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Last updated on 2024-06-16.

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David Zhang

Bioinformatics software engineer with experience operating across the entire software development lifecycle. Skilled in prototyping and benchmarking innovative solutions, as well as implementing, testing, and integrating software into production-ready pipelines.

Work Experience

Senior bioinformatics engineer

CoSyne Therapeutics

London, UK (hybrid)

Present - 2024

Senior bioinformatics software engineer

Congenica

Hinxton, UK (hybrid)

2024 - 2022

  • Goal: Developing, benchmarking and productionising bioinformatic pipelines for the precision oncology product.
  • Engineering nextflow and snakemake pipelines that perform alignment, variant calling, driver annotation and therapy matching using solid tumour sequencing data.

Bioinformatician internship (2 months)

Verge Genomics

London, UK (remote)

2021

  • Goal: Set up an aberrant splicing detection pipeline for drug target discovery in C9orf72 ALS patients.
  • Used docker to setup a reproducible workflow for running aberrant splicing analyses on an AWS instance.

Research Technician

University College London

London, UK

2017 - 2016

  • Goal: Investigate the impact of genetic variation on the age of onset of dementia and cognition within Down syndrome patients.

Education

PhD, Bioinformatics

University College London

London, UK

2022 - 2017

  • Thesis: Using transcriptomics to improve the genetic diagnosis rate of rare disease patients.
  • Developed and released software that facilitate transcriptomic analyses with a focus on diagnostics.

MSc, Neuroscience

University College London

London, UK

2016 - 2015

  • Thesis: The role of mitochondrial dysfunction in Xerodoma pigmentosum
  • Grade: Merit (68%)
  • Awarded post-graduate support scheme bursary (£10,000)

BSc, Biomedical science

University College London

London, UK

2015 - 2012

  • Thesis: Investigating the function of CYFIP1 in the development of rat hippocampal neurons.
  • Grade: 2:1 (69%)

H.S.

Queen Elizabeth’s School

Barnet, UK

2012 - 2007

  • Grades: Maths (A*), Biology (A*), Chemistry (A*), Sociology (A).

Software & programming

Portfolio website

N/A

N/A

Present - 2022

  • My website is built using Django/Bootstrap 5, deployed with Heroku and showcases the five projects I’m most fond of.

Rust packages

N/A

N/A

2024

  • tuni: Unify transcripts across different samples. Author.

Python packages

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N/A

2023 - 2021

  • codino converts a codon design to the expected amino acid frequencies, and vice versa. Author.
  • autogroceries: Use Selenium to automate your grocery shop. Author.
  • stravaboard: A dashboard for flexibly displaying and tracking Strava runs built using Streamlit. Author.

R packages

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2022 - 2020

  • ggtranscript: Visualising transcript structure and annotation using ggplot2. Author.
  • megadepth: BigWig and BAM related utilities. An R wrapper for the megadepth software developed by Chris Wilks. Co-author.
  • dasper: Detection of aberrant splicing events in RNA-sequencing. Author,

Data science blog

N/A

N/A

2021

  • Chess-related blog post was selected for the hand-on-tutorials column in Towards Data Science, which displays pieces that highlight best practices of data science.
  • Applied popular data science packages in python to analyse chess.com data.

Selected Publications

A complete list of publications is available via Google Scholar

ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2

Bioinformatics

N/A

2022

Developmental Consequences of Defective ATG7-Mediated Autophagy in Humans

The New England Journal of Medicine

N/A

2021

  • Collier J, Guissart C, Oláhová M, Sasorith S, Piron-Prunier F, Suom Fi, Zhang D, Martinez-Lopez N, Leboucq N, Bahr A, Azzarello-Burri S, Reich S, Schöls L, Polvikoski TM, Meyer P, Larrieu L, Schaefer AM, Alsaif HS, Alyamani S, Zuchner S, Barbosa IA, Deshpande C, Pyle A, Rauch A, Synofzik M, Alkuraya FS, Rivier F, Ryten M, McFarland R, Delahodde A, McWilliams TG, Koenig M, and Taylor RW.
  • Role: Co-first author
  • DOI: https://doi.org/10.1093/bioinformatics/btac409

Megadepth: efficient coverage quantification for BigWigs and BAMs

Bioinformatics

N/A

2021

Incomplete annotation of disease-associated genes is limiting our understanding of Mendelian and complex neurogenetic disorders.

Science advances

N/A

2020

  • Zhang D, Guelfi S, Ruiz SG, Costa B, Reynolds RH, D’Sa K, Liu W, Courtin T, Peterson A, Jaffe AE, Hardy J, Botia JA, Collado-Torres L and Ryten M.
  • Role: First Author.
  • DOI: https://doi.org/10.1126/sciadv.aay8299