Publications

2010

Inference in particle tracking experiments by passing messages between images. M. Chertkov, L. Kroc, F. Krzakala, M. Vergassola & L. Zdeborova, Proceed. Nat. Acad. Sciences, 107, 7663-7368, 2010.

Phase transitions in the distribution of bipartite entanglement of a random pure state. C. Nadal, S.N. Majumdar & M. Vergassola, Phys. Rev. Lett., 104, 110501, 2010.

Quantifying biomolecule diffusivity using an optimal Bayesian method. G. Voisinne, A. Alexandrou & J.B. Masson, Biophysical Journal, 98, 596-605, 2010.

Bacterial strategies for chemotaxis response. A. Celani & M. Vergassola, Proceed. Nat. Acad. Sciences, 107, 1391-1396, 2010.

2009

Chasing information to search in random environments. J.B. Masson, M. Bailly-Bechet, M. Vergassola, J. Phys. A, vol 42 p 434009 special issue on random search problems. 

Repulsion and metabolic switches in the collective behavior of bacterial colonies. A. Sekowska, J.B. Masson, A. Celani, A. Danchin, M. Vergassola, Biophys. J., vol 97 p 688-698, August 2009

Inferring maps of forces inside cell membrane microdomains. Masson JB, Casanova D, Türkcan S, Voisinne G, Popoff MR, Vergassola M, Alexandrou A. Phys Rev Lett. 102 048103. 2009.
Featured in Virtual Journal of Biol. Phys. Research – Feb. 1, 2009, Volume 17, Issue 3;
Virtual Journal of Nanoscale Science & Technology – Feb. 9, 2009, Volume 19, issue 6.

The Listeria transcriptional landscape from saprophytism to virulence. Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H, Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy M, Vergassola M, Nahori MA, Soubigou G, Régnault B, Coppée JY, Lecuit M, Johansson J, Cossart P. Nature. 459 950-6 2009.

Large deviations of the maximum eigenvalue for Wishart and Gaussian random matrices. Majumdar SN, Vergassola M. Phys Rev Lett. 102 060601 2009.

Phase-field model for the Rayleigh-Taylor instability of immiscible fluids. Celani A, Mazzino A, Muratore-Ginanneschi P, L. Vozella Journal of Fluid Mechanics 622 115-134, 2009.

Extended Fano model of extraordinary electromagnetic transmission through subwavelength hole arrays in the terahertz domain J-B Masson, A Podzorov, G Gallot, Optics Express 2009, Vol 17, issue 17, pp 15280-15291.

2008

Message-passing algorithms for the prediction of protein domain interactions from protein-protein interaction data. M. Iqbal, A.A. Freitas, C.G. Johnson, M. Vergassola, Bioinformatics, 24 2064-70, 2008.

Collective behavior in the invasion of a network of channels by a wetting liquid. X. C. Wang , C. N. Baroud, J.-B Masson, Journal of Colloidal and Interface Science, 36 445-50 2008.

A model for thermal exchange in axons during action potential propagation J.-B Masson & G..Gallot European Biophysical Journal, 27 1001-6, 2008.

Anomalies in the vanishing of the extraordinary transmission through subwavelength hole array.J.-B Masson, A. Podzorov & G. Gallot, Optics Express, 16, 4719-30, 2008

The equivalent size of cloud condensation nuclei. Celani A, Mazzino A, Tizzi M New Journal of Physics 10 075021, 2008

Two-dimensional elastic turbulence. Berti S, Bistagnino A, Boffetta G Celani A Musacchio S Physical Review E 77 055306, 2008

A simple model of genetic oscillations through regulated degradation Bottani S, Grammaticos B., Chaos, Solitons and Fractals, 38, 1468-1482, 2008.

Cellular reactions to gene dosage imbalance: genomic, transcriptomic and proteomic effects. Veitia R, Bottani S, Birchler J. Trends in Genetics, 24, 390-397, 2008. 

How winding is the coast of Britain? Conformal invariance of rocky shorelines Boffetta G, Celani A, Dezzani D, Seminara A Geophysical Research Letters 35, L03615, 2008.

2007

Infotaxis as a strategy for searching without gradients. M. Vergassola, E. Villermaux & B.I. Shraiman Nature, 445, 406-409, 2007. 

Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets. P. Mandin*, F. Repoila*, M. Vergassola*, T. Geissmann & P. Cossart Nucleic Acids Research, 35: 962-74 2007 (*Equal contributions). 

Causes for the intriguing presence of tRNAs in phages. M. Bailly-Bechet, M. Vergassola & EPC Rocha 2007 Genome Research, 17, 1486-1495, 2007. 

Transcription factor concentrations versus binding site affinities in the yeast S. cerevisiae. E. Aurell, A. Fouquier d’Herouel, C. Malmnas & M. Vergassola Physical Biology, 4: 134-143, 2007. 

Sinuosities in vascular structures J.-B Masson & J.-L Martin European Physical Journal Applied Physics, 40, No 3 (2007). 

Direct observation of ligand transfer and bond formation in cytochrome c oxidase using mid-infrared chirped pulse up conversion J. Treuffet, K. J. Kubarych, J.-C. Lambry, E. Pilet, J.-B. Masson, J.-L. Martin, M. H. Vos, M. Joffre, & A. Alexandrou Proc. Nat. Acad. Sci. USA, 104, 15705-15710 (2007) 

Ionic contrast terahertz near-field imaging of axonal activity and water fluxes J.-B. Masson, M.-P. Sauviat, J.-L. Martin & G. Gallot Proceedings of the SPIE 6441 (2007) 

True near field versus contrast near field imaging. II. imaging with a probe J.-B. Masson & G. Gallot Optics Express 15, 3078 (2007). 

Inverse turbulent cascades and conformally invariant curves. Bernard D, Boffetta G, Celani A, Falkovich G, Phys. Rev. Lett., 98(2), 024501, 2007. 

Nonlinear dynamics of the viscoelastic Kolmogorov flow. A. Bistagnino, G. Boffetta, A. Celani, A. Mazzino, A. Puliafito, M. Vergassola, J. Fluid Mechanics, 590, 61-80, 2007, 

The frontiers of computing in turbulence: challenges and perspectives. Celani A. Journal of Turbulence, 8 (34), 1-9, 2007. 

Point-source scalar turbulence Celani A, Afonso MM, Mazzino A Journal of fluid Mechanics 583 189-198 2007. 

The Eulerian description of dilute collisionless suspension Boffetta G, Celani A, De Lillo, Musacchio S, EPL 78(1) 14001, 2007 

Droplet condensation in two-dimensional Bolgiano turbulence
Celani A Mazzino A, Seminara A, Tizzi M Journal of Turbulence 8(17) 1-9 2007.

Analysis of a minimal model for p53 oscillations Bottani S, Grammaticos B Journal of Theoretical Biology 249(2) 235-245, 2007

2005-2006

Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages. Fischer G, Rocha EPC, Brunet F, Vergassola M, Dujon B PLoS Gen. 2: 253-261, 2006.

True near field versus contrast near field imaging.  J.-B. Masson & G. Gallot Optics Express 14, 11566 (2006).

Ionic contrast terahertz time resolved imaging of frog auricular heart muscle electrical activity .
J.-B Masson & Guilhem Gallot, Appl. Phys. Lett. 89, 153904 (2006)

Coupling between surface plasmons in subwavelength hole arrays. 
J.-B. Masson & G. Gallot, Phys. Rev. B. 73, 121401(R) (2006).

Ionic Contrast Terahertz Near Field Imaging of Axonal Activity and Water Fluxes
.  J.-B. Masson, M.-P Sauviat, J.-L Martin & G. Gallot Proc. Nat. Acad. Sci. USA 103, 4808 (2006).

Codon usage domains over bacterial chromosomes
Bailly-Bechet M, Danchin A, Iqbal M, Marsili M, Vergassola M PLoS Computational Biology 2(4): 263-275, 2006. 

Terahertz achromtatic quater wave plate.  J.-B. Masson & G. Gallot Opt. Lett. 31, 265 (2006).

Mecanisms involved in the swelling of the erythrocytes caused by pacific and caribbean ciguatoxins. M.-P. Sauviat, R.B.-L. Garrec, J.-B. Masson, R.L. Lewis, J.-P. Vernoux, J. Molgoe, D. Laurent, E. Benoit Blood Cells Molecules and Diseases 36, 1 (2006).

Cooperative evolution in protein complexes of yeast from comparative analyses of its interaction network. Vergassola M, Vespignani A, Dujon B Proteomics 5(12): 3116-3119, 2005. 

VirR, a response regulator critical for Listeria monocytogenes virulence Mandin P, Fsihi H, Dussurget O, Vergassola M, Milohanic E, Toledo-Arana A, Lasa I, Johansson J, Cossart P Molecular Microbiology 57(5): 1367-1380, 2005. 

Shear effects on passive scalar spectra
Celani A, Cencini M, Vergassola M, Villermaux E, Vincenzi D Journal of Fluid Mechanics 523: 99-108 2005.

The viscoelastic Kolmogorov flow: eddy viscosity and linear stability Boffetta G, Celani A, Mazzino A, Puliafito A, Vergassola M Journal of Fluid Mechanics 523: 161-170 2005. 

An evolutionary and functional assessment of regulatory network motifs Mazurie A, Bottani S, Vergassola M Genome Biology 6(4): Art. No. R35 2005.