Consultancy

As an experienced bioinformatician and data scientist, I offer consultancy services across a range of bioinformatics and data analytics projects, with a particular focus on cancer genomics, high-throughput sequencing, and healthcare data analytics. My expertise spans the entire data analysis pipeline, from experimental planning to data interpretation, ensuring comprehensive support tailored to your research needs.

Consultancy services are available in the following areas:

1. RNA Sequencing (RNAseq) Analysis

I offer expertise in both bulk and single-cell RNA sequencing projects, providing end-to-end support that covers:

• Experimental Design: Assistance with choosing between bulk vs. single-cell RNAseq, and conducting power analysis to ensure optimal experimental setup.
• Sample Processing & Sequencing: Guidance on sample processing, sequencing submission, and setup to maximize data quality.
• Data Quality Control (QC): Thorough QC checks to ensure data integrity and reliability.
• Data Processing: Alignment, quantification, and analysis of RNAseq data using cutting-edge tools.
• Differential Expression Analysis: Identifying differentially expressed genes across conditions and samples.
• Gene Set Enrichment Analysis: Functional interpretation of RNAseq data through pathway and gene set enrichment analysis.
• Unsupervised Clustering & Data Visualization: Extracting patterns and insights from complex datasets.
• Data Interpretation & Reporting: Detailed reports to help you draw meaningful biological insights from your data.
• Data Upload & Sharing: Assistance with preparing data for sharing and open access repositories to support transparent and reproducible research.

2. Whole Genome/Whole Exome Sequencing (WGS/WXS) and Variant Calling

I provide comprehensive consultancy services for projects requiring whole-genome or whole-exome sequencing, offering support in:

• Experimental Planning: Advising on sequencing depth, sample pairing strategies, and the choice between short-read and long-read technologies.
• Sample Processing & Sequencing: Guidance on sample preparation and sequencing submission protocols.
• Data QC & Pre-processing: Ensuring high-quality data with rigorous quality checks and processing steps.
• Variant Calling: Detection of single nucleotide variants (SNVs), insertions/deletions (indels), and structural variants.
• Variant Effect Prediction: Interpreting the functional impact of genetic variants using state-of-the-art tools and databases.
• Mutational Signature Analysis: Characterizing mutational processes active in your dataset.
• Driver Gene Identification: Identifying key driver mutations relevant to disease or phenotype.
• Data Interpretation: Integrating results into a biological context, helping you uncover meaningful insights.
• Data Management & Sharing: Preparing data for upload to relevant repositories, ensuring compliance with data sharing standards.

3. Machine Learning and Predictive Analytics in Healthcare

With a strong background in healthcare analytics and data science, I offer consultation in:

• Supervised and Unsupervised Machine Learning: Building predictive models for healthcare datasets, including patient stratification, outcome prediction, and biomarker discovery.
• Text Mining and Natural Language Processing (NLP): Extraction of insights from clinical notes and unstructured healthcare data.
• Predictive Modelling: Developing models for risk factor identification and outcome prediction in various healthcare settings.
• Data Integration: Combining multi-omics datasets with clinical data to identify potential biomarkers and predictors of disease.
• Data Visualization & Interpretation: Creating clear, actionable visualizations to communicate complex findings.

4. Bioinformatics Pipeline Development

Leveraging my extensive experience in high-performance computing (HPC) and pipeline development, I offer services in:

• Workflow Development: Building custom bioinformatics workflows for processing next-generation sequencing data.
• High-Performance Computing (HPC) Support: Assistance with optimizing computational workflows for HPC environments.
• Automated Data Processing: Developing scripts and pipelines for data automation and analysis.

Professional Experience and Credentials

With a strong interdisciplinary background in cancer bioinformatics, data analytics, and machine learning, my consultancy work is informed by:

• Extensive Academic Experience: Positions as Senior Lecturer in Data Science and Analytics at Sheffield Hallam University and an Honorary Senior Lectureship in Bioinformatics at the University of Sheffield.
• Research Leadership: Active involvement in high-impact projects such as the Genomics England 100,000 Genomes Project, the GUSTO phase II clinical trial, and collaborative research on cancer genomics.
• Advance HE Fellowship (FHEA): Recognizing my commitment to professionalism in learning and teaching in higher education.
• Certified Carpentries Instructor: Trained to teach foundational coding and data science skills.

Confidentiality and Data Security

I am experienced in handling sensitive and confidential data across both academic and commercial projects. All discussions, documents, and data are treated with the utmost confidentiality and securely stored on password-protected, dedicated filestores.

Get in Touch

I welcome inquiries from researchers, clinicians, and organizations seeking bioinformatics or data science support. Please contact me to discuss your project, specific needs, or for more information on rates and availability.

• Email: l.quayle@shu.ac.uk or drlquayle@gmail.com
• Website: www.lewisdoesdata.com
• LinkedIn: linkedin.com/in/lewis-quayle
• ResearchGate: researchgate.net/profile/Lewis-Quayle
• GitHub: github.com/lquayle88