Studholme, David J, Ibanez, Selena, MacLean, Daniel, Dangl, Jeffery L, Chang, Jeff H, Rathjen, John P
Abstract Background Pseudomonas syringae is a widespread bacterial pathogen that causes disease on a broad range of economically important plant species. Pathogenicity of P. syringae strains is...
MacLean, Daniel, Burrell, Michael A, Studholme, David J, Jones, Alexandra ME
Abstract Background We have created a software implementation of a published and verified method for assigning probabilities to potential phosphorylation sites on peptides using mass spectrometric...
A toolkit for analysing large-scale plant small RNA datasets (2008)
Moxon, Simon, Schwach, Frank, Dalmay, Tamas, MacLean, Dan, Studholme, David J., Moulton, Vincent
Summary: Recent developments in high-throughput sequencing technologies have generated considerable demand for tools to analyse large datasets of small RNA sequences. Here, we describe a suite of...
David J Studholme, Neil D Rawlings, Alan J Barrett, Alex Bateman, Alex Bateman
Background: We wished to compare two databases based on sequence similarity: one that aims to be comprehensive in its coverage of known sequences, and one that specialises in a relatively small...
G8: a novel domain associated with polycystic kidney disease and non-syndromic hearing loss (2006)
He, Quan-yuan, Liu, Xiang-hua, Li, Qiang, Studholme, David J., Li, Xuan-wen, Liang, Song-ping
Summary: We report a novel protein domain—G8—which contains five repeated β-strand pairs and is present in some disease-related proteins such as PKHD1, KIAA1199, TMEM2 as well as other...
Protein domains and architectural innovation in plant-associated Proteobacteria (2005)
Studholme, David J, Downie, J Allan, Preston, Gail M
Abstract Background Evolution of new complex biological behaviour tends to arise by novel combinations of existing building blocks. The functional and evolutionary building blocks of the proteome are...
Protein domains and architectural innovation in plant-associated Proteobacteria (2005)
Studholme, David J, Downie, J Allan, Preston, Gail M
Background Evolution of new complex biological behaviour tends to arise by novel combinations of existing building blocks. The functional and evolutionary building blocks of the proteome are protein...
Research article Protein domains and architectural innovation in plant-associated (2005)
Bmc Genomics, David J Studholme, J Allan Downie, Gail M Preston
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Bmc Genomics, David J Studholme, J. Allan Downie, Gail M Preston, David J. Studholme, J. Allan Downie, ...
This Provisional PDF corresponds to the article as it appeared upon acceptance. The fully-formatted
Research article Protein domains and architectural innovation in plant-associated (2005)
Bmc Genomics, David J Studholme, J Allan Downie, Gail M Preston
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
InterPro, progress and status in 2005 (2005)
Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
InterPro, progress and status in 2005 (2005)
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
Studholme, David J, Bentley, Stephen D, Kormanec, Jan
Abstract Background Streptomyces coelicolor is a bacterium with a vast repertoire of metabolic functions and complex systems of cellular development. Its genome sequence is rich in genes that encode...
Novel protein domains and motifs in the marine planctomycete Rhodopirellula baltica (2004)
Studholme, David J., Fuerst, John A., Bateman, Alex
The planctomycetes are a phylum of bacteria that have a unique cell compartmentalisation and yeast-like budding cell division and peptidoglycan-less proteinaceous cell walls. We wished to further our...
Novel protein domains and motifs in the marine planctomycete Rhodopirellula baltica (2004)
Studholme, David J., Fuerst, John A., Bateman, Alex
The planctomycetes are a phylum of bacteria that have a unique cell compartmentalisation and yeast-like budding cell division and peptidoglycan-less proteinaceous cell walls. We wished to further our...
The Pfam protein families database (2004)
Bateman, Alex, Coin, Lachlan, Durbin, Richard, Finn, Robert D., Hollich, Volker, Griffiths-Jones, Sam, ...
Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for...
Studholme, David J, Pau, Richard N
Abstract Background The transition metal molybdenum is essential for life. Escherichia coli imports this metal into the cell in the form of molybdate ions, which are taken up via an ABC transport...
A comparison of Pfam and MEROPS: Two databases, one comprehensive, and one specialised. (2003)
Studholme, David J, Rawlings, Neil D, Barrett, Alan J, Bateman, Alex
Abstract Background We wished to compare two databases based on sequence similarity: one that aims to be comprehensive in its coverage of known sequences, and one that specialises in a relatively...
Studholme, David J., Wigneshwereraraj, Siva R., Gallegos, María-Trinidad, Buck, Martin
The genome sequence of the extremely thermophilic bacterium Aquifex aeolicus encodes alternative sigma factor ςN (ς54, RpoN) and five potential ςN-dependent transcriptional activators. Although A....
The Bacterial Enhancer-Dependent ς54 (ςN) Transcription Factor
Buck, Martin, Gallegos, María-Trinidad, Studholme, David J., Guo, Yuli, Gralla, Jay D.
A comparison of Pfam and MEROPS: Two databases, one comprehensive, and one specialised.
Studholme, David J, Rawlings, Neil D, Barrett, Alan J, Bateman, Alex
The Pfam protein families database
Bateman, Alex, Coin, Lachlan, Durbin, Richard, Finn, Robert D., Hollich, Volker, Griffiths-Jones, Sam, ...
Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for...
Tucker, Nicholas P., D'Autréaux, Benoît, Studholme, David J., Spiro, Stephen, Dixon, Ray
The Escherichia coli nitric oxide sensor NorR was shown to bind to the promoter region of the norVW transcription unit, forming at least two distinct complexes detectable by gel retardation. Three...
InterPro, progress and status in 2005
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
Studholme, David J., Wigneshwereraraj, Siva R., Gallegos, María-Trinidad, Buck, Martin
The genome sequence of the extremely thermophilic bacterium Aquifex aeolicus encodes alternative sigma factor ςN (ς54, RpoN) and five potential ςN-dependent transcriptional activators. Although A....
The Bacterial Enhancer-Dependent ς54 (ςN) Transcription Factor
Buck, Martin, Gallegos, María-Trinidad, Studholme, David J., Guo, Yuli, Gralla, Jay D.
A comparison of Pfam and MEROPS: Two databases, one comprehensive, and one specialised.
Studholme, David J, Rawlings, Neil D, Barrett, Alan J, Bateman, Alex
The Pfam protein families database
Bateman, Alex, Coin, Lachlan, Durbin, Richard, Finn, Robert D., Hollich, Volker, Griffiths-Jones, Sam, ...
Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for...
Tucker, Nicholas P., D'Autréaux, Benoît, Studholme, David J., Spiro, Stephen, Dixon, Ray
The Escherichia coli nitric oxide sensor NorR was shown to bind to the promoter region of the norVW transcription unit, forming at least two distinct complexes detectable by gel retardation. Three...
InterPro, progress and status in 2005
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...