Research & Academic Profile

Maria
Kalyva

Researcher and computational biologist with experience in cancer genomics, transcriptomics and bioinformatics. Passionate about interdisciplinary work and innovation.

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01 — About

Hi! I am Maria. I finished my bachelor's degree in molecular biology in Crete, Greece, with an interest in species evolution and computational biology.

I then did my PhD at EMBL-EBI, Cambridge, becoming an expert in cancer genomics and cancer evolution.

I'm currently a fellow between UCL and the Crick Institute, using long-read RNA technologies to understand transcriptomic diversity in multi-regional cancer patient data.

Maria Kalyva at Cambridge graduation

PhD graduation · Cambridge

Maria Kalyva at Brooklyn Bridge

ASHG Conference · Washington DC

Location

London, United Kingdom

Expertise

Single-cell · Multi-omics · Cancer Genomics

02 — Skills

03 — Tools

Python · Simulation

ClonalSim

github.com/cortes-ciriano-lab/ClonalSim

An object-oriented Python simulator for clonal expansions implementing a Wright-Fisher model with selection. Developed as part of the MSI tumour evolution project. Simulates mutant cell counts per generation via binomial sampling, supports variable mutation rates for MMRD hypermutated contexts, and converts population arrays into treeswift-compatible tree objects for downstream phylogenetic analysis. Includes Approximate Bayesian Computation integration for parameter inference.

Wright-Fisher Clonal Dynamics MSI / MMRD ABC Phylogenetics

04 — Education

Sep 2019 — Jan 2024

PhD in Cancer Genomics and Evolution

University of Cambridge & EMBL-EBI

Thesis: "Elucidating the evolutionary dynamics of MSI tumours at the single-cell level". College Senior Scholarship recipient (2020–2023).

2014 — 2018

BSc in Molecular Biology (Top 10%)

University of Crete

Erasmus traineeship at University College London. World Hellenic Biomedical Association Scholarship (2018).

05 — Publications

Kalyva M, McGranahan N. (2026).

Redefining cancer drivers with tissue-specific context.

Cancer Cell (in press)

Kalyva M, Kildisiute G, Elmentaite R, et al. (2024).

Transcriptional signals of transformation in human cancer.

Genome Medicine

Van Egeren D, Kamaz B, Liu S, Kalyva M, et al. (2022).

Transcriptional differences between JAK2-V617F and wild-type bone marrow cells in myeloproliferative neoplasms.

Experimental Hematology

Van Egeren D, Escabi J, Nguyen M, Kalyva M, et al. (2021).

Reconstructing lineage histories and differentiation trajectories of individual cancer cells in myeloproliferative neoplasms.

Cell Stem Cell

Sekar S, Tomasini L, Proukakis C, Kalyva M, et al. (2020).

Complex mosaic structural variations in human fetal brains.

Genome Research

Perez-Rodriguez D, Kalyva M*, et al. (*equal contribution) (2019).

Investigation of somatic CNVs in brains of synucleinopathy cases using targeted SNCA analysis and single cell sequencing.

Acta Neuropathologica Communications

06 — Awards & Scholarships

College Senior Scholarship

Fitzwilliam College, University of Cambridge (2020–2023)

World Hellenic Biomedical Association Scholarship

2018

07 — Contact

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touch.

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