Barquist, L., Burge, S. W., & Gardner, P. P. (2016). Studying RNA homology and conservation with infernal: From single sequences to RNA families. In A. Bateman, S. Draghici, E. Khurana, S. Orchard & W. R. Pearson (Eds.), Current protocols in bioinformatics. (pp. 12.13.1-12.13.25). Wiley. doi: 10.1002/cpbi.4

Chapter in Book - Research

Hertel, J., Fasold, M., Nitsche, A., Erb, I., Prieto, P., Kedra, D., … Gardner, P. P., & Stadler, P. F. (2015). Noncoding RNAs in the chicken genome. In M. Schmid, J. Smith & D. W. Burt (Eds.), Third report on chicken genes and chromosomes 2015. (pp. 89-91). Basel, Switzerland: Karger. doi: 10.1159/isbn.978-3-318-05569-6

Chapter in Book - Research

Bollback, J. P., Gardner, P. P., & Nielsen, R. (2007). Estimating the history of mutations on a phylogeny. In D. A. Liberles (Ed.), Ancestral sequence reconstruction. Oxford University Press. doi: 10.1093/acprof:oso/9780199299188.003.0006

Chapter in Book - Research

Cooper, H. B., Krause, K. L., & Gardner, P. P. (2023). Finding priority bacterial ribosomes for future structural and antimicrobial research based upon global RNA and protein sequence analysis. PeerJ, 11, e14969. doi: 10.7717/peerj.14969

Journal - Research Article

Gardner, P. P., Paterson, J. M., McGimpsey, S., Ashari-Ghomi, F., Umu, S. U., Pawlik, A., Gavryushkin, A., & Black, M. A. (2022). Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software. Genome Biology, 23, 56. doi: 10.1186/s13059-022-02625-x

Journal - Research Article

Bhandari, B. K., Lim, C. S., & Gardner, P. P. (2021). TISIGNER.com: Web services for improving recombinant protein production. Nucleic Acids Research, 49, W654-W661. doi: 10.1093/nar/gkab175

Journal - Research Article

Bhandari, B. K., Lim, C. S., Remus, D. M., Chen, A., van Dolleweerd, C., & Gardner, P. P. (2021). Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites. PLoS Computational Biology, 17(10), e1009461. doi: 10.1371/journal.pcbi.1009461

Journal - Research Article

Sitter, T. L., Vaughan, A. L., Schoof, M., Jackson, S. A., Glare, T. R., Cox, M. P., Fineran, P. C., Gardner, P. P., & Hurst, M. R. H. (2021). Evolution of virulence in a novel family of transmissible mega-plasmids. Environmental Microbiology, 23(9), 5289-5304. doi: 10.1111/1462-2920.15595

Journal - Research Article

Smith, L. M., Jackson, S. A., Malone, L. M., Ussher, J. E., Gardner, P. P., & Fineran, P. C. (2021). The Rcs stress response inversely controls surface and CRISPR–Cas adaptive immunity to discriminate plasmids and phages. Nature Microbiology, 6, 162-172. doi: 10.1038/s41564-020-00822-7

Journal - Research Article

Bhandari, B. K., Gardner, P. P., & Lim, C. S. (2020). Solubility-Weighted Index: Fast and accurate prediction of protein solubility. Bioinformatics, 36(18), 4691-4698. doi: 10.1093/bioinformatics/btaa578

Journal - Research Article

Biggs, H., Parthasarathy, P., Gavryushkina, A., & Gardner, P. P. (2020). ncVarDB: A manually curated database for pathogenic non-coding variants and benign controls. Database, baaa105. doi: 10.1093/database/baaa105

Journal - Research Article

Gemmell, N. J., Rutherford, K., Prost, S., Tollis, M., Winter, D., Macey, J. R., … Gardner, P. P., … Hore, T. A., … Dussex, N., Taylor, H., Abe, H., Bond, D. M., … Ngatiwai Trust Board. (2020). The tuatara genome reveals ancient features of amniote evolution. Nature, 584, 403-409. doi: 10.1038/s41586-020-2561-9

Journal - Research Article

Malone, L. M., Warring, S. L., Jackson, S. A., Warnecke, C., Gardner, P. P., Gumy, L. F., & Fineran, P. C. (2020). A jumbo phage that forms a nucleus-like structure evades CRISPR-Cas DNA targeting but is vulnerable to type III RNA-based immunity. Nature Microbiology, 5, 48-55. doi: 10.1038/s41564-019-0612-5

Journal - Research Article

Gardner, P. P., Watson, R. J., Morgan, X. C., Draper, J. L., Finn, R. D., Morales, S. E., & Stott, M. B. (2019). Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies. PeerJ, 7, e6160 . doi: 10.7717/peerj.6160

Journal - Research Article

Sackton, T. B., Grayson, P., Cloutier, A., Hu, Z., Liu, J. S., Wheeler, N. E., Gardner, P. P., … Edwards, S. V. (2019). Convergent regulatory evolution and loss of flight in paleognathous birds. Science, 364(6435), 74-78. doi: 10.1126/science.aat7244

Journal - Research Article

Wheeler, N. E., Blackmore, T., Reynolds, A. D., Midwinter, A. C., Marshall, J., French, N. P., … Gardner, P. P., & Biggs, P. J. (2019). Genomic correlates of extraintestinal infection are linked with changes in cell morphology in Campylobacter jejuni. Microbial Genomics, 5(2), 1-12. doi: 10.1099/mgen.0.000251

Journal - Research Article

Wheeler, N. E., Gardner, P. P., & Barquist, L. (2018). Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica. PLoS Genetics, 14(5), e1007333. doi: 10.1371/journal.pgen.1007333

Journal - Research Article

Umu, S. U., & Gardner, P. P. (2017). A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life. Bioinformatics, 33(7), 988-996. doi: 10.1093/bioinformatics/btw728

Journal - Research Article

Lindgreen, S., Adair, K. L., & Gardner, P. P. (2016). An evaluation of the accuracy and speed of metagenome analysis tools. Scientific Reports, 6, 19233 . doi: 10.1038/srep19233

Journal - Research Article

Umu, S. U., Poole, A. M., Dobson, R. C. J., & Gardner, P. P. (2016). Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea. eLIFE, 5, e13479. doi: 10.7554/eLife.13479

Journal - Research Article

Wheeler, N. E., Barquist, L., Kingsley, R. A., & Gardner, P. P. (2016). A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes. Bioinformatics, 32(23), 3566-3574. doi: 10.1093/bioinformatics/btw518

Journal - Research Article

Gardner, P. P., & Eldai, H. (2015). Annotating RNA motifs in sequences and alignments. Nucleic Acids Research, 43(2), 691-698. doi: 10.1093/nar/gku1327

Journal - Research Article

Gardner, P. P., Fasold, M., Burge, S. W., Ninova, M., Hertel, J., Kehr, S., … Stadler, P. F. (2015). Conservation and losses of non-coding RNAs in avian genomes. PLoS ONE, 10(3), e0121797. doi: 10.1371/journal.pone.0121797

Journal - Research Article

Nawrocki, E. P., Burge, S. W., Bateman, A., Daub, J., Eberhardt, R. Y., Eddy, S. R., … Gardner, P. P., … Finn, R. D. (2015). Rfam 12.0: Updates to the RNA families database. Nucleic Acids Research, 43(D1), D130-D137. doi: 10.1093/nar/gku1063

Journal - Research Article

Lindgreen, S., Umu, S. U., Lai, A. S.-W., Eldai, H., Liu, W., McGimpsey, S., … Gardner, P. P. (2014). Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling. PLoS Computational Biology, 10(10), e1003907. doi: 10.1371/journal.pcbi.1003907

Journal - Research Article

Tang, Y., Nielsen, H., Masquida, B., Gardner, P. P., & Johansen, S. D. (2014). Molecular characterization of a new member of the lariat capping twin-ribozyme introns. Mobile DNA, 5, 25. doi: 10.1186/1759-8753-5-25

Journal - Research Article

Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., … Avian Genome Consortium, including Gardner, P. P., … Wang, J. (2014). Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346(6215), 1311-1320. doi: 10.1126/science.1251385

Journal - Research Article

Barquist, L., Langridge, G. C., Turner, D. J., Phan, M.-D., Turner, A. K., Bateman, A., … Gardner, P. P. (2013). A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium. Nucleic Acids Research, 41(8), 4549-4564. doi: 10.1093/nar/gkt148

Journal - Research Article

Burge, S. W., Daub, J., Eberhardt, R., Tate, J., Barquist, L., Nawrocki, E. P., … Gardner, P. P., & Bateman, A. (2013). Rfam 11.0: 10 years of RNA families. Nucleic Acids Research, 41(D1), D226-D232. doi: 10.1093/nar/gks1005

Journal - Research Article

Kingsley, R. A., Kay, S., Connor, T., Barquist, L., Sait, L., Holt, K. E., … Gardner, P. P., … Dougan, G. (2013). Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar. mBio, 4(5), e00565-13. doi: 10.1128/mBio.00565-13

Journal - Research Article

Hoeppner, M. P., Gardner, P. P., & Poole, A. M. (2012). Comparative analysis of RNA families reveals distinct repertoires for each domain of life. PLoS Computational Biology, 8(11), e1002752. doi: 10.1371/journal.pcbi.1002752

Journal - Research Article

Widmann, J., Stombaugh, J., McDonald, D., Chocholousova, J., Gardner, P., Iyer, M. K., … Knight, R. (2012). RNASTAR: An RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs. RNA, 18(7), 1319-1327. doi: 10.1261/rna.032052.111

Journal - Research Article

Chaudhuri, R. R., Yu, L., Kanji, A., Perkins, T. T., Gardner, P. P., Choudhary, J., … Grant, A. J. (2011). Quantitative RNA-seq analysis of the campylobacter jejuni transcriptome. Microbiology, 157(10), 2922-2932. doi: 10.1099/mic.0.050278-0

Journal - Research Article

Gardner, P. P., Barquist, L., Bateman, A., Nawrocki, E. P., & Weinberg, Z. (2011). RNIE: Genome-wide prediction of bacterial intrinsic terminators. Nucleic Acids Research, 39(14), 5845-5852. doi: 10.1093/nar/gkr168

Journal - Research Article

Gardner, P. P., Daub, J., Tate, J., Moore, B. L., Osuch, I. H., Griffiths-Jones, S., … Bateman, A. (2011). Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Research, 39(Suppl. 1), D141-D145. doi: 10.1093/nar/gkq1129

Journal - Research Article

Nygaard, S., Braunstein, A., Malsen, G., Van Dongen, S., Gardner, P. P., Krogh, A., … Jeffares, D. C. (2010). Long- and short-term selective forces on malaria parasite genomes. PLoS Genetics, 6(9), e1001099. doi: 10.1371/journal.pgen.1001099

Journal - Research Article

Gardner, P. P., Daub, J., Tate, J. G., Nawrocki, E. P., Kolbe, D. L., Lindgreen, S., … Bateman, A. (2009). Rfam: Updates to the RNA families database. Nucleic Acids Research, 37(Suppl. 1), D136-D140. doi: 10.1093/nar/gkn766

Journal - Research Article

Perkins, T. T., Kingsley, R. A., Fookes, M. C., Gardner, P. P., James, K. D., Yu, L., … Dougan, G. (2009). A strand-specific RNA-seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genetics, 5(7), e1000569. doi: 10.1371/journal.pgen.1000569

Journal - Research Article

Mourier, T., Carret, C., Kyes, S., Christodoulou, Z., Gardner, P. P., Jeffares, D. C., … Pain, A. (2008). Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum. Genome Research, 18(2), 281-292. doi: 10.1101/gr.6836108

Journal - Research Article

Freyhult, E. K., Bollback, J. P., & Gardner, P. P. (2007). Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA. Genome Research, 17(1), 117-125. doi: 10.1101/gr.5890907

Journal - Research Article

Lindgreen, S., Gardner, P. P., & Krogh, A. (2007). MASTR: Multiple alignment and structure prediction of non-coding RNAs using simulated annealing. Bioinformatics, 23(24), 3304-3311. doi: 10.1093/bioinformatics/btm525

Journal - Research Article

Weiler, C., Gardner, P. P., Hedegaard, M. M., & Vinther, J. (2007). Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes. BMC Genomics, 8, 244. doi: 10.1186/1471-2164-8-244

Journal - Research Article

Lindgreen, S., Gardner, P. P., & Krogh, A. (2006). Measuring covariation in RNA alignments: Physical realism improves information measures. Bioinformatics, 22(24), 2988-2995. doi: 10.1093/bioinformatics/btl514

Journal - Research Article

Freyhult, E., Gardner, P. P., & Moulton, V. (2005). A comparison of RNA folding measures. BMC Bioinformatics, 6, 241. doi: 10.1186/1471-2105-6-241

Journal - Research Article

Freyhult, E., Moulton, V., & Gardner, P. (2005). Predicting RNA structure using mutual information. Applied Bioinformatics, 4(1), 53-59. doi: 10.2165/00822942-200504010-00006

Journal - Research Article

Gardner, P. P., Wilm, A., & Washietl, S. (2005). A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Research, 33(8), 2433-2439. doi: 10.1093/nar/gki541

Journal - Research Article

Gardner, P. P., & Giegerich, R. (2004). A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics, 5, 140. doi: 10.1186/1471-2105-5-140

Journal - Research Article

Edvardsson, S., Gardner, P. P., Poole, A. M., Hendy, M. D., Penny, D., & Moulton, V. (2003). A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction. Bioinformatics, 19(7), 865-873. doi: 10.1093/bioinformatics/btg080

Journal - Research Article

Gardner, P. P., Holland, B. R., Moulton, V., Hendy, M., & Penny, D. (2003). Optimal alphabets for an RNA world. Proceedings of the Royal Society of London: Series B, 270(1520), 1177-1182. doi: 10.1098/rspb.2003.2355

Journal - Research Article

Rakonjac, J., Ward, L. J. H., Schiemann, A. H., Gardner, P. P., Lubbers, M. W., & O'Toole, P. W. (2003). Sequence diversity and functional conservation of the origin of replication in lactococcal prolate phages. Applied & Environmental Microbiology, 69(9), 5104-5114. doi: 10.1128/AEM.69.9.5104-5114.2003

Journal - Research Article

Buchka, S., Hapfelmeier, A., Gardner, P. P., Wilson, R., & Boulesteix, A. (2021). On the optimistic performance evaluation of newly introduced bioinformatic methods [Short report]. Genome Biology, 22(1). doi: 10.1186/s13059-021-02365-4

Journal - Research Other

Smith, L. M., Jackson, S. A., Gardner, P. P., & Fineran, P. C. (2021). SorTn-seq: A high-throughput functional genomics approach to discovering regulators of bacterial gene expression. Nature Protocols, 16, 4382-4418. doi: 10.1038/s41596-021-00582-6

Journal - Research Other

da Fonseca, R. R., Couto, A., Machado, A. M., Brejova, B., Albertin, C. B., Silva, F., Gardner, P., … Gilbert, M. T. P. (2020). A draft genome sequence of the elusive giant squid, Architeuthis dux [Data note]. GigaScience, 9(1), giz152. doi: 10.1093/gigascience/giz152

Journal - Research Other

Jose, B. R., Gardner, P. P., & Barquist, L. (2019). Transcriptional noise and exaptation as sources for bacterial sRNAs. Biochemical Society Transactions, 47(2), 527-539. doi: 10.1042/bst20180171

Journal - Research Other

Weber, L. M., Saelens, W., Cannoodt, R., Soneson, C., Hapfelmeier, A., Gardner, P. P., … Robinson, M. D. (2019). Essential guidelines for computational method benchmarking. Genome Biology, 20(1), 125. doi: 10.1186/s13059-019-1738-8

Journal - Research Other

Dickie, I. A., Boyer, S., Buckley, H., Duncan, R. P., Gardner, P., Hogg, I. D., … Morales, S. E., … Weaver, L. (2018). Towards robust and repeatable sampling methods in eDNA based studies. Molecular Ecology Resources, 18(5), 940-952. doi: 10.1111/1755-0998.12907

Journal - Research Other

Coray, D., Wheeler, N. E., Heinemann, J. A., & Gardner, P. P. (2017). Why so narrow: Distribution of anti-sense regulated, type I toxin-antitoxin systems compared with type II and type III systems. RNA Biology, 14(3), 275-280. doi: 10.1080/15476286.2016.1272747

Journal - Research Other

Finn, R. D., Gardner, P. P., & Bateman, A. (2012). Making your database available through Wikipedia: The pros and cons. Nucleic Acids Research, 40(D1), D9-D12. doi: 10.1093/nar/gkr1195

Journal - Research Other

Gardner, P. P. (2012). Three years of RNA families. RNA Biology, 9(1), 2-3. doi: 10.4161/rna.9.1.18979

Journal - Research Other

Bateman, A., Agrawal, S., Birney, E., Bruford, E. A., Bujnicki, J. M., Cochrane, G., … Gardner, P. P., … Zwieb, C. (2011). RNAcentral: A vision for an international database of RNA sequences. RNA, 17(11), 1941-1946. doi: 10.1261/rna.2750811

Journal - Research Other

Gardner, P. P., Bateman, A., & Poole, A. M. (2010). SnoPatrol: How many snoRNA genes are there? Journal of Biology, 9(1), 4. doi: 10.1186/jbiol211

Journal - Research Other

Logan, D. W., Sandal, M., Gardner, P. P., Manske, M., & Bateman, A. (2010). Ten simple rules for editing wikipedia. PLoS Computational Biology, 6(9), e1000941. doi: 10.1371/journal.pcbi.1000941

Journal - Research Other

Gardner, P. P. (2009). The use of covariance models to annotate RNAs in whole genomes. Briefings in Functional Genomics, 8(6), 444-450. doi: 10.1093/bfgp/elp042

Journal - Research Other

Gardner, P. P., & Bateman, A. G. (2009). A home for RNA families at RNA Biology. RNA Biology, 6(1), 2-4. doi: 10.4161/rna.6.1.7635

Journal - Research Other

Daub, J., Gardner, P. P., Tate, J., Ramsköld, D., Manske, M., Scott, W. G., … Bateman, A. (2008). The RNA WikiProject: Community annotation of RNA families. RNA, 14(12), 2462-2464. doi: 10.1261/rna.1200508

Journal - Research Other

Gardner, P. P., & Vinther, J. (2008). Mutation of miRNA target sequences during human evolution. Trends in Genetics, 24(6), 262-265. doi: 10.1016/j.tig.2008.03.009

Journal - Research Other

Munch, K., Gardner, P. P., Arctander, P., & Krogh, A. (2006). A hidden Markov model approach for determining expression from genomic tiling micro arrays. BMC Bioinformatics, 7, 239. doi: 10.1186/1471-2105-7-239

Journal - Research Other

Vinther, J., Hedegaard, M. M., Gardner, P. P., Andersen, J. S., & Arctander, P. (2006). Identification of miRNA targets with stable isotope labeling by amino acids in cell culture. Nucleic Acids Research, 34(16), e107. doi: 10.1093/nar/gkl590

Journal - Research Other

Moulton, V., Gardner, P. P., Pointon, R. F., Creamer, L. K., & Jameson, G. B. (2000). RNA folding argues against a hot-start origin of life. Journal of Molecular Evolution, 51(4), 416-421. doi: 10.1007/s002390010104

Journal - Research Other