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

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

The Bethe approximation for solving the inverse Ising problem: a comparison with other inference methods

(2012) Federico Ricci-Tersenghi   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Mean-Field Theory for the Inverse Ising Problem at Low Temperatures

(2012) H. Chau Nguyen et al.   PHYSICAL REVIEW LETTERS

Inverse Ising Inference Using All the Data

(2012) Erik Aurell et al.   PHYSICAL REVIEW LETTERS

Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis

(2012) T. Nugent et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis

(2012) A. E. Dago et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomics-aided structure prediction

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

The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future

(2012) Helen M. Berman et al.   STRUCTURE

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

(2011) David T. Jones et al.   BIOINFORMATICS

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

(2011) I. Pagani et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

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

Intrinsic limitations of the susceptibility propagation inverse inference for the mean field Ising spin glass

(2010) Enzo Marinari et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Learning generative models for protein fold families

(2010) Sivaraman Balakrishnan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments

(2010) Lukas Burger et al.   PLoS Computational Biology

Small-correlation expansions for the inverse Ising problem

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

Constraint satisfaction problems and neural networks: A statistical physics perspective

(2009) Marc Mézard et al.   JOURNAL OF PHYSIOLOGY-PARIS

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

High-resolution protein complexes from integrating genomic information with molecular simulation

(2009) Alexander Schug et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Statistical physics of pairwise probability models

(2009) Yasser Roudi   Frontiers in Computational Neuroscience

Inference algorithms for gene networks: a statistical mechanics analysis

(2008) A Braunstein et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Identification of direct residue contacts in protein-protein interaction by message passing

(2008) M. Weigt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA