Publications & Communications

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Peer Reviewed Journals

• Bolteau M, Chebouba L, David L, Bourdon J, Guziolowski C. Boolean Network Models of Human Preimplantation Development. J Comput Biol. 2024 May 29. doi: 10.1089/cmb.2024.0517. Epub ahead of print. PMID: 38814745.

• Le Bars S, Bolteau M, Bourdon J, Guziolowski C. Predicting weighted unobserved nodes in a regulatory network using answer set programming. BMC Bioinformatics. 2023 Aug 25;24(Suppl 1):321. doi: 10.1186/s12859-023-05429-3. PMID: 37626282; PMCID: PMC10463596.

• Lefebvre M, Gaignard A, Folschette M, Bourdon J, Guziolowski C. Large-scale regulatory and signaling network assembly through linked open data. Database (Oxford). 2021 Jan 18;2021:baaa113. doi: 10.1093/database/baaa113. PMID: 33459761

• Folschette M, Legagneux V, Poret A, Chebouba L, Guziolowski C, Théret N. A pipeline to create predictive functional networks: application to the tumor progression of hepatocellular carcinoma. BMC Bioinformatics. 2020 Jan 14;21(1):18. doi: 10.1186/s12859-019-3316-1. 

• Razzaq M, Paulevé L, Siegel A, Saez-Rodriguez J, Bourdon J, Guziolowski C. Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data. PLoS Comput Biol. 2018 Oct 29;14(10):e1006538. (Web access)

• Fourati S, Talla A, Mahmoudian M, Burkhart JG, Klén R, Henao R, Yu T, Aydın Z,Yeung KY, Ahsen ME, Almugbel R, Jahandideh S, Liang X, Nordling TEM, Shiga M, Stanescu A, Vogel R; Respiratory Viral DREAM Challenge Consortium, Pandey G, Chiu C, McClain MT, Woods CW, Ginsburg GS, Elo LL, Tsalik EL, Mangravite LM, Sieberts SK. A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection. Nat Commun. 2018 Oct 24;9(1):4418. doi: 10.1038/s41467-018-06735-8. (Web access)

• L Chebouba, D Boughaci, C Guziolowski. Proteomics versus clinical data and stochastic local search based variable selection for Acute Myeloid Leukemia patients' classification. Journal of Medical Systems 42 (7) 2018 (web access). 

• B Miannay, S Minvielle, F Magrangeas & C Guziolowski. Constraints on signaling networks logic reveal functional subgraphs on Multiple Myeloma OMIC data. BMC Systems Biology BMC series – open, 12(Suppl 3):32 2018. (web access)

• L Chebouba, B Miannay, D Boughaci and C Guziolowski. Discriminate the response of Acute Myeloid Leukemia patients to treatment by using proteomics data and Answer Set Programming. BMC Bioinformatics 2018 19(Suppl 2):59 doi: https://doi.org/10.1186/s12859-018-2034-4 (web access)

• A. Poret, C. Guziolowski. Therapeutic target discovery using Boolean network attractors: improvements of kali. Royal Society Open Science 5(2):171852 2018 DOI: 10.1098/rsos.171852. (web access)

• B Miannay, S Minvielle, O Roux, P Drouin, H Avet-Loiseau, C Guérin-Charbonnel, W Gouraud, M Attal, T Facon, N C Munshi, P Moreau, L Campion, F Magrangeas & C Guziolowski. Logic programming reveals alteration of key transcription factors in multiple myeloma. Scientific Reports 2017. 7(1) 9257 doi:10.1038/s41598-017-09378-9. (web access)

• L. Fippo Fitime, O. Roux, C. Guziolowski†, L. Paulevé†. Identification of Bifurcation Transitions in Biological Regulatory Networks using Answer-Set Programming, Algorithms Mol Biol. 2017 Jul 20;12:19. doi: 10.1186/s13015-017-0110-3. (web access)

• S. Videla, J. Saez-Rodriguez, C. Guziolowski, A. Siegel, caspo: a toolbox for automated reasoning on the response of logical signaling networks families, Bioinformatics 2017 Mar 15;33(6):947-950, (web access)

• M. Ostrowski, L. Paulevé, T. Schaub, A. Siegel, C. Guziolowski, Boolean Network Identification from Perturbation Time Series Data combining Dynamics Abstraction and Logic Programming, Biosystems, 2016, Nov; 149:139-153 (web access) 

• V. Acuña, A. Aravena, C. Guziolowski, D. Eveillard, A. Siegel, A. Maass. "Deciphering transcriptional regulations coordinating the response to environmental changes". BMC Bioinformatics, 17:35 , 2016. (Web access) 

• A. Kittas, A. Delobelle, S. Schmitt, K. Breuhahn, C. Guziolowski, N. Grabe. "Directed random walks and constraint programming reveal active pathways in HGF signaling". FEBS Journal,  2016 Jan; 283(2):350-60. doi: 10.1111/febs.13580. (Web access)

• Sven Thiele; Luca Cerone; Julio Saez-Rodriguez; Anne Siegel; Carito Guziolowski†; Steffen Klamt†. "Extended Notions of Sign Consistency to Relate Experimental Data to Signaling and Regulatory Network Topologies".  BMC Bioinformatics 2015 , 16:345 (Web access)

• S. Videla, I. Konokotina, L. Alexopoulos, J. Saez-Rodriguez, T. Schaub, A. Siegel, C. Guziolowski "Designing experiments to discriminate families of logic models". Frontiers in Bioengineering and Biotechnology, 2015, DOI=10.3389/fbioe.2015.00131 (Web access)

• S Videla, C Guziolowski, F Eduati, S Thiele, M Gebser, J Nicolas, J Saez-Rodriguez, T Schaub, A Siegel. "Learning Boolean logic models of signaling networks with Answer Set Programming" Theoretical Computer Science, vol. 599 pp 79-101 2014 (Web access)

• C. Guziolowski*, S. Videla*, F. Eduati, S. Thiele, T. Cokelaer, A. Siegel; J. Saez-Rodriguez. "Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming". Bioinformatics 2013; 29 (18) :2320-6. doi: 10.1093/bioinformatics/btt393 (Web access)

• C. Guziolowski, A. Kittas,  F. Dittmann, N. Grabe. "Automatically generating causal networks linking growth factor stimuli to functional cell state changes".  FEBS Journal 2012, 279, 18:3462-74. (pdf) (Web access)

• C Guziolowski, S Blachon, T Baumuratova, G Stoll, O Radulescu, A Siegel. "Designing Logical Rules to Model the Response of Biomolecular Networks with Complex Interactions: An Application to Cancer Modeling". IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no.5, pp. 1223-1234,  2010. (preprint.pdf) (Web access)

• C Guziolowski, A Bourde, F Moreews, A Siegel. "BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks. BMC Genomics 2009, 10:244 doi:10.1186/1471-2164-10-244. (Web access)

• P Veber, C Guziolowski, M Le Borgne, O Radulescu, and A Siegel. "Inferring the role of transcription factors in regulatory networks". BMC Bioinformatics 2008 9: 228 doi:10.1186/1471-2105-9-228. (Web access)

• C Guziolowski, P Veber, M Le Borgne, O Radulescu, and A Siegel. "Checking Consistency Between Expression Data and Large Scale Regulatory Networks: A Case Study" Journal of Biological Physics and Chemistry 7 2007 37-43 (preprint.pdf). Technical Report RR-6190 INRIA (link). RIAMS'06: Réseaux d'interaction, analyse, modélisation et simulation. Lyon, France 2006. (slides)

• G.Didier and C.Guziolowski. "Mapping Sequences by Parts"Algorithms for Molecular Biology 2007, 2:11doi:10.1186/1748-7188-2-11. (Web access)

• M.Latorre, H.Silva, J.Saba, C.Guziolowski, P.Vizoso, V.Martinez, J.Maldonado, A.Morales, R.Caroca, V.Cambiazo, R.Campos-Vargas, M.Gonzalez, A.Orellana, J.Retamales, L.A.Meisel "JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow" BMC Bioinformatics 2006,7:513 doi:10.1186/1471-2105-7-513 (Web access)

Conference Proceedings

• Bolteau, M., Bourdon, J., David, L., Guziolowski, C. (2023). Inferring Boolean Networks from Single-Cell Human Embryo Datasets. In: Guo, X., Mangul, S., Patterson, M., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2023. Lecture Notes in Computer Science(), vol 14248. Springer, Singapore. https://doi.org/10.1007/978-981-99-7074-2_34

• Le Bars S., Bourdon J., Guziolowski C. (2020) Comparing Probabilistic and Logic Programming Approaches to Predict the Effects of Enzymes in a Neurodegenerative Disease Model. In: Abate A., Petrov T., Wolf V. (eds) Computational Methods in Systems Biology. CMSB 2020. Lecture Notes in Computer Science, vol 12314. Springer, Cham. https://doi.org/10.1007/978-3-030-60327-4_8

• Misbah Razzaq, Roland Kaminiski, Javier Romero, Torsten Schaub, Jeremie Bourdon and Carito Guziolowski: Computing Diverse Boolean Networks from Phosphoproteomic Time Series Data. In CMSB 2018, Brno, Czech Republic, September 2018. LNCS, vol 11095, pp 59-74 (Web access).

• Bertrand Miannay, Stéphane Minvielle, Olivier Roux, Florence Magrangeas, Carito Guziolowski: Constraints On Signaling Networks Logic Reveal Functional Subgraphs On Multiple Myeloma OMIC Data. Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics,  BCB 2017, Boston, MA, USA, August 20-23, 2017, pp 768-69 (Web access).

• Louis Fippo Fitime, Christian Schuster, Peter Angel, Olivier Roux, and Carito Guziolowski. Integrating time-series data in large-scale discrete cell-based models. In A. Abate and D. Safranek (Eds.): HSB 2015 - 4th International Workshop on Hybrid Systems Biology, Madrid, Spain. LNCS 9271, pp. 75–95, 2016 (Web access).

• Max Ostrowski*, Loïc Paulevé*, Torsten Schaub, Anne Siegel, and Carito Guziolowski. Boolean Network Identification from Multiplex Time Series Data. In CMSB 2015 - 13th conference on Computational Methods for Systems Biology, Nantes, France, September 2015. LNBI 9308, pp 170-181.(Web access)

• S. Videla*, C. Guziolowski*, F. Eduati, S. Thiele, N. Grabe, J. Saez-Rodriguez, and A. Siegel. "Revisiting the Training of Logic Models of Protein Signaling Networks with a Formal Approach based on Answer Set Programming". LNCS 7605, Computational Methods in Systems Biology, pp 342-361, 2012. (Web access)

• M Gebser, C Guziolowski, M Ivanchev, T Schaub, A Siegel, S Thiele, P Veber. "Repair and Prediction (under Inconsistency) in Large Biological Networks with Answer Set Programming". Proceeding of the Twelfth International Conference on Principles of Knowledge Representation and Reasoning (KR’10), Toronto, Canada, pp. 497-507, AIII Press, 2010 (selection rate : 25.1% (53/211)) (Web access)

• S Blachon, G Stoll, C Guziolowski, A Zinovyev, E Barillot, A Siegel, O Radulescu "Method for relating inter-patient gene copy numbers variations with gene expression via gene influence networks", BMIINT'09: Biomedical Informatics & Intelligent Methods in the support of Genomic Medicine, Thessaloniki, Grece, AIAI, pp 72-87  2009. (Web access )

• C Guziolowski, J Gruel, O Radulescu, A Siegel 'Curating a large-scale regulatory network by evaluating its consistency with expression datasets', CIBB'08: 5th International Conference on Bioinformatics and Biostatistics, Salerno, Italy 2008, Lecture Notes in Computer Science, Springer vol. 5488, pp. 144-155 2009 (selected paper) (slides) (Web access )

• A Siegel, M Le Borgne, O Radulescu, C Guziolowski, P Veber ''Qualitative response of interaction networks: application to the validation of biological models', Contribution to minisymposium New Research in Bioinformatics. ICIAM'07: 6th International Congress on Industrial and Applied Mathematics, PAMM, vol. 7, no. 1, pp. 1121803-1121804, Zurich 2007.

Book Chapters

• Razzaq M., Chebouba L., Le Jeune P., Mhamdi H., Guziolowski C., Bourdon J. (2019) Logic and Linear Programs to Understand Cancer Response. In: Liò P., Zuliani P. (eds) Automated Reasoning for Systems Biology and Medicine. Computational Biology, vol 30. Springer, Cham (Web access)

*  Equal contributions

† Corresponding authors

Non peer reviewed publications or peer reviewed without proceedings  

• A. Aravena, C, Guziolowski, A. Siegel, A. Maass. "Using Mutual Information and Answer Set Programming to refine PWM based transcription regulation network", JOBIM, Rennes, 2012 (download PDF).

• A. Siegel, C. Guziolowski, P. Veber, O. Radulescu, M. Le Borgne. "Optimiser un plan d'expérience à partir de modèles qualitatifs?" BioFutur 2006, 275:27 (preprint.pdf)

PhD Thesis

• Carito Guziolowski.  Analysis of Large-Scale Biological Networks with Constraint-Based approaches over Static Models.  PhD Thesis, INRIA - University of Rennes 1, France, Jan 2010 (.pdf)

HDR Thesis

• Carito Guziolowski. Modeling Biological Networks as Logic Programs.  HDR Thesis, LS2N - Nantes University, France, Jan 2024 (.pdf)

Other communications

Posters

• • Safferling K, Westphal K, Guziolowski C, Halama N, Grabe N. "Dermal-Epidermal Crosstalk: Quantification of Proliferation in Wound Healing using a 3D in-vitro Model" 41st Annual ESDR Meeting, J Invest Dermatol. 2011 Sep;131(2):5 (Download PDF) .

  • Guziolowski, C., Dittmann, F., Grabe, N., "Linking growth factor stimuli to cellular processes", ICSB : International Conference in Systems Biology, Heidelberg, Germany, 2011.

  • Guziolowski, C., Dittmann, F., Grabe, N., "High dimensional RNA data in protein networks?", Systems Biology of Human Disease, Boston, US, 2011.

  • Guziolowski, C., Hernandez, S., Grabe, N., "A Global Reaction Map of Signaling in Wound Healing", Systems Biology of Mammalian Cells, Freiburg, Germany, 2010.

  • Guziolowski, C., Veber, P., Le Borgne, M., Radulescu, O., Siegel, A. "Analysing regulatory networks using a qualitative approach", Genomes to Systems, Manchester, UK, 2008.

Oral communications

• • Virtual Liver Retreat 2011: "Automatically inferring causal networks linking growth factor stimuli to functional cell state changes by integrating growth factor stimulation experiments with pathway databases". Hünfeld, Germany, November 2011.

  • Workshop in Gen2Bio: Les rencontres Biotech organisées par OUEST-genopole. "Plugin BioQuali pour Cytoscape: un nouvel outil mis en place sur la plate-forme", La Boule, France, March 2009. (slides.pdf)

  • JOBIM 2008 satellite meeting : Dynamical modelling and simulation of biological networks: "Adding missing post-transcriptional regulations to a regulatory network".Lille, France, July 2008. (slides.pdf)

  • Cinquièmes Rencontres autour de la plate-forme Bio-informatique Genouest: "Bio-Quali : tool for analysing regulatory networks". Rennes, France, October 2007. (slides.pdf)

  • 2nd International Course in Yeast Systems Biology, ICYSB : "Inferring the role of transcription factors in regulatory networks". Goteborg, Sweden, June 2007. (slides.pdf)

  • C Guziolowski, P Veber, M Le Borgne, O Radulescu, A Siegel 'Checking Consistency Between Expression Data and Large Scale Regulatory Networks: A Case Study' , RIAMS'06: Réseaux d'interaction, analyse, modélisation et simulation. Lyon, France 2006. (file.pdf) (slides)

Oral communications given as internal seminars

• • Seminar at the European Bioinformatics Institute: "Generating and optimizing signaling networks". Cambridge, UK, April 2012

  • Seminar at the Institute de Recherche en Communications et Cybernetique de Nantes: "Constraint-based modeling of large-scale biological systems". Nantes, France, March 2012

  • Seminar at Laboratorie Bordelais de Recherche en Informatique: "Constraint-based modeling of large-scale biological systems". Bordeaux, France, January 2012.

  • Seminar at Laboratoire d'Informatique, Signaux et Systèmes de Sophia-Antipolis: "Constraint-based modeling of large-scale biological systems". Nice, France, December 2011.

  • Seminar at Institute of Systems and Synthetic Biology: "Constraint-based modeling of large-scale biological systems". Evry, France, October 2011. (slides.pdf)

  • Seminar at Max Plank Institute Magdeburg: "Analysis of Large-Scale Biological Networks with Constraint-Based Approaches over Static Models". Magdeburg, Germany, July 2011. (slides.pdf)

  • Bioinformatic seminar at the Symbiose team, INRIA Rennes - Bretagne Atlantique, 2008. (slides.pdf)