John Vivian

Principal Research Scientist / Bioinformatician

I currently hold the position of Principal Research Scientist at Ideaya Biosciences, focusing on bioinformatics in the cancer therapeutic space. My primary responsibility revolves around MTAP-deleted synthetic lethality, internal bioinformatics infrastructure, and analysis. I am hoping to advance our team's statistical modeling, drawing on my background in Bayesian inference and interest in neural networks,

Senior Bioinformatics Scientist

Building bioinformatics pipelines to visualize flow cytometry data for customers on a personalized dashboards. Frontend/backend, database, software development, algorithmic refinement, data visualization, research, and statistical analysis.

Senior Bioinformatics Scientist

Applying computational expertise to generate insights into the immune responses of oncology patients from one of the world’s largest database of precise, comprehensive antibody and T cell receptor repertoires. Performing analyses on hundreds of millions of antibody sequences, writing scalable bioinformatics pipelines in Python/Nextflow, and developing methods for assays.

Bioinformatics Scientist II

Bioinformatics Scientist I

Graduate Student Researcher

Worked for the Computational Genomics Lab with a focus on distributed computing for large-scale genomics projects and applications. Developed a series of analysis pipelines with emphases on portability, reproducibility, efficiency, and scalability.

Summer Workshop Teacher

Created and taught a week-long bioinformatics bootcamp to undergraduates from around the country. Taught the basics of Git, cloud computing, shell, Python, notebooks, visualization, and gave lectures on evolution, mutation, and next generation sequencing. Materials.

Teacher's Assistant

Python Programming for Biologists (BME-160). I taught six hours of section a week, held office hours, and graded homework.

Graduate Student Researcher

Ran and analyzed single-molecule biological nanopore experiments for determining the effectiveness of improving accuracy by “rereading.” Created a hidden markov model to detect differences in methylation state and quantified improved accuracy by rereading.

Junior Specialist

Ran and analyzed single-molecule biological nanopore experiments for distinguishing epigenetic modifications on cytosine. Created scientific figures and videos for publications. Designed and modeled prototype nanopore device in AutoCAD.

University of California Santa Cruz

Bioinformatics

Univeristy of California Santa Cruz

Biomolecular Engineering & Bioinformatics

Dynamic Factor Model Dashboard

A dashboard for visualizing and analyzing Dynamic Factor Models allowing researchers and policy makers to evaluate and compare (for example) pandemic dynamics across time and geography.

Scalable & Efficient Workflow Engine

A scalable, efficient, cross-platform pipeline management system written entirely in Python and designed around the principles of functional programming.

RNA-Seq Quantification

A scalable and modular RNA-seq quantification workflow. Used to process over 20,000 samples on 32,000 cores.

Gene Expression Outlier Detection

A Bayesian model for identifying gene expression outliers for individual single samples (N-of-1) when compared to a cohort of background datasets.

FASTQ Pairing

Very fast FASTQ pairing algorithms written in Rust. Used to correct improperly paired FASTQ files.