Search Results for author: Erik Aurell

Found 9 papers, 1 papers with code

Temporal epistasis inference from more than 3,500,000 SARS-CoV-2 Genomic Sequences

no code implementations24 Dec 2021 Hong-Li Zeng, Yue Liu, Vito Dichio, Erik Aurell

We use Direct Coupling Analysis (DCA) to determine epistatic interactions between loci of variability of the SARS-CoV-2 virus, segmenting genomes by month of sampling.

Mutation frequency time series reveal complex mixtures of clones in the world-wide SARS-CoV-2 viral population

no code implementations7 Sep 2021 Hong-Li Zeng, Yue Liu, Vito Dichio, Kaisa Thorell, Rickard Nordén, Erik Aurell

We compute the allele frequencies of the alpha (B. 1. 1. 7), beta (B. 1. 351) and delta (B. 167. 2) variants of SARS-CoV-2 from almost two million genome sequences on the GISAID repository.

Time Series

Statistical Genetics in and out of Quasi-Linkage Equilibrium (Extended)

no code implementations4 May 2021 Vito Dichio, Hong-Li Zeng, Erik Aurell

Our goals here are to clarify under which conditions the QLE phase can be expected to hold in population biology and how the stability of the QLE phase is lost.

Symmetries of quantum evolutions

no code implementations13 Jan 2021 Giulio Chiribella, Erik Aurell, Karol Życzkowski

Our no-go theorem implies that any time symmetric formulation of quantum theory must either restrict the set of the allowed evolutions, or modify the operational interpretation of quantum states and processes.

Quantum Physics Mathematical Physics Mathematical Physics

Quantum information in Hawking radiation

no code implementations28 Dec 2020 Erik Aurell, Michał Eckstein, Paweł Horodecki

In contrast, the single-mode thermality of Hawking radiation originating from microscopic black holes, expected to evaporate through several quanta, is not excluded, though there are constraints on modes' frequencies.

Information Retrieval General Relativity and Quantum Cosmology High Energy Physics - Theory Quantum Physics 83C57, 81P45, 81V80

Inferring epistasis from genomic data with comparable mutation and outcrossing rate

no code implementations30 Jun 2020 Hong-Li Zeng, Eugenio Mauri, Vito Dichio, Simona Cocco, Remi Monasson, Erik Aurell

We consider a population evolving due to mutation, selection and recombination, where selection includes single-locus terms (additive fitness) and two-loci terms (pairwise epistatic fitness).

Improving contact prediction along three dimensions

no code implementations3 Mar 2014 Christoph Feinauer, Marcin J. Skwark, Andrea Pagnani, Erik Aurell

Correlation patterns in multiple sequence alignments of homologous proteins can be exploited to infer information on the three-dimensional structure of their members.

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

1 code implementation20 Jan 2014 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 data.

A novel local search based on variable-focusing for random K-SAT

no code implementations9 Oct 2013 Rémi Lemoy, Mikko Alava, Erik Aurell

A Variable-based Focused Metropolis Search (V-FMS) is then applied to random 3-SAT.

Cannot find the paper you are looking for? You can Submit a new open access paper.