Kasia Kedzierska

Kasia Kedzierska

DPhil Candidate in Genomic Medicine and Statistics

Wellcome Trust Centre for Human Genetics

University of Oxford

Hello! đź‘‹

My research interest lies at the intersection of Machine Learning and Biology and Healthcare. The rapid advancements in technology, especially those enabling investigating genomics at single cell resolution, coupled with the progress in Machine Learning, have rendered computational biology an exceptionally captivating and invigorating field of study. Within this space, I’m particularly interested in Multimodal and Generative Models.

For my PhD at the University of Oxford I studied the cancer of the uterus and the role chromatin organisation plays in its initiation and progression. During my studies I interned at Novo Nordisk Research Centre in Oxford where I worked with NLP and knowledge graphs to identify potential new drug candidates.

Recently, I joined Microsoft Research New England as an intern where I am mentored by Alex Lu, Ava Amini, and Lorin Crawford. During the course of the internship I am working with Foundation Models in Computational Biology.

If you find anything on this website interesting or just fancy a chat about the intersection of biology, healthcare and Machine Learning be sure to reach out!

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, Generative Models
  • Single cell genomics
  • Cancer, Tumor heterogeneity
  • PhD in Genomic Medicine and Statistics, in progress

    University of Oxford

  • MSc in Biotechnology, 2018

    Warsaw University of Technology

Recent Publications

The full list of publications is available on Google Scholar or here.
Functional analysis reveals driver cooperativity and novel mechanisms in endometrial carcinogenesis
The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability
We found no evidence that rs1800734 or other MLH1 SNPs were associated with the risk of MSI EC. We found the rs1800734 risk allele had no effect on MLH1 methylation or expression in ECs. We propose that MLH1 hypermethylation occurs by different mechanisms in CRC and EC.
The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability

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


Microsoft Research New England
Intern @ BioML
May 2023 – Present Cambirdge, MA, US
I’m working on Foundation Models in Computational Biology and I am privileged to be mentored by Alex Lu, Ava Amini and Lorin Crawford.
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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