PublicationsThe lists of publications (of different types) given below are mainly to keep track of old papers and papers by PhD students without Erik Aurell as co-author. They therefore not updated very frequently. More regularly updated lists of papers co-authored by Erik Aurell can found through his Google scholar page or through the KTH data base DIVA, for instance from here. |
| Recent papers and publications Conference proceedings & book chapters Selected earlier publications |
Recent papers and publications |
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Erik Aurell, Federica Montana Thermal power of heat flow through a qubit arXiv:1901.05896 (2019) Chen-Yi Gao, Fabio Cecconi, Angelo Vulpiani, Hai-Jun Zhou, Erik Aurell DCA for genome-wide epistasis analysis: the statistical genetics perspective Physical biology (2019) Chen-Yi Gao, Hai-Jun Zhou, Erik Aurell Correlation-compressed direct-coupling analysis Physical Review E 98 (3), 032407 (2018) Erik Aurell, Global Estimates of Errors in Quantum Computation by the Feynman-Vernon Formalism J Statistical Physics 171 (5), 745-767 (2018) Erik Aurell, Characteristic functions of quantum heat with baths at different temperatures Physical Review E 97 (6), 062117 (2018) Erik Aurell, Unified picture of strong-coupling stochastic thermodynamics and time reversals Phys. Rev. E 97, 042112 (2018) Erik Aurell, Eduardo Dominguez, David Machado, Roberto Mulet, Exploring the diluted ferromagnetic p-spin model with a Cavity Master Equation Physical Review E 97 (5), 050103 (2018) Erik Aurell, Stefano Bo, Steady diffusion in a drift field: A comparison of large-deviation techniques and multiple-scale analysis Phys. Rev. E 96, 032140 (2017) Erik Aurell On work and heat in time-dependent strong coupling Entropy(2017) Yingying Xu, Erik Aurell, Jukka Corander, Yoshiyuki Kabashima, Statistical properties of interaction parameter estimates in direct coupling analysis [arXiv:1704.01459](2017) Marcin J. Skwark , Nicholas J. Croucher , Santeri Puranen, Claire Chewapreecha, Maiju Pesonen, Ying Ying Xu, Paul Turner, Simon R. Harris, Stephen B. Beres, James M. Musser, Julian Parkhill, Stephen D. Bentley, Erik Aurell and Jukka Corander, Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis PLOS Genetics(2017) Alexandre Maes, Celine Gracia, Nicolas Innocenti, Kaiyang Zhang, Erik Aurell, and Eliane Hajnsdorf, Landscape of RNA polyadenylation in E. coli Nucleic Acids Research(2016) Erik Aurell, Gino Del Ferraro, Eduardo Dominguez, Roberto Mulet A Cavity Master Equation for the continuous time dynamics of discrete spins models Phys. Rev. E 95, 052119 (2017) Eduardo Dominguez, Gino Del Ferraro, Federico Ricci-Tersenghi A simple analytical description of the non-stationary dynamics in Ising spin systems Journal of Statistical Mechanics: Theory and Experiment (2017) Erik Aurell, The Maximum Entropy Fallacy Redux? PLOS Comp. Bio.,1004777 (2016) Erik Aurell, Nicolas Innocenti, Hai-Jun-Zhou, The Bulk and The Tail of Minimal Absent Words in Genome Sequences Physical Biology 13, 2(2016) Erik Aurell, Gino Del Ferraro Causal analysis, Correlation-Response and Dynamic cavity Journal of Physics: Conference Series 699, 012002(2016) Raffaele Marino, Erik Aurell Advective-diffusive motion on large scales from small-scale dynamics with an internal symmetry Phys. Rev. E 93, 062147(2016) Qin Li, Anders Wennborg, Erik Aurell, Erez Dekel, Jie-Zhi Zou, Yuting Xu, Sui Huang, and Ingemar Ernberg Dynamics inside the cancer cell attractor reveal cell heterogeneity, limits of stability, and escape PNAS vol. 113 no. 10(2016) Erik Aurell, Stefano Bo, Marcelo Dias, Ralf Eichhorn and Raffaele Marino Diffusion of a Brownian ellipsoid in a force field EPL, 114 30005(2016) Raffaele Marino, Ralf Eichhorn, Erik Aurell, Entropy production of a Brownian ellipsoid in the overdamped limit Phys. Rev. E 93, 012132(2016) Gino Del Ferraro, Chuang Wang, Dani Martì , Marc Mézard, Cavity Method: Message Passing from a Physics Perspective [arXiv:1409.3048](2015) Nicolas Innocenti, Son Nguyen, Aymeric Fouquier d'Hérouël, Erik Aurell, An observation of circular RNAs in bacterial RNA-seq data [arXiv:1606.04576](2016) Raffaele Marino, Giorgio Parisi, Federico Ricci-Tersenghi, The Backtracking Survey Propagation Algorithm for Solving Random K-SAT Problems Nat. Commun. 7,12996(2015) Yueheng Lan, Erik Aurell, The stochastic thermodynamics of a rotating Brownian particle in a gradient flow Scientific Reports 5, Article number: 12266(2015) Gino Del Ferraro, Chuang Wang, Hai-Jun Zhou, Erik Aurell, On one-step replica symmetry breaking in the Edwards-Anderson spin glass model Journal of Statistical Mechanics: Theory and Experiment(2016) Gino Del Ferraro, Erik Aurell, Dynamic message-passing approach for kinetic spin models with reversible dynamics Phys. Rev. E 92, 010102(2015) Nicolas Innocenti, Francis Repoila, Erik Aurell, Detection and quantitative estimation of spurious double stranded DNA formation during reverse transcription in tagRNA-seq RNA Biology (2015) Erik Aurell, Jakub Zakrzewski, Karol Życzkowski, Time reversals of irreversible quantum maps J. Phys. A: Math. Theor. 48 (2015) 38FT01, and in the special collection on IOPSCIENCE(2015) IOPcollections (2016) (2016) Nicolas Innocenti, Monica Golumbeanu, Aymeric Fouquier d'Hérouël, Caroline Lacoux, Rémy A. Bonnin, Sean P Kennedy, Françoise Wessner, Pascale Serror, Philippe Bouloc, Francis Repoila and Erik Aurell Whole genome mapping of 5' ends in bacteria by tagged sequencing: A comprehensive view in Enterococcus faecalis RNA 21: 1018-1030(2015) Rémi Lemoy, Mikko Alava, Erik Aurell A novel local search for random K-SAT Phys. Rev. E 91, 013305 (2015) Erik Aurell, Ralf Eichhorn, On the von Neumann entropy of a bath linearly coupled to a driven quantum system New Journal of Physics 17 065007(2015) Saikat Chatterjee, David Koslicki, Siyuan Dong, Nicolas Innocenti, Lu Cheng, Yueheng Lan, Mikko Vehkaperä, Mikael Skoglund, Lars K. Rasmussen, Erik Aurell and Jukka Corander, SEK: sparsity exploiting k-mer-based estimation of bacterial community composition Bioinformatics (2014) 30 (17): 2423-2431. [arXiv:1407.0387](2014) Ralf Eichhorn and Erik Aurell, Stochastic thermodynamics Phys. Scr. 89 (2014) 048001.(2014) Christoph Feinauer, Marcin J. Skwark, Andrea Pagnani, Erik Aurell, Improving contact prediction along three dimensions PLoS Comput Biol 10(10): e1003847. [arXiv:1403.0379](2014) Magnus Ekeberg, Tuomo Hartonen, Erik Aurell, Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences Journal of Computational Physics Volume 276: 341-356 [arXiv:1401.4832](2014) Gino Del Ferraro, Erik Aurell Perturbative large deviation analysis of non-equilibrium dynamics J. Phys. Soc. Japan 83 084001 [arXiv:1401.4685](2014) Erik Aurell The physics of distributed information systems J. Phys.: Conf. Ser. 473 012017(2013) Nicolas Innocenti, Erik Aurell, Lognormality and oscillations in the coverage of high-throughput transcriptomic data towards gene ends J. Stat. Mech. (2013) P10013 (2013) [arXiv:1303.4229] Lu-Lu Wu, Hai-Jun Zhou, Mikko Alava, Erik Aurell, Pekka Orponen, Witness of unsatisfiability for a random 3-satisfiability formula Phys. Rev. E 87, 052807 (2013) Stefano Bo, Erik Aurell, Ralf Eichhorn, Antonio Celani Optimal stochastic transport in inhomogeneous thermal environments EPL 103 10010 (2013) [arXiv:1303.3206] Adriano Barra, Gino Del Ferraro, Daniele Tantari Mean field spin glasses treated with PDE techniques Eur. Phys. J. B. (2013) 86:332 (2013) S. Koelling, N. Innocenti, J. Bogdanowicz, W. Vandervorst Optimal laser positioning for laser-assisted atom probe tomography Ultramicroscopy 132, p. 70-74 (2013) Elena Agliari, Adriano Barra, Gino Del Ferraro, Francesco Guerra, Daniele Tantari Anergy in self-directed B lymphocytes from a statistical mechanics perspective Journal of Theoretical Biology 05/2014; 375. (2013) Janusz Bogdanowicz, Matthieu Gilbert, Nicolas Innocenti, Sebastian Koelling, Benoit Vanderheyden, Wilfried Vandervorst Light absorption in conical silicon particles Optics Express, Vol. 21, Issue 3, pp. 3891-3896 (2013) Magnus Ekeberg, Cecilia Lövkvist, Yueheng Lan, Martin Weigt, Erik Aurell Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models Phys. Rev. E 87, 012707 (2013) Hong-Li Zeng, Mikko Alava, Erik Aurell, John Hertz, Yasser Roudi Maximum likelihood reconstruction for Ising models with asynchronous updates Phys. Rev. Lett. 110, 210601 (2013) Joseph Xu Zhou, M. D. S. Aliyu, Erik Aurell, Sui Huang, Quasi-potential landscape in complex multi-stable systems J. R. Soc. Interface rsif20120434 (2012) Antonio Celani, Stefano Bo, Ralf Eichhorn, Erik Aurell Anomalous thermodynamics at the micro-scale Phys. Rev. Lett. 109, 260603 (2012) Mikko Vehkaperä, Yoshiyuki Kabashima, Saikat Chatterjee, Erik Aurell, Mikael Skoglund, Lars Rasmussen, Analysis of Sparse Representations Using Bi-Orthogonal Dictionaries Information Theory Workshop ITW 2012, Lausanne, Switzerland [arXiv:1204.4065] (2012) Erik Aurell, Krzysztof Gawȩdzki, Carlos Mejía-Monasterio, Roya Mohayaee, Paolo Muratore-Ginanneschi, Refined Second Law of Thermodynamics for fast random processes J. Stat. Phys. 147(3) (2012) Erik Aurell, Carlos Mejía-Monasterio, Paolo Muratore-Ginanneschi Boundary layers in stochastic thermodynamics Phys. Rev. E 85, 020103(R) (2012) Erik Aurell, Hamed Mahmoudi Dynamic mean-field and dynamic cavity for diluted Ising systems Phys. Rev. E 85, 031119 (2012) Erik Aurell, Magnus Ekeberg Inverse Ising inference using all the data Phys. Rev. Lett. 108, 090201 (2012) Erik Aurell, Carlos Mejía-Monasterio, Paolo Muratore-Ginanneschi, Optimal protocols and optimal transport in stochastic thermodynamics Phys. Rev. Lett. 106, 250601 (2011) Erik Aurell, Hamed Mahmoudi, Three lemmas on the dynamic cavity method Communications in Theoretical Physics, 56:1, pp. 157-162 (2011) Sebastian Koelling, Nicolas Innocenti, Andreas Schulze, Matthieu Gilbert, AJay Kumar Kambham, and Wilfried Vandervorst, In-situ observation of non-hemispherical tip shape formation during laser-assisted atom probe tomography J. Appl. Phys. 109, 104909 (2011) Sebastian Koelling, Nicolas Innocenti, Geert Hellings, Matthieu Gilbert, Ajay Kumar Kambham, Kristin De Meyer, Wilfried Vandervorst, Characteristics of cross-sectional atom probe analysis on semiconductor structures Ultramicroscopy 111(6):540-545 (2011) Anita Göndör, Alejandro Fernandez Woodbridge, Chenxi Shi, Erik Aurell, Marta Imreh, Rolf Ohlsson, Window into the Complexities of Chromosome Interactomes Cold Spring Harb. Symp. Quant. Biol. 75: 493-500 (2011) Aymeric Fouquier d'Hérouël, Françoise Wessner, David Halpern, Joseph Ly-Vu, Sean Kennedy, Pascale Serror, Erik Aurell, Francis Repoila, A simple and efficient method to search for selected primary transcripts: noncoding- and antisense RNAs in the human pathogen Enterococcus faecalis Nucl. Acids Res. 39(7):e46 (2011) Erik Aurell, Hamed Mahmoudi, A message-passing scheme for non-equilibrium stationary states J. Stat. Mech P04014 (2011) Hong-Li Zeng, Erik Aurell, Mikko Alava, Hamed Mahmoudi, Network inference using asynchronously updated kinetic Ising model Phys. Rev. E 83, 041135 (2011) John Hertz, Yasser Roudi, Andreas Thorning, Joanna Tyrcha, Erik Aurell, Hong-Li Zeng, Inferring network connectivity using kinetic Ising models BMC Neuroscience 2010, 11(Suppl 1):P51 (2010) Supriya Krishnamurthy, John Ardelius, Erik Aurell, Mads Dam, Rolf Stadler, Fetahi Wuhib, The Accuracy of Tree-based Counting in Dynamic Networks Proceeding of the 29th ACM SIGACT-SIGOPS symposium on Principles of distributed computing (2010) Vishwambhar Rathi, Erik Aurell, Lars Rasmussen, Mikael Skoglund, Bounds on Thresholds related to Maximum Satisfiability of Regular Random formulas 6th International symposium on turbo codes & iterative information processing, 2010. [arXiv:1004.2425] Vishwambhar Rathi, Erik Aurell, Lars Rasmussen, Mikael Skoglund, Bounds on Threshold of Regular Random k-SAT SAT 2010 [arXiv:1002.1290] Erik Aurell, Charles Ollion, Yasser Roudi, Dynamics and performance of susceptibility propagation on synthetic data Eur. Phys. J. B 77(4): 587-595 (2010) Aymeric Fouquier d'Hérouël, Anna Birgersdotter, Maria Werner, FR-like EBNA1 binding sites in the human genome Virology 405(2): 524-529 (2010) Maria Werner, Erik Aurell, A computational study of the lambda-lac mutants Phys. Biol. 6 046007 (2009) Yasser Roudi, Erik Aurell, John Hertz, Statistical physics of pairwise probability models Front. Comput. Neurosci. 3 22 [arXiv:0905.1410] (2009) Seung Ki Baek, Petter Minnhagen, Sebastian Bernhardsson, Kweon Choi, Beom Jun Kim, Flow improvement caused by agents who ignore traffic rules Phys. Rev. E 80, 016111 (2009) Seung Ki Baek, Petter Minnhagen, Hiroyuki Shima, Beom Jun Kim, Phase transition of q-state clock model on heptagonal lattices Phys. Rev. E 80, 011133 (2009) Seung Ki Baek, Hiroyuki Shima, Beom Jun Kim, Curvature-induced frustration in the XY Model on hyperbolic surfaces Phys. Rev. E 79, 060106(R) (2009) Erik Aurell, René Pfitzner, Gaussian Belief with dynamic data and in dynamic network Euro. Phys. Lett. 87 68004 Maria Werner, Szabolcs Semsey, Kim Sneppen, Sandeep Krishna Dynamics of Uptake and Metabolism of Small Molecules in Cellular Response Systems PLoS ONE 4(3): e4923 (2009) Mikko Alava, John Ardelius, Erik Aurell, Petteri Kaski, Supriya Krishnamurthy, Pekka Orponen, Sakari Seitz, Circumspect descent prevails in solving random constraint satisfaction problems PNAS 105(40) 15253-15257 (2008) Supriya Krishnamurthy, Sameh El-Ansary, Erik Aurell, Seif Haridi, Comparing Maintenance Strategies for Overlays [arXiv:0710.0386] Proc. 16th Euromicro Conference on Parallel, Distributed and Network-Based Processing (PDP 2008) 473-482 Supriya Krishnamurthy, Sameh El-Ansary, Erik Aurell, Seif Haridi, An Analytical Study of a Structured Overlay in the presence of Dynamic Membership [arXiv:0710.0270] IEEE/ACM Transactions on Networking 16 814-825 (2008) Maria Werner, LiZhe Zhu, Erik Aurell, Cooperative action in eukaryotic gene regulation: physical properties of a viral example Physical Review E 76 061909 (2007) [arXiv:0706.1852] Maria Werner, Ingemar Ernberg, JieZhi Zou, Jenny Almqvist, Erik Aurell, Epstein-Barr virus latency switch in human B-cells: a physico-chemical model BMC Systems Biology 1:40 (2007) John Ardelius, Erik Aurell, Supriya Krishnamurthy, Clustering of solutions in hard satisfiability problems J Stat Phys; Theo Exp: P10012 (2007) Erik Aurell, Aymeric Fouquier d'Hérouël, Claes Malmnäs, Massimo Vergassola, Transcription factor concentrations versus binding site affinities in the yeast S. cerevisiae Phys. Biol. 4 134-143 (2007) John Ardelius, Erik Aurell, Behavior of heuristics on large and hard satisfiability problems Phys. Rev. E 74, 037702 (2006) Erik Aurell, Paolo Muratore-Ginanneschi, Optimal hedging of Derivatives with transaction costs International Journal of Theoretical and Applied Finance vol. 9, No. 7, 1051-1069 [physics/0509150] (2006) Uriel Frisch, Jeremie Bec, Erik Aurell, "Locally homogeneous turbulence" Is it an inconsistent framework? Physics of Fluids 17:081706 (2005) Alain Noullez, Sergey N. Gurbatov, Erik Aurell, Sergey I. Simdyankin, The global picture of self-similar and not self-similar decay in Burgers Turbulence Physical Review E71, 056305 (2005) Guglielmo Lacorata, Erik Aurell, Bernard Legras, Angelo Vulpiani, Evidence for a k**(-5/3) spectrum from the EOLE Lagrangian balloons in the low stratosphere Journal of the Atmospheric Sciences 61:2936-2942 (2004) Erik Aurell, Paolo Muratore-Ginanneschi, Growth-Optimal Strategies with Quadratic Friction Over Finite-Time Investment Horizons International J. of Theoretical and Applied Finance 7:645-657 (2004) Adam Ameur, Erik Aurell, Mats Carlsson, Jakub Orzechowski Westholm, Global gene expression analysis by combinatorial optimization In Silico Biology 4, 0020 (2004) |
Conference proceedings & book chapters |
| Nicolas Innocenti, Sebastian Koelling, Wilfried Vandervorst, Benoit Vanderheyden, Fsec Laser Solid Interactions on Nanoscale Semiconducting Objects and Their Impact on Imaging with 3D-atomic Resolution in the Atomprobe MRS Spring Meeting 2011 Erik Aurell, Duccio Fanelli, Sergey N. Gurbatov, A.Yu. Moshkov, The non-linear regime of the gravitational instability. The inner structure of the pancake Frontiers of Nonlinear Physics (2005) Supriya Krishnamurthy, Sameh El-Ansary, Erik Aurell, Seif Haridi, A statistical theory of Chord under Churn 4th International Workshop on Peer-to-Peer Systems (IPTPS 2005) cs.NI/0501069 Sameh El-Ansary, Erik Aurell, Seif Haridi, A Physics-inspired Performace Evaluation of a Structured Peer-to-Peer Overlay Network The International Conference on Parallel and Distributed Computing and Networks (PDCN 2005) Maria Werner, Numerical solution to the master equation using the linear noise approximation International Conference on Biological Physics (ICBP 2004) Daniel Hasselrot, Erik Aurell, Comparison of transcription factor binding site models using correlation with gene expression International Conference on Biological Physics (ICBP 2004) [abstracts] Erik Aurell, Uri Gordon, Scott Kirkpatrick, Comparing Beliefs, Surveys and Random Walks Eighteenth Annual Conference on Neural Information Processing Systems (NIPS 2004) [cond-mat/0406217] Sameh El-Ansary, Erik Aurell, Per Brand, Seif Haridi, Experience with a physics-style approach for the study of self properties in structured overlay networks Proceedings of SELF-STAR: International Workshop on Self-* Properties in Complex Information Systems (2004) Sameh El-Ansary, Erik Aurell, A physics-style approach to scaling in distributed systems LNCS Post-Proceedings of the Global Computing, Springer-Verlag (2004) |
Selected earlier publications |
2003 |
| M. Ehrenberg, J. Elf, E. Aurell, R. Sandberg and J. Tegner, Systems Biology is Taking Off Genome Research 13, 2377-2380 (2003) |
2002 |
| E. Aurell, S. Brown, J. Johansson and K. Sneppen, Stability puzzles in Phage lambda Physical Review E 65, 051914 (2002) E. Aurell and K. Sneppen, Epigenetics as a first exit problem Physical Review Letters 88, 048101 (2002) A. Kozlov, F. Ullen, P. Fagerstedt, E. Aurell, A. Lansner and S. Grillner, Mechanisms for lateral turns in lamprey in response to descending unilateral commands: a modeling study Biological Cybernetics 86, 1-14 (2002) |
2001 |
| A. Kozlov, E. Aurell, G.N. Orlovsky, T. Deliagina, P.V.
Zelenin, J. Hellgren-Kotaleski and S. Grillner, Modeling control of body orientation in the lamprey Biological Cybernetics 84, 323-330 (2001) |
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