Expert Bioinformatics Consultant

I bring 20 years of experience in answering biological questions using bioinformatics in both corporate and academia. I apply my energy and experience to turn your research question into actionable tasks, publication ready figures, and reproducible code.

I’m very knowledgeable about cancer biology and oncology, and passionate about biology in general.

Bespoke analysis at extremely competetitive prices!

survivalgraphspgc1 — High expression of glutamine metabolism genes is associated with reduced survival in all patients (all subtypes, left) and ERBB2-enriched patients (right).

exampleheatmap — This heatmap shows some of the differentially expressed genes between WT and KO (left and right, respectively). The blue/red column shows the magnitude of changes in expression (down and up, respectively). The light brown column shows p-value (lighter is more significant).

examplevolcanoplot — This volcano shows the differece in expression of genes between WT and KO. Genes donwregulated and upregulated in KO are to the right and left respectively. The horizontal axix shows fold change, while the vertical axis shows logged p-value

examplegoscatterplot — Functional enrichment of gense upregulated in KO animals.

exampletcgaplot — This shows the distribution of PDK1 in TCGA breast cancer data, where we can see the expression is different in the different cancer types.

glioblastomafunction — Functional enrichment of genes up- and down- regulated by a candidate modulator of cancer (left & right). We can see this modulator seems related to migration.

About Me

I love using computational tools to solve biological problems and questions.

Demonstrated success in research, software development, and collaborations to identify clinically meaningful insights.

I have experience in both academic and corporate positions as a bioinformatician, and an academic publication history. I’m an expert in creating pipelines and processing data using multiple programming languages (R, Python, MATLAB, PERL, UNIX shell) while complying with regulations for sensitive patient data and creating documented, reproducible code.

I’m an expert at cloud computing (AWS) and using High-Performance Computing (HPC) clusters. Proficient in creating complex pipelines using workflow managers like WDL, Nextflow, luigi.

In my time at McGill University, I discovered that I don’t like being a Group Leader, but I love helping solve interesting biological questions in a research environment.

In my corporate role, I was responsible for developing genomic pipelines using Python/R, AWS cloud, and Docker. This development was done coordinating with biologists, medical scientists and bioinformaticians on multiple levels, so I am well versed with presenting my work to people from different fields.

In addition to the previously mentioned skills, I mentored junior bioinformaticians in both corporate and academic environments, something I greatly enjoyed.

Biological Data Types: DNAseq, copy number estimation, RNA expression (RNAseq, transcriptomics), single cell RNAseq analysis (scRNA), metabolomics
Programming languages: Python, R, Perl, MATLAB, Linux/Bash
Tools: Amazon Web Services (AWS), workflow languages (WDL, Nextflow), Bitbucket/git version control, containerization (Docker), HPC, Design Control in software development (Codebeamer)
Regulatory: IEC 62304 (Medical device software Life Cycle processes).
Data Analytics: Multi-omics exploratory data analysis and integration, machine learning, graphical models, statistics
Communication: Cross-disciplinary collaboration with biologists, bioinformaticians, and clinicians

What Services I'm Providing

Bioinformatics analysis, at multiple levels

Dataset analysis

Going from raw data (raw reads in FASTQ files) to identifying mutations (DNA-seq), differentially expressed genes and pathways (RNA-seq/proteomics). Figures and methodogy provided.

Interpertation of gene lists

What do the results mean functionally and biologically? Are they linked to a pathway or transcription factors? Gene network construction and machine learning to dive into your data. Literature review and comparison to published datasets.

Software/pipeline development

If you’ve got a piece of software written by someone (who’s left the lab), I’d be happy to modernize and update it for you. Pipeline construction from scratch in Nextflow to fit your cloud or HPC environment.