Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models

Methods of integrating data to uncover genotype–phenotype interactions

(2015) Marylyn D. Ritchie et al.   NATURE REVIEWS GENETICS

Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners

(2014) Carlo Baldassi et al.   PLoS One

A General Pairwise Interaction Model Provides an Accurate Description of In Vivo Transcription Factor Binding Sites

(2014) Marc Santolini et al.   PLoS One

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

(2014) Sergey Ovchinnikov et al.   eLife

Emerging landscape of oncogenic signatures across human cancers

(2013) Giovanni Ciriello et al.   NATURE GENETICS

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanism-independent method for predicting response to multidrug combinations in bacteria

(2012) Kevin Wood et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Statistical mechanics for natural flocks of birds

(2012) W. Bialek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) David T. Jones et al.   BIOINFORMATICS

Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data

(2011) Jan Krumsiek et al.   BMC Systems Biology

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

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

Statistical mechanics of letters in words

(2010) Greg J. Stephens et al.   PHYSICAL REVIEW E

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

Covariance-regularized regression and classification for high dimensional problems

(2009) Daniela M. Witten et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Maximum Entropy Reconstructions of Dynamic Signaling Networks from Quantitative Proteomics Data

(2009) Jason W. Locasale et al.   PLoS One

Pairwise Maximum Entropy Models for Studying Large Biological Systems: When They Can Work and When They Can't

(2009) Yasser Roudi et al.   PLoS Computational Biology

A Maximum Entropy Model Applied to Spatial and Temporal Correlations from Cortical Networks In Vitro

(2008) A. Tang et al.   JOURNAL OF NEUROSCIENCE

Reverse engineering the genotype–phenotype map with natural genetic variation

(2008) Matthew V. Rockman   NATURE

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