List of works - Paul Gardner

A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria.

scientific article

A benchmark of multiple sequence alignment programs upon structural RNAs

scientific article

A comparison of RNA folding measures.

scientific article

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

scientific article

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

scientific article published on 19 December 2016

A comprehensive comparison of comparative RNA structure prediction approaches

scientific article

A draft genome sequence of the elusive giant squid, Architeuthis dux

scientific article published on 01 January 2020

A hidden Markov model approach for determining expression from genomic tiling micro arrays

scientific article

A jumbo phage that forms a nucleus-like structure evades CRISPR-Cas DNA targeting but is vulnerable to type III RNA-based immunity

scientific article published on 09 December 2019

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

scientific article published on 8 August 2016

A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction

scientific article published in May 2003

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

scientific article

An evaluation of function of multicopy non-coding RNAs in mammals using ENCODE/FANTOM data and comparative genomics.

scientific article published on 3 April 2018

An evaluation of the accuracy and speed of metagenome analysis tools

scientific article published on 18 January 2016

An evaluation of the accuracy and speed of metagenome analysis tools

bioRxiv

An introduction to RNA databases

scientific article published on January 2014

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

scientific article published on 05 October 2021

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

scientific article published on 17 October 2017

Annotating RNA motifs in sequences and alignments

scientific article

Author Correction: An evaluation of the accuracy and speed of metagenome analysis tools

scientific article published on 20 April 2020

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

scientific article

Comparative analysis of RNA families reveals distinct repertoires for each domain of life

scientific article

Complete Genome Sequences of Two Geographically Distinct Legionella micdadei Clinical Isolates

scientific article published on June 2017

Conservation and losses of non-coding RNAs in avian genomes

scientific article

Convergent regulatory evolution and loss of flight in paleognathous birds

scientific article published on 01 April 2019

Convergent regulatory evolution and the origin of flightlessness in palaeognathous birds

Evolution of virulence in a novel family of transmissible mega‐plasmids

scientific article published in 2021

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

scientific article published on 27 August 2013

Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum

scientific article

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

article

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

scientific article

Identification of miRNA targets with stable isotope labeling by amino acids in cell culture.

scientific article

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

scientific article published on 04 January 2019

Long- and short-term selective forces on malaria parasite genomes

scientific article

MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing

scientific article

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

scientific article published on 8 May 2018

Machine learning identifies signatures of host adaptation in the bacterial pathogenSalmonella enterica

scholarly article published 17 October 2017

Making your database available through Wikipedia: the pros and cons ⬇️

scientific article published on December 5, 2011

Molecular characterization of a new member of the lariat capping twin-ribozyme introns

scientific article

Multiple alignment and structure prediction of non-coding RNA sequences

Mutation of miRNA target sequences during human evolution

scientific article published on 09 May 2008

Optimal alphabets for an RNA world

scientific article (publication date: 7 June 2003)

Predicting RNA structure using mutual information

scientific article published in January 2005

Publisher Correction: The tuatara genome reveals ancient features of amniote evolution

scientific article published on 18 August 2020

Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome

scientific article published on 4 August 2011

RNA Biology. Letter from the editor

scientific article published in January 2013

RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs

scientific article

RNAcentral: A vision for an international database of RNA sequences

scientific article (publication date: November 2011)

RNIE: genome-wide prediction of bacterial intrinsic terminators

scientific article published on 7 April 2011

Rfam 11.0: 10 years of RNA families

scientific article

Rfam 12.0: updates to the RNA families database

scientific article

Rfam: Wikipedia, clans and the "decimal" release

scientific article

Rfam: updates to the RNA families database

scientific article

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

scientific article

Sequence diversity and functional conservation of the origin of replication in lactococcal prolate phages.

scientific article

Simulating the RNA-world and computational ribonomics

2003 doctoral thesis by Paul Phillip Gardner at Massey University

SnoPatrol: how many snoRNA genes are there?

scientific article

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

scientific article published on 17 February 2020

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

scientific article published on 20 June 2016

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

scientific article published on 16 February 2022

Ten simple rules for editing Wikipedia ⬇️

scientific article

The Gene Ontology Resource: 20 years and still GOing strong

article

The RNA WikiProject: community annotation of RNA families ⬇️

scientific article

The tuatara genome reveals ancient features of amniote evolution

scientific article published on 5 August 2020

The use of covariance models to annotate RNAs in whole genomes

scientific article

Third Report on Chicken Genes and Chromosomes 2015.

scientific article published on 14 July 2015

Towards robust and repeatable sampling methods in eDNA-based studies

scientific article published on 26 May 2018

Transcriptional noise and exaptation as sources for bacterial sRNAs

scientific article published on 05 March 2019

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

scientific article

Two covariance models for iron-responsive elements ⬇️

scientific article published on September 1, 2011

Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes

scientific article

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

scientific article published on 9 January 2017

List of works by Paul Gardner

A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria.

A benchmark of multiple sequence alignment programs upon structural RNAs

A comparison of RNA folding measures.

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

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

A comprehensive comparison of comparative RNA structure prediction approaches

A draft genome sequence of the elusive giant squid, Architeuthis dux

A hidden Markov model approach for determining expression from genomic tiling micro arrays

A jumbo phage that forms a nucleus-like structure evades CRISPR-Cas DNA targeting but is vulnerable to type III RNA-based immunity

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

A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction

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

An evaluation of function of multicopy non-coding RNAs in mammals using ENCODE/FANTOM data and comparative genomics.

An evaluation of the accuracy and speed of metagenome analysis tools

An evaluation of the accuracy and speed of metagenome analysis tools

An introduction to RNA databases

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

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

Annotating RNA motifs in sequences and alignments

Author Correction: An evaluation of the accuracy and speed of metagenome analysis tools

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

Comparative analysis of RNA families reveals distinct repertoires for each domain of life

Complete Genome Sequences of Two Geographically Distinct Legionella micdadei Clinical Isolates

Conservation and losses of non-coding RNAs in avian genomes

Convergent regulatory evolution and loss of flight in paleognathous birds

Convergent regulatory evolution and the origin of flightlessness in palaeognathous birds

Evolution of virulence in a novel family of transmissible mega‐plasmids

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

Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum

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

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

Identification of miRNA targets with stable isotope labeling by amino acids in cell culture.

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

Long- and short-term selective forces on malaria parasite genomes

MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing

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

Machine learning identifies signatures of host adaptation in the bacterial pathogenSalmonella enterica

Making your database available through Wikipedia: the pros and cons ⬇️

Molecular characterization of a new member of the lariat capping twin-ribozyme introns

Multiple alignment and structure prediction of non-coding RNA sequences

Mutation of miRNA target sequences during human evolution

Optimal alphabets for an RNA world

Predicting RNA structure using mutual information

Publisher Correction: The tuatara genome reveals ancient features of amniote evolution

Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome

RNA Biology. Letter from the editor

RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs

RNAcentral: A vision for an international database of RNA sequences

RNIE: genome-wide prediction of bacterial intrinsic terminators

Rfam 11.0: 10 years of RNA families

Rfam 12.0: updates to the RNA families database

Rfam: Wikipedia, clans and the "decimal" release

Rfam: updates to the RNA families database

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

Sequence diversity and functional conservation of the origin of replication in lactococcal prolate phages.

Simulating the RNA-world and computational ribonomics

SnoPatrol: how many snoRNA genes are there?

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

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

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

Ten simple rules for editing Wikipedia ⬇️

The Gene Ontology Resource: 20 years and still GOing strong

The RNA WikiProject: community annotation of RNA families ⬇️

The tuatara genome reveals ancient features of amniote evolution

The use of covariance models to annotate RNAs in whole genomes

Third Report on Chicken Genes and Chromosomes 2015.

Towards robust and repeatable sampling methods in eDNA-based studies

Transcriptional noise and exaptation as sources for bacterial sRNAs

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

Two covariance models for iron-responsive elements ⬇️

Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes

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