DPhil candidate in Genomic Medicine and Statistics

University of Oxford, Wellcome Trust Centre for Human Genetics

About me

I’m a PhD student in Genomic Medicine and Statistics at the Wellcome Centre for Human Genetics, University of Oxford in the Church and Wedge groups. Currently, I joined Computational Biology Department at Novo Nordisk Research Centre in Oxford as an intern, where I am working with NLP methods and knowledge graphs.

I’m interested in tumor heterogeneity, cancer genomics and epigenetics. You can read more about my DPhil project here. Briefly, I am investigating the role of chromatin organisation in endometrial cancer. In my research I rely heavily on statistical machine learning.

I like data viz and I believe that a good figure can help convey the message but a bad one can confuse a reader. In my free time I tend to look at various data trying to make sense of it. I describe some of my projects, for example exploration of COVID-19 mortlity figures, in the posts on this website. I recently became interested in the generative art, I write about my experiences with it in generative aRt.

I strongly believe that in order to advance science we have to constantly learn from each other, share our knowledge, findings and discuss and test our assumptions. I am the President of the #NGSchool Society. We are a group of computational biologists based all over Europe and beyond - our aim is promote and support science, with emphasis on bioinformatics. We focus our efforts on bridging the gap between Western and Eastern Europe in the area of R&D. Each year, we organise cutting-edge affordable training in computational biology. I am extremely proud of the efforts of our team of volunteers, especially during the 18 long months of pandemic. Despite the difficulties and uncertainties of life in the pandemic we manage to organise online tutorials (in topics such as Python, R, version control, reproducibility and many more), conference and a hackathon. Next year, fingers crossed, we are planning to organise a summer school and a conference in person. You can find more about our projects here or on our website.

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

Interests
  • Tumor heterogeneity
  • Cancer genomics
  • Epigenetics
  • Machine Learning
Education
  • 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

Projects

You can read about my recent projects below. Those include my past work and DPhil project, as well as my volunteer work and hobbies.

My Generative aRt

My Generative aRt

I got interested in creating generative aRt. Generative art - according to Wikipedia it’s the art that is in part, or in whole, created with the use of an autonomous system.

Chromatin organisation in the context of tumor evolution in endometrial cancer

Chromatin organisation in the context of tumor evolution in endometrial cancer

I seek to understand the chromatin organisation in endometrial cancer. My goal is to link the genetic (changes in DNA sequence) perturbations to epigenetic (changes other than DNA sequence) modifications. For one, I want to understand how mutations in the SWI/Snf complex influence chromatin structure in uterine cancer and how they link to disease progression.

SONiCS

SONiCS

Stutter mONte Carlo Simulation - SONiCS in short, is an algorithm design to determine the genotype of a Short Tandem Repeats (STR) given a noisy input. It performs dense forward simulations of the PCR of STR from capture experiments and dermines the most probable genotype.

NGSchool Society

NGSchool Society

NGSchool Society was established to support science, with emphasis on computational biology and strengthening the bioinformatics community. We organise in-person and virtual training events, conferences and much more.

Recent Publications

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Experience

 
 
 
 
 
Intern
Aug 2021 – Nov 2021 Oxford, UK
I am working with NLP based methods to screen biomedical articles to identify potential therapeutic targets. I build classifiers to further improve the performance of in-house pipelines, analyse the results and create visualisations to communicate the results to broader audience.
 
 
 
 
 
PhD student
Oct 2018 – Oct 2022 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.
 
 
 
 
 
Visiting Graduate Student
Jul 2017 – Aug 2018 Charlottesville, VA, 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
 
 
 
 
 
Visiting Graduate Student
Jul 2016 – Jun 2017 Charlottesville, VA, USA
Project: Epigenetic regulation in prostate cancer. Working with Pten-null mice as a model for prostate cancer and various genomic methods such as RNA-seq, ATAC-seq, and ChIP-seq for histone modifications allowed for investigation of the molecular mechanisms of tumor formation. For example, by analyzing co-binding patterns of crucial transcription factors, we were able to confirm that AP1 potentiates chromatin accessibility for AR, thus allowing for increased expression of AR-dependant genes. A similar conclusion can be drawn for Sox-AR pair based on our preliminary results.
 
 
 
 
 
Research Assistant
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.

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