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List of works by David J. Studholme

A Boolean model of the Pseudomonas syringae hrp regulon predicts a tightly regulated system

scientific article

A Grain Rot of Rice in Iran Caused by a Xanthomonas Strain Closely Related to X. sacchari

scientific article published on 09 April 2020

A codon-optimized green fluorescent protein for live cell imaging in Zymoseptoria tritici

scientific article published on June 2015

A comparison of Pfam and MEROPS: two databases, one comprehensive, and one specialised ⬇️

scientific article published on May 9, 2003

A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528

scientific article published on 24 August 2009

A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528.

scientific article

A draft genome sequence of Pseudomonas syringae pv. tomato T1 reveals a type III effector repertoire significantly divergent from that of Pseudomonas syringae pv. tomato DC3000.

scientific article

A highly specific tool for identification of pv. based on five Xvm-specific coding sequences

A toolkit for analysing large-scale plant small RNA datasets

scientific article

Application of 'next-generation' sequencing technologies to microbial genetics

scientific article published on April 2009

Application of high-throughput DNA sequencing in phytopathology

scientific article published on January 2011

Application of high‐throughput genome sequencing to intrapathovar variation in Pseudomonas syringae ⬇️

scientific article published on April 1, 2011

Ash leaf metabolomes reveal differences between trees tolerant and susceptible to ash dieback disease.

scientific article published on 19 December 2017

Assessing the performance of the Oxford Nanopore Technologies MinION.

scientific article published on March 2015

AzeR, a transcriptional regulator that responds to azelaic acid in Pseudomonas nitroreducens

scientific article published on 01 January 2020

Bioinformatic identification of novel regulatory DNA sequence motifs in Streptomyces coelicolor

scientific article

Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles.

scientific article

Comparative genome analysis provides insights into the evolution and adaptation of Pseudomonas syringae pv. aesculi on Aesculus hippocastanum

scientific article

Construction and high-throughput phenotypic screening ofZymoseptoria tritici over-expression strains

scientific article published on June 2015

Coping with Environmental Eukaryotes; Identification of Pseudomonas syringae Genes during the Interaction with Alternative Hosts or Predators

scientific article published on 21 April 2018

Correction: Studholme et al., Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 clade. Genes 2011, 2, 1050-1065.

scientific article published on 11 January 2012

Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome

scientific article

DNA binding activity of the Escherichia coli nitric oxide sensor NorR suggests a conserved target sequence in diverse proteobacteria

scientific article

Data management challenges for artificial intelligence in plant and agricultural research

scientific article published in 2023

De novo assembly of short sequence reads

scientific article published on 19 August 2010

De novoassembly of thePseudomonas syringaepv.syringaeB728a genome using Illumina/Solexa short sequence reads

scientific article published on 09 December 2008

Deep sequencing of small RNAs in plants: applied bioinformatics ⬇️

scientific article published on December 19, 2011

Deletion of a previously uncharacterized flagellar-hook-length control gene fliK modulates the sigma54-dependent regulon in Campylobacter jejuni

scientific article published in September 2007

Development of molecular markers tightly linked to Pvr4 gene in pepper using next-generation sequencing.

scientific article

Differences in carbon source utilisation distinguish Campylobacter jejuni from Campylobacter coli

scientific article

Domain architectures of sigma54-dependent transcriptional activators

scientific article

Draft Genome Sequence of Beneficial Rice Rhizosphere Isolate Pseudomonas aeruginosa PUPa3.

scientific article published on 3 July 2014

Draft Genome Sequence of Erwinia toletana, a Bacterium Associated with Olive Knots Caused by Pseudomonas savastanoi pv. Savastanoi

scientific article published on 9 May 2013

Draft Genome Sequence of Pseudomonas syringae pv. syringae ALF3 Isolated from Alfalfa

scientific article published on 11 February 2016

Draft Genome Sequence of the Enteropathogenic Bacterium Campylobacter jejuni Strain cj255

scientific article

Draft Genome Sequences of Achromobacter piechaudii GCS2, Agrobacterium sp. Strain SUL3, Microbacterium sp. Strain GCS4, Shinella sp. Strain GWS1, and Shinella sp. Strain SUS2 Isolated from Consortium with the Hydrocarbon-Producing Alga Botryococcus b

scientific article published in 2016

Draft Genome Sequences of Pathotype Strains for Three Pathovars Belonging to Three Xanthomonas Species

scientific article published on 27 September 2018

Draft Genome Sequences of Two Strains of Xanthomonas arboricola pv. celebensis Isolated from Banana Plants

scientific article published on 11 February 2016

Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 Clade

scientific article published on 02 December 2011

Draft genome sequence of Pseudomonas fuscovaginae, a broad-host-range pathogen of plants

scientific article

Draft genome sequence of Pseudomonas syringae pathovar syringae strain FF5, causal agent of stem tip dieback disease on ornamental pear

scientific article published on July 2012

Draft genome sequence of Xanthomonas axonopodis pathovar vasculorum NCPPB 900.

scientific article

Draft genome sequences of Phytophthora kernoviae and Phytophthora ramorum lineage EU2 from Scotland

scientific article published on 22 September 2015

Draft genome sequences of seven isolates of Phytophthora ramorum EU2 from Northern Ireland

scientific article published on 22 September 2015

Environmental fluctuations accelerate molecular evolution of thermal tolerance in a marine diatom.

scientific article published on 30 April 2018

Evidence for large complex networks of plant short silencing RNAs

scientific article

Evolution. Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

scientific article published in February 2015

Exploitation of sulfonylurea resistance marker and non-homologous end joining mutants for functional analysis in Zymoseptoria tritici

scientific article published on June 2015

Finding sRNA generative locales from high-throughput sequencing data with NiBLS.

scientific article

Functionality of purified sigma(N) (sigma(54)) and a NifA-like protein from the hyperthermophile Aquifex aeolicus.

scientific article

G8: a novel domain associated with polycystic kidney disease and non-syndromic hearing loss

scientific article

Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana

scientific article

Genome Resequencing of Laboratory Stocks of Burkholderia pseudomallei K96243

Genome Sequence of Staphylococcus aureus Ex1, Isolated from a Patient with Spinal Osteomyelitis.

scientific article

Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

scientific article published on 5 October 2015

Genome characterization of a novel Burkholderia cepacia complex genomovar isolated from dieback affected mango orchards

scientific article

Genome evolution following host jumps in the Irish potato famine pathogen lineage

scientific article published in December 2010

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

scientific article

Genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes

scientific article published on 08 May 2009

Genome sequences of 12 isolates of the EU1 lineage of Phytophthora ramorum, a fungus-like pathogen that causes extensive damage and mortality to a wide range of trees and other plants

scientific article published on 06 February 2017

Genome sequences of six Phytophthora species associated with forests in New Zealand.

scientific article published on 22 November 2015

Genome sequencing reveals a new lineage associated with lablab bean and genetic exchange between Xanthomonas axonopodis pv. phaseoli and Xanthomonas fuscans subsp. fuscans

scientific article

Genome-Enabled Phylogeographic Investigation of the Quarantine Pathogen Ralstonia solanacearum Race 3 Biovar 2 and Screening for Sources of Resistance Against Its Core Effectors

scientific article published on May 2015

Genome-wide sequencing data reveals virulence factors implicated in banana Xanthomonas wilt

scientific article

Genome-wide sequencing of Phytophthora lateralis reveals genetic variation among isolates from Lawson cypress (Chamaecyparis lawsoniana) in Northern Ireland

scientific article published on 5 June 2013

Genome-wide sequencing reveals two major sub-lineages in the genetically monomorphic pathogen xanthomonas campestris pathovar musacearum

scientific article published on 04 July 2012

Genome-wide survey of Arabidopsis natural variation in downy mildew resistance using combined association and linkage mapping

scientific article

Genomics-Informed Molecular Detection of Xanthomonas vasicola pv. vasculorum Strains Causing Severe Bacterial Leaf Streak of Corn

scientific article published on 10 January 2020

Haustorium formation and a distinct biotrophic transcriptome characterize infection of Nicotiana benthamiana by the tree pathogen Phytophthora kernoviae

scientific article published on 20 May 2021

Heterologous expression of pyruvate decarboxylase in Geobacillus thermoglucosidasius

scientific article published on 27 March 2008

High-Quality Draft Genome Sequence of the Causal Agent of the Current Panama Disease Epidemic

scientific article published on 05 September 2019

Identification of possible virulence marker from Campylobacter jejuni isolates

scientific article

Identifying molecular markers suitable for Frl selection in tomato breeding

scientific article published on 07 July 2018

Improved method for genotyping the causative agent of crayfish plague (Aphanomyces astaci) based on mitochondrial DNA

scientific article published on 12 April 2019

In silico analysis of the sigma54-dependent enhancer-binding proteins in Pirellula species strain 1.

scientific article published in January 2004

Integrated bioinformatic and phenotypic analysis of RpoN-dependent traits in the plant growth-promoting bacterium Pseudomonas fluorescens SBW25.

scientific article published on December 2007

InterPro, progress and status in 2005

scientific article

Investigating the beneficial traits of Trichoderma hamatum GD12 for sustainable agriculture-insights from genomics

scientific article (publication date: 2013)

Isolation of Salmonella mutants resistant to the inhibitory effect of Salicylidene acylhydrazides on flagella-mediated motility

scientific article

MANSC: a seven-cysteine-containing domain present in animal membrane and extracellular proteins

scientific article

Marker development for the genetic study of natural variation in Arabidopsis thaliana

scientific article published in November 2007

Mechanism of action of the Escherichia coli phage shock protein PspA in repression of the AAA family transcription factor PspF.

scientific article

Morphological Variation and Inter-Relationships of Quantitative Traits in Enset (Ensete ventricosum (welw.) Cheesman) Germplasm from South and South-Western Ethiopia

scientific article

Multidimensional Protein Identification Technology (MudPIT) Analysis of Ubiquitinated Proteins in Plants

article

Multiple candidate effectors from the oomycete pathogen Hyaloperonospora arabidopsidis suppress host plant immunity

scientific article

NCD3G: a novel nine-cysteine domain in family 3 GPCRs

scientific article published in September 2004

New genotyping method for the causative agent of crayfish plague ( Aphanomyces astaci ) based on whole genome data

scientific article published on 25 June 2018

Nonagricultural reservoirs contribute to emergence and evolution of Pseudomonas syringae crop pathogens

scientific article published on 21 May 2013

PhosCalc: a tool for evaluating the sites of peptide phosphorylation from mass spectrometer data

scientific article

Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana

scientific article published on 24 February 2009

Phylogenetic analysis of transformable strains of thermophilic Bacillus species

scientific article published in March 1999

Phylogenetic analysis of transformable strains of thermophilic Bacillus species

scholarly article by David J. Studholme published in March 1999

PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis

scientific article

Progress in metagenomics requires a balanced appraisal of the available technologies.

scientific article

Protein domains and architectural innovation in plant-associated Proteobacteria

scientific article

Pseudomonas fluorescens NZI7 repels grazing by C. elegans, a natural predator

scientific article published on 21 February 2013

Pseudomonas syringae pv. actinidiae (PSA) isolates from recent bacterial canker of kiwifruit outbreaks belong to the same genetic lineage

scientific article

Pseudomonas syringae strains naturally lacking the classical P. syringae hrp/hrc Locus are common leaf colonizers equipped with an atypical type III secretion system

scientific article

Publisher Correction: Environmental fluctuations accelerate molecular evolution of thermal tolerance in a marine diatom

scientific article published in Nature Communications

Recently published Streptomyces genome sequences

scientific article published on September 2014

SDE5, the putative homologue of a human mRNA export factor, is required for transgene silencing and accumulation of trans-acting endogenous siRNA.

scientific article published in April 2007

SNP-based genotyping and whole-genome sequencing reveal previously unknown genetic diversity in <i>Xanthomonas vasicola</i> pv. <i>musacearum</i>, causal agent of banana xanthomonas wilt, in its presumed Ethiopian origin

scientific article published on 27 November 2020

Salmonella Gallinarum field isolates from laying hens are related to the vaccine strain SG9R.

scientific article published on 27 August 2013

Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome

scientific article

Some (bacilli) like it hot: genomics of Geobacillus species

scientific article

The C-Terminal 12 Amino Acids of ςN Are Required for Structure and Function

scientific article published in 1999

The Genome of Peronospora belbahrii Reveals High Heterozygosity, a Low Number of Canonical Effectors, and TC-Rich Promoters

scientific article published on 01 April 2020

The alternative sigma factor σ28 of the extreme thermophile Aquifex aeolicus restores motility to an Escherichia coli fliA mutant

article published in 2000

The biology of enhancer-dependent transcriptional regulation in bacteria: insights from genome sequences

scholarly article by David J. Studholme published in May 2000

The plant pathogen Pseudomonas syringae pv. tomato is genetically monomorphic and under strong selection to evade tomato immunity

scientific article

The rulB gene of plasmid pWW0 is a hotspot for the site-specific insertion of integron-like elements found in the chromosomes of environmental Pseudomonas fluorescens group bacteria

scientific article

Transfer of Xanthomonas campestris pv. arecae and X. campestris pv. musacearum to X. vasicola (Vauterin) as X. vasicola pv. arecae comb. nov. and X. vasicola pv. musacearum comb. nov. and Description of X. vasicola pv. vasculorum pv. nov

scientific article published on 10 January 2020

Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis

scientific article published in Nature

Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects

scientific article published on January 2013

miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii

scientific article

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