- IBISC / Computer Science, Université Paris-Saclay, Univ. Évry, Évry-Courcouronnes, France
- Computational complexity, Design and analysis of algorithms, Dynamical systems, Graph theory, Systems biology
Marker and source-marker reprogramming of Most Permissive Boolean networks and ensembles with BoNesis
Reprogramming of locally-monotone Boolean networks with BoNesisRecommended by Sergiu Ivanov based on reviews by Ismail Belgacem and 1 anonymous reviewer
Reprogramming of cellular networks is a well known challenge in computational biology consisting first of all in properly representing an ensemble of networks having a role in a phenomenon of interest, and secondly in designing strategies to alter the functioning of this ensemble in the desired direction. Important applications involve disease study: a therapy can be seen as a reprogramming strategy, and the disease itself can be considered a result of a series of adversarial reprogramming actions. The origins of this domain go back to the seminal paper by Barabási et al.  which formalized the concept of network medicine.
An abstract tool which has gathered considerable success in network medicine and network biology are Boolean networks: sets of Boolean variables, each equipped with a Boolean update function describing how to compute the next value of the variable from the values of the other variables. Despite apparent dissimilarity with the biological systems which involve varying quantities and continuous processes, Boolean networks have been very effective in representing biological networks whose entities are typically seen as being on or off. Particular examples are protein signalling networks as well as gene regulatory networks.
The paper  by Loïc Paulevé presents a versatile tool for tackling reprogramming of Boolean networks seen as models of biological networks. The problem of reprogramming is often formulated as the problem of finding a set of perturbations which guarantee some properties on the attractors. The work  relies on the most permissive semantics , which together with the modelling assumption allows for considerable speed-up in the practically relevant subclass of locally-monotone Boolean networks.
The paper is structured as a tutorial. It starts by introducing the formalism, defining 4 different general variants of reprogramming under the most permissive semantics, and presenting evaluations of their complexity in terms of the polynomial hierarchy. The author then describes the software tool BoNesis which can handle different problems related to Boolean networks, and in particular the 4 reprogramming variants. The presentation includes concrete code examples with their output, which should be very helpful for future users.
The paper  introduces a novel scenario: reprogramming of ensembles of Boolean networks delineated by some properties, including for example the property of having a given interaction graph. Ensemble reprogramming looks particularly promising in situations in which the biological knowledge is insufficient to fully determine all the update functions, i.e. in the majority of modelling situations. Finally, the author also shows how BoNesis can be used to deal with sequential reprogramming, which is another promising direction in computational controllability, potentially enabling more efficient therapies [4,5].
- Barabási A-L, Gulbahce N, Loscalzo J (2011) Network medicine: a network-based approach to human disease. Nature Reviews Genetics, 12, 56–68. https://doi.org/10.1038/nrg2918
- Paulevé L (2023) Marker and source-marker reprogramming of Most Permissive Boolean networks and ensembles with BoNesis. arXiv, ver. 2 peer-reviewed and recommended by Peer Community in Mathematical and Computational Biology. https://doi.org/10.48550/arXiv.2207.13307
- Paulevé L, Kolčák J, Chatain T, Haar S (2020) Reconciling qualitative, abstract, and scalable modeling of biological networks. Nature Communications, 11, 4256. https://doi.org/10.1038/s41467-020-18112-5
- Mandon H, Su C, Pang J, Paul S, Haar S, Paulevé L (2019) Algorithms for the Sequential Reprogramming of Boolean Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16, 1610–1619. https://doi.org/10.1109/TCBB.2019.2914383
- Pardo J, Ivanov S, Delaplace F (2021) Sequential reprogramming of biological network fate. Theoretical Computer Science, 872, 97–116. https://doi.org/10.1016/j.tcs.2021.03.013