Systems Biology  (and Computational Linguistics)

Application of the Reachability Analysis for the Iron Homeostasis Study.
A. Rocca, T. Dang, Fanchon E, J-M. Moulis.
Lecture Notes in Bioinformatics, LNCS/LNBI 9957, 67-84, 2016. [pdf thru ResearchGate]
Multi-scale modelling of erythropoiesis and of hemoglobin production.
Bouchnita A, Rocca A, Fanchon E, Koury M J, Moulis J-M, Volpert V.
Journal of Inorganic and Organometallic Polymers and Materials, 26, 1362-1379, 2016. [Read on-line, pdf thru ResearchGate]
Molecular mechanisms underlying COPD-muscle dysfunction unveiled through a systems medicine approach.
Marín de Mas I, Fanchon E, Papp B, Kalko S, Roca J, Cascante M.
Bioinformatics, 33, 95-103, 2017. (doi: 10.1093/bioinformatics/btw566).
HepatoDyn: a Dynamic Model of Hepatocyte Metabolism that Integrates 13C Isotopomer Data.
Carles Foguet, Silvia Marin, Vitaly A Selivanov, Eric Fanchon, Pedro de Atauri, Marta Cascante.
PLoS Computational Biology, 12, e1004899 (doi: 10.1371/journal.pcbi.1004899), 2016.
Reduction and Fixed Points of Boolean Networks and Linear Network Coding Solvability.
Gadouleau M, Richard A, Fanchon É.
IEEE Transactions on Information Theory, 62, 2504-2519, 2016. [pdf on arXiv]
Exploiting the Eigenstructure of Linear Systems to speed up Reachability Computations.
Rocca A, Dang T, Fanchon É. 3rd International Workshop on Hybrid Systems and Biology (HSB 2014), Vienna, 2014.
Lecture Notes in Bioinformatics, LNCS/LNBI 7699, 111-127, 2015. [pdf]
Iron for proliferation of cell lines and hematopoietic progenitors: nailing down the intracellular functional iron concentration.
Pourcelot E, Lénon M, Mobilia N, Cahn J-Y, Arnaud J, Fanchon E, Moulis J-M, Mossuz P.
BBA - Molecular Cell Research, 1853, 1596-1605, 2015.
Logical Modeling and Analysis of Regulatory Genetic Networks in a Non Monotonic Framework.
Mobilia M, Rocca A, Chorlton S, Fanchon É, Trilling L.
[Bioinformatics and Biomedical Engineering, 3rd International Conference, IWBBIO 2015, Granada, Spain, April 2015].
Lecture Notes in Bioinformatics, LNCS/LNBI 9043, 599-612, 2015.
ASP for construction and validation of regulatory biological networks.
Rocca A, Mobilia N, Fanchon É, Ribeiro T, Trilling L, Inoue K.
In: Logical Modeling of Biological Systems. L Fariñas del Cerro & K Inoue (eds), Wiley-ISTE, 167-206, 2014.
Cellular Iron Regulation in Animals: Need and Use of Suitable Models.
Pourcelot E, Mobilia N, Donzé A, Louis F, Maler O, P. Mossuz, Fanchon É, Moulis J-M.
In: Nutzen-Risiko-Bewertung von Mineralstoffen and Spurenelementen. Biochemische, physiologische und toxikologische Aspekte. A Hartwig, B Köberle & B Michalke (eds), KIT Scientific Publishing, 73-89, 2014. [full book].
Producing a Set of Models for the Iron Homeostasis Network.
Mobilia N, Donzé A, Moulis, J-M, Fanchon É.
[2nd International Workshop on Hybrid Systems and Biology (HSB 2013), Taormina, Italy, sept 2013].
Electronic Proceedings in Theoretical Computer Science, 125, 92-98. [pdf on arXiv]
On the number of different dynamics in Boolean networks with deterministic update schedules.
Aracena J, Demongeot J, Fanchon É, Montalva M.
Mathematical Biosciences, 242, 188-194, 2013.
Formal Methods for Hopfield-like networks.
Ben Amor H, Corblin F, Fanchon E, Elena A, Trilling L, Demongeot J, Glade G.
Acta Biotheoretica, 61, 21-39, 2013. [pdf]
On the number of update digraphs and its relation with the feedback arc sets and tournaments.
Aracena J, Demongeot J, Fanchon E, Montalva M.
Discrete Applied Mathematics, 161, 1345-1355, 2013. [preprint]
A Model of the Cellular Iron Homeostasis Network Using Semi-Formal Methods for Parameter Space Exploration.
Mobilia N, Donzé A, Moulis, J-M, Fanchon E.
[1st International Workshop on Hybrid Systems and Biology (HSB 2012), Newcastle, UK, sept 2012].
Electronic Proceedings in Theoretical Computer Science, 92, 42-57. [pdf on arXiv]
Automatic inference of regulatory and dynamical properties from incomplete gene interaction and expression data.
Corblin F, Fanchon E, Trilling L, Chaouiya C and Thieffry D.
Information Processing in Cells and Tissues. Lecture Notes in Computer Science, 7223, 25-30, 2012.
Investigating metalloproteinases MMP-2 and MMP-9 mechanosensitivity to feedback loops involved in the regulation on in vitro angiogenesis by endogenous mechanical stresses.
Minh-Uyen Dao Thi, Candice Trocmé, Marie-Paule Montmasson, Eric Fanchon, Bertand Toussaint, Philippe Tracqui.
Acta Biotheoretica, 60, 21-40, 2012.
How many Maxwell's demons, and where?
Eric Fanchon, Klil Ha-Horesh Neori, and Avshalom C. Elitzur.
In: Probability in Physics, Y. Ben-Menahem and M. Hemmo (eds), The Frontier collection, Springer, 2012.
Robustness Analysis and Behavior Discrimination in Enzymatic Reaction Networks.
Alexandre Donzé, Eric Fanchon, Lucie Gattepaille, Oded Maler, Philippe Tracqui.
PLoS ONE, 2011.
Combinatorics on update digraphs in Boolean networks.
Aracena J, Fanchon E, Montalva M, Noual M.
Discrete Applied Mathematics, 159, 401-409, 2011.
Determination, Optimization and Taxonomy of Regulatory Networks: The Example of Arabidopsis thaliana Flower Morphogenesis.
Glade N, Elena A, Corblin F, Fanchon E, Demongeot J, Ben-Amor H.
IEEE AINA' 11 & BLSMC' 11, Singapore, IEEE Proceedings, Piscataway, 2011. [pdf]
Computing with bacterial constituents, cells and populations: from bioputing to bactoputing.
Norris V, Zemirline A, Amar P, Audinot JN, Ballet P, Ben Jacob E, Bernot G, Beslon G, Cabin A, Fanchon E, Giavitto J-L, Glade N, Greussay P, Grondin Y, Foster JA, Hutzler G, Kepes F, Michel O, Molina F, Signorini J, Stano P, Thierry AR.
Theory in Biosciences, 130, 211-228, 2011. [pdf]
Connections and Integration with SAT Solvers: A Survey and a Case Study in Computational Biology.
Corblin F, Bordeaux L, Fanchon E, Hamadi Y, Trilling L.
In: Hybrid Optimization: the 10 years of CP-AI-OR, P. van Hentenryck and M. Milano (eds.), Springer, 2011. [book contents] [pdf]
Applications of a formal approach to decipher discrete genetic networks.
Corblin F, Fanchon E, Trilling L.
BMC Bioinformatics, 11, 385, 2010.
A declarative constraint-based method for analyzing discrete genetic regulatory networks.
Corblin F, Tripodi S, Fanchon E, Ropers D, Trilling L.
Biosystems, 98, 91-104, 2009.
From bioputing to bactoputing : computing with bacteria.
Norris V, Zemirline A, Amar P, Ballet P, Ben Jacob E, Bernot G, Beslon G, Fanchon E, Giavitto J, Glade N, Greussay P, Grondin Y, Foster J, Hutzler G, Kepes F, Michel O, Misevic G, Molina F, Signorini J et Stano P.
Proceedings of the Spring School on Modelling Complex Biological Systems in the Context of Genomics, 123-150, Lille, 2008.  [pdf] [complete proceedings, 2.4Mb]
A SAT-based approach to decipher Gene Regulatory Networks
Corblin F, Bordeaux L, Hamadi Y, Fanchon E, Trilling L.
Integrative Post-Genomics, RIAMS, Lyon, 2007.  [pdf]
Modélisation de réseaux biologiques discrets en Programmation Logique par Contraintes
Corblin F, Fanchon E, Trilling L.
Technique et Science Informatiques, n° spécial Modélisation et simulation pour la post-génomique, Edition Lavoisier, Hermes Sciences, vol. 26, 73-98, 2007. [pdf]
Modeling the molecular network controlling adhesion between human endothelial cells: Inference and simulation using constraint logic programming
Fanchon E, Corblin F, Trilling L, Hermant B, Gulino D.
Computational Methods in Systems Biology, Lecture Notes in Bioinformatics, 3082, 104-118, 2005. [pdf]
Semantically-Based Text Authoring and the Concurrent Documentation of Experimental Protocols
Brun C, Dymetman M, Fanchon E, Lhomme S, Pogodalla S.
Proceedings of the 2003 ACM symposium on Document engineering. [pdf]
Controlled Authoring of Biological Experiment Reports
Brun C, Fanchon E, Dymetman M, Lhomme S.
10th conference of the Association for Computational Linguistics, 2003.  [pdf]


Protein crystallography / Synchrotron radiation diffraction 

Roth M, Carpentier P, Kaikati O, Joly J, Charrault P, Pirocchi M, Kahn R, Fanchon E, et al.
FIP: a highly automated beamline for multiwavelength anomalous diffraction experiments 
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 58: 805-814 Part 5 MAY 2002.  [PubMed]
Carpentier P, Boesecke P, Bois JM, Chesne ML, Fanchon E, et al.
Soft x-ray diffraction up to wavelengths of 6.0 angstrom becomes feasible at ID1 of ESRF 
ACTA PHYSICA POLONICA A 101 (5): 603-612 MAY 2002
Michel G, Chantalat L, Fanchon E, et al.
The iota-carrageenase of Alteromonas fortis - A beta-helix fold-containing enzyme for the degradation of a highly polyanionic polysaccharide 
JOURNAL OF BIOLOGICAL CHEMISTRY 276 (43): 40202-40209 OCT 26 2001  [PubMed]  [free full text @ JBC]
Carpentier P, Capitan M, Chesne ML, Fanchon E, et al.
Anomalous diffraction with soft X-ray synchrotron radiation: DANES from pentakismethylammonium undecachlorodibismuthate at the K absorption edge of chlorine 
JOURNAL OF ALLOYS AND COMPOUNDS 328 (1-2): 64-70 OCT 4 2001  [doi (full text)]
Bertrand JA, Fanchon E, Martin L, et al.
"Open" structures of MurD: Domain movements and structural similarities with folylpolyglutamate synthetase 
JOURNAL OF MOLECULAR BIOLOGY 301 (5): 1257-1266 SEP 1 2000  [PubMed]
Carpentier P, Berthet-Colominas C, Capitan M, Chesne ML, Fanchon E, et al.
Anomalous X-ray diffraction with soft X-ray synchrotron radiation 
CELLULAR AND MOLECULAR BIOLOGY 46 (5): 915-935 JUL 2000  [PubMed]
Kahn R, Carpentier P, Berthet-Colominas C, Capitan M, Chesne ML, Fanchon E, et al.
Feasibility and review of anomalous X-ray diffraction at long wavelengths in materials research and protein crystallography 
JOURNAL OF SYNCHROTRON RADIATION 7: 131-138 Part 3 MAY 2000  [PubMed]
Bertrand JA, Auger G, Martin L, Fanchon E, et al.
Determination of the MurD mechanism through crystallographic analysis of enzyme complexes 
JOURNAL OF MOLECULAR BIOLOGY 289 (3): 579-590 JUN 11 1999  [PubMed]
Ferrer JL, Simon JP, Berar JF, Caillot B, Fanchon E, et al.
D2AM, a beamline with a high-intensity point-focusing fixed-exit monochromator for multiwavelength anomalous diffraction experiments 
JOURNAL OF SYNCHROTRON RADIATION 5: 1346-1356 Part 6 NOV 1 1998  [PubMed]
Auger G, Martin L, Bertrand J, Ferrari P, Fanchon E, et al.
Large-scale preparation, purification, and crystallization of UDP-N-acetyluramoyl-L-alanine: D-glutamate ligase from Escherichia coli 
PROTEIN EXPRESSION AND PURIFICATION 13 (1): 23-29 JUN 1998  [PubMed]
Bertrand JA, Auger G, Fanchon E, et al.
Crystal structure of UDP-N-acetylmuramoyl-L-alanine: D-glutamate ligase from Escherichia coli 
EMBO JOURNAL 16 (12): 3416-3425 JUN 16 1997  [PubMed]
Duée E, Olivier-Deyris L, Fanchon E, et al.
Comparison of the structures of wild-type and a N313T mutant of Escherichia coli glyceraldehyde 3-phosphate dehydrogenases: Implication for NAD binding and cooperativity 
JOURNAL OF MOLECULAR BIOLOGY 257 (4): 814-838 APR 12 1996  [PubMed]
OLIVIER L, BUISSON G, FANCHON E, et al.
CRYSTALLIZATION AND PRELIMINARY-X-RAY DIFFRACTION STUDIES OF ESCHERICHIA-COLI GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 51: 245-247 Part 2 MAR 1 1995  [PubMed]
FERRER JL, ROTH M, FANCHON E, et al.
THERMAL BILAYER MONOCHROMATOR CRYSTAL FOR A HIGH-RESOLUTION MULTIWAVELENGTH ANOMALOUS DIFFRACTION BEAMLINE AT THE EUROPEAN SYNCHROTRON-RADIATION FACILITY 
REVIEW OF SCIENTIFIC INSTRUMENTS 66 (2): 2089-2091 Part 2 FEB 1995
DUÉE ED, FANCHON E, VICAT J, et al.
REFINED CRYSTAL-STRUCTURE OF THE 2[4FE-4S] FERREDOXIN FROM CLOSTRIDIUM-ACIDURICI AT 1.84-ANGSTROM RESOLUTION 
JOURNAL OF MOLECULAR BIOLOGY 243 (4): 683-695 NOV 4 1994  [PubMed]
SIMON JP, GEISSLER E, HECHT AM, BLEY F, LIVET F, ROTH M, FERRER JL, FANCHON E, COHEN-ADDAD C, THIERRY JC
MULTIWAVELENGTH ANOMALOUS DIFFRACTION AND DIFFUSE-SCATTERING BEAM LINE PROJECT ON A BENDING MAGNET AT ESRF 
REVIEW OF SCIENTIFIC INSTRUMENTS 63 (1): 1051-1054 Part 2B JAN 1992  [cat.inist.fr (not free...)]
FANCHON E, HENDRICKSON WA
EFFECT OF THE ANISOTROPY OF ANOMALOUS SCATTERING ON THE MAD PHASING METHOD 
ACTA CRYSTALLOGRAPHICA SECTION A 46: 809-820 Part 10 OCT 1 1990  [PubMed]  [free full text @ iucr]  [doi]

Physics / Material science

FANCHON E, HODEAU JL, VICAT J, et al.
3-DIMENSIONAL ONE-DIMENSIONAL TRANSITION IN THE CS+ SUBLATTICE OF THE MIXED-VALENCE CSTI8O16 HOLLANDITE - STRUCTURES AT 297-K AND 673-K 
JOURNAL OF SOLID STATE CHEMISTRY 92 (1): 88-100 MAY 1991  [doi (full text)]
FANCHON E, VICAT J, HODEAU JL, et al.
COMMENSURATE ORDERING AND DOMAINS IN THE Ba1.2Ti6.8Mg1.2O16 HOLLANDITE 
ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE 43: 440-448 Part 5 OCT 1 1987  [free full text @ iucr]
FANCHON E, VICAT J, QUI DT, et al.
ABSOLUTE STRUCTURE OF LiH2AsO4 
ACTA CRYSTALLOGRAPHICA SECTION C-CRYSTAL STRUCTURE COMMUNICATIONS 43: 1022-1025 Part 6  [free full text @ iucr]  [doi]
FANCHON E, HALOUANI F, DAOUD A, et al.
STRUCTURE OF PIPERAZINE DI-MU-CHLOROBIS[TRIAQUACHLORONICKEL(II)]DICHLORIDE 
ACTA CRYSTALLOGRAPHICA SECTION C-CRYSTAL STRUCTURE COMMUNICATIONS 43: 829-831 Part 5 MAY 15 1987  [free full text @ iucr]  [doi]
VICAT J, FANCHON E, STROBEL P, TRAN QUI D
THE STRUCTURE OF K1.33Mn8O16 AND CATION ORDERING IN HOLLANDITE-TYPE STRUCTURES 
ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE 42: 162-167 Part 2 APR 1 1986  [free full text @ iucr]  [doi]