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Kasia Kedzierska
For my PhD @ University of Oxford, I studied cancer of the uterus and chromatin organisation in disease progression. Over the summer, I joined the bioML team at the Microsoft Research New England as an intern where I worked on Foundation Models in single-cell biology.
Previously, I worked with NLP methods and knowledge graphs during my internship @ Novo Nordisk Research Centre in Oxford. Using Transfer Learning and YOLO model I built a framework to identify sea pens from a video footage of an ocean floor @ Turing Data Study Group.
With extensive domain knowledge in Computational Biology complemented by my experience in Data Science & Machine Learning I am eager to drive advancements at the crossroads of these disciplines.
Research Experience
Intern @ Microsoft Research New England, Cambridge, Massachusetts, USA
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2023
During the summer I investigated the potential of the Foundation Models in the space of single cell biology. I was mentored by Alex Lu, Ava Amini, and Lorin Crawford.
Intern @ Novo Nordisk Research Centre Oxford, Oxford, United Kingdom
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2021
I worked with NLP and knowledge graphs to screen biomedical articles to identify and prioritise therapeutic targets. To increase the impact of the analysis and increase reach I built and deployed an interactive dashboard (using R Shiny) to allow colleagues within the company to investigate and visualise the results directly in real-time.
DPhil Researcher @ Wellcome Centre for Human Genetics, Big Data Institute, University of Oxford, UK
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present - 2018
In my PhD project I looked at how chromatin organization influences disease initiation and progression in uterine cancer using multimodal data. I was also working on building and refining ML models of cancer evolution, specifically identyfing evolutionary trajectories in the cancer of the uterus.
Visiting Graduate Student @ Ratan group, University of Virginia, USA
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2018 - 2017
I carried out the research for my Master thesis Analysis of the mutational burden across gene sets in cancer in which I modeled somatic mutations background distribution using germline variation. I also developed SONiCS - algorithm to genotype Short Tandem Repeats (STRs) using dense forward simulations of the polymerase chain reaction (PCR).
Visiting Graduate Student @ Pemberton group, University of Virginia, USA
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2017 - 2016
Investigated epigenetic regulation in prostate cancer using mouse models of primary, invasive and metastatic tumors. I planned, carried out experimental wokrd and analysed results of RNA-seq, ChIP-seq and ATAC-seq assays.
Research Assistant @ Zebrafish Developmental Genomics, IIMCB, Warsaw, Poland
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2016 - 2015
I worked on the project: Elucidating gene regulatory network of zebrafish heart development using genomics. I was responsible for both computational and experimental aspects of the project.
Education
DPhil in Genomic Medicine and Statistics @ Nuffield Department of Medicine, Brasenose College
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present - 2018
PhD fully funded by the Wellcome Trust Four-year PhD Studentships in Science
M. Sc. Eng., Biotechnology @ Warsaw University of Technology
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2018 - 2015
Master thesis Analysis of the mutational burden across gene sets in cancer awarded the title of The Best Master Thesis in Bioinformatics defended in 2018.
B. Sc. Eng., Biotechnology @ Warsaw University of Technology
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2015 - 2011
Biotechnology of drugs and cosmetics.
Publications
Full list of publication is available through my Google Scholar profile scholar.google.com/citations?user=Yv6poTwAAAAJ.
Assessing the limits of zero-shot foundation models in single-cell biology @ bioRxiv
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2023
K. Z. Kedzierska, L. Crawford, A. P. Amini, A. X. Lu
Data Study Group Final Report: CEFAS - Automated identification of sea pens using OpenCV and machine learning @ Zenodo
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2023
In alphabetical order: M. Asthana, R. Blackwell, S. Davis, A. Downie, J. Forsyth, K. Kedzierska, R. Mestre, Z. Reza, J. Ribeiro, P. Palola, Y. Said
Functional analysis reveals driver cooperativity and novel mechanisms in endometrial carcinogenesis @ EMBO Molecular Medicine
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2023
M. Brown, A. Leon, K. Kedzierska, C. Moore, H. L. Belnoue‐Davis, S. Flach, J. P. Lydon, F. J. DeMayo, A. Lewis, T. Bosse, I. Tomlinson, D. N. Church
Discordant prognosis of mismatch repair deficiency in colorectal and endometrial cancer reflects variation in antitumour immune response and immune escape @ The Journal of pathology
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2022
M. A. Glaire, N. AJ. Ryan, M. E. Ijsselsteijn, K. Kedzierska, S. Obolenski, R. Ali, E. J. Crosbie, T. Bosse, N. F. D. Miranda, D. N. Church
Multi-omics analyses of early liver injury reveals cell-type-specific transcriptional and epigenomic shift @ BMC Genomics
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2021
M. Migdal, E. Tralle, K. A. Nahia, L. Bugajski, K. Z. Kedzierska, F. Garbicz, K. Piwocka, C. L. Winata, M. Pawlak
The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability @ Clinical Epigenetics
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2020
H. Russell, K. Kedzierska, D. D. Buchanan, R. Thomas, E. Tham, M. Mints, A. Keränen, G. G. Giles, M. C. Southey, R. L. Milne, I. Tomlinson, D. Church, A. B. Spurdle, T. A. O’Mara and A. Lewis
Prognostic integrated image-based immune and molecular profiling in early-stage Endometrial Cancer @ Cancer Immunology Research
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2020
N. Horeweg, M. de Bruyn, R. A. Nout, E. Stelloo, K. Kedzierska, A. León-Castillo, A. Plat, K. D. Mertz, M. Osse, I. M. Jürgenliemk-Schulz, L. C.H.W. Lutgens, J. J. Jobsen, E. M. van der Steen-Banasik, V. T. Smit, C. L. Creutzberg, T. Bosse, H. W. Nijman, V. H. Koelzer and D. N. Church
Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development @ Genome Research
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2019
M. Pawlak, K. Z. Kedzierska, M. Migdal, K. A. Nahia, J. A. Ramilowski, L. Bugajski, K. Hashimoto, A. Marconi, K. Piwocka, P. Carninci and C. L. Winata
Genomic analysis of DNA repair genes and androgen signaling in prostate cancer @ BMC Cancer
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2018
K. Jividen, K. Z. Kedzierska, C.-S. Yang, K. Szlachta, A. Ratan and B. M. Paschal
SONiCS: PCR stutter noise correction in genome-scale microsatellites @ Bioinformatics
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2018
K. Z. Kedzierska, L. Gerber, D. Cagnazzi, M. Krützen, A. Ratan, L. Kistler
Posters, and Talks
Chromatin modfiers in endometrial cancer, Poster @ Biology of Genomes 2023, Cold Spring Harbor, NY, USA
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2023
Systematic characterisation of chromatin modifiers in endometrial cancer, Poster @ European Association for Cancer Research 2022 Congress, Seville, Spain
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2022
Analysis of the mutational burden across gene sets in cancer, Invited talk @ Polish Bioinformatics Society Symposium, Cracow, Poland
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2019
Differential mutation analysis across gene sets in cancers, Poster @ Biology of Genomes 2018, Cold Spring Harbor, NY, USA
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2018
Epigenetic regulation of prostate cancer, Talk @ Visiting Graduate Traineeship Program Grantees Symposium, Charlottesville, VA, USA
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2017
Awards
JXTX + CSHL 2023 Biology of Genomes Scholarship @ JXTX Foundation, Cold Spring Harbor Laboratory
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2023
Awarded to outstanding graduate students in genomics and data sciences.
Graduate Prize in the ‘Outstanding work outside degree’ category @ Nuffield Department of Medicine, University of Oxford
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2022
Each year Nuffield Department of Medicine, based on nominations, awards selected PhD students based on their performance within and outside of their degree.
Senior Hulme Scholarship @ Brasenose College, University of Oxford
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2023 - 2021
Senior Hulme Scholarship is awarded by Brasenose College, University of Oxford to DPhil students whose academic performance is deemed to be exceptional.
Best Master Thesis in Bioinformatics @ Polish Bioinformatics Society
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2019 - 2018
Analysis of the mutational burden across gene sets in cancer - Best Master Thesis defended in Bioinformatics in 2018 in Poland.
Visiting Graduate Traineeship Program, now known as BioLAB @ Fulbright Poland
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2017 - 2016
The Visiting Research Graduate Traineeship Program offered 12-month research traineeships for outstanding, qualified students from the life sciences at selected institutions in the United States.
Grasz o Staz @ PwC Poland
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2015
“Grasz o Staz” competition was a national, prestigious and highly competitive (1:25 success rate) scholarship program in Poland organized by PwC.
Teaching Experience
Unsupervised learning @ NGSchool2022: Machine Learning in Computational Biology, Jablonna, Poland
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2022
I co-led, with Kaspar Märtens, lecture and tutorial sessions on unsupervised learning and its use cases in computational biology. All materials are availble at github.com/kzkedzierska/ngs22_unsupervised.
Data visualization in bioinformatics - hackathon mentor @ Online hackathon NGSprint, Discord
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2021
I led the hackathon in data viusalisation with emphasis on computational biology. Teaching materials are available at github.com/kzkedzierska/NGSprint_data_viz.
Online tutorials: Python for Data Science and Introduction to Python @ NGSeminars, YouTube
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2020
I led two Python tutorials: Introduction to Python kasia.codes/talk/intro_to_python/ and Python for Data Science kasia.codes/talk/py4ds/.
Unsupervised learning, Introduction to Python @ #NGSchool2019: Machine Learning for Biomedicine, Ostróda, Poland
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2019
Tutor for the Introduction to Python (3 h workshop) and for the Unsupervised learning (1,5 h lecture).
Introduction to R @ Wellcome Centre for Human Genetics, Oxford, UK
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2019
8 week course in Introduction to R, Data Manipulation, Data Visualisation and RNA-seq data analysis.
Introduction to Managing Code with Git @ Wellcome Centre for Human Genetics, Oxford, UK
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2019
I led a 2-hour introduction to working with Git. Materials, including slides and exercises are available at kasia.codes/talk/into_to_git/.
ATAC-seq workshop @ #NGSchool2017: Single-cell Sequencing, Jachranka, Poland
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2017
Invited speaker
Attended Workshops, Summer Schools
Sea pen identification from video footage challenge @ Turing Data Study Group @ The Alan Turing Institute, London, UK
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2022
Machine Learning Summer School @ Imperial College London, University College London, London, UK
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2019
Grants
Visegrad Grant to organise NGSchool2022 @ Visegrad Fund
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2022 - 2020
32,190 EUR awarded towards organising affordable training and conference focusing on ML application in Computational Biology. During this project I managed an international team of volunteers and led the organisation of summer school, conference, online seminars and hackathon.
Visegrad Grant to organise NGSchool2019 @ Visegrad Fund
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2019
23,500 EUR awarded towards organising #NGSchool2019 allowed to keep the cost of attenting the school to the minimum and record the lectures for broader access.
Non profit work
President @ NGSchool Society
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2022 - 2018
The goal of the Society is to promote and support science, with emphasis on computational biology.
President @ Warsaw Society of Biotechnology
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2016 - 2015
Symbioza’s aim is to integrate biotechnology community in Poland starting from the youngest generations, and promotion and popularization of biotechnology.