A Comparison of the Maximum Entropy Principle Across Biological Spatial Scales

Derivations of the Core Functions of the Maximum Entropy Theory of Ecology

(2019) Alexander B. Brummer et al.   Entropy

Comparison of two maximum entropy models highlights the metabolic structure of metacommunities as a key determinant of local community assembly

(2019) Jason Bertram et al.   ECOLOGICAL MODELLING

An Introduction to the Non-Equilibrium Steady States of Maximum Entropy Spike Trains

(2019) Rodrigo Cofré et al.   Entropy

Maximum Entropy Theory of Ecology: A Reply to Harte

(2018) Marco Favretti   Entropy

Maximum Entropy and Theory Construction: A Reply to Favretti

(2018) John Harte   Entropy

Information Entropy Production of Maximum Entropy Markov Chains from Spike Trains

(2018) Rodrigo Cofré et al.   Entropy

Inverse statistical physics of protein sequences: a key issues review

(2018) Simona Cocco et al.   REPORTS ON PROGRESS IN PHYSICS

Collective Behavior of Social Bots Is Encoded in Their Temporal Twitter Activity

(2018) Andrej Duh et al.   Big Data

Genomes OnLine database (GOLD) v.7: updates and new features

(2018) Supratim Mukherjee et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Remarks on the Maximum Entropy Principle with Application to the Maximum Entropy Theory of Ecology

(2017) Marco Favretti   Entropy

Mutation effects predicted from sequence co-variation

(2017) Thomas A Hopf et al.   NATURE BIOTECHNOLOGY

Inferring structural connectivity using Ising couplings in models of neuronal networks

(2017) Balasundaram Kadirvelu et al.   Scientific Reports

PRANAS: A New Platform for Retinal Analysis and Simulation

(2017) Bruno Cessac et al.   Frontiers in Neuroinformatics

On the Entropy of Protein Families

(2016) John P. Barton et al.   JOURNAL OF STATISTICAL PHYSICS

Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes

(2016) R. R. Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

meteR: anrpackage for testing the maximum entropy theory of ecology

(2016) Andrew J. Rominger et al.   Methods in Ecology and Evolution

A Strong Test of the Maximum Entropy Theory of Ecology

(2015) Xiao Xiao et al.   AMERICAN NATURALIST

Statistical Mechanics of the US Supreme Court

(2015) Edward D. Lee et al.   JOURNAL OF STATISTICAL PHYSICS

Thermodynamics and signatures of criticality in a network of neurons

(2015) Gašper Tkačik et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) Richard R. Stein et al.   PLoS Computational Biology

On Theory in Ecology

(2014) Pablo A. Marquet et al.   BIOSCIENCE

Empirical tests of within- and across-species energetics in a diverse plant community

(2014) Erica A. Newman et al.   ECOLOGY

Parameter Estimation for Spatio-Temporal Maximum Entropy Distributions: Application to Neural Spike Trains

(2014) Hassan Nasser et al.   Entropy

Exact computation of the maximum-entropy potential of spiking neural-network models

(2014) R. Cofré et al.   PHYSICAL REVIEW E

Dynamical maximum entropy approach to flocking

(2014) Andrea Cavagna et al.   PHYSICAL REVIEW E

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

(2014) Marc Santolini et al.   PLoS One

Quantifying selection in immune receptor repertoires

(2014) Yuval Elhanati et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Maximum information entropy: a foundation for ecological theory

(2014) John Harte et al.   TRENDS IN ECOLOGY & EVOLUTION

Searching for Collective Behavior in a Large Network of Sensory Neurons

(2014) Gašper Tkačik et al.   PLoS Computational Biology

The simplest maximum entropy model for collective behavior in a neural network

(2013) Gašper Tkačik et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Collective Motion of Humans in Mosh and Circle Pits at Heavy Metal Concerts

(2013) Jesse L. Silverberg et al.   PHYSICAL REVIEW LETTERS

A pairwise maximum entropy model accurately describes resting-state human brain networks

(2013) Takamitsu Watanabe et al.   Nature Communications

High-order social interactions in groups of mice

(2013) Yair Shemesh et al.   eLife

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

TRY - a global database of plant traits

(2011) J. KATTGE et al.   GLOBAL CHANGE BIOLOGY

Gibbs distribution analysis of temporal correlations structure in retina ganglion cells

(2011) J.C. Vasquez et al.   JOURNAL OF PHYSIOLOGY-PARIS

Are Biological Systems Poised at Criticality?

(2011) Thierry Mora et al.   JOURNAL OF STATISTICAL PHYSICS

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

(2011) Michael Remmert et al.   NATURE METHODS

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

Sparse low-order interaction network underlies a highly correlated and learnable neural population code

(2011) E. Ganmor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Towards a unification of unified theories of biodiversity

(2010) Brian J. McGill   ECOLOGY LETTERS

Plant traits, species pools and the prediction of relative abundance in plant communities: a maximum entropy approach

(2010) Grégory Sonnier et al.   JOURNAL OF VEGETATION SCIENCE

Sparse coding and high-order correlations in fine-scale cortical networks

(2010) Ifije E. Ohiorhenuan et al.   NATURE

Curvature in metabolic scaling

(2010) Tom Kolokotrones et al.   NATURE

Wiener–Granger Causality: A well established methodology

(2010) Steven L. Bressler et al.   NEUROIMAGE

Maximum entropy models for antibody diversity

(2010) T. Mora et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biodiversity scales from plots to biomes with a universal species-area curve

(2009) John Harte et al.   ECOLOGY LETTERS

Prediction of Spatiotemporal Patterns of Neural Activity from Pairwise Correlations

(2009) O. Marre et al.   PHYSICAL REVIEW LETTERS

The Brain's Default Network

(2008) Randy L. Buckner et al.   Annals of the New York Academy of Sciences

A Small World of Neuronal Synchrony

(2008) Shan Yu et al.   CEREBRAL CORTEX

MAXIMUM ENTROPY AND THE STATE-VARIABLE APPROACH TO MACROECOLOGY

(2008) J. Harte et al.   ECOLOGY

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

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

Spatio-temporal correlations and visual signalling in a complete neuronal population

(2008) Jonathan W. Pillow et al.   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