The core bioinformatics group is embedded into the research of the institute. We provide computational support for any area of modern biology, from sequence similarity searches to analysing genome-wide screening and NGS data. As we are integrated in the institute we are able to provide the closest possible collaborations and develop new tools and techniques based on novel discoveries within the institute.

Current research focuses:
• Analysis of NGS data (DNA-Seq, RNA-Seq and ChIP-Seq)
• Extracting biological meaning from genome-wide experiments (screens, microarray, NGS)
• Large scale RNAi screen mapping, annotation and analysis
• Functional prediction through the detection of weak sequence similarities

Experience and skills:
• Analysis of ChIP-Seq data (peak calling and motif detection)
• Analysis of RNA-Seq data (expression profiling)
• Analysis of DNA-Seq data (detection of sequence varients)
• Mapping and identification of BACs through NGS
• Re-mapping of microarray probes to newer version of genome and transcriptome
• Annotation of proteomics mass spectrometry data
• Sequence analysis through inter-species conservation
• Large scale BLAST searches, and subsequent analysis for the detection of orthologs
• Design of shRNAs, siRNAs and esiRNAs
• Large scale domain detection through both sequence conservation and structural conservation
• Functional analysis through distant homology
• Multiple sequence alignments and phylogenetic analysis
• Providing bioinformatics software and tools to users through web interfaces or local installations

Resources:
• HMMerThread Database of remotely conserved domains
• ProFAT (currently being relocated - will be enabled shortly...)
• Xenopus Search tools
• EST databases

Plain English:
Modern molecular biology has become heavily dependent on computers, both to analyse data, and to provide access to external data resources and the means to display them. The core bioinformatics group provides embedded expert support for research scientists to understand these resources better, and to help with the interpretation and use of information and tools. Based on the needs of the institute we work to improve tools and develop new computational methods to aid biological research.

Selected publications:

• Rodriguez R, Miller KM, Forment JV, Bradshaw CR, Nikan M, Britton S, Oelschlaegel T, Xhemalce B, Balasubramanian S, Jackson SP (2012) Small-molecule-induced DNA damage identifies alternative DNA structures in human genes. Nat Chem Biol [in press]

• Harrigan JA, Belotserkovskaya R, Coates J, Dimitrova DS, Polo SE, Bradshaw CR, Fraser P and Jackson SP (2011) Replication stress induces 53BP1-containing OPT domains in G1 cells. J Cell Biol 193(1), 97-108

• Bradshaw CR, Surendranath V, Henschel R, Mueller M and Habermann HH (2011) HMMerThread: Detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition.
PLoS ONE 6(3): e17568

• Collinet C, Stöter M, Bradshaw CR, Samusik N, Rink JC, Kenski D, Habermann B, Buchholz F, Henschel R, Mueller MS, Nagel WE, Fava E, Kalaidzidis Y and Zerial M (2010) Systems survey of endocytosis by multiparametric image analysis.
Nature 464(7286), 243-9

• Erler A, Wegmann S, Elie-Caille C, Bradshaw CR, Maresca M, Seidel R, Habermann B, Muller DJ and Stewart AF (2009) Conformational adaptability of Redbeta during DNA annealing and implications for its structural relationship with Rad52.
J Mol Biol 391(3), 586-98

• Bradshaw CR, Surendranath V and Habermann B (2006) ProFAT: a web-based tool for the functional annotation of protein sequences. BMC Bioinformatics 7, 466