Bioinformatics Support Unit

Staff Profile

Dr Simon Cockell

Senior Lecturer Bioinformatics

Background

Background

My background is in experimental molecular biology, particularly the scaffolding of signal transduction processes. Since leaving the lab to pursue a Bioinformatics career, I have gained an MRes degree in the subject, and spent 15 years in the Bioinformatics Support Unit providing practical support to a wide array of researchers. I led the BSU for 9 years (2011-2020), before being appointed as Senior Lecturer in Bioinformatics in the School of Biomedical, Nutritional and Sports Sciences.

Roles and Responsibilities

Senior Lecturer in Bioinformatics in the School of Biomedical, Nutritional and Sport Sciences.

Director of Research, School of Biomedical, Nutritional and Sport Sciences.

Qualifications

B.Sc. (Hons) - Biochemistry and Genetics - University of Nottingham, 1999
Ph.D. - Genetics - University of Leicester, 2004
M.Res. - Bioinformatics and Computational Biology - University of Leeds, 2005

Research

Research Interests

I have been a professional bioinformatician for more than 15 years, during which time I have contributed to a large number of collaborative projects as a researcher and an investigator. My recent research career has seen me involved as a co-investigator on a number of large multi-omics investigations of complex disease. Many of these projects have used bulk RNA-Seq to characterise pathological states or to stratify disease, and increasingly these studies are looking to use single-cell and spatial transcriptomics to refine the detail of these systems even further.

My research revolves around a small number of central themes, all involving the analysis of biological data:

  • Integration of disparate biological data
  • Molecular characterisation of complex disease
  • High-throughput sequencing analysis, particulatly functional genomics techniques such as RNA-Seq, ChIP-Seq etc

In recent years, I have been involved in a number of large projects connected to one or more of these themes, including the following:

  • Psoriasis Stratification to Optimise Relevant Therapy (PSORT) - MRC, co-Investigator
  • Liver Investigation: Testing Marker Utility in Steatohepatitis (LITMUS) - EU (IMI), co-Investigator
  • Elucidating Pathways of Steatohepatitis (EPoS) - EU (H2020), co-Investigator
  • An in silico based approach to improve the efficacy and precision of drug REPurpOsing TRIALs for a mechanism-based patient cohort with predominant cerebro-cardiovascular phenotypes (REPO-TRIAL) - EU (H2020), co-Investigator
  • Strategic Training Awards for Research Skills - Newcastle University Bioinformatics Skills Schools (NUBASS) - BBSRC, Principal Investigator


Teaching

My teaching responsibilities are:

Module Leadership
  • CSC8309 – Genome Scale Data Analytics
Postgraduate Teaching
  • CSC8325 – An Introduction to Bioinformatics Theory and Practice
  • CSC8326 – Advanced Bioinformatics Theory and Practice
  • MSC8001 – Introduction to Healthcare Science, Professional Practice and Clinical Leadership
Undergraduate Teaching
  • CMB2000 - Essential Skills in Biomedical Research
  • BGM2062 - Advanced Protein Analysis
  • BGM2063 - Approaches to Analysis of Genes and Genomes
  • BMS3025 - Bioinformatics
  • CSC3424 - Bioinformatics
Previous teaching
CSC8313 – Bioinformatics Theory and Practice (2005-2019), MMB8023 – Systems Biology MRes strand (2011 – 2018), GNM8007 – Bioinformatics, Interpretation, Statistics and Data Quality Assurance (2017 – 2018)

Bioinformatics Training
I have prepared and delivered training courses in bioinformatics and programming to life science researchers for many years.

During Coronavirus crisis of 2020 I produced the live-streamed “Lockdown Learning” series. My YouTube channel has >4,000 subscribers and my tutorial videos have >180,000 views.


Publications