Expertise

The BSU has expertise in the following areas, and software packages:

High-Throughput Sequence Analysis
  • BWA, Bowtie and other aligners for all NGS platforms and applications
  • Mira, Velvet and SPAdes for de novo assembly, including HGAP for PacBio data
  • Tophat, Cufflinks, DESeq and Trinity (among others) for RNA-Seq analysis, including single-cell expression analysis with Monocle
  • GATK, VarScan and MuTect for variant calling
  • MACS, SISSRs and other peak callers for ChIP-Seq analysis
  • Bismark for bisulphite sequencing
  • Kraken and QIIME for metagenomics sequence classification
Microarray Analysis
  • Experience with data from all major array platforms (Affymetrix, Illumina, Nimblegen & Agilent)
  • Varying data types, including expression, methylation (450K), MEDIP-ChIP, and tiling arrays
  • GeneSpring GX
  • BioConductor/R
Proteomics Analysis
  • Bioinformatic screening for potential protein-protein interactions
  • Analysis of SILAC data using MaxQuant
  • 2D-GE analysis
Further Expertise
  • Remote homology and domain detection using HMMs
  • Database design
  • Custom pipeline creation
  • Custom software engineering

As well as these analysis services, we also provide training courses and bespoke 1-to-1 training for researchers and industry. We provide an introduction to Linux/Next-Generation Sequencing course at least annually (currently this course runs approximately every nine months). We also run a Bioconductor course in conjunction with Colin Gillespie. More courses will be added to our portfolio in the coming year. Full details available on the “Courses” page of this site.

To contact a member of the BSU directly, please contact Dr Simon Cockell (Unit Head), or see the individual staff pages, listed below.

Unit Staff
  • Simon Cockell, Unit Manager
  • Robert Stones, BSU Experimental Scientific Officer (ESO)
  • John Casement, BSU analyst
  • Ben Allen, Systems Analyst
  • Sirintra Nakjang, ESO (NICR)
  • Graham Smith, ESO (ICM)
  • Jannetta Steyn, ESO (IGM)
  • Andrew Skelton, Musculoskeletal Research Group analyst

The Bioinformatics Support Unit is one of a number of facilities available for research and commercial use at Newcastle University. A full list of University Research Facilities can be found on the Services for Business web pages.