@inproceedings{MHP-HSB16,
  address = {Grenoble France},
  month = oct,
  optvolume = 9957,
  series = {Lecture Notes in Computer Science},
  publisher = {Springer},
  opteditor = {Cinquemani, Eugenio and
               Donz{\'{e}, Alexandre}},
  acronym = {{HSB}'16},
  booktitle = {{P}roceedings of the 5th
           {I}nternational {W}orkshop on 
           {H}ybrid {S}ystems {B}iology},
  author = {Mandon, Hugues and Haar, Stefan and Paulev{\'e}, Lo{\"i}c},
  title = {{Relationship between the Reprogramming Determinants of Boolean Networks and their Interaction Graph}},
  pages = {113-127},
  year = {2016},
  doi = {10.1007/978-3-319-47151-8_8},
  pdf = {http://www.lsv.fr/Publis/PAPERS/PDF/MHP-HSB16.pdf},
  url = {http://www.lsv.fr/Publis/PAPERS/PDF/MHP-HSB16.pdf},
  abstract = {In this paper, we address the formal characterization of tar- gets triggering cellular trans-differentiation in the scope of Boolean net- works with asynchronous dynamics. Given two fixed points of a Boolean network, we are interested in all the combinations of mutations which allow to switch from one fixed point to the other, either possibly, or in- evitably. In the case of existential reachability, we prove that the set of nodes to (permanently) flip are only and necessarily in certain connected components of the interaction graph. In the case of inevitable reachabil- ity, we provide an algorithm to identify a subset of possible solutions.}
}

@comment{{B-arxiv16,
  author =		Bollig, Benedikt, 
  affiliation = 	aff-LSVmexico,
  title =    		One-Counter Automata with Counter Visibility, 
  institution = 	Computing Research Repository, 
  number =    		1602.05940, 
  month = 		feb, 
  nmonth =     		2,
  year = 		2016, 
  type = 		RR, 
  axeLSV = 		mexico,
  NOcontrat = 		"",
  
  url =			http://arxiv.org/abs/1602.05940, 
  PDF =			"http://www.lsv.fr/Publis/PAPERS/PDF/B-arxiv16.pdf",
  lsvdate-new =  	20160222,
  lsvdate-upd =  	20160222,
  lsvdate-pub =  	20160222,
  lsv-category = 	"rapl",
  wwwpublic =    	"public and ccsb",
  note = 		18~pages, 

  abstract = "In a one-counter automaton (OCA), one can read a letter
    from some finite alphabet, increment and decrement the counter by
    one, or test it for zero. It is well-known that universality and
    language inclusion for OCAs are undecidable. We consider here OCAs
    with counter visibility: Whenever the automaton produces a letter,
    it outputs the current counter value along with~it. Hence, its
    language is now a set of words over an infinite alphabet. We show
    that universality and inclusion for that model are in PSPACE, thus
    no harder than the corresponding problems for finite automata, which
    can actually be considered as a special case. In fact, we show that
    OCAs with counter visibility are effectively determinizable and
    closed under all boolean operations. As~a~strict generalization, we
    subsequently extend our model by registers. The general nonemptiness
    problem being undecidable, we impose a bound on the number of
    register comparisons and show that the corresponding nonemptiness
    problem is NP-complete.",
}}

@inproceedings{MHP-cmsb17,
  address = {Darmstadt, Germany},
  month = sep,
  year = 2017,
  volume = {10545},
  series = {Lecture Notes in Bioinformatics},
  publisher = {Springer-Verlag},
  editor = {Feret, J{\'e}r{\^o}me and Koeppl, Heinz},
  acronym = {{CMSB}'17},
  booktitle = {{P}roceedings of the 15th
           {C}onference on
           {C}omputational {M}ethods in {S}ystem {B}iology
	   ({CMSB}'17)},
  author = {Mandon, Hugues and Haar, Stefan and Paulev{\'e}, Lo{\"i}c},
  title = {{Temporal Reprogramming of Boolean Networks}},
  pages = {179-195},
  pdf = {https://hal.inria.fr/hal-01589251/document},
  doi = {10.1007/978-3-319-67471-1\_11},
  abstract = {Cellular reprogramming, a technique that opens huge opportunities in modern and regenerative medicine, heavily relies on identifying key genes to perturb. Most of computational methods focus on finding mutations to apply to the initial state in order to control which attractor the cell will reach. However, it has been shown, and is proved in this article, that waiting between the perturbations and using the transient dynamics of the system allow new reprogramming strategies. To identify these temporal perturbations, we consider a qualitative model of regulatory networks, and rely on Petri nets to model their dynamics and the putative perturbations. Our method establishes a complete characterization of temporal perturbations, whether permanent (mutations) or only temporary, to achieve the existential or inevitable reachability of an arbitrary state of the system. We apply a prototype implementation on small models from the literature and show that we are able to derive temporal perturbations to achieve trans-differentiation.}
}

@inproceedings{MSHPP-cmsb19,
  address = {Trieste, Italy},
  month = sep,
  volume = {11773},
  series = {Lecture Notes in Bioinformatics},
  publisher = {Springer-Verlag},
  editor = {Luca Bortolussi and Guido Sanguinetti},
  acronym = {{CMSB}'19},
  booktitle = {{P}roceedings of the 17th
           {C}onference on
           {C}omputational {M}ethods in {S}ystem {B}iology
	   ({CMSB}'19)},
  author = {Mandon, Hugues and Su, Cui and Haar, Stefan and Pang, Jun and Paulev{\'e}, Lo{\"i}c},
  title = {Sequential Reprogramming of Boolean Networks Made Practical},
  pages = {3-19},
  doi = {10.1007/978-3-030-31304-3_1},
  year = 2019,
  abstract = {We address the sequential reprogramming of gene regulatory networks modelled as Boolean networks. We develop an attractor-based sequential reprogramming method to compute all sequential reprogramming paths from a source attractor to a target attractor, where only attractors of the network are used as intermediates. Our method is more practical than existing reprogramming methods as it incorporates several practical constraints: (1) only biologically observable states, viz. attractors, can act as intermediates; (2) certain attractors, such as apoptosis, can be avoided as intermediates; (3) certain nodes can be avoided to perturb as they may be essential for cell survival or difficult to perturb with biomolecular techniques; and (4) given a threshold \(k\), all sequential reprogramming paths with no more than \(k\) perturbations are computed. We compare our method with the minimal one-step reprogramming and the minimal sequential reprogramming on a variety of biological networks. The results show that our method can greatly reduce the number of perturbations compared to the one-step reprogramming, while having comparable results with the minimal sequential reprogramming. Moreover, our implementation is scalable for networks of more than 60 nodes.}
}

@article{MSPPHP-ipl19,
  publisher = {ACM Press},
  journal = {IEEE/ACM Transaction on Computational Biology and Bioinformatics},
  author = {Mandon, Hugues and Su, Cui and Pang, Jun and Paul, Soumya and Haar, Stefan and Paulev{\'e}, Lo{\"i}c},
  title = {Algorithms for the Sequential Reprogramming of Boolean Networks},
  volume = {16},
  number = {5},
  pages = {1610--1619},
  year = 2019,
  pdf = {https://hal.archives-ouvertes.fr/hal-02113864/file/main.pdf},
  url = {https://hal.archives-ouvertes.fr/hal-02113864}
}

@phdthesis{mandon-phd2019,
  author = {Hugues Mandon},
  title = {{Algorithms for Cell Reprogramming Strategies in Boolean Networks}},
  school = {{\'E}cole Normale Sup{\'e}rieure Paris-Saclay, France},
  type = {Th{\`e}se de doctorat},
  year = 2019,
  month = dec,
  url = {https://tel.archives-ouvertes.fr/tel-02412717},
  pdf = {https://hal.archives-ouvertes.fr/tel-02412717/document}
}

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