Rothamsted Research

where knowledge grows

The Applied Bioinformatics (AB) group, established in 2012, is one of Rothamsted's core capabilities. We are an applied group in the sense that we apply computational and bioinformatics methods on challenging biological questions that underpin Rothamsted science. We provide bioinformatics support and training on data intensive research projects and also put a strong emphasis on bioinformatics R&D to develop novel approaches to analyse complex data from crops, insects, pathogens and metagenomes.

AB 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, QTLNetMiner is a web application for searching and ranking candidate genes for traits such as “flowering time” or “drought tolerance”. 

AB 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  (QTLNetMiner, Ondex).
  • Bioinformatics software platforms (Galaxy, Geneious) being used by Rothamsted scientists.

AB group develops tools & resoruces

  • QTLnetMiner QTLNetMiner is a web-based tool for candidate gene discovery in plant and animal genomes using data mining and network-based approaches.
  • Ondex is an open-source framework for the integration and visualisation of biological databases using a labelled & directed multi-graph.

AB 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

Science Team

Group Leader

Keywan Hassani-Pak

Staff

Ambrose Andongabo
David Hughes
Robert King
Ajit Singh
Asier Gonzalez

Open Positions

See below

Past Members

Chris Love
Nathalie Castells
Paul Verrier
Jun Wang
Pierre Carion
Maria Esch