751 citations · 1.1k across the 4 of their papers we have counts for
4 papers
On a Multilocus Wright-Fisher Model with Mutation and a Svirezhev-Shahshahani Gradient-like Selection Dynamics
Erik Aurell, Magnus Ekeberg, Timo Koski
In this paper we introduce a multilocus diffusion model of a population of haploid, asexually reproducing individuals. The model includes parent-dependent mutation and interloc…
Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences
Magnus Ekeberg, Tuomo Hartonen, Erik Aurell
Direct-Coupling Analysis is a group of methods to harvest information about coevolving residues in a protein family by learning a generative model in an exponential family from dat…
Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models
Magnus Ekeberg, Cecilia Lövkvist, Yueheng Lan +2
Spatially proximate amino acids in a protein tend to coevolve. A protein's three-dimensional (3D) structure hence leaves an echo of correlations in the evolutionary record. Reverse…
Inverse Ising inference using all the data
Erik Aurell, Magnus Ekeberg
We show that a method based on logistic regression, using all the data, solves the inverse Ising problem far better than mean-field calculations relying only on sample pairwise cor…