Netadis – Early Stage Researchers’ publications

Extended Plefka Expansion for Stochastic Dynamics
B. Bravi, P. Sollich, M. Opper
Phys. A., arXiv:1509.07066 (2015)

The unconventionality of Nature: Biology, from Noise to Functional Randomness, Unconventional Computation & Natural Computation Conference (UCNC)
B. Bravi, G. Longo
Auckland (NZ) 31/8 – 4/9/2015, proceedings in Springer LNCS 9252, C. Calude and M.J. Dinneen (Eds.), pp. 3-34 (2015)

Inferring hidden states in a random  kinetic ising model: replica analysis
L. Bachschmid-Romano and M. Opper, Journal of Statistical Mechanics: Theory and Experiment, 2014(6):P06013, 2014.

Belief propagation and replicas for inference and learning in a kinetic Ising model with hidden spins
Battistin C, Hertz J, Tyrcha J, Roudi Y.
Journal of Statistical Mechanics: Theory and Experiment. 2015

Variational perturbation and extended Plefka approaches to dynamics on random networks: the case of the kinetic Ising model” by Bachschmid-Romano, Ludovica; Battistin, Claudia; Opper, Manfred; Roudi, Yasser (to be submitted)

L Bachschmid-Romano, C Battistin, M Opper, Y Roudi. On variational and extended Plefka approach to the dynamics of Ising spin glasses. 2016. (Manuscript in preparation)

Non-equilibrium statistical mechanics of the heat bath for two Brownian particles
Caterina De Bacco, Fulvio Baldovin,Enzo Orlandini and Ken Sekimoto, PRL 112, 180605 (2014)

Shortest node-disjoint paths on random graphs
De Bacco, C., Franz, S., Saad, D., & Yeung, C. H. (2014). arXiv preprint arXiv:1401.8096

The average number of distinct sites visited by a random walker on random graphs, C. De Bacco, P. Sollich, S. Majumdar, Journal of Physics A: 48.20 (2015): 205004; 2014

The edge-disjoint path problem on random graphs by message-passing, F.Altarelli, A. Braunstein, L. Dall’Asta, C. De Bacco and S. Franz, PloS one 10.12 (2015).

A matrix product algorithm for stochastic dynamics on locally tree-like graphs, Barthel, C. De Bacco, S. Franz, http://arxiv.org/abs/1508.03295

Mean field spin glasses treated with PDE techniques
Adriano Barra, Gino Del Ferraro, Daniele Tantari
Eur. Phys. J. B (2013) 86: 332
DOI: 10.1140/epjb/e2013-40334-6

“Anergy in self-directed B lymphocytes from a statistical mechanics perspective
Elena Agliari , Adriano Barra , Gino Del Ferraro , Francesco Guerra , Daniele Tantari, Journal of Theoretical Biology,Volume 375, 21 June 2015, Pages 21–31

Perturbative large deviation analysis of non-equilibrium dynamics
Gino Del Ferraro and Erik Aurell
arXiv:1401.4685v1 [cond-mat.stat-mech] 19 Jan 2014

Causal analysis, Correlation-Response and Dynamic cavity. Erik Aurell and G. Del Ferraro. arXiv:1512.00763. Accepted in Journal of the Physical Society of Japan (JPSJ).

On one-step replica symmetry breaking in the Edwards-Anderson spin glass model”. G. Del Ferraro, Chuang Wang, Hai-Jun Zhou, Erik Aurell. arXiv:1507.00574. Under review in Journal of Statistical Mechanics: Theory and Experiment (JSTAT)

Cavity Method: Message Passing from a Physics perspective
G. Del Ferraro, Chuang Wang, Dani Martì, Marc Mézard. Book chapter of ”Statistical Physics, Optimization, Inference, and Message-Passing Algorithms”. Eds.: F. Krzakala, F. Ricci-Tersenghi, L. Zdeborova, R. Zecchina, E. W. Tramel, L. F. Cuglian- dolo (Oxford University Press, to appear). Published in “Oxford University Press”, see also arXiv:1409.3048.

Dynamic message-passing approach for kinetic spin models with reversible dynamics G. Del Ferraro, Erik Aurell. Phys. Rev. E 92, 010102(R).

Improving contact prediction along three dimensions
Christoph Feinauer, Marcin J. Skwark, Andrea Pagnani, Erik Aurell
arxiv.org/abs/1403.0379, 5 Mar 2014

Zinc finger proteins and the 3D organization of chromosomes.
Feinauer CJ, Hofmann A, Goldt S, Liu L, Máté G, Heermann DW.
Adv Protein Chem Struct Biol. 2013;90:67-117. doi: 10.1016/B978-0-12-410523-2.00003-1. PubMed PMID: 23582202.

Fast and accurate multivariate gaussian modeling of protein families: predicting residue contacts and protein-interaction partners.
Baldassi C, Zamparo M, Feinauer C, Procaccini A, Zecchina R, Weigt M, Pagnani
A., PLoS One. 2014 Mar 24;9(3):e92721. doi: 10.1371/journal.pone.0092721. eCollection 2014. PubMed PMID: 24663061; PubMed Central PMCID: PMC3963956.

Modelling the emergence of polarity patterns for the intercellular transport of auxin in plants.
Grigolon S, Sollich P, Martin OC. 2015 J. R. Soc. Interface 12: 20141223.

Identifying relevant positions in proteins by Critical Variable Selection
Silvia Grigolon, Silvio Franz, Matteo Marsili, Mol. BioSyst.,2016
http://arxiv.org/abs/1503.03815

Silvia Grigolon, Modelling and inference for biological systems : from auxin dynamics in plants to protein sequences, D. Thesis, September 2015, theses.fr/2015PA112178

Silvia Grigolon, Barbara Bravi, Peter Sollich, Olivier C. Martin, ARF response to auxin signalling in plants: an operating principle for stability yet dynamical sensitivity, in preparation.

Silvia Grigolon, Francesca Di Patti, Andrea De Martino and Enzo Marinari
Heliyon, 2 (2016) e00095

Minimal contagious sets in random regular graphs
Alberto Guggiola, Guilhem Semerjian, arXiv:1407.7361

Rare events statistics of random walks on networks: localization and other dynamical phase transitions, Caterina De Bacco, Alberto Guggiola, Reimer Kühn, Pierre Paga, J. Phys. A (arxiv: http://arxiv.org/pdf/1506.08436.pdf)

Haimovici A, Marsili M, Criticality of mostly informative samples: a Bayesian model selection approach, Journal of Statistical Mechanics: Theory and Experiment, 2015

Martirosyan A, Figliuzzi M, Marinari E, De Martino A. Probing the Limits to MicroRNA-Mediated Control of Gene Expression. PLoS Comput. Biol. 12(1): e1004715, 2016.

Inference for interacting linear waves in ordered and random media, P Tyagi, A Pagnani, F Antenucci, M Ibánez Berganza and L Leuzzi, Tyagi et al J. Stat. Mech. (2015) P05031 doi:10.1088/1742-5468/2015/05/P05031

CODES AND SOFTWARES 

  • Grigolon, F. Di Patti, A. De Martino and E. Marinari, Gillespie’s C-codes for the revisited Feed-Forward Loop described in 4. Available at: chimera.roma1.infn.it/SYSBIO/
  • Grigolon, P. Sollich and O. C. Martin, Codes described in 1 available on the webpage of the paper.

POSTERS

Inferring hidden states in a random kineticising model: replica analysis
Ludovica Bachschmid-Romano and Manfred Opper

BP for learning networks with hidden units
C. Battistin, Y. Roudi, J. Tyrcha, J. Hertz

Gaussian average method for the kinetic Ising model
Claudia Battistin & Yasser Roudi

Mean field spin glasses treated with PDE techniques
A. Barra, G. Del Ferraro, D. Tantari

Review of Protein Residue Contact Inference
C. Feinauer, A. Pagnani, R. Zecchina

Accurate contact prediction in proteins: using pseudolikelihoods with gap term to infer Potts models
Christoph Feinauer , Marcin J. Skwark, Erik Aurell

Modeling the emergence of polarity patterns in meristemic auxin transport
Silvia Grigolon , Peter Sollich and Olivier C. Martin

Mapping between sequence and response paces in the olfactory system in Drosophila
Alberto Guggiola, Matteo Marsili

Information Processing in Post-Transcriptional Networks
Araks Martirosyan, Matteo Figliuzzi, Andrea De Martino, Enzo Marinari

Heterogeneity, interactions and credit risk
Reimer Kuehn and Pierre Paga

Investigating random laser through study of disordered systems
Payal Tyagi and Luca Leuzzi

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