Jan Verburg

Genetics and Molecular Medicine (PhD) - 3 Years (Full-time)

Year of study: 3

  • MRC Human Genetics Unit
  • Institute of Genetics and Cancer
  • College of Medicine and Veterinary Medicine

Contact details

PhD supervisor:

Address

Street

Institute of Genetics and Cancer
The University of Edinburgh
Western General Hospital
Crewe Road
Edinburgh
EH4 2XU

City
Edinburgh
Post code
EH4 2XU

Availability

  • Available at office hours: 09:00 - 17:00.

Biography

Background

PhD professional with strong affinity for mechanisms underlying mutational processes in genomic biology. Experience with analysing genomic and genetic data using self-designed frameworks, statistical skills and programming languages such as R, python, perl and UNIX shell scripting. Seeking a role within academia to build on current research and contribute to a deeper understanding of mutagenic processes and their effect on human disease.

Qualifications

  • MSc - Biology of Disease, Bioinformatics profile, Utrecht Universtiy, The Netherlands

    • Bioinformatics profile

    • Major Research Project: ‘Cyclin E overexpression leads to coping with Chk1 inhibition despite increased sensitivity’

    • Minor Research Project: ‘Somatic mutations at regulatory regions cause a decrease in gene expression in murine liver cancer’. ERASMUS+ funded.

    • Writing Assignment (literature review): ‘Beyond MYCN and ALK: therapeutic targets in Neuroblastoma’
  • BSc - Biomedical Sciences, Utrecht University, The Netherlands
    • Dissertation: ‘ATR - CHK1 mediated DNA damage response and drug resistance in cancer’

Responsibilities & affiliations

  • Member of the Genetics Society (UK)
  • Member of IGC Post Graduate Society

Postgraduate teaching

Jan 2023: Teaching assistant at workshop ‘High-dimensional Statistics’, Ed-DaSH, Edinburgh, UK

  • Assisted with teaching four day workshop on high dimensional statistics hosted on ‘The Carpentries’ platform

  • Solved coding issues or errors that participants were having

  • Answered questions by participants on high-dimensional statistical frameworks

 

Nov & June 2022: Teaching assistant at workshop ‘Workflows with Snakemake’, Ed-DaSH, Edinburgh, UK

  • Guided participants throughout three day hands-on workshop on workflow management using Snakemake

  • Teached part of course programme

  • Supported answering questions on workflow management

  • Solved coding issues or errors that participants were having on the fly

  • Contributed with optimising exercises on The Carpentries course platform

Project activity

Current Project (2021 - present)

Apr 2021-present: PhD researcher on MRC funded project, MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh

  • Experienced R programmer with proficiency in python, perl and UNIX shell scripting languages as well as well-versed in common bioinformatics software such as samtools, bedtools, tabix, igv, UCSC LiftOver and Sigprofiler

  • Trained in statistical analyses of biological data, including extensive knowledge on permutation, bootstrapping and simulation of biological processes

  • Developed a novel framework that lends itself to subsequent statistical analyses

  • Detailed record keeping on a web-based collaborative platform

  • Assertive project management

  • Version control with GitLab

  • Participated at extensive statistical workshops on statistical frameworks, including ‘Academy for PhD Training in Statistics’ (APTS) module on ‘Computer Intensive Statistics’ and ‘High-dimensional Statistics’

  • Presented work at regular department wide meetings and collective group meetings

  • Contributed to papers (in progress) and presented research in an international consortium (Edinburgh UK, Cambridge UK, Heidelberg GER and Barcelona ES)

  • Assisted in teaching of workshops on ‘high-dimensional statistics’ and ‘workflow management with Snakemake’

  • Created and presented posters at international conferences

  • Successfully applied for additional funding for additional training and conference attendance

  • Designed computational pipelines using Snakemake

  • Computational environment control with Conda and Mamba

  • Familiar with common biological data sources such as Ensembl, UCSC Genome Browser, ICGC, PCAWG and TCGA

  • Experienced with the interpretation and creation of mutational signatures 

  • Figure creation with Adobe Illustrator

  • Interdisciplinary collaboration with group members

  • Submitted written work within deadlines

Past projects (2018-2021)

Jan 2021 - Apr 2021:  PhD researcher on MRC funded rotation project, MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh

  • Developed a classifier for determining DNA repair deficiency in tumours with Dr Ewing

  • Assembled a combined data set with copy number calls from CNVkit and CLImAT, and structural variant calls from Manta of 244 whole genome sequenced ovarian tumours

  • Workflow management with Snakemake

  • Computational environment with Conda

  • Pipeline execution and development on SGE cluster and jupyter notebooks

  • Created structural variant signatures

  • Interpreted structural variant and single base substitution mutational signatures

  • Designed machine learning models using NMF, SVM and neural network approaches using python scikit-learn to detect and classify DNA repair deficiency in ovarian tumours

  • Assessed machine learning model accuracy and efficiency

Oct 2020 - Dec 2020:  PhD researcher on MRC funded rotation project, MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh

  • Conducted project on secondary protein structures

  • Workflow management with Snakemake

  • Maintained computational environment with Conda

  • Interpretation of protein data bank (PDB) files and variant effect predictors (VEPs)

  • Wrote custom python and R scripts for analysing deep mutational scanning (DMS) data sets

  • Statistical analyses in R

April 2020 – Aug 2020: MSc student on literature review project, Princess Maxima Centre for Paediatric Oncology, Utrecht University

  • Performed systematic literature search

  • Provided overview on current research on neuroblastoma in literature

  • In-depth evaluation of genetic landscape in neuroblastoma

  • Produced new potential targets for treatment of neuroblastoma tumours based on evidence in primary literature sources

Oct 2019 – April 2020: MSc student on ERASMUS+ funded bioinformatics internship, MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh and Utrecht University

  • Internship: ‘Somatic mutations in regulatory regions’, Taylor group, MRC HGU, Institute of Genetics and Cancer, Edinburgh

  • Shell scripting (R, Python, Bash) on LSF and SGE based  high performance computer clusters

  • Devised pipelines using management tool Snakemake

  • Ensured reproducibility by maintaining computational environments using Conda

  • Designed computational analyses

  • Performed unbiased (hypothesis free) screens

  • Executed expression analyses using dimensionality reduction techniques

  • Statistical analyses in R

  • Presented work at international consortium meeting

  • Successfully applied for ERASMUS+ funding for duration of project

Sep 2018 – Aug 2019: MSc student on internship, Utrecht University

  • Internship: ‘Replication stress in cancer’, Regenerative Medicine Utrecht, Utrecht

  • Maintained cell cultures

  • Conducted colony formation assays and quantified results using custom scripts for ImageJ software

  • Identified DNA replication fork speed using DNA fibre spreading assays. Analysed fibres with immunofluorescent DNA staining approaches for confocal microscopy and quantified with ImageJ software

  • Performed quantitative real-time PCR

  • Executed DNA damage analysis with cell line containing tetracycline-repressible construct using confocal microscopy. Quantified results with custom script for imageJ software

  • Designed and performed 72 hour live cell imaging experiments with RPE cell lines containing FUCCI cell cycle reporter construct

  • Wrote custom R script to determine cell cycle checkpoints from live cell imaging data to overcome systematic challenges when using imageJ software plugin TrackMate

  • Statistical analyses in R

Apr 2018 - July 2018: BSc student on project, Utrecht University

  • Maintained cell cultures

  • Performed flow cytometry experiments and analysed data with FlowJo

  • Conducted MTT assays

  • Immunofluorescence assays analysed with confocal microscope and imageJ 

  • Statistical analyses with IBM SPSS

  • Evaluated and interpreted results in bachelor thesis

Nov 2017 – Jan 2018: BSc student on project, Utrecht University

  • Full time research project at research group, UMC Utrecht, NL

  • Designing hypothesis driven experiments

  • Cloning Renilla-Firefly Luciferase constructs

  • Performing bioluminescence assays

  • Interpretation and presentation of results in collaborative meetings

  • Paper writing with intend to publish

  • Presenting results at national conference

Current project grants

MRC Human Genetics Unit doctoral training programme (DTP), UKRI, Institute of Genetics and Cancer, University of Edinburgh

Past project grants

Recipient of ERASMUS+ funding for a six months project at the Martin Taylor Researchgroup, MRC Human Genetics Unit: ' The impact of mutations at transcription factor binding sites and promoters on gene expression in cancer'. (Oct 2019 - April 2020)

Conference details

2024

  • Apr -  Mutations In Time And Space, Edinburgh, UK. Presenter (poster) ‘Embracing indel ambiguity reveals collateral translesion mutagenesis in melanoma skin cancer’

2023

  • Dec - CSHL Genome Informatics, Cold Spring Harbor, USA. Presenter (poster) ‘Accurate comparison of insertion and deletion mutation rates using sequence composition correction with novel sequence ambiguity scoring’

  • Nov - EMBL Cancer Genomics, Heidelberg, GER. Presenter (poster), same as above

2022

  • Apr - Functional Regulatory Genomics and Disease, Genetics Society UK, Edinburgh, UK

  • Feb - Liver Cancer Evolution consortium meeting, Cambridge, UK. Presenter (talk) ‘Insertion and deletion landscape in LCE data’

2021

  • Nov - EMBL Cancer Genomics, Heidelberg, GER

  • May - EACR Bioinformatics In Cancer, Virtual

  • May - Liver Cancer Evolution consortium meeting, Edinburgh, UK

2020

  • Feb - Liver Cancer Evolution consortium meeting, Edinburgh, UK. Presenter (talk) ‘Somatic mutations at regulatory regions cause a decrease in gene expression in murine liver cancer’

2019

  • Nov - A Century Of Genetics, Genetics Society UK, Edinburgh, UK

2018

  • Nov - Student Research Conference 2018, The Hague, NL. Presenter (talk) 'Cytotoxic cells modulate the innate antiviral immune response'

Organiser

June 2023: PhD Retreat, Newcastle, United Kingdom

  • Led the organisation of one-day conference for current PhD students at the Institute of Genetics and Cancer, Edinburgh,UK

  • Designed programme and acted as first point of contact

  • Invited and welcomed guest speakers

  • Budgeted available funds

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