ACE: adaptive cluster expansion for maximum entropy graphical model inference

Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models

(2016) Hugo Jacquin et al.   PLoS Computational Biology

Structure of Finite-RSB Asymptotic Gibbs Measures in the Diluted Spin Glass Models

(2015) Dmitry Panchenko   JOURNAL OF STATISTICAL PHYSICS

Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1

(2015) Matteo Figliuzzi et al.   MOLECULAR BIOLOGY AND EVOLUTION

HIV-1 assembly, release and maturation

(2015) Eric O. Freed   NATURE REVIEWS MICROBIOLOGY

Scaling laws describe memories of host–pathogen riposte in the HIV population

(2015) John P. Barton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From residue coevolution to protein conformational ensembles and functional dynamics

(2015) Ludovico Sutto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences

(2014) Magnus Ekeberg et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Large pseudocounts andL2-norm penalties are necessary for the mean-field inference of Ising and Potts models

(2014) J. P. Barton et al.   PHYSICAL REVIEW E

Improving Contact Prediction along Three Dimensions

(2014) Christoph Feinauer et al.   PLoS Computational Biology

The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing

(2014) Jaclyn K. Mann et al.   PLoS Computational Biology

Translating HIV Sequences into Quantitative Fitness Landscapes Predicts Viral Vulnerabilities for Rational Immunogen Design

(2013) Andrew L. Ferguson et al.   IMMUNITY

Ising models for neural activity inferred via selective cluster expansion: structural and coding properties

(2013) John Barton et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Beyond Inverse Ising Model: Structure of the Analytical Solution

(2013) Iacopo Mastromatteo   JOURNAL OF STATISTICAL PHYSICS

Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes

(2013) Karthik Shekhar et al.   PHYSICAL REVIEW E

Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction

(2013) Simona Cocco et al.   PLoS Computational Biology

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

Bethe–Peierls approximation and the inverse Ising problem

(2012) H Chau Nguyen et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Adaptive Cluster Expansion for the Inverse Ising Problem: Convergence, Algorithm and Tests

(2012) S. Cocco et al.   JOURNAL OF STATISTICAL PHYSICS

Inverse Ising Inference Using All the Data

(2012) Erik Aurell et al.   PHYSICAL REVIEW LETTERS

Genomics-aided structure prediction

(2012) J. I. Sulkowska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The inverse Ising problem for one-dimensional chains with arbitrary finite-range couplings

(2011) Giacomo Gori et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Adaptive Cluster Expansion for Inferring Boltzmann Machines with Noisy Data

(2011) S. Cocco et al.   PHYSICAL REVIEW LETTERS

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-dimensional Ising model selection using ℓ 1 -regularized logistic regression

(2010) Pradeep Ravikumar et al.   ANNALS OF STATISTICS

A weakly informative default prior distribution for logistic and other regression models

(2009) Andrew Gelman et al.   Annals of Applied Statistics

Small-correlation expansions for the inverse Ising problem

(2009) Vitor Sessak et al.   Journal of Physics A-Mathematical and Theoretical

Replay of rule-learning related neural patterns in the prefrontal cortex during sleep

(2009) Adrien Peyrache et al.   NATURE NEUROSCIENCE

Ising model for neural data: Model quality and approximate methods for extracting functional connectivity

(2009) Yasser Roudi et al.   PHYSICAL REVIEW E

Neuronal couplings between retinal ganglion cells inferred by efficient inverse statistical physics methods

(2009) S. Cocco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA