Rothamsted Research

where knowledge grows

The Bioinformatics group, established in 2012, is one of Rothamsted's core capabilities providing support and undertaking R&D. We support bioinformatics users to access and use a range of state-of-the-art Bioinformatics platforms and systems. We collaborate and apply computational and bioinformatics approaches to help tackle challenging biological questions. Our research focuses on the development of novel approaches for knowledge discovery, data mining and candidate gene prioritization to bridge the genotype to phenotype gap.  

Bioinformatics group collaborates

  • to manage, process and analyse the Next Generation Sequencing data using state-of-the-art bioinformatics tools and technologies. 
  • to find value in complex biological data. We have worked on projects aiming to identify differentially expressed genes, co-expressed genes, copy number variations and significant SNPs in genome re-sequencing projects, etc. 
  • to integrate data from ‘omics experiments with information hidden in various public databases. We can also help build networks to visualise and explore complex interactions and quantitative datasets using free tools like Ondex (www.ondex.org). 
  • to build web applications and public resources for different communities. For example, KnetMiner is a web application for searching and ranking candidate genes for traits such as “flowering time” or “drought tolerance”. 

Bioinformatics group provides training

  • Data management solutions for next generation sequencing (NGS) data and phenotypic trait information from field experiments.
  • Primary analysis of high-throughput NGS data including de novo transcriptome assemblies, re-sequencing projects, expression analysis (RNA-seq) and metagenomics.
  • Integration and exploration of large biological datasets to facilitate the systematic discovery of candidate genes  (KnetMiner, Ondex).
  • Bioinformatics software platforms (Galaxy, Geneious) being used by Rothamsted scientists.

Bioinformatics group develops tools & resources

  • KnetMiner is a suite of tools and resources to help scientists with the biological interpretation of RNA-seq, QTL and GWAS outputs. We provide KnetMiner web servers for several crop, pathogen and animal species. 
  • Ondex is an open-source framework for the integration and visualisation of biological databases using a labelled & directed multi-graph.

Bioinformatics group supports bioinformatics platforms

  • Galaxy is an open, web-based platform for data intensive biological research. Our own in-house Galaxy instance can be used to perform, reproduce, and share complete analyses.
  • Geneious is a DNA, RNA and protein sequence alignment, assembly and analysis software platform, integrating bioinformatics and molecular biology tools into a simple interface.
  • DeCypher© biocomputing systems accelerate sequence comparison by combining optimized bioinformatics applications with powerful FPGA-based accelerator cards. A single DeCypher server can provide the performance equivalent of hundreds of CPU cores.

Selected Papers

Bioinformatics Training

We provide Bioinformatics training on a range of topics.

Team

Grant-funded Team

  • Marco Brandizi

Students

  • Monika Mistry
  • Lisa Lill

Past Members

  • Nathalie Castells
  • Pierre Carion
  • Maria Esch