stadler PF.

PLoS One. 2015 Mar 30;10(3):e0121797. doi: 10.1371/journal.pone.0121797. eCollection 2015.

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