Erik Aurell

Professor (fixed-term)

Research outputs

  1. 2019
  2. Published

    Thermal power of heat flow through a qubit

    Aurell, E. & Montana, F., 19 Apr 2019, In : Physical Review E. 99, 4, p. 1-14 042130.

    Research output: Contribution to journalArticleScientificpeer-review

  3. 2018
  4. Published

    Correlation-compressed direct-coupling analysis

    Gao, C. Y., Zhou, H. J. & Aurell, E., 11 Sep 2018, In : Physical Review E. 98, 3, p. 1-15 032407.

    Research output: Contribution to journalArticleScientificpeer-review

  5. Published

    Characteristic functions of quantum heat with baths at different temperatures

    Aurell, E., 7 Jun 2018, In : Physical Review E. 97, 6, p. 1-9 062117.

    Research output: Contribution to journalArticleScientificpeer-review

  6. Published

    Unified picture of strong-coupling stochastic thermodynamics and time reversals

    Aurell, E., 9 Apr 2018, In : Physical Review E. 97, 4, p. 1-10 042112.

    Research output: Contribution to journalArticleScientificpeer-review

  7. Published

    Global Estimates of Errors in Quantum Computation by the Feynman–Vernon Formalism

    Aurell, E., 2018, In : Journal of Statistical Physics. 171, 5, p. 745–767 23 p.

    Research output: Contribution to journalArticleScientificpeer-review

  8. 2017
  9. Published

    On work and heat in time-dependent strong coupling

    Aurell, E., 1 Nov 2017, In : Entropy. 19, 11, p. 1-17 595.

    Research output: Contribution to journalArticleScientificpeer-review

  10. Published

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

    Aurell, E. & Bo, S., 27 Sep 2017, In : Physical Review E. 96, 3, p. 1-12 032140.

    Research output: Contribution to journalArticleScientificpeer-review

  11. Published

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

    Aurell, E., Del Ferraro, G., Dominguez, E. & Mulet, R., 12 May 2017, In : Physical Review E. 95, 5, p. 1-14 14 p., 052119.

    Research output: Contribution to journalArticleScientificpeer-review

  12. Published

    Landscape of RNA polyadenylation in E. coli

    Maes, A., Gracia, C., Innocenti, N., Zhang, K., Aurell, E. & Hajnsdorf, E., 17 Mar 2017, In : Nucleic Acids Research. 45, 5, p. 2746-2756 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  13. Published

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

    Skwark, M. J., Croucher, N. J., Puranen, S., Chewapreecha, C., Pesonen, M., Xu, Y., Turner, P., Harris, S. R., Beres, S. B., Musser, J. M. & 4 othersParkhill, J., Bentley, S. D., Aurell, E. & Corander, J., 1 Feb 2017, In : PLoS Genetics. 13, 2, e1006508.

    Research output: Contribution to journalArticleScientificpeer-review

  14. Published

    SuperDCA for genome-wide epistasis analysis

    Puranen, S., Pesonen, M., Pensar, J., Xu, Y. Y., Lees, J. A., Bentley, S. D., Croucher, N. J., Corander, J. & Aurell, E., 2017, In : bioRxiv.

    Research output: Contribution to journalArticleScientific

  15. 2016
  16. Published

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

    Del Ferraro, G., Wang, C., Zhou, H-J. & Aurell, E., Jul 2016, In : Journal of Statistical Mechanics: Theory and Experiment. 2016, 7, 32 p., 073305.

    Research output: Contribution to journalArticleScientificpeer-review

  17. Published

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

    Marino, R. & Aurell, E., 30 Jun 2016, In : Physical Review E. 93, 6, p. 1-15 062147.

    Research output: Contribution to journalArticleScientificpeer-review

  18. Published

    Diffusion of a Brownian ellipsoid in a force field

    Aurell, E., Bo, S., Dias, M., Eichhorn, R. & Marino, R., 1 May 2016, In : EPL. 114, 3, 30005.

    Research output: Contribution to journalArticleScientificpeer-review

  19. Published

    The Maximum Entropy Fallacy Redux?

    Aurell, E., 1 May 2016, In : PLoS computational biology. 12, 5, p. 1-7 e1004777.

    Research output: Contribution to journalArticleScientificpeer-review

  20. Published

    Causal analysis, Correlation-Response, and Dynamic cavity

    Aurell, E. & Ferraro, G. D., 6 Apr 2016, In : Journal of Physics: Conference Series. 699, 1, p. 1-12 012002.

    Research output: Contribution to journalArticleScientificpeer-review

  21. Published

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

    Aurell, E., Innocenti, N. & Zhou, H. J., 4 Apr 2016, In : Physical Biology. 13, 2, p. 1-10 026004.

    Research output: Contribution to journalArticleScientificpeer-review

  22. Published

    Entropy production of a Brownian ellipsoid in the overdamped limit

    Marino, R., Eichhorn, R. & Aurell, E., 19 Jan 2016, In : Physical Review E. 93, 1, p. 1-15 012132.

    Research output: Contribution to journalArticleScientificpeer-review

  23. 2015
  24. Published

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

    Innocenti, N., Repoila, F. & Aurell, E., 2015, In : RNA BIOLOGY. 12, 9, p. 1067-1069

    Research output: Contribution to journalArticleScientificpeer-review

  25. Published

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

    Del Ferraro, G. & Aurell, E., 2015, In : Physical Review E. 92, 1, p. 1-7 010102.

    Research output: Contribution to journalArticleScientificpeer-review

  26. Published

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

    Lemoy, R., Alava, M. & Aurell, E., 2015, In : Physical Review E. 91, 1, p. 1-6 013305.

    Research output: Contribution to journalArticleScientificpeer-review

  27. Published

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

    Aurell, E. & Eichhorn, R., 2015, In : New Journal of Physics. 17, 8 June 2015, p. 065007

    Research output: Contribution to journalArticleScientificpeer-review

  28. Published

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

    Lan, Y. & Aurell, E., 2015, In : Scientific Reports. 5, p. 1-10 12266.

    Research output: Contribution to journalArticleScientificpeer-review

  29. Published

    Time reversals of irreversible quantum maps

    Aurell, E., Zakrzewski, J. & Zyczkowski, K., 2015, In : Journal of Physics A: Mathematical and Theoretical. 48, 38, p. 0000038

    Research output: Contribution to journalArticleScientificpeer-review

  30. Published

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

    Innocenti, N., Golumbeanu, M., "D'Herouel", A. F., Lacoux, C., Bonnin, R. A., Kennedy, S. P., Wessner, F., Serror, P., Bouloc, P., Repoila, F. & 1 othersAurell, E., 2015, In : RNA: A PUBLICATION OF THE RNA SOCIETY. 21, 5, p. 1018-1030

    Research output: Contribution to journalArticleScientificpeer-review

  31. 2014
  32. Published

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

    Ekeberg, M., Hartonen, T. & Aurell, E., 1 Nov 2014, In : Journal of Computational Physics. 276, p. 341-356 16 p.

    Research output: Contribution to journalArticleScientificpeer-review

  33. Published

    Perturbative large deviation analysis of non-equilibrium dynamics

    Ferraro, G. D. & Aurell, E., 15 Aug 2014, In : Journal of the Physical Society of Japan. 83, 8, p. 1-13 084001.

    Research output: Contribution to journalArticleScientificpeer-review

  34. Published

    Improving Contact Prediction along Three Dimensions

    Feinauer, C., Skwark, M. J., Pagnani, A. & Aurell, E., 2014, In : PLoS computational biology. 10, 10, p. 1-13 e1003847.

    Research output: Contribution to journalArticleScientificpeer-review

  35. Published

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

    Chatterjee, S., Koslicki, D., Dong, S., Innocenti, N., Cheng, L., Lan, Y., Vehkaperä, M., Skoglund, M., Rasmussen, L. K., Aurell, E. & 1 othersCorander, J., 2014, In : Bioinformatics. 30, 17, p. 24232431

    Research output: Contribution to journalArticleScientificpeer-review

  36. Published

    Stochastic thermodynamics

    Eichhorn, R. & Aurell, E., 2014, In : Physica Scripta. 89, 4, p. 048001

    Research output: Contribution to journalArticleScientific

  37. 2013
  38. Published

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

    Ekeberg, M., Lövkvist, C., Lan, Y., Weigt, M. & Aurell, E., 2013, In : Physical Review E. 87

    Research output: Contribution to journalArticleScientificpeer-review

  39. Published

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

    Innocenti, N. & Aurell, E., 2013, In : Journal of Statistical Mechanics: Theory and Experiment. 2013, 10

    Research output: Contribution to journalArticleScientificpeer-review

  40. Published

    Maximum likelihood reconstruction for Ising Models with Asynchronous Updates

    Zeng, H-L., Alava, M., Aurell, E., Hertz, J. & Roudi, Y., 2013, In : Physical Review Letters. 110, 21, p. 1-5 210601.

    Research output: Contribution to journalArticleScientificpeer-review

  41. Published

    Optimal stochastic transport in inhomogeneous thermal environments

    Bo, S., Aurell, E., Eichhorn, R. & Celani, A., 2013, In : EPL. 103

    Research output: Contribution to journalArticleScientificpeer-review

  42. Published

    The physics of distributed information systems

    Aurell, E., 2013, ELC International Meeting on Inference, Computation, and Spin Glasses (ICSG2013), 28-30 July 2013, Sapporo, Japan. IOP Publishing

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  43. Published

    Witness of unsatisfiability for a random 3-satisfiability formula

    Wu, L-L., Zhou, H-J., Alava, M., Aurell, E. & Orponen, P., 2013, In : Physical Review E. 87, 5, p. 1-10 052807.

    Research output: Contribution to journalArticleScientificpeer-review

  44. 2012
  45. Published

    Anomalous thermodynamics at the microscale

    Celani, A., Bo, S., Eichhorn, R. & Aurell, E., 27 Dec 2012, In : Physical Review Letters. 109, 26, 260603.

    Research output: Contribution to journalArticleScientificpeer-review

  46. Published

    Dynamic mean-field and cavity methods for diluted Ising systems

    Aurell, E. & Mahmoudi, H., 16 Mar 2012, In : Physical Review E. 85, 3, 031119.

    Research output: Contribution to journalArticleScientificpeer-review

  47. Published

    Analysis of Sparse Representations Using Bi-Orthogonal Dictionaries

    Vehkaperä, M., Kabashima, Y., Chatterjee, S., Aurell, E., Skoglund, M. & Rasmussen, L. K., 2012, ITW Information Theory Workshop (ITW 2012) ITW, Lausanne, Switzerland, September 3-7, 2012. IEEE, p. 647-651

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

  48. Published

    Boundary layers in stochastic thermodynamics

    Aurell, E., Mejía-Monasterio, C. & Muratore-Ginanneschi, P., 2012, In : Physical Review E. 85, 2, p. 020103

    Research output: Contribution to journalArticleScientificpeer-review

  49. Published

    Dynamic mean-field and dynamic cavity for diluted Ising systems

    Aurell, E. & Mahmoudi, H., 2012, In : Physical Review E. 85, 3, p. 031119

    Research output: Contribution to journalArticleScientificpeer-review

  50. Published

    Inverse Ising inference using all the data

    Aurell, E. & Ekeberg, M., 2012, In : Physical Review Letters. 108, 9, p. 090201

    Research output: Contribution to journalArticleScientificpeer-review

  51. Published

    Quasi-potential landscape in complex multi-stable systems

    Zhou, J. X., Aliyu, M. D. S., Aurell, E. & Huang, S., 2012, In : Journal of the Royal Society Interface. 9, 77, p. 3539-3553

    Research output: Contribution to journalArticleScientificpeer-review

  52. Published

    Refined Second Law of Thermodynamics for fast random processes

    Aurell, E., Gawedzki, K., Mejia-Monasterio, C., Mohayaee, R. & Muratore-Ginanne, P., 2012, In : Journal of Statistical Physics. 147, 3, p. 487-505

    Research output: Contribution to journalArticleScientificpeer-review

  53. 2011
  54. Published

    A message-passing scheme for non-equilibrium stationary states

    Aurell, E. & Mahmoudi, H., 2011, In : Journal of Statistical Mechanics: Theory and Experiment. 2011, 4, p. pp. P04014

    Research output: Contribution to journalArticleScientificpeer-review

  55. Published

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

    "d'Herouel", A. F., Wessner, F., Halpern, D., Ly-Vu, J., Kennedy, S., Serror, P., Aurell, E. & Repoila, F., 2011, In : COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY. 39, p. 1-14

    Research output: Contribution to journalArticleScientificpeer-review

  56. Published

    Network inference using asynchronously updated kinetic Ising Model

    Zeng, H-L., Aurell, E., Alava, M. & Mahmoudi, H., 2011, In : Physical Review E. 83, 4, p. 1-6 041135.

    Research output: Contribution to journalArticleScientificpeer-review

  57. Published

    Optimal protocols and optimal transport in stochastic thermodynamics

    Aurell, E., Mejia-Monasterio, C. & Muratore-Ginanneschi, P., 2011, In : Physical Review Letters. 106, 25, p. 1-4

    Research output: Contribution to journalArticleScientificpeer-review

  58. Published

    Three lemmas on the dynamic cavity method

    Aurell, E. & Mahmoudi, H., 2011, In : COMMUNICATIONS IN THEORETICAL PHYSICS. 56, 1, p. 157-162

    Research output: Contribution to journalArticleScientificpeer-review

  59. Published

    Window into the Complexities of Chromosome Interactomes

    Göndör, A., Woodbridge, A. F., Shi, C., Aurell, E., Imreh, M. & Ohlsson, R., 2011, In : COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY. p. 493-500

    Research output: Contribution to journalArticleScientificpeer-review

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