Steve Checkley
Profile
Interdisciplinary scientist turned research software engineer.
Education

PhD Systems Biology

University of Manchester (2011)

B.Sc (hons) Microbiology

Liverpool John Moore's University (2000)

Experience

UKRI - Research Software Engineer

March 2023 - current

  • Development of bioinformatics pipelines using Nextflow.

  • Management of industry commercialisation projects to deliver research software into production.


    • SEDA pds - Associate Principal Scientist

    Nov 2022 - Mar 2023

  • Delivery of literature reviews and non-compartmental analysis for drug pharmacokinetic studies to clients in the pharmaceutical industry.


    • Certara QSP - Research Scientist

    Feb 2020 - Nov 2022

  • I delivered scientific programming support to researchers building quantitative systems pharmacology models for clients in the pharmaceutical industry.

  • Development of models of chronic lymphocytic leukaemia as part of a large immunooncology platform model developed for a pharmaceutical industry consortium.

  • Development of pipelines for parameter optimization and sensitivity analysis of large ordinary differential equation models using R and MATLAB.

  • Implementation of methods for generating virtual patient populations from ordinary differential equation models.

  • Implementation of numerical deconvolution methods for calculating drug absorption.

  • Supporting colleagues with adapting code for parallel computing using MATLAB parallel server.


    • STFC - Data Scientist

    Jun 2017 - Jan 2020

  • I delivered data science consultancy projects working collaboratively with IBM Research and industry clients using high-performance computing clusters.

  • I implemented a bioinformatics pipeline for a large Agrochemicals manufacturer to annotate L1000 genomics data, perform pathway enrichment and output biochemical network visualisation to investigate biomarkers of toxicology. The work was published in a collaborative paper with IBM Research.

  • I implemented a data pipeline using Apache Airflow to collate client data combined with public API’s for application in supply chain logistics.

  • I developed a social media scraping and sentiment analysis pipeline in collaboration with IBM Watson.

  • I developed a clustering pipeline using DBSCAN for investigating fault detection in acoustic engineering.

  • I managed the delivery of machine learning models to a pharmaceutical industry consortium as part of the EU-funded ADDoPT program for improving drug manufacturing processes, and co-authored a paper on the work in the Journal of Pharmaceutical Innovation.


    • Certara Simcyp - Research Scientist

    Sep 2016 - Jun 2017

  • I implemented mathematical models of neutropenia, supporting contract research projects for clients in the pharmaceutical industry.


    • STFC - Research Scientist

    Dec 2015 - Sep 2016

  • Working in collaboration with IBM Research, I was responsible for identifying opportunities to work with industry and academic partners to apply high-performance computing in genomics.


    • AstraZeneca - Senior Scientist

    Mar 2012 - Jun 2015

  • Working primarily in the oncology disease area, I developed quantitative systems pharmacology models in collaboration with experimental scientists, DMPK modellers, and clinical teams.

  • My work was applied to phase 1 clinical trials to enable dose scheduling and drug efficacy prediction for clinicians, and published in Nature Scientific Reports.

  • I contributed to the development of models of the intestinal free mucus pharmacokinetic efficacy relationship for gastrointestinal limited drugs, which was published in the Journal of Drug Metabolism and Pharmacokinetics.

  • I project managed outsourced modelling and simulation projects, coordinating third-party organisations in the US, Russia, and Sweden for oncology and cardiovascular research programs.


    • Unilever - Research Assistant

    Mar 2003 - Sep 2007

  • Microbiology support for home and personal care products.


    • ConvaTec - Research Assistant

    Mar 2001 - Mar 2003

  • QC microbiology screening for wound healing products and environmental monitoring of clean room facilities.


    • Unilever - Research Assistant

    Jun 2000 - Mar 2001

  • Microbiology support for consumer study trials of oral care products.

    • Skills
    • Python
    • R
    • Shiny
    • Flask
    • Matlab
    • Nextflow
    • Copasi
    • ODE based mechanistic modelling
    • Numerical optimization
    • Sensitivity analysis
    • Virtual patient simulation
    • Quantitative systems pharmacology
    • Development of hpc data pipelines
    • Molecular biology
    • Microbiology
    • Drug discovery for oncology
    © 2024 Steve Checkley