Computational Biology Support
The Computational Biology Support team (CBS) provides bioinformatics support and collaborative data analysis solutions to researchers across the CRUK Manchester Institute. Our core activities reside at the interface between biology, computer science and statistics, particularly in the application of high-throughput omics technologies. The primary goal of the CBS team is to build and maintain an infrastructure that enables the application of advanced bioinformatics analysis to cutting-edge scientific research within CRUK MI.
A major aspect of our work has been to develop pipelines and computational approaches for analysing high-throughput datasets generated from next generation sequencing (NGS) and mass-spectrometry platforms. Most of the workflows that we developed utilise a combination of open-source and custom-built software tools running on the on-site high performance computing facility provided by the Scientific Computing team. Working closely with the SciCom team, we are currently building automated pipelines to handle routine tasks associated with the pre-processing of deep sequencing dataset, freeing valuable time for the more challenging downstream analysis and results interpretation.
We offer data analysis support to a wide range of NGS and proteomics applications, including RNA-seq, ChIP-seq, small RNA-seq, whole genome sequencing, whole exome sequencing, targeted re-sequencing, genome-wide CRISPR/Cas9 knockout screen, protein identification and label-free quantitative proteomics. In addition to these, we also provide custom support to tasks such as re-analysis of published or public domain data (e.g. TCGA), data submission to public data repositories, generating preliminary results for grant writing.
We encourage users interested in using our service to get in touch and discuss their requirements with us in advance. This allows us to assist in the design of experiments and provide the most effective data analysis solution for the project.
Since its inception in 2015, the CBS team has contributed to a number of publications in a broad range of journals:
Carter L, Rothwell DG, Mesquita B, Smowton C, Leong HS…Miller C, Hughes A, Blackhall F, Dive C, Brady G. (2017)
Molecular analysis of circulating tumor cells identifies distinct copy-number profiles in patients with chemosensitive and chemorefractory small-cell lung cancer.
Nature Medicine 23(1):114-119. PubMed abstract
Tape CJ, Ling S, Dimitriadi M, McMahon KM, Worboys JD, Leong HS, Norrie IC, Miller CJ, Poulogiannis G, Lauffenburger DA, Jørgensen C. (2016)
Oncogenic KRAS regulates tumor cell signaling via stromal reciprocation.
Cell 165(4) 910-920. PubMed abstract
Williamson S, Metcalf R, Trapani F, Mohan S, Antonello J, Abbott B, Leong HS, Chester C , Simms N, Polanski R, Nonaka D, Priest L, Fusi A, Carlsson F, Carlsson A, Hendrix M, Seftor R, Mrs. Elisabeth Seftor, Rothwell D, Hughes A, Hicks J, Miller C, Kuhn P, Brady G, Simpson K, Blackhall F, Dive C. (2016)
Vasculogenic Mimicry in Small Cell Lung Cancer.
Nature Communication 7:13322. PubMed abstract
Draper J, Sroczynska P, Tsoulaki O, Leong HS, Fadlullah MZH, Miller C, Kouskoff V, Lacaud G. (2016)
RUNX1B expression is highly heterogeneous and distinguishes megakaryocytic and erythroid lineage fate in adult mouse hematopoiesis.
Plos Genetics 12(1):e1005814. PubMed abstract
Somerville TD, Wiseman DH, Spencer GJ, Huang X, Lynch JT, Leong HS, Williams EL, Cheesman E, Somervaille TC. (2015)
Frequent derepression of the mesenchymal transcription factor gene FOXC1 in acute myeloid leukaemia. Cancer Cell 14:329-342. PubMed abstract
Rothwell DG, Smith N, Morris D, Leong HS, Li Y, Hollebecque A, Ayub M, Carter L, Antonello J, Franklin L, Miller C, Blackhall F, Dive C, Brady G. (2016)
Genetic profiling of tumours using both circulating free DNA and circulating tumour cells isolated from the same preserved whole blood sample.
Molecular Oncology 10(4):566-74. PubMed abstract
- Head of Computational Biology Support Team
- Computational Biologist/Genomics analyst
- Computational Biologist/Genomics analyst/Prostate cancer support