Kasia Kedzierska

Kasia Kedzierska

DPhil Candidate in Genomic Medicine and Statistics

Wellcome Trust Centre for Human Genetics

University of Oxford

About me

My name is Kasia* Kedzierska; I am a computational biologist and I use Data Science and Machine Learning to answer biological questions.

For my PhD, I’m looking at the cancer of the uterus, and I’m trying to understand what role chromatin organisation plays in its initiation and progression. Here, you can read more about my DPhil (Oxford speak for PhD) project. In 2021, I took a break from my research and joined Computational Biology Department at Novo Nordisk Research Centre in Oxford as an intern, where I worked with NLP methods and knowledge graphs. Since returning to my studies, I’ve been working on adapting what I learned during the internship and building ML models of cancer evolution.

I like data viz, and I believe that a good figure can help convey the message but a whereas one can confuse a reader. In my free time, I look at variou s data trying to make sense of it. I describe some of my projects, for example exploring COVID-19 mortality figures, in the posts on this website.

I’m a founder, and for a while, I was the President of the NGSchool Society - an organisation that aims to promote and support science with an emphasis on bioinformatics. We focus our efforts on bridging the gap between Western and Eastern Europe in the area of R&D. Each year, NGSchool organises cutting-edge affordable training in computational biology. To learn more about it check out NGSchool website.

Before coming to Oxford, I worked as a research assistant in the Ratan group at the University of Virginia and the Zebrafish Developmental Genomics group at the International Institute of Molecular and Cell Biology in Warsaw. I studied for BScEng and MSc in Biotechnology at the Warsaw University of Technology in Poland.

*Actually, my full name is Katarzyna Kedzierska, or Katarzyna Zofia Kedzierska (including my middle name). In Polish, we usually have a shorter version of a name that we go by and reserve the full legal name (here: Katarzyna) for official occasions, or when we get in trouble with our parents. Here you can find recordings on how to pronounce my shorter name: Kasia or longer: Katarzyna.

  • Machine Learning
  • Tumor heterogeneity
  • Cancer genomics
  • Epigenetics
  • PhD in Genomic Medicine and Statistics, in progress

    University of Oxford

  • MSc in Biotechnology, 2018

    Warsaw University of Technology

  • BScEng in Biotechnology, 2014

    Warsaw University of Technology

Recent Publications

The full list of publications is available on Google Scholar or here.

Talks and tutorials

Unsupervised learning
Lecture and tutorial prepared and taught jointly by me and Kaspar Märtens at the NGSchool2022 in September 2022 in Jablonna, Poland.
Unsupervised learning
Data visualization in bioinformatics
I mentored hackathon during NGSprint where during the first part I taught data visualisation principles (with focus on use cases in computational biology) and introduction to interactivity with plotly and R Shiny. In the second part, participants applied their knowledge to visaulise the TCGA LGG data set.
Data visualization in bioinformatics


Wellcome Centre for Human Genetics
PhD student @ University of Oxford
Oct 2018 – Present Oxford, UK
  • PhD project: Functional and evolutionary characterisation of chromatin organisation in endometrial cancer
  • Together with Andrew Kwok, we are running Old Road Dhil Journal Club - computational biology and genomics JC.
Computational Biology Department
Intern @ Novo Nordisk Research Centre in Oxford
Aug 2021 – Nov 2021 Oxford, UK
I worked with NLP based methods to screen biomedical articles to identify potential therapeutic targets. I built classifiers to further improve the performance of in-house pipelines, analyse the results and create visualisations to communicate the results to broader audience.
Ratan Group
Visiting Graduate Student @ University of Virginia
Jul 2017 – Aug 2018 Charlottesville, Virginia, USA
  • Conducted research towards Master’s thesis titled: “Analysis of the mutational burden across gene sets in cancer” defended in September 2018 at the Warsaw University of Technology
  • Developed SONiCS - a tool for genotyping short tandem repeats (STRs) profiled using capture assays, SONiCS on GitHub
  • Before I joined Aakrosh Ratan’s group, I worked on epigenetic regulation in prostate cancer in Pemberton group, also at UVa. By joining Ratan’s group I fully transitioned from experimental to computational biology.
Laboratory of Zebrafish Developmental Genomics
Research Assistant @ International Institute of Molecular and Cell Biology
Jul 2015 – Jun 2016 Warsaw, Poland
Project: Elucidating gene regulatory network of zebrafish heart development using genomics. My initial contribution was towards genotyping mutants, harvesting tissues and library preparations for RNA-seq and ATAC-seq. Later, I became more involved in designing the experiments and improving the protocols. For example, I proposed HRMA as more efficient and straightforward method for genotyping zebrafish mutants. I was responsible for both, the computational and experimental aspects of the project. The manuscript entitled “Dynamics Of Cardiomyocyte Transcriptome And Chromatin Landscape Demarcates Key Events Of Heart Development” has been published in Genome Research.


  • Roosevelt Drive, Oxford, Oxfordshire, OX3 7BN
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