Erik Aurell

Peer-reviewed scientific articles

Journal article-refereed, Original research

Cavity master equation for the continuous time dynamics of discrete-spin models

Aurell, E.; Del Ferraro, Gino; Dominguez, E.; Mulet, R.

2017 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)

ISSN: 2470-0045

Steady diffusion in a drift field A comparison of large-deviation techniques and multiple-scale analysis

Aurell, Erik; Bo, Stefano

2017 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)

ISSN: 2470-0045

Landscape of RNA polyadenylation in E. coli

Maes, Alexandre; Gracia, Céline; Innocenti, Nicolas; Zhang, Kaiyang; Aurell, Erik; Hajnsdorf, Eliane

2017 in NUCLEIC ACIDS RESEARCH (Oxford University Press)

ISSN: 0305-1048

Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis

Skwark, Marcin J.; Croucher, Nicholas J.; Puranen, Santeri; Chewapreecha, Claire; Pesonen, Maiju; Xu, Yingying; Turner, Paul; Harris, Simon R.; Beres, Stephen B.; Musser, James M.; Parkhill, Julian; Bentley, Stephen D.; Aurell, Erik; Corander, Jukka

2017 in PLOS GENETICS (Public Library of Science)

ISSN: 1553-7390

Causal analysis, Correlation-Response, and Dynamic cavity

Aurell, Erik; Ferraro, Gino Del

2016 in Journal of Physics: Conference Series (IOP Publishing Ltd.)

ISSN: 1742-6588

The bulk and the tail of minimal absent words in genome sequences

Aurell, Erik; Innocenti, Nicolas; Zhou, Hai Jun

2016 in PHYSICAL BIOLOGY (IOP Publishing Ltd.)

ISSN: 1478-3967

Diffusion of a Brownian ellipsoid in a force field

Aurell, Erik; Bo, Stefano; Dias, Marcelo; Eichhorn, Ralf; Marino, Raffaele

2016 in EPL (IOP Publishing Ltd.)

ISSN: 0295-5075

The Maximum Entropy Fallacy Redux?

Aurell, Erik

2016 in PLOS COMPUTATIONAL BIOLOGY (Public Library of Science)

ISSN: 1553-734X

On one-step replica symmetry breaking in the Edwards-Anderson spin glass model

Del Ferraro, Gino; Wang, Chuang; Zhou, Hai-Jun; Aurell, Erik

2016 in JOURNAL OF STATISTICAL MECHANICS: THEORY AND EXPERIMENT (IOP PUBLISHING LTD)

ISSN: 1742-5468

Advective-diffusive motion on large scales from small-scale dynamics with an internal symmetry

Marino, Raffaele; Aurell, Erik

2016 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)

ISSN: 1539-3755

Entropy production of a Brownian ellipsoid in the overdamped limit

Marino, Raffaele; Eichhorn, Ralf; Aurell, Erik

2016 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)

ISSN: 1539-3755

On the von Neumann entropy of a bath linearly coupled to a driven quantum system

Aurell, Erik; Eichhorn, Ralf

2015 in NEW JOURNAL OF PHYSICS (IOP PUBLISHING LTD)

ISSN: 1367-2630

Time reversals of irreversible quantum maps

Aurell, Erik; Zakrzewski, Jakub; Zyczkowski, Karol

2015 in JOURNAL OF PHYSICS A: MATHEMATICAL AND THEORETICAL (IOP PUBLISHING LTD)

ISSN: 1751-8113

Dynamic message-passing approach for kinetic spin models with reversible dynamics

Del Ferraro, Gino; Aurell, Erik

2015 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)

ISSN: 1539-3755

Whole-genome mapping of 5 ' RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis

Innocenti, Nicolas; Golumbeanu, Monica; "D'Herouel", Aymeric Fouquier; Lacoux, Caroline; Bonnin, Remy A.; Kennedy, Sean P.; Wessner, Francoise; Serror, Pascale; Bouloc, Philippe; Repoila, Francis; Aurell, Erik

2015 in RNA: A PUBLICATION OF THE RNA SOCIETY (Cold Spring Harbor Laboratory Press)

ISSN: 1355-8382

Detection and quantitative estimation of spurious double stranded DNA formation during reverse transcription in bacteria using tagRNA-seq

Innocenti, Nicolas; Repoila, Francis; Aurell, Erik

2015 in RNA BIOLOGY (Landes Bioscience)

ISSN: 1547-6286

The stochastic thermodynamics of a rotating Brownian particle in a gradient flow

Lan, Yuehang; Aurell, Erik

2015 in SCIENTIFIC REPORTS (NATURE PUBLISHING GROUP)

ISSN: 2045-2322

Local search methods based on variable focusing for random K-satisfiability

Lemoy, Remi; Alava, Mikko; Aurell, Erik

2015 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)

ISSN: 2470-0045

SEK: sparsity exploiting k-mer-based estimation of bacterial community composition

Chatterjee, Saikat; Koslicki, David; Dong, Siyuan; Innocenti, Nicolas; Cheng, Lu; Lan, Yueheng; Vehkaperä, Mikko; Skoglund, Mikael; Rasmussen, Lars K.; Aurell, Erik; Corander, Jukka

2014 in BIOINFORMATICS (OXFORD UNIV PRESS INC)

ISSN: 1367-4803

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

Ekeberg, Magnus; Hartonen, Tuomo; Aurell, Erik

2014 in JOURNAL OF COMPUTATIONAL PHYSICS (Academic Press Inc.)

ISSN: 0021-9991

Improving Contact Prediction along Three Dimensions

Feinauer, Christoph; Skwark, Marcin J.; Pagnani, Andrea; Aurell, Erik

2014 in PLOS COMPUTATIONAL BIOLOGY (Public Library of Science)

ISSN: 1553-734X

Perturbative large deviation analysis of non-equilibrium dynamics

Ferraro, Gino Del; Aurell, Erik

2014 in JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN (Physical Society of Japan)

ISSN: 0031-9015

Optimal stochastic transport in inhomogeneous thermal environments

Bo, Stefano; Aurell, Erik; Eichhorn, Ralf; Celani, Antonio

2013 in EPL (IOP Publishing Ltd.)

ISSN: 0295-5075

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

Ekeberg, Magnus; Lövkvist, Cecilia; Lan, Yueheng; Weigt, Martin; Aurell, Erik

2013 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)

ISSN: 1539-3755

Lognormality and oscillations in the coverage of high-throughput transcriptomic data towards gene ends

Innocenti, Nicolas; Aurell, Erik

2013 in JOURNAL OF STATISTICAL MECHANICS: THEORY AND EXPERIMENT (IOP PUBLISHING LTD)

Witness of unsatisfiability for a random 3-satisfiability formula

Wu, Lu-Lu; Zhou, Hai-Jun; Alava, Mikko; Aurell, Erik; Orponen, Pekka

2013 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)

ISSN: 1539-3755

Maximum likelihood reconstruction for Ising Models with Asynchronous Updates

Zeng, Hong-Li; Alava, Mikko; Aurell, Erik; Hertz, John; Roudi, Yasser

2013 in PHYSICAL REVIEW LETTERS (AMERICAN PHYSICAL SOC)

ISSN: 0031-9007

Refined Second Law of Thermodynamics for fast random processes

Aurell, Erik; Gawedzki, Krzysztof; Mejia-Monasterio, Carlos; Mohayaee, Roya; Muratore-Ginanne, Paolo

2012 in JOURNAL OF STATISTICAL PHYSICS (Springer New York)

ISSN: 0022-4715

Boundary layers in stochastic thermodynamics

Aurell, Erik; Mejía-Monasterio, Carlos; Muratore-Ginanneschi, Paolo

2012 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)

ISSN: 1539-3755

Dynamic mean-field and dynamic cavity for diluted Ising systems

Aurell, Erik; Mahmoudi, Hamed

2012 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)

ISSN: 1539-3755

Dynamic mean-field and cavity methods for diluted Ising systems

Aurell, Erik; Mahmoudi, Hamed

2012 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)

ISSN: 1539-3755

Inverse Ising inference using all the data

Aurell, Erik; Ekeberg, Magnus

2012 in PHYSICAL REVIEW LETTERS (AMERICAN PHYSICAL SOC)

ISSN: 0031-9007

Anomalous thermodynamics at the microscale

Celani, Antonio; Bo, Stefano; Eichhorn, Ralf; Aurell, Erik

2012 in PHYSICAL REVIEW LETTERS (AMERICAN PHYSICAL SOC)

ISSN: 0031-9007

Quasi-potential landscape in complex multi-stable systems

Zhou, Joseph Xu; Aliyu, M.D.S.; Aurell, Erik; Huang, Sui

2012 in JOURNAL OF THE ROYAL SOCIETY INTERFACE (Royal Society of London)

ISSN: 1742-5689

Optimal protocols and optimal transport in stochastic thermodynamics

Aurell, Erik; Mejia-Monasterio, Carlos; Muratore-Ginanneschi, Paolo

2011 in PHYSICAL REVIEW LETTERS (AMERICAN PHYSICAL SOC)

ISSN: 0031-9007

Three lemmas on the dynamic cavity method

Aurell, Erik; Mahmoudi, Hamed

2011 in COMMUNICATIONS IN THEORETICAL PHYSICS (IOP Publishing Ltd.)

ISSN: 0253-6102

A message-passing scheme for non-equilibrium stationary states

Aurell, Erik; Mahmoudi, Hamed

2011 in JOURNAL OF STATISTICAL MECHANICS: THEORY AND EXPERIMENT (IOP PUBLISHING LTD)

A simple and efficient method to search for selected primary transcripts: noncoding- and antisense RNAs in the human pathogen Enterococcus faecalis

"d'Herouel", Aymeric Fouquier; Wessner, Franoise; Halpern, David; Ly-Vu, Joseph; Kennedy, Sean; Serror, Pascale; Aurell, Erik; Repoila, Francis

2011 in COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY (Cold Spring Harbor Laboratory Press)

ISSN: 0091-7451

Window into the Complexities of Chromosome Interactomes

Göndör, Anita; Woodbridge, Alejandro Fernandez; Shi, Chenxi; Aurell, Erik; Imreh, Marta; Ohlsson, Rolf

2011 in COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY (Cold Spring Harbor Laboratory Press)

ISSN: 0091-7451

Network inference using asynchronously updated kinetic Ising Model

Zeng, Hong-Li; Aurell, Erik; Alava, Mikko; Mahmoudi, Hamed

2011 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)

ISSN: 1539-3755

Dynamics and Performance of Susceptibility Propagation on Synthetic Data

Aurell, Erik; Ollion, Charles; Roudi, Yasser

2010 in EUROPEAN PHYSICAL JOURNAL B (SPRINGER)

ISSN: 1434-6028

Circumspect descent prevails in solving random constraint satisfaction problems

Alava, Mikko; Ardelius, John; Aurell, Erik; Kaski, Petteri; Krishnamurthy, Supriya; Orponen, Pekka

2008 in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (NATL ACAD SCIENCES)

An Analytical Study of a Structured Overlay in the presence of Dynamic Membership

Krishnamurthy, Supriya; El-Ansary, Sameh; Aurell, Erik; Haridi, Seif

2008 in IEEE/ACM Transactions on Networking (NATL ACAD SCIENCES)

Conference proceedings

The physics of distributed information systems

Aurell, Erik

2013

ISSN: 1742-6588

Analysis of Sparse Representations Using Bi-Orthogonal Dictionaries

Vehkaperä, Mikko; Kabashima, Yoshiyuki; Chatterjee, Saikat; Aurell, Erik; Skoglund, Mikael; Rasmussen, Lars K.

2012

ISBN: 978-1-4673-0224-1

The Accuracy of Tree-based Counting in Dynamic Networks

Krishnamurthy, Supriya; Ardelius, John; Aurell, Erik; Dam, Mads; Stadler, Rolf; Wuhib, Fetahi

2010

Bounds on Threshold of Regular Random $k$-SAT

Rathi, Vishwambhar; Aurell, Erik; Rasmussen, Lars; Skoglund, Mikael

2010

ISSN: 0302-9743

Bounds on Thresholds Related to Maximum Satisfiability of Regular Random Formulas

Rathi, Vishwambhar; Aurell, Erik; Rasmussen, Lars; Skoglund, Mikael

2010

Non-refereed scientific articles

Unrefereed journal articles

Stochastic thermodynamics

Eichhorn, Ralf; Aurell, Erik

2014 in PHYSICA SCRIPTA (IOP Publishing Ltd.)

ISSN: 0031-8949