Erik Aurell
Adjunct Professor, Science at Aalto University School of Business
Biography
Aalto University School of Business
Peer-reviewed scientific articles
Journal article-refereed, Original researchCavity 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: 2470-0045Steady diffusion in a drift field A comparison of large-deviation techniques and multiple-scale analysis
Aurell, Erik; Bo, Stefano2017 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)ISSN: 2470-0045Landscape of RNA polyadenylation in E. coli
Maes, Alexandre; Gracia, Céline; Innocenti, Nicolas; Zhang, Kaiyang; Aurell, Erik; Hajnsdorf, Eliane2017 in NUCLEIC ACIDS RESEARCH (Oxford University Press)ISSN: 0305-1048Interacting 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, Jukka2017 in PLOS GENETICS (Public Library of Science)ISSN: 1553-7390Causal analysis, Correlation-Response, and Dynamic cavity
Aurell, Erik; Ferraro, Gino Del2016 in Journal of Physics: Conference Series (IOP Publishing Ltd.)ISSN: 1742-6588The bulk and the tail of minimal absent words in genome sequences
Aurell, Erik; Innocenti, Nicolas; Zhou, Hai Jun2016 in PHYSICAL BIOLOGY (IOP Publishing Ltd.)ISSN: 1478-3967Diffusion of a Brownian ellipsoid in a force field
Aurell, Erik; Bo, Stefano; Dias, Marcelo; Eichhorn, Ralf; Marino, Raffaele2016 in EPL (IOP Publishing Ltd.)ISSN: 0295-5075The Maximum Entropy Fallacy Redux?
Aurell, Erik2016 in PLOS COMPUTATIONAL BIOLOGY (Public Library of Science)ISSN: 1553-734XOn one-step replica symmetry breaking in the Edwards-Anderson spin glass model
Del Ferraro, Gino; Wang, Chuang; Zhou, Hai-Jun; Aurell, Erik2016 in JOURNAL OF STATISTICAL MECHANICS: THEORY AND EXPERIMENT (IOP PUBLISHING LTD)ISSN: 1742-5468Advective-diffusive motion on large scales from small-scale dynamics with an internal symmetry
Marino, Raffaele; Aurell, Erik2016 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)ISSN: 1539-3755Entropy production of a Brownian ellipsoid in the overdamped limit
Marino, Raffaele; Eichhorn, Ralf; Aurell, Erik2016 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)ISSN: 1539-3755On the von Neumann entropy of a bath linearly coupled to a driven quantum system
Aurell, Erik; Eichhorn, Ralf2015 in NEW JOURNAL OF PHYSICS (IOP PUBLISHING LTD)ISSN: 1367-2630Time reversals of irreversible quantum maps
Aurell, Erik; Zakrzewski, Jakub; Zyczkowski, Karol2015 in JOURNAL OF PHYSICS A: MATHEMATICAL AND THEORETICAL (IOP PUBLISHING LTD)ISSN: 1751-8113Dynamic message-passing approach for kinetic spin models with reversible dynamics
Del Ferraro, Gino; Aurell, Erik2015 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)ISSN: 1539-3755Whole-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, Erik2015 in RNA: A PUBLICATION OF THE RNA SOCIETY (Cold Spring Harbor Laboratory Press)ISSN: 1355-8382Detection and quantitative estimation of spurious double stranded DNA formation during reverse transcription in bacteria using tagRNA-seq
Innocenti, Nicolas; Repoila, Francis; Aurell, Erik2015 in RNA BIOLOGY (Landes Bioscience)ISSN: 1547-6286The stochastic thermodynamics of a rotating Brownian particle in a gradient flow
Lan, Yuehang; Aurell, Erik2015 in SCIENTIFIC REPORTS (NATURE PUBLISHING GROUP)ISSN: 2045-2322Local search methods based on variable focusing for random K-satisfiability
Lemoy, Remi; Alava, Mikko; Aurell, Erik2015 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)ISSN: 2470-0045SEK: 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, Jukka2014 in BIOINFORMATICS (OXFORD UNIV PRESS INC)ISSN: 1367-4803Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences
Ekeberg, Magnus; Hartonen, Tuomo; Aurell, Erik2014 in JOURNAL OF COMPUTATIONAL PHYSICS (Academic Press Inc.)ISSN: 0021-9991Improving Contact Prediction along Three Dimensions
Feinauer, Christoph; Skwark, Marcin J.; Pagnani, Andrea; Aurell, Erik2014 in PLOS COMPUTATIONAL BIOLOGY (Public Library of Science)ISSN: 1553-734XPerturbative large deviation analysis of non-equilibrium dynamics
Ferraro, Gino Del; Aurell, Erik2014 in JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN (Physical Society of Japan)ISSN: 0031-9015Optimal stochastic transport in inhomogeneous thermal environments
Bo, Stefano; Aurell, Erik; Eichhorn, Ralf; Celani, Antonio2013 in EPL (IOP Publishing Ltd.)ISSN: 0295-5075Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models
Ekeberg, Magnus; Lövkvist, Cecilia; Lan, Yueheng; Weigt, Martin; Aurell, Erik2013 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)ISSN: 1539-3755Lognormality and oscillations in the coverage of high-throughput transcriptomic data towards gene ends
Innocenti, Nicolas; Aurell, Erik2013 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, Pekka2013 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)ISSN: 1539-3755Maximum likelihood reconstruction for Ising Models with Asynchronous Updates
Zeng, Hong-Li; Alava, Mikko; Aurell, Erik; Hertz, John; Roudi, Yasser2013 in PHYSICAL REVIEW LETTERS (AMERICAN PHYSICAL SOC)ISSN: 0031-9007Refined Second Law of Thermodynamics for fast random processes
Aurell, Erik; Gawedzki, Krzysztof; Mejia-Monasterio, Carlos; Mohayaee, Roya; Muratore-Ginanne, Paolo2012 in JOURNAL OF STATISTICAL PHYSICS (Springer New York)ISSN: 0022-4715Boundary layers in stochastic thermodynamics
Aurell, Erik; Mejía-Monasterio, Carlos; Muratore-Ginanneschi, Paolo2012 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)ISSN: 1539-3755Dynamic mean-field and dynamic cavity for diluted Ising systems
Aurell, Erik; Mahmoudi, Hamed2012 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)ISSN: 1539-3755Dynamic mean-field and cavity methods for diluted Ising systems
Aurell, Erik; Mahmoudi, Hamed2012 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)ISSN: 1539-3755Inverse Ising inference using all the data
Aurell, Erik; Ekeberg, Magnus2012 in PHYSICAL REVIEW LETTERS (AMERICAN PHYSICAL SOC)ISSN: 0031-9007Anomalous thermodynamics at the microscale
Celani, Antonio; Bo, Stefano; Eichhorn, Ralf; Aurell, Erik2012 in PHYSICAL REVIEW LETTERS (AMERICAN PHYSICAL SOC)ISSN: 0031-9007Quasi-potential landscape in complex multi-stable systems
Zhou, Joseph Xu; Aliyu, M.D.S.; Aurell, Erik; Huang, Sui2012 in JOURNAL OF THE ROYAL SOCIETY INTERFACE (Royal Society of London)ISSN: 1742-5689Optimal protocols and optimal transport in stochastic thermodynamics
Aurell, Erik; Mejia-Monasterio, Carlos; Muratore-Ginanneschi, Paolo2011 in PHYSICAL REVIEW LETTERS (AMERICAN PHYSICAL SOC)ISSN: 0031-9007Three lemmas on the dynamic cavity method
Aurell, Erik; Mahmoudi, Hamed2011 in COMMUNICATIONS IN THEORETICAL PHYSICS (IOP Publishing Ltd.)ISSN: 0253-6102A message-passing scheme for non-equilibrium stationary states
Aurell, Erik; Mahmoudi, Hamed2011 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, Francis2011 in COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY (Cold Spring Harbor Laboratory Press)ISSN: 0091-7451Window into the Complexities of Chromosome Interactomes
Göndör, Anita; Woodbridge, Alejandro Fernandez; Shi, Chenxi; Aurell, Erik; Imreh, Marta; Ohlsson, Rolf2011 in COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY (Cold Spring Harbor Laboratory Press)ISSN: 0091-7451Network inference using asynchronously updated kinetic Ising Model
Zeng, Hong-Li; Aurell, Erik; Alava, Mikko; Mahmoudi, Hamed2011 in PHYSICAL REVIEW E (AMER PHYSICAL SOC)ISSN: 1539-3755Dynamics and Performance of Susceptibility Propagation on Synthetic Data
Aurell, Erik; Ollion, Charles; Roudi, Yasser2010 in EUROPEAN PHYSICAL JOURNAL B (SPRINGER)ISSN: 1434-6028Circumspect descent prevails in solving random constraint satisfaction problems
Alava, Mikko; Ardelius, John; Aurell, Erik; Kaski, Petteri; Krishnamurthy, Supriya; Orponen, Pekka2008 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, Seif2008 in IEEE/ACM Transactions on Networking (NATL ACAD SCIENCES)Conference proceedingsThe physics of distributed information systems
Aurell, Erik2013 ISSN: 1742-6588Analysis of Sparse Representations Using Bi-Orthogonal Dictionaries
Vehkaperä, Mikko; Kabashima, Yoshiyuki; Chatterjee, Saikat; Aurell, Erik; Skoglund, Mikael; Rasmussen, Lars K.2012 ISBN: 978-1-4673-0224-1The Accuracy of Tree-based Counting in Dynamic Networks
Krishnamurthy, Supriya; Ardelius, John; Aurell, Erik; Dam, Mads; Stadler, Rolf; Wuhib, Fetahi2010 Bounds on Threshold of Regular Random $k$-SAT
Rathi, Vishwambhar; Aurell, Erik; Rasmussen, Lars; Skoglund, Mikael2010 ISSN: 0302-9743Bounds on Thresholds Related to Maximum Satisfiability of Regular Random Formulas
Rathi, Vishwambhar; Aurell, Erik; Rasmussen, Lars; Skoglund, Mikael2010 Non-refereed scientific articles
Unrefereed journal articlesStochastic thermodynamics
Eichhorn, Ralf; Aurell, Erik2014 in PHYSICA SCRIPTA (IOP Publishing Ltd.)ISSN: 0031-8949
Cavity master equation for the continuous time dynamics of discrete-spin models
Steady diffusion in a drift field A comparison of large-deviation techniques and multiple-scale analysis
Landscape of RNA polyadenylation in E. coli
Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis
Causal analysis, Correlation-Response, and Dynamic cavity
The bulk and the tail of minimal absent words in genome sequences
Diffusion of a Brownian ellipsoid in a force field
The Maximum Entropy Fallacy Redux?
On one-step replica symmetry breaking in the Edwards-Anderson spin glass model
Advective-diffusive motion on large scales from small-scale dynamics with an internal symmetry
Entropy production of a Brownian ellipsoid in the overdamped limit
On the von Neumann entropy of a bath linearly coupled to a driven quantum system
Time reversals of irreversible quantum maps
Dynamic message-passing approach for kinetic spin models with reversible dynamics
Whole-genome mapping of 5 ' RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis
Detection and quantitative estimation of spurious double stranded DNA formation during reverse transcription in bacteria using tagRNA-seq
The stochastic thermodynamics of a rotating Brownian particle in a gradient flow
Local search methods based on variable focusing for random K-satisfiability
SEK: sparsity exploiting k-mer-based estimation of bacterial community composition
Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences
Improving Contact Prediction along Three Dimensions
Perturbative large deviation analysis of non-equilibrium dynamics
Optimal stochastic transport in inhomogeneous thermal environments
Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models
Lognormality and oscillations in the coverage of high-throughput transcriptomic data towards gene ends
Witness of unsatisfiability for a random 3-satisfiability formula
Maximum likelihood reconstruction for Ising Models with Asynchronous Updates
Refined Second Law of Thermodynamics for fast random processes
Boundary layers in stochastic thermodynamics
Dynamic mean-field and dynamic cavity for diluted Ising systems
Dynamic mean-field and cavity methods for diluted Ising systems
Inverse Ising inference using all the data
Anomalous thermodynamics at the microscale
Quasi-potential landscape in complex multi-stable systems
Optimal protocols and optimal transport in stochastic thermodynamics
Three lemmas on the dynamic cavity method
A message-passing scheme for non-equilibrium stationary states
A simple and efficient method to search for selected primary transcripts: noncoding- and antisense RNAs in the human pathogen Enterococcus faecalis
Window into the Complexities of Chromosome Interactomes
Network inference using asynchronously updated kinetic Ising Model
Dynamics and Performance of Susceptibility Propagation on Synthetic Data
Circumspect descent prevails in solving random constraint satisfaction problems
An Analytical Study of a Structured Overlay in the presence of Dynamic Membership
The physics of distributed information systems
Analysis of Sparse Representations Using Bi-Orthogonal Dictionaries
The Accuracy of Tree-based Counting in Dynamic Networks
Bounds on Threshold of Regular Random $k$-SAT
Bounds on Thresholds Related to Maximum Satisfiability of Regular Random Formulas
Non-refereed scientific articles
Unrefereed journal articlesStochastic thermodynamics
Eichhorn, Ralf; Aurell, Erik2014 in PHYSICA SCRIPTA (IOP Publishing Ltd.)ISSN: 0031-8949
Stochastic thermodynamics
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