Deciphering the diversity of small RNAs in plants: the long and short of it (2009)
Schwach, Frank, Moxon, Simon, Moulton, Vincent, Dalmay, Tamas
RNA silencing is a complex and highly conserved regulatory mechanism that is now known to be involved in such diverse processes as development, pathogen control, genome maintenance and response to...
Szittya, Gyorgy, Moxon, Simon, Santos, Dulce M, Jing, Runchun, Fevereiro, Manuel PS, Moulton, Vincent, ...
Abstract Background High-throughput sequencing technology is capable to identify novel short RNAs in plant species. We used Solexa sequencing to find new microRNAs in one of the model legume species,...
A scoring matrix approach to detecting miRNA target sites (2008)
Moxon, Simon, Moulton, Vincent, Kim, Jan T
Abstract Background Experimental identification of microRNA (miRNA) targets is a difficult and time consuming process. As a consequence several computational prediction methods have been devised in...
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...
Moxon, Simon, Jing, Runchun, Szittya, Gyorgy, Schwach, Frank, Rusholme Pilcher, Rachel L., Moulton, Vincent, ...
In plants there are several classes of 21–24-nt short RNAs that regulate gene expression. The most conserved class is the microRNAs (miRNAs), although some miRNAs are found only in specific...
Pfam: clans, web tools and services (2006)
Robert D. Finn, Jaina Mistry, Benjamin Schuster-böckler, Sam Griffiths-jones, Volker Hollich, Timo Lassmann, ...
Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are...
Pfam: clans, web tools and services (2006)
Finn, Robert D., Mistry, Jaina, Schuster-Böckler, Benjamin, Griffiths-Jones, Sam, Hollich, Volker, Lassmann, Timo, ...
Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are...
Rfam: annotating non-coding RNAs in complete genomes (2005)
Griffiths-Jones, Sam, Moxon, Simon, Marshall, Mhairi, Khanna, Ajay, Eddy, Sean R., Bateman, Alex
Rfam is a comprehensive collection of non-coding RNA (ncRNA) families, represented by multiple sequence alignments and profile stochastic context-free grammars. Rfam aims to facilitate the...
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...
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...
Rfam: annotating non-coding RNAs in complete genomes
Griffiths-Jones, Sam, Moxon, Simon, Marshall, Mhairi, Khanna, Ajay, Eddy, Sean R., Bateman, Alex
Rfam is a comprehensive collection of non-coding RNA (ncRNA) families, represented by multiple sequence alignments and profile stochastic context-free grammars. Rfam aims to facilitate the...
Pfam: clans, web tools and services
Finn, Robert D., Mistry, Jaina, Schuster-Böckler, Benjamin, Griffiths-Jones, Sam, Hollich, Volker, Lassmann, Timo, ...
Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are...
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...
Rfam: annotating non-coding RNAs in complete genomes
Griffiths-Jones, Sam, Moxon, Simon, Marshall, Mhairi, Khanna, Ajay, Eddy, Sean R., Bateman, Alex
Rfam is a comprehensive collection of non-coding RNA (ncRNA) families, represented by multiple sequence alignments and profile stochastic context-free grammars. Rfam aims to facilitate the...
Pfam: clans, web tools and services
Finn, Robert D., Mistry, Jaina, Schuster-Böckler, Benjamin, Griffiths-Jones, Sam, Hollich, Volker, Lassmann, Timo, ...
Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are...
High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families
Szittya, Gyorgy, Moxon, Simon, Santos, Dulce M, Jing, Runchun, Fevereiro, Manuel PS, Moulton, Vincent, ...
Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening
Moxon, Simon, Jing, Runchun, Szittya, Gyorgy, Schwach, Frank, Rusholme Pilcher, Rachel L., Moulton, Vincent, ...
In plants there are several classes of 21–24-nt short RNAs that regulate gene expression. The most conserved class is the microRNAs (miRNAs), although some miRNAs are found only in specific...