laboratoire de physique statistique

En Fr

Publications

Rechercher

Simona COCCO

P U B L I C A T I O N S

2016

DOI

On the Entropy of Protein Families - Barton, John P. and Chakraborty, Arup K. and Cocco, Simona and Jacquin, Hugo and Monasson, Remi
JOURNAL OF STATISTICAL PHYSICS 162, 1267-1293 (2016)

LPS

DOI

Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models - Jacquin, Hugo and Gilson, Amy and Shakhnovich, Eugene and Cocco, Simona and Monasson, Remi
PLOS COMPUTATIONAL BIOLOGY 12, (2016)

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DOI

ACE: adaptive cluster expansion for maximum entropy graphical model inference - Barton, J. P. and De Leonardis, E. and Coucke, A. and Cocco, S.
BIOINFORMATICS 32, 3089-3097 (2016)

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DOI

Direct coevolutionary couplings reflect biophysical residue interactions in proteins - Coucke, Alice and Uguzzoni, Guido and Oteri, Francesco and Cocco, Simona and Monasson, Remi and Weigt, Martin
JOURNAL OF CHEMICAL PHYSICS 145, (2016)

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DOI

Neural assemblies revealed by inferred connectivity-based models of prefrontal cortex recordings - Tavoni, G. and Cocco, S. and Monasson, R.
JOURNAL OF COMPUTATIONAL NEUROSCIENCE 41, 269-293 (2016)

LPS

2015

Protein and RNA Structure Prediction by Integration of Co-Evolutionary Information into Molecular Simulation - De Leonardis, Eleonora and Lutz, Benjamin and Cocco, Simona and Monasson, Remi and Szurmant, Hendrik and Weigt, Martin and Schug, Alexander
BIOPHYSICAL JOURNAL 108, 13A-14A (2015)

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DOI

Learning Probabilities From Random Observables in High Dimensions: The Maximum Entropy Distribution and Others - Obuchi, Tomoyuki and Cocco, Simona and Monasson, Remi
JOURNAL OF STATISTICAL PHYSICS 161, 598-632 (2015)

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DOI

Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction - De Leonardis, Eleonora and Lutz, Benjamin and Ratz, Sebastian and Cocco, Simona and Monasson, Remi and Schug, Alexander and Weigt, Martin
NUCLEIC ACIDS RESEARCH 43, 10444-10455 (2015)

LPS

DOI

Distinguishing the immunostimulatory properties of noncoding RNAs expressed in cancer cells - Tanne, Antoine and Muniz, Luciana R. and Puzio-Kuter, Anna and Leonova, Katerina I. and Gudkov, Andrei V. and Ting, David T. and Monasson, Remi and Cocco, Simona and Levine, Arnold J. and Bhardwaj, Nina and Greenbaum, Benjamin D.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 112, 15154-15159 (2015)

LPS

2014

DOI

Reconstruction and Identification of DNA Sequence Landscapes from Unzipping Experiments at Equilibrium - Barbieri, Carlo and Cocco, Simona and Jorg, Thomas and Monasson, Remi
BIOPHYSICAL JOURNAL 106, 430-439 (2014)

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DOI

Quantitative theory of entropic forces acting on constrained nucleotide sequences applied to viruses - Greenbaum, Benjamin D. and Cocco, Simona and Levine, Arnold J. and Monasson, Remi
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 111, 5054-5059 (2014)

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DOI

Stochastic Ratchet Mechanisms for Replacement of Proteins Bound to DNA - Cocco, S. and Marko, J. F. and Monasson, R.
PHYSICAL REVIEW LETTERS 112, (2014)

LPS

DOI

Large pseudocounts and L-2-norm penalties are necessary for the mean-field inference of Ising and Potts models - Barton, J. P. and Cocco, S. and De Leonardis, E. and Monasson, R.
PHYSICAL REVIEW E 90, (2014)

LPS

2013

DOI

Ising models for neural activity inferred via selective cluster expansion: structural and coding properties - Barton, John and Cocco, Simona
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT , (2013)

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DOI

From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction - Cocco, Simona and Monasson, Remi and Weigt, Martin
PLOS COMPUTATIONAL BIOLOGY 9, (2013)

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DOI

Trend and fluctuations: Analysis and design of population dynamics measurements in replicate ecosystems - Hekstra, Doeke R. and Cocco, Simona and Monasson, Remi and Leibler, Stanislas
PHYSICAL REVIEW E 88, (2013)

LPS

2012

DOI

Adaptive Cluster Expansion for the Inverse Ising Problem: Convergence, Algorithm and Tests - Cocco, S. and Monasson, R.
JOURNAL OF STATISTICAL PHYSICS 147, 252-314 (2012)

LPS

2011

DOI

Adaptive Cluster Expansion for Inferring Boltzmann Machines with Noisy Data - Cocco, S. and Monasson, R.
PHYSICAL REVIEW LETTERS 106, (2011)

LPS

DOI

On the trajectories and performance of Infotaxis, an information-based greedy search algorithm - Barbieri, C. and Cocco, S. and Monasson, R.
EPL 94, (2011)

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DOI

High-dimensional inference with the generalized Hopfield model: Principal component analysis and corrections - Cocco, S. and Monasson, R. and Sessak, V.
PHYSICAL REVIEW E 83, (2011)

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