Profile picture
Administrative data

Markus Kirolos Youssef

markus.youssef@epfl.ch

Expertise

Topological data analysis · computational and applied topology · homotopy theory of discrete structures · network science · statistical analysis of high-dimensional biological data · scientific software in Python

Mission

Developing mathematically rigorous and computationally practical tools for detecting geometric and topological structure in complex data, with a focus on biology. My work connects algebraic topology with data-driven applications, and I collaborate closely with experimental biologists to turn topological invariants into usable screening statistics.

Current Work


  • Ring scores: axiomatic invariants of compact metric spaces that quantify circular structure, with a stability theorem and persistence-based constructions; applications to single-cell RNA sequencing data.
  • Obstructions to Quillen model structures on categories with intrinsic discrete homotopy theories via the notion of segmented categories. 
Markus Kirolos Youssef is a mathematician working at the interface of topology, data analysis and biology. Born in Vienna, he studied mathematics at the University of Vienna (BSc 2016, MSc in Geometry and Topology 2019), with a master's thesis on ring structures in networks that became the basis of the ringity package. After research internships at the Acoustics Research Institute and the Austrian Institute of Technology, he joined the Barcelona Supercomputing Center (2019 to 2020), where he co-developed a graphlet-based algorithm for probabilistic molecular networks. From 2020 to 2023 he was a Marie Skłodowska-Curie fellow at the University of Lausanne, analysing bulk and single-cell sequencing and DNA-methylation data for cancer-biology and epigenetics projects, with a secondment at the University of Helsinki.

He completed his PhD in mathematics at EPFL in August 2026 under the supervision of Prof. Kathryn Hess, with a thesis on obstructions to model structures in discrete homotopy theory and on ring scores for detecting circular structure in data. Since September 2026 he has been a scientist (postdoctoral researcher) in the Laboratory for Topology and Neuroscience.

Curriculum vitae

  • 2026 to present: Scientist (Postdoctoral Researcher), Laboratory for Topology and Neuroscience, EPFL
  • 2023 to 2026: PhD in Mathematics, EPFL (supervisor: Prof. Kathryn Hess). Thesis: On the Non-Existence of Model Structures and the Existence of Ring Scores: Two Studies in Combinatorial Topology (doi:10.5075/epfl-thesis-12216)
  • 2020 to 2023: Marie Skłodowska-Curie Fellow (research software engineer, bioinformatics and cancer biology), University of Lausanne; secondment at the University of Helsinki (2022)
  • 2019 to 2020: Research Intern, Barcelona Supercomputing Center / UPC
  • 2016 to 2019: MSc in Geometry and Topology, University of Vienna
  • 2012 to 2016: BSc in Mathematics, University of Vienna
  • Languages: German and Arabic (native), English (fluent), Spanish (proficient), French (basic)
  • Links: ORCID · Google Scholar · GitHub

Professionals experiences

Scientist (Postdoctoral Researcher)

Continuation of the doctoral research on ring scores and on obstructions to model structures in discrete homotopy theory; maintenance of the ringity package.

2026–2026

EPFL, Laboratory for Topology and Neuroscience, Lausanne

Doctoral Assistant

Topological data analysis of bulk and single-cell gene-expression data, benchmarked on synthetic and experimental datasets; author and maintainer of the ringity package; joint first author of a single-cell manuscript and coordinated its submission; three years of teaching assistance. Supervisor: Prof. Kathryn Hess.

2023–2026

EPFL, Laboratory for Topology and Neuroscience, Lausanne

Marie Skłodowska-Curie Fellow (Research Software Engineer, Bioinformatics and Cancer Biology)

Built and maintained Python and R analyses for experimental biologists across three labs (supervisors: Prof. G.-P. Dotto, Prof. K. Hess, Prof. G. Ciriello); quality control, normalisation and batch-effect handling of bulk and single-cell RNA-seq and DNA-methylation data; co-author on the resulting publications. Secondment at the University of Helsinki (Prof. J. Kaprio, 2022): statistical and machine-learning analysis of population-scale twin-cohort methylation data.

2020–2023

University of Lausanne (UNIL), Lausanne

Research Intern, Network Biology and Scientific Software

Co-developed a graphlet-based open-source algorithm for probabilistic molecular networks (Python/C++, HPC), published in Bioinformatics. Supervisor: Prof. Nataša Pržulj.

2019–2020

Barcelona Supercomputing Center / Universitat Politècnica de Catalunya, Barcelona

Research Intern, Signal Processing and Computer Vision

Python pipelines on noisy sensor data: room-geometry reconstruction from echo recordings, an inverse problem, implemented and stress-tested (ARI, Dr. José Luis Romero); image-analysis pipeline (AIT, Dr. Svorad Štolc).

2017–2017

Acoustics Research Institute (Austrian Academy of Sciences) and Austrian Institute of Technology, Vienna

Education

Mathematics

| Thesis: On the Non-Existence of Model Structures and the Existence of Ring Scores: Two Studies in Combinatorial Topology (thesis no. 12216)

2023 – 2026 EPFL, Lausanne
Directed by Prof. Kathryn Hess

Mathematics (Geometry and Topology)

| Thesis on ring structures in networks, the basis of the ringity package

2016 – 2019 University of Vienna
Directed by Prof. Herbert Edelsbrunner (IST Austria) and Dr. Jörg Menche (CeMM)

Mathematics

| With a research stay at the Acoustics Research Institute of the Austrian Academy of Sciences

2012 – 2016 University of Vienna

Awards

Marie Skłodowska-Curie Fellowship (Innovative Training Network, grant 859860)

European Commission

2020

Austrian Physics Olympiad, national finalist

Österreichische Physikolympiade

2012

Selected publications

On the Non-Existence of Model Structures and the Existence of Ring Scores: Two Studies in Combinatorial Topology (PhD thesis)

Markus Kirolos Youssef
Published in EPFL thesis no. 12216 in 2026

Topology identifies concurrent cyclic processes in single-cell transcriptomics and androgen receptor function

Kelly Maggs*, Markus K. Youssef*, Cyril Pulver, Jovan Isma, Tâm J. Nguyên, Matthias Arzt, Wouter Karthaus, Heather A. Harrington, Kathryn Hess, G. Paolo Dotto
Published in bioRxiv (preprint, under review); joint first author with Kelly Maggs in 2025

ANKRD1 is a mesenchymal-specific driver of cancer-associated fibroblast activation bridging androgen receptor loss to AP-1 activation

Luigi Mazzeo, Soumitra Ghosh, Emery Di Cicco, Jovan Isma, Daniele Tavernari, Anastasia Samarkina, Paola Ostano, Markus K. Youssef, Christian Simon, G. Paolo Dotto
Published in Nature Communications 15:1038 in 2024

Androgen receptor is a determinant of melanoma targeted drug resistance

Anastasia Samarkina, Markus K. Youssef, Paola Ostano, Soumitra Ghosh, Min Ma, Beatrice Tassone, Tatiana Proust, Giovanna Chiorino, Mitchell P. Levesque, Sandro Goruppi, et al.
Published in Nature Communications 14:6498 in 2023

DNA methylation sites in early adulthood characterised by pubertal timing and development: a twin study

Emir Sehovic, Stephanie M. Zellers, Markus K. Youssef, Aino Heikkinen, Jaakko Kaprio, Miina Ollikainen
Published in Clinical Epigenetics 15:181 in 2023

Probabilistic graphlets capture biological function in probabilistic molecular networks

Sergio Doria-Belenguer, Markus K. Youssef, René Böttcher, Noël Malod-Dognin, Nataša Pržulj
Published in Bioinformatics 36(Suppl. 2):i804-i812 in 2020

Research

Current Research Fields

My research has two directions.
  • Applied topology and data analysis: ring scores, numerical invariants of compact metric spaces that measure how closely a space resembles a circle, built in analogy with the role of H0 persistent homology in clustering. Axioms, a stability theorem and persistence-based constructions. Applications as screening statistics for circular gene-set projections in single-cell RNA-seq data.
  • Homotopy theory of discrete structures: obstructions to Quillen model structures on categories with intrinsic discrete homotopy theories, in particular x-homotopy on graphs. Various obstruction arguments extended via segmented categories to simplicial, cubical, A- and x-homotopy. Results have been formalized in Lean.

Teaching & PhD

Teaching and PhD thesis

Teaching: teaching assistant at EPFL for three years (2023 to 2026), alongside the doctoral research.

PhD thesis: On the Non-Existence of Model Structures and the Existence of Ring Scores: Two Studies in Combinatorial Topology, EPFL, 2026 (thesis no. 12216), supervised by Prof. Kathryn Hess. Private defense June 2026, public defense August 2026. doi:10.5075/epfl-thesis-12216