Publications and talks

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My preprints/reprints at the Los Alamos Preprint Archive (cond-mat) (q-bio)


In Review

Reviewed

Proceedings



Refereed Journals



2015

Satya Swarup Samal, Dima Grigoriev, Holger Fröhlich, Andreas Weber, Ovidiu Radulescu. A geometric method for model reduction of biochemical networks with polynomial rate functions.
Bulletin of Mathematical Biology, in press.

 

Radulescu, O., Vakulenko, S., Grigoriev, D.. Model reduction of biochemical reactions networks by tropical analysis methods.
Mathematical Model of Natural Phenomena 10(3), 124-138 (2015).

 

Marc-Antoine Fardin, Ovidiu Radulescu, Alexander Morozov, Olivier Cardoso, Julien Browaeys, Sandra Lerouge. Stress diffusion in shear banding wormlike micelles,
Journal of Rheology 59(6):1335 (2015).

 

Radulescu, O., Samal, S.S. Naldi, A., Grigoriev, D. and Weber, A.: Symbolic dynamics of biochemical pathways as finite states machines. In: Roux, O. and Bourdon, J. (ed.)
Computational Methods in Systems Biology: 13th International Conference, CMSB 2015, Nantes, France, September 16-18, 2015, Proceedings. Lecture Notes in Computer Science,

vol. 9308, pp. 104-120. Springer (2015).

 

Samal, S.S., Grigoriev, D., Fröhlich, H., Radulescu, O.. Analysis of reaction network systems using tropical geometry. In: Gerdt, V.P., Koepf, W., Seiler, W.M., Vorozhtsov, E.V. (eds.)
Computer Algebra in Scientific Computing - 17th International Workshop (CASC 2015). Lecture Notes in Computer Science, vol. 9301, pp. 422-437. Springer, Aachen, Germany (Sep 2015).

2014

Samal, S.S., Radulescu, O., Grigoriev, D., Fröhlich, H., Weber, A.. A tropical method based on newton polygon approach for algebraic analysis of biochemical reaction networks.
 In: 9th European Conference on Mathematical and Theoretical Biology (2014).

 

Sylvain Soliman, Francois Fages, and Ovidiu Radulescu. A constraint solving approach to model reduction by tropical equilibration. Algorithms for Molecular Biology, 9(1):24, 2014.

 

Vincent Noel, Dima Grigoriev, Sergei Vakulenko, and Ovidiu Radulescu. Tropicalization and tropical equilibration of chemical reactions. In G Litvinov and S Sergeev, editors,
Tropical and Idempotent Mathematics and Applications, volume 616 of Contemporary Mathematics, pages 261-277, American Mathematical Soc., 2014.


2013


P.Sen, H.J. Vial, and O.Radulescu. Kinetic modelling of phospholipid synthesis in Plasmodium knowlesi unravels crucial steps and relative importance of multiple pathways.
BMC Systems Biology 2013, 7:123
(link).


GCP Innocentini, M.Forger,  A.F.Ramos, O.Radulescu, JEM Hornos. Multi-modality and flexibility of stochastic gene expression. In press, Bulletin of Mathematical Biology.


V.Noel, S.Vakulenko, O.Radulescu. A hybrid mammalian cell cycle model. EPTCS (2013) 125: 68-83 (preprint).


V.Noel, D.Grigoriev, S.Vakulenko, O.Radulescu. Tropicalization and tropical equilibration of chemical reactions. In press, Contemporary Mathematics, Tropical and Idempotent Mathematics and Applications, GL Litvinov and S. Sergeev, AMS.
 
(preprint


2012


O.Radulescu, A.N.Gorban, A.Zinovyev, V.Noel. Reduction of dynamical biochemical reaction networks in computational biology. Frontiers in Bioinformatics

and Computational Biology (2012) 3.  (preprint)(link).

O.Radulescu, GCP Innocentini, JEM Hornos. Relating network rigidity, time scale hierarchies, and expression noise in gene networks, Physical Reviews E 85 (2012) 041919. (preprint).

S.Vakulenko, O.Radulescu. Flexible and robust patterning by centralized gene networks,  Fundamenta Informaticae 119 (2012) 1-25. (preprint).


S.Vakulenko, O.Radulescu. Flexible and robust networks, Journal of Bioinformatics and Computational Biology 2 (2012) 1241011. (preprint).


M.L. Ferguson, D. Le Coq, M. Jules, S. Aymerich, O.Radulescu, N. Declerck, C.A. Royer. Reconciling molecular regulatory mechanisms with noise
patterns of bacterial metabolic promoters in induced and repressed states, Proceedings of the National Academy of Sciences USA, 109, 155, 2012.
(link).

V.Noel, D.Grigoriev, S.Vakulenko, O.Radulescu, Tropical geometries and dynamics of biochemical networks. Application to hybrid cell cycle models.
SASB 2011, Electronic Notes in Theoretical Computer Science
Volume 284, 20 June 2012, Pages 75–91. (preprint).

V.Noel, D.Grigoriev, S.Vakulenko, O.Radulescu. Hybrid models of the cell cycle molecular machinery. EPTCS (2012) 92: 88-105 (preprint).

2011


V.Noel, S.Vakulenko, O.Radulescu,
Algorithm for Identification of Piecewise Smooth Hybrid Systems: Application to Eukaryotic Cell Cycle Regulation.
 WABI 2011, in press
Lecture Notes in Computer Science 6833 Springer 2011, ISBN 978-3-642-23037-0. (preprint).


A.Crudu, A.Debussche, A.Muller, O.Radulescu, Convergence of stochastic gene networks to hybrid piecewise deterministic processes,
  in press Annals of Applied Probability. (preprint
).


Ovidiu Radulescu, Anne Siegel, Elisabeth Pécou, Clément Chatelain, Sandrine Lagarrigue. Genetically regulated metabolic
networks: Gale-Nikaido modules and differential inequalities, in Transactions in Computational Systems Biology XIII, LNBI 6575, Springer 2011
(preprint).


2010

Baumuratova T, Surdez D, Delyon B, Stoll G, Delattre O, Radulescu O, Siegel A. Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network. 
BMC Systems Biology (2010) 2;4(1):146. (link).


Carito Guziolowski, Sylvain Blacho, Tatiana Baumuratova, Gautier Stoll, Ovidiu Radulescu, Anne Siegel. Designing Logical Rules to
Model the Response of Biomolecular Networks with Complex Interactions: An Application to Cancer Modeling. IEEE/ACM Trans.
Comp. Bio. Bioinformatics, 99 (2010) 1545-5963
(link)


A.N. Gorban, O.Radulescu, A. Zinovyev, Asymptotology of Chemical Reaction Networks,

Chemical Engineering Science, Chem.Eng.Sci. 65 (2010) 2310-2324. (link). (preprint).


2009


S.Vakulenko, Manu, J.Reinitz, O.Radulescu, Size Regulation in the Segmentation of Drosophila: Interacting Interfaces between

Localized Domains of Gene Expression Ensure Robust Spatial Patterning, Phys.Rev.Lett. (2009) 103, 168102. (link). also selected by
Virtual Journals, Vir.J.Bio.Phys.Res. (2009) 18,9
(link) (preprint)(supplemental).

 

A.Crudu, A.Debussche, O.Radulescu, Hybrid stochastic simplifications for multiscale gene networks, BMC Systems Biology (2009) 3:89. (link).

 

P. Blavy, F. Gondret, H. Guillou, S. Lagarrigue, P.G.P., Martin, J. van Milgen, O. Radulescu and Siegel, A. A minimal model for hepatic fatty acid

balance during fasting: Application to PPAR alpha-deficient mice, Journal of Theoretical Biology, 261 (2009), pp. 266-278.

 

B.Lasne, O.Radulescu, S.Lerouge, Echelles de temps et instabilités dans un système rhéofludifiant de micelles géantes,

à paraitre dans Rhéologie, revue du GFR.

 

Manu, S.Surkova, AV.Spirov, V.Gursky, H.Janssens, A.Kim, O.Radulescu, CE.Vanario-Alonso, 

D.H.Sharp, M.Samsonova, J.Reinitz. Canalization of gene expression and domain shifts in the Drosophila

blastoderm by dynamical attractors,  PLoS Computational Biology 2009 (link).

 

Manu, S.Surkova, AV.Spirov, V.Gursky, H.Janssens, A.Kim, O.Radulescu, CE.Vanario-Alonso, 

D.H.Sharp, M.Samsonova, J.Reinitz. Canalization of gene expression in the Drosophila blastoderm by

gap genes cross regulation,  PLoS Biology 2009 (link).

 

Carito Guziolowski, Jeremy Gruel, Ovidiu Radulescu, Anne Siegel, Curating a Large-Scale Regulatory Network by Evaluating its Consistency with Expression Datasets, accepted LNBI/LNCS series, Springer (preprint).

2008

Christophe Lavelle, Hugues Berry, Guillaume Beslon, Francesco Ginelli, Jean-Louis Giavitto, Zoi Kapoula, André Le Bivic, Nadine Peyrieras, Ovidiu Radulescu, Adrien Six, Véronique Thomas-Vaslin,  Paul Bourgine, "From Molecules to Organisms: Towards Multiscale Integrated Models of Biological Systems", Theoretical Biology Insights 2008, 1:13-22.

O.Radulescu, A.N.Gorban, A.Zinovyev,  A.Lilienbaum, "Robust simplifications of multiscale biochemical networks", BMC 
Systems Biology, 2008, 2:86. (link) highlighted "most accessed" by BMC in november 2008.
 

Dynamic and static limitation in reaction networks, revisited

A.N.Gorban and O. Radulescu, invited paper Advances in Chemical Engineering, Vol 34, 103-173, 2008. (preprint)

 

Inferring the role of transcription factors as inducers or repressors in regulatory

networks Ph. Veber, C. Guziolowski, M. Le Borgne, O.Radulescu, and A.Siegel BMC Bioinformatics 2008, 9:228. (preprint)

2007

Checking Consistency Between Expression Data and Large Scale Regulatory Networks: A Case Study
C.Guziolowski, P.Veber, M. Le Borgne, O.Radulescu, A.Siegel, J.Biol.Phys.Chem. 2007, Volume 7, Number 2, p.p. 37-43. (
preprint
)

Dynamical robustness of biological networks with hierarchical distribution of time scales.
A.Gorban, O. Radulescu IET Systems Biology (2007) 1: 238-246. (preprint)

Optimiser un plan d’expérience à partir de modèles qualitatifs.
A. Siegel, C.Vargas, Ph. Veber, O. Radulescu, M. le Borgne Biofutur, (2007) 27-31

Theoremes limites pour des processus de Markov a sauts. Synthese des resultats et applications en biologie moleculaire
O. Radulescu, A. Muller, A. Crudu, TSI (Technique et Science Informatiques) (2007) 26/3-4: 443-469. (preprint)

2006

Topology and static response of interaction networks in molecular biology.
O. Radulescu, S. Lagarrigue, A. Siegel, , M. Le Borgne, P. Veber, Royal Society Interfaces, 3 (2006) 185-196 (preprint)

Qualitative analysis of the relation between DNA microarray data and behavioral models of regulation networks.
A. Siegel, O. Radulescu, M. Le Borgne, P. Veber, J. Ouy, S. Lagarrigue, Biosystems 84 (2006) 153-174. (preprint)

1990-2004

Complex Qualitative Models in Biology: a new approach.
Ph.Veber, M. Le Borgne, A. Siegel, O. Radulescu, Complexus 2 (2004-5) 140-151. (preprint)

Theory of Phasons in Aperiodic Crystals
T. Janssen, O Radulescu, Ferroelectrics 305 (2004) 179-184, (
reprint
).

Timescales in shear banding of wormlike micelles.
O.Radulescu, P.D.Olmsted, J.P.Decruppe, S.Lerouge, J.F.Berret, G.Porte, Europhys. Lett. 62 (2) (2003) 230-236. (
preprint
)

Dynamics of modulated and composite aperiodic crystals: the signature of the inner polarization in the neutron coherent inelastic scattering.
O Radulescu, T Janssen, and J Etrillard, Eur.Phys.J. B 29 (2002) 385 (
reprint
).

Phasons, sliding modes and friction.
T. Janssen, O. Radulescu, and A.N. Rubtsov, Eur.Phys.J. B 29 (2002) 85-95 (
reprint
).

Models of Commensurate and Incommensurate Composites
O Radulescu, Ferroelectrics 250 (2001) 43-46, (
preprint
).

Matched Asymptotic Solutions for the Steady Banded Flow of the Johnson-Segalman Model in Various Geometries
O Radulescu and PD Olmsted, Journal of non-Newtonian Fluid Mechanics 91 (2000) 141-162 (
preprint
), (reprint).

The Johnson-Segalman model with a diffusion term: a mechanism for stress selection
PD Olmsted, O Radulescu, and CYD Lu,
Journal of Rheology 44 (2000) 257-275
(preprint), (reprint).

One-dimensional quasicrystals related to decagonal Al-Co-Ni
S Ritsch, O Radulescu, C Beeli, K Hiraga, R Luck, and DH Warrington, Philosophical Magazine Letters 80 (2000) 107-118

Shear-banding in reaction-diffusion models
O Radulescu and PD Olmsted,
Rheologica Acta 38 (1999) 606-613
, (reprint).

Sliding mode and analyticity breaking in the double-chain model of incommensurate composites
O Radulescu and T Janssen, PHYSICAL REVIEW B-CONDENSED MATTER 60 (1999) 12737- 12745, (
preprint
).

Pinning and phonon localization in Frenkel-Kontorova models on quasiperiodic substrates
TS vanErp, A Fasolino, O Radulescu, and T Janssen, PHYSICAL REVIEW B-CONDENSED MATTER 60 (1999) 6522- 6528, (
preprint
).

Arithmetic properties of spectra produced by Farey hierarchies of approximants
O Radulescu and T Janssen, JOURNAL OF MATHEMATICAL PHYSICS 40 (1999) 1317- 1333., (
reprint
).

Domain wall motion in aperiodic crystal systems and magnetoelectrics
T Janssen and O Radulescu, Zeitschrift fur Physik B 104 (1997) 657-660.

Dynamics of lattice vibrations for 1-D commensurate and incommensurate composites with harmonic interaction
O Radulescu and T Janssen, Journal of Physics A 30 (1997) 4199-4214, (
reprint
).

Coincidence quasilattices and coincidence modules for icosahedral quasicrystals
DH Warrington, O Radulescu and R Luck, Acta Crystallographica A53 (1997) 314-328.

Twins of quasicrystals and of rational approximants
O Radulescu and DH Warrington, Materials Science Forum 207-209 (1996) 329-332.

An elementary approach to the crystallography of twins in icosahedral quasicrystals
O Radulescu, Journal de Physique I France 5 (1995) 719-728.

Arithmetic properties of quasicrystals, coincidence modules and coincidence quasilattices
O Radulescu and DH Warrington Acta Crystallographica A51 (1995) 134-156.

A classification of the periodic directions in the rational approximants of icosahedral quasicrystals
O Radulescu, Journal de Physique I France 3 (1993) 2099-2113.

A visibility threshold for rational approximants
O Radulescu and M Kléman, Journal of Non-crystalline Solids 153-154 (1993) 227-231.

Périodicité et quasi-périodicité dans les structures à ordre local icosahédrique
O Radulescu and M Kléman, Comptes-rendus de l'Académie des Sciences t.315 II (1992) 1629.

On the bond orientational order in icosahedral phases
O Radulescu and R Manaila, Physica Status Solidi (b) 161 (1990) 65.

On the transition-metal quasisublattice in icosahedral Al-Cr-Fe phases
R Manaila, V Florescu, A Jianu and O Radulescu, Philosophical Magazine B 60 (1989) 589-599.

Conference Proceedings


S.Soliman, F.Fages, O.Radulescu. A Constraint Solving Approach to Tropical Equilibration and Model Reduction. In Proceedings of the ninth Workshop on Constraint Based Methods for Bioinformatics WCB'13, colocated with CP 2013, pages 27–36, 2013.

V.Noel, D.Grigoriev, S.Vakulenko, O.Radulescu. Hybrid models of the cell cycle molecular machinery, HSB-2012, Newcastle, September 2012  (preprint).

V.Noel, D.Grigoriev, S.Vakulenko, O.Radulescu. Tropicalization of systems biology models, TROPICAL-12, Moscow, August 2012. (abstract).

Ovidiu Radulescu, Alexander Gorban, and Andrei Zinovyev. Pruning, pooling and limiting steps in metabolic
networks. Proceedings of Evry school
2010 "Modelling Complex Biological Systems in the Context of Genomics". (preprint).

Sylvain Blachon, Gautier Stoll, Carito Guziolowski, Andrei Zinovyev, Emmanuel Barillot, Anne Siegel, Ovidiu Radulescu: Method for Relating Inter-patient Gene
Copy Numbers Variations with Gene Expression via Gene Influence Networks. AIAI Workshops 2009: 72-87

Static and Dynamic properties of commensurate ans incommensurate composites
O Radulescu and T Janssen, in Proceedings of the International Conference on Aperiodic Crystals Aperiodic '97, M de Boissieu, JL Verger-Gaugry and R Currat edts., World Scientific (1998).

Phason flips and reconstruction of grain boundaries in quasicrystals
O Radulescu, DH Warrington and R Luck, in Proceedings of the International Conference on Aperiodic Crystals Aperiodic '97, M de Boissieu, JL Verger-Gaugry and R Currat edts., World Scientific (1998).

Recent talks


Tropical approaches to multi-scaleness of chemical reactions  (Montpellier, 2013) (slides)
Hybrid models of the cell cycle molecular machinery (Newcastle, 2012) (slides

Talks 2005-2007

Aspects stochastiques de la dynamique de reseaux en biologie moleculaire (in French) (slides)

Raisonnements qualitatifs sur reseaux : applications en genomique fonctionnelle, seminaire Institut Curie 2005, (in French) (slides)

Concentration and spectral robustness of biological networks, ECCS'05 (in English) (slides)

New qualitative approaches in molecular biology, Bangalore meeting 2006 (in English) (slides)

Hierarchies and modules in complex biological systems, ECCS conference september 2006 (in English) (slides)

Modèles mathématiques de la complexité en biologie moléculaire et en mécanique des fluides
Habilitation à diriger des recherches soutenue le 11/12/2006 (document de synthèse)(slides)(live)

Improving model consistency by qualitative equations, INRIA-NIH meeting Bethesda April 2007 (in English) (slides)

Interfaces and shear banding, Euromech meeting on "Shear Banding" London September 2007 (in English) (slides)

Hierarchical models in systems biology, CEA-EDF-INRA School "Model Reduction" Rocquencourt October 2007 (in English) (slides)

Mathématiques des cellules, conférence grand public dans le "Festival des sciences" de Rennes Metropole, Octobre 2007 (in french) (slides)



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Ovidiu.Radulescu@univ-rennes1.fr

Last modified 20 january 2007