Academic CV

An academic CV is available here.


Articles

  • High order expression dependencies finely resolve cryptic states and subtypes in single cell data

    Abel Jansma, Yuelin Yao, Jareth Wolfe, Luigi Del Debbio, Sjoerd V Beentjes, Chris P Ponting, and Ava Khamseh, Molecular Systems Biology 2025

    [ paper | preprint | code | Twitter thread ]

    tl;dr We introduce Stator, a new computational method that reveals hidden cell states in single-cell data by analysing how genes work together, rather than just looking at where cells cluster. Unlike traditional methods, Stator can label a single cell with multiple states simultaneously-like being both a neuron and in a specific phase of cell division-giving us a more complete picture of what cells are doing. Stator even finds substructure within homogeneous populations!


  • The Fast Möbius Transform: An algebraic approach to information decomposition

    Abel Jansma, Pedro Mediano, and Fernando Rosas, 2024

    [ paper | code | Twitter thread ]

    tl;dr We present a way to calculate how information is shared between multiple variables in complex systems, distinguishing between redundant, synergistic, and unique information. By leveraging algebraic properties of information decomposition, the method makes previously intractable analyses possible. We demonstrate this on brain activity data, and baroque music compositions.


  • A Mereological Approach to Higher-Order Structure in Complex Systems: from Macro to Micro with Möbius

    Abel Jansma, 2024

    [ paper | code | Twitter thread ]

    tl;dr We present a unified mathematical framework to describe how breaking down complex systems (like brains, molecules, or social networks) into parts determines what kinds of interactions we can discover between those parts. Using an algebraic method called Möbius inversion, this relates large-scale observations to microscopic and "higher-order" interactions.


  • Superdense Coding and Stabiliser Codes with Ising-coupled Entanglement

    Abel Jansma, 2024

    [ paper | code ]

    tl;dr We introduce a new family of quantum states that contain the statistics of strongly coupled Ising models in their entanglement structure. These states enable quantum communication protocols and error correction codes that might offer some advantages over traditional ones.


  • A compositional game to fairly divide homogeneous cake

    Abel Jansma, 2023

    [ paper | code | Mathstodon thread ]

    tl;dr Ever wonder how to split a cake fairly when people can't all be in the same room? Here's a solution: after each cut, make whoever has the biggest piece do the next cutting. While most cake-cutting research assumes that people prefer different flavors and toppings, we argue that even splitting a plain cake is tricky - naive approaches end up super unfair. This "biggest piece cuts next" rule ensures everyone gets exactly their fair share.


  • Higher-order in-and-outeractions reveal synergy and logical dependence beyond Shannon-information

    Abel Jansma, Entropy 2023

    [ paper | preprint | code | Twitter thread ]

    tl;dr By relating higher-order Ising interactions to concepts from algebra and information theory, we can better detect and measure interactions in complex systems - from logic gates to gene networks. The paper shows these new measures can distinguish between systems that look identical using traditional methods.



Talks and Conferences

  • A Compositional Approach to Higher-order Structure in Complex Systems - Centre for Complexity Science, Imperial College London, April 2024. Slides
  • Plant Communication: Fact vs. Lore - Multispecies Research Unit, Trust Berlin, March 2024.
  • A unified approach to higher-order structure in complex systems - University of Leipzig, Feb 2024.
  • From Genetic Hypergraphs to Persistent Quantum Entanglement - Max Planck Institute for Mathematics in the Sciences, seminar, Oct 2023.
  • A Compositional Game to Fairly Divide Homogeneous Cake - Applied Category Theory 2023, Aug 2023. Poster
  • The information theory of higher-order interactions - Dutch Institute for Emergent Phenomena, Institute for Advanced Study, June 2023. Slides
  • Higher-Order Interactions and Their Duals Reveal Synergy and Logical Dependence beyond Shannon-Information - DEMICS23, Max Planck Institute for the Physics of Complex Systems, June 2023. Slides
  • Cybergenetic networks in the mouse brain: higher-order gene regulation and Boolean logic - IGC Biomedical Genomics section meeting, Dec 2021.
  • Cybergenetic in-and-outeractions: Searching for strange loops in the mouse brain - De Las Cuevas Group, University of Innsbruck, Sep 2021.
  • Genetic Interactions and Information Lattices - Mathematical Quantum Physics group, University of Innsbruck, Juli 2021.
  • Model-free estimation of higher-order interactions - CSHL Biology of Genomes conference, May 2021. Poster
  • Complex Gene Regulation: Higher-order interactions in single-cell expression data - European Mathematical Genetics Meeting, April 2021. Slides | Video
  • Higher-order interactions in single-cell expression data - IGC Biomedical Genomics section meeting, March 2021. Slides
  • Complex gene regulation: higher-order interactions in single-cell expression data - CSHL Network Biology conference, March 2021. Poster
  • A maximally noncommittal physicist looks at genetic interactions - Biomedical Genomics section meeting, May 2020. Slides
  • Computational biology journal club - Helped organise and present, IGC May 2019 - Sep 2020.
  • Introduction to the do-calculus - Helped organise and present at the Causality book club, IGC April 2019.
  • Ethics in biomedicine - Workshop for Ponting-Lab, October 2019.
  • Distillation for Olfactory Design - Mediamatic Odorama nights, March 2017.
  • SPUI25 in spe - Organised and hosted multiple events at cultural centre SPUI25, Jan-Sep 2017.
  • Debates on science and technology in society - Organised and hosted monthly debates at the Betabreak events, Dec 2014 - Jan 2016.


PhD Thesis

Higher-order interactions in single-cell gene expression: towards a cybergenetic semantics of cell state University of Edinburgh, A. Jansma 2023.


MSc Thesis

E8 symmetry structures in the Ising model University of Amsterdam, A. Jansma 2018.


Code

Stator: cell state inference from gene expression data Github, 2023
Training RBMs with parallel tempering Github, 2019
Leaf venation simulation (ran by ~700 users) Openprocessing.org, 2014.
Firefly synchronisation (ran by ~5k users) Openprocessing.org, 2014.
Flocking simulations with predators (ran by ~16k users, forked ~25 times) Openprocessing.org, 2013.


Outreach

Over vogels en vuurvliegjes Quantumuniverse.nl 2019.
Solitonen in het zwembad Quantumuniverse.nl 2019.
Distillation 101 Mediamatic.net 2016.