Richard J. Edwards

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Correction: SLiMEnrich: computational assessment of protein–protein interaction data as a source of domain-motif interactions

Sobia Idrees, Åsa Pérez-Bercoff, Richard J. Edwards, 2018, PeerJ.

An expert system for convective heat transfer measurements using a transient analysis

Richard J. Edwards, Ali R. Uzel, Bryan L. Button, 1989 .

ELM—the database of eukaryotic linear motifs

Richard J. Edwards, Aidan Budd, Allegra Via, 2011, Nucleic Acids Res..

GASP: Gapped Ancestral Sequence Prediction for proteins

Richard J. Edwards, Denis C. Shields, D. Shields, 2004, BMC Bioinformatics.

Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia

Richard J. Edwards, Maria Victoria Schneider, Malcolm J. McConville, 2017, Briefings Bioinform..

SLiMSearch 2.0: biological context for short linear motifs in proteins

Richard J. Edwards, Denis C. Shields, Norman E. Davey, 2011, Nucleic Acids Res..

CompariMotif: quick and easy comparisons of sequence motifs

Richard J. Edwards, Denis C. Shields, Norman E. Davey, 2008, Bioinform..

Investigating the 3D Conformation of N-Terminally Constrained Oligopeptides

Richard J. Edwards, Denis C. Shields, Itizar Frades, 2004, Spanish Bioinformatics Conference.

Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery

Richard J. Edwards, Denis C. Shields, Norman E. Davey, 2009, Bioinform..

SLiMSearch: A Webserver for Finding Novel Occurrences of Short Linear Motifs in Proteins, Incorporating Sequence Context

Richard J. Edwards, Denis C. Shields, Norman E. Davey, 2010, PRIB.

Absolute Net Charge and the Biological Activity of Oligopeptides

Richard J. Edwards, Marc Devocelle, Denis C. Shields, 2006, J. Chem. Inf. Model..

BADASP: predicting functional specificity in protein families using ancestral sequences

Richard J. Edwards, Denis C. Shields, D. Shields, 2005, Bioinform..

QSLiMFinder: improved short linear motif prediction using specific query protein data

Richard J. Edwards, Nicolas Palopoli, Kieren T. Lythgow, 2015, Bioinform..

A study into the feasibility of an intelligent knowledge based system (IKBS) in computational fluid mechanics (CFM)

Richard J. Edwards, B. L. Button, A. R. Uzel, 1988 .

Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins

Richard J. Edwards, Denis C. Shields, Norman E. Davey, 2010, BMC Bioinformatics.

SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs

Richard J. Edwards, Denis C. Shields, Norman E. Davey, 2010, Nucleic Acids Res..

The SLiMDisc server: short, linear motif discovery in proteins

Richard J. Edwards, Denis C. Shields, Norman E. Davey, 2007, Nucleic Acids Res..

SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks

Richard J. Edwards, Denis C. Shields, Kevin T. O'Brien, 2015, F1000Research.

SLiMFinder: A Probabilistic Method for Identifying Over-Represented, Convergently Evolved, Short Linear Motifs in Proteins

Richard J. Edwards, Denis C. Shields, Norman E. Davey, 2007, PloS one.

SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent

Richard J. Edwards, Denis C. Shields, Norman E. Davey, 2006, Nucleic acids research.

SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions

Richard J. Edwards, Denis C. Shields, Toby J. Gibson, 2012, Nucleic acids research.

Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture

Richard J. Edwards, N. Deshpande, H. Ertan, 2019, PeerJ.

Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture.

Richard J. Edwards, N. Deshpande, H. Ertan, 2019, PeerJ.

Evaluation of whether accelerated protein evolution in chordates has occurred before, after, or simultaneously with gene duplication.

Richard J. Edwards, C. O'Dushlaine, D. Shields, 2006, Molecular biology and evolution.

Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C

Richard J. Edwards, Erez Lieberman Aiden, Timothy P. L. Smith, 2020, GigaScience.

Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome

Richard J. Edwards, Erez Lieberman Aiden, L. Hillier, 2020, bioRxiv.

Quantitative Proteomics of the Infectious and Replicative Forms of Chlamydia trachomatis

Richard J. Edwards, N. Thomson, P. Skipp, 2016, PloS one.

Protein interactions with the platelet integrin αIIb regulatory motif

Richard J. Edwards, D. Murphy, N. Moran, 2010, Proteomics.

A phased chromosome-level genome and full mitochondrial sequence for the dikaryotic myrtle rust pathogen, Austropuccinia psidii

Richard J. Edwards, R. Park, P. Tobias, 2022, bioRxiv.

Draft genome assembly of the invasive cane toad, Rhinella marina

Richard J. Edwards, E. Holmes, R. Shine, 2018, GigaScience.

An intrinsically disordered proteins community for ELIXIR

Silvio C. E. Tosatto, Richard J. Edwards, Norman E. Davey, 2019, F1000Research.

SLiM-Enrich: computational assessment of protein–protein interaction data as a source of domain-motif interactions

Richard J. Edwards, Åsa Pérez-Bercoff, Sobia Idrees, 2018, PeerJ.

An intrinsically disordered proteins community for ELIXIR [version 1; peer review: 2 approved]

Richard J. Edwards, Philippe Le Mercier, J. M. Hancock, 2020 .

Contrasting Patterns of Single Nucleotide Polymorphisms and Structural Variation Across Multiple Invasions

Richard J. Edwards, W. Sherwin, L. Rollins, 2022, bioRxiv.

A chromosome-level genome resource for studying virulence mechanisms and evolution of the coffee rust pathogen Hemileia vastatrix

Richard J. Edwards, R. Park, P. Surana, 2022, bioRxiv.

mGluRs in C. elegans

Richard J. Edwards, T. Ishihara, J. Dillon, 2015 .

Complete genome sequences of pooled genomic DNA from 10 marine bacteria using PacBio long-read sequencing.

Richard J. Edwards, T. Thomas, Wei-Zhi Song, 2019, Marine genomics.

An investigation into the structure and function of VanS proteins involved in the two-component VanS/VanR regulatory system controlling antibiotic resistance

Richard J. Edwards, 2014 .

Metabotropic Glutamate Receptors

Richard J. Edwards, T. Ishihara, R. Edwards, 2015, The Journal of Biological Chemistry.

Selective Toxicity of the Anthelmintic Emodepside Revealed by Heterologous Expression of Human KCNMA1 in Caenorhabditis elegans

Richard J. Edwards, Caitríona Murray, L. Holden-Dye, 2011, Molecular Pharmacology.

Evolutionary genomics: Insights from the invasive European starlings

Richard J. Edwards, W. Sherwin, L. Rollins, 2023, Frontiers in Genetics.

Shotgun Proteomic Analysis of Emiliania huxleyi, a Marine Phytoplankton Species of Major Biogeochemical Importance

Richard J. Edwards, P. Skipp, R. Edwards, 2011, Marine Biotechnology.

Bioinformatic discovery of novel bioactive peptides.

Richard J. Edwards, Marc Devocelle, Niamh Moran, 2007, Nature chemical biology.

A Simple Method for Genome-Wide Screening for Advantageous Insertions of Mobile DNAs in Escherichia coli

Richard J. Edwards, J. Brookfield, R. Sockett, 2002, Current Biology.

The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology

Richard J. Edwards, Erez Lieberman Aiden, J. Keilwagen, 2023, bioRxiv.

Limited Introgression between Rock-Wallabies with Extensive Chromosomal Rearrangements

Richard J. Edwards, Jason G. Bragg, M. Kirkpatrick, 2021, Molecular biology and evolution.

Fluorescent protein‐mediated colour polymorphism in reef corals: multicopy genes extend the adaptation/acclimatization potential to variable light environments

Richard J. Edwards, J. Wiedenmann, F. Oswald, 2015, Molecular ecology.

Horizontal Transposon Transfer and Its Implications for the Ancestral Ecology of Hydrophiine Snakes

Richard J. Edwards, Alastair J. Ludington, D. Adelson, 2021, bioRxiv.

The Australian dingo is an early offshoot of modern breed dogs

Richard J. Edwards, J. Keilwagen, A. Omer, 2022, Science advances.

Tandem repeat copy-number variation in protein-coding regions of human genes

Richard J. Edwards, C. O'Dushlaine, R. Edwards, 2005, Genome Biology.

Biochar alters the soil microbiome and soil function: results of next‐generation amplicon sequencing across Europe

Richard J. Edwards, F. Miglietta, G. Taylor, 2017 .

Antarctic desert soil bacteria exhibit high novel natural product potential, evaluated through long-read genome sequencing and comparative genomics.

Richard J. Edwards, B. Ferrari, T. Amos, 2020, Environmental microbiology.

Computational Prediction of Disordered Protein Motifs Using SLiMSuite.

Åsa Pérez-Bercoff, Richard J. Edwards, Richard J Edwards, 2020, Methods in molecular biology.

Computational identification and analysis of protein short linear motifs.

Richard J. Edwards, Norman E. Davey, Richard J Edwards, 2010, Frontiers in bioscience.

First in family Rhabdiasidae: the reference-guided genome assembly of an invasive parasite, the cane toad lungworm (Rhabdias pseudosphaerocephala)

Richard J. Edwards, Gregory P. Brown, R. Shine, 2023, bioRxiv.

Correlation of probiotic Lactobacillus salivarius growth phase with its cell wall-associated proteome.

Richard J. Edwards, D. Fitzgerald, F. Shanahan, 2005, FEMS microbiology letters.

Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C

Richard J. Edwards, Jason G. Bragg, J. Bragg, 2021, bioRxiv.

Desert Dingo (Canis lupus dingo) genome provides insights into their role in the Australian ecosystem

Richard J. Edwards, J. Keilwagen, A. Omer, 2020, bioRxiv.

The Extracellular Domain of Two-component System Sensor Kinase VanS from Streptomyces coelicolor Binds Vancomycin at a Newly Identified Binding Site

Richard J. Edwards, D. Roper, C. Lockey, 2020, Scientific Reports.

Parallel Evolution in Streptococcus pneumoniae Biofilms

Richard J. Edwards, Raju V. Misra, S. Gharbia, 2016, Genome biology and evolution.

Transiently beneficial insertions could maintain mobile DNA sequences in variable environments.

Richard J. Edwards, J. Brookfield, 2003, Molecular biology and evolution.

Plant adaptation or acclimation to rising CO2? Insight from first multigenerational RNA‐Seq transcriptome

Richard J. Edwards, F. Miglietta, G. Taylor, 2016, Global change biology.

Do epigenetic changes drive corticosterone responses to alarm cues in larvae of an invasive amphibian?

Richard J. Edwards, R. Shine, P. Waters, 2020, Integrative and comparative biology.

Intergenerational effects of manipulating DNA methylation in the early life of an iconic invader

Richard J. Edwards, Gregory P. Brown, J. Devore, 2021, Philosophical Transactions of the Royal Society B.

Transcriptome analysis of human brain tissue identifies reduced expression of complement complex C1Q Genes in Rett syndrome

Richard J. Edwards, Amelia A. Assareh, A. Assareh, 2016, BMC Genomics.

Computational prediction of short linear motifs from protein sequences.

Richard J. Edwards, Richard J Edwards, Nicolas Palopoli, 2015, Methods in molecular biology.

Interactome-wide prediction of short, disordered protein interaction motifs in humans.

Richard J. Edwards, Norman E. Davey, Kevin T. O'Brien, 2012, Molecular bioSystems.

High risk human papilloma viruses (HPVs) are present in benign prostate tissues before development of HPV associated prostate cancer

Richard J. Edwards, L. Lutze-Mann, J. Lawson, 2017, Infectious Agents and Cancer.

Phylogenetic Tree Rooting

Richard J. Edwards, Richard J. Edwards, 2019, Encyclopedia of Bioinformatics and Computational Biology.

Responses of the Emiliania huxleyi Proteome to Ocean Acidification

Richard J. Edwards, P. Skipp, B. Jones, 2013, PloS one.

Metaproteomics reveals methyltransferases implicated in dichloromethane and glycine betaine fermentation by ‘Candidatus Formimonas warabiya’ strain DCMF

Richard J. Edwards, H. Ertan, M. Manefield, 2022, Frontiers in Microbiology.

A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes

Richard J. Edwards, Jason G. Bragg, B. Schwessinger, 2023, bioRxiv.

Long read data analysis workshop

Richard J. Edwards, Marc R. Wilkins, Tim Kahlke, 2018 .

Isolation and molecular characterisation of Dunaliella tertiolecta with truncated light-harvesting antenna for enhanced photosynthetic efficiency

Richard J. Edwards, R. Terauchi, M. J. Terry, 2020, Algal Research.

Horizontal transfer and southern migration: the tale of Hydrophiinae′s marine journey.

Richard J. Edwards, Alastair J. Ludington, D. Adelson, 2021 .

Transcript‐ and annotation‐guided genome assembly of the European starling

Richard J. Edwards, Gregory F Ball, Scott J. Werner, 2021, bioRxiv.

HSP-4 endoplasmic reticulum (ER) stress pathway is not activated in a C. elegans model of ethanol intoxication and withdrawal

Richard J. Edwards, L. Holden-Dye, V. O’Connor, 2012, Invertebrate Neuroscience.

High risk human papilloma viruses (HPVs) are present in benign prostate tissues before development of HPV associated prostate cancer

Richard J. Edwards, L. Lutze-Mann, J. Lawson, 2017, Infectious Agents and Cancer.

BUSCOMP: BUSCO compilation and comparison – Assessing completeness in multiple genome assemblies

Richard J. Edwards, Richard J. Edwards, 2019 .

The Extracellular Domain of Two-component System Sensor Kinase VanS from Streptomyces coelicolor Binds Vancomycin at a Newly Identified Binding Site

Richard J. Edwards, D. Roper, A. M. Dixon, 2020, Scientific Reports.

The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology

Richard J. Edwards, Erez Lieberman Aiden, J. Keilwagen, 2023, GigaScience.

SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks

Richard J. Edwards, Kevin T. O'Brien, D. Shields, 2015, F1000Research.

The SLiMDisc server: short, linear motif discovery in proteins

Richard J. Edwards, Norman E. Davey, D. Shields, 2007, Nucleic Acids Res..