This is a list of recent publications.
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Articles

Fouquier d'Hérouel A., Wessner F., Halpern D., Ly-Vu J., Kennedy S. P., Serror P., Aurell E. and Repoila F. (2011):

A simple and efficient method to search for selected primary transcripts: non-coding and antisense rnas in the human pathogen enterococcus faecalis.

Nucleic Acids Research: 39, e46

Göndör A., Woodbridge A. F., Shi C., Aurell E., Imreh M. and Ohlsson R. (2011):

Window into the complexities of chromosome interactomes.

Cold Spring Harb Symp Quant Biol sqb.2010.75.049, Published in Advance April 5, 2011.

Brüderle D., Petrovici M. A., Vogginger B., Ehrlich M., Pfeil T., Millner S., Grübl A., Wendt K., Müller E., Schwartz M.-O., Oliveira D. H. d., Jeltsch S., Fieres J., Schilling M., Müller P., Breitwieser O., Petkov V., Muller L., Davison A. P., Krishnamurthy P., Kremkow J., Lundqvist M., Muller E., Partzsch J., Scholze S., Zühl L., Mayr C., Destexhe A., Diesmann M., Potjans T. C., Lansner A., Schüffny R., Schemmel J. and Meier K. (2011):

A comprehensive workflow for general-purpose neural modeling with highly configurable neuromorphic hardware systems.

Biol Cybern: 104, 263-296

Aurell E., Mej\'ia-Monasterio C. and Muratore-Ginanneschi P. (2011):

Optimal protocols and optimal transport in stochastic thermodynamics.

Phys Rev Lett, Accepted May 17

Aurell E. and Mahmoudi H. (2011):

A message-passing scheme for non-equilibrium stationary states.

J. Stat. Mech., P04014

Aurell E. and Mahmoudi H. (2011):

Three lemmas on the dynamic cavity method.

Communications in Theoretical Physics, Accepted May 17

Kamali Sarvestani I., Lindahl M., Hellgren Kotaleski J. and Ekeberg Ö. (2011):

The arbitration-extension hypothesis: a hierarchical interpretation of the functional organization of the basal ganglia.

Front. Syst. Neurosci.: 5, 13

Zeng H.-L., Aurell E., Alava M. and Mahmoudi H. (2011):

Network inference using asynchronously updated kinetic ising model.

Phys Rev E, in press, [arXiv:1011.6216]

Koelling S., Innocenti N., Hellings G., Gilbert M., Kambham A., Meyer K. D. and Vandervorst W. (2011):

Characteristics of cross-sectional atom probe analysis on semiconductor structures.

Ultramicroscopy, in press

Lundqvist M., Herman P. and Lansner A. (2011):

Theta and gamma power increases and alpha/beta power decreases with memory load in an attractor network model.

J Cogn Neurosci, Accepted

Silverstein D. and Lansner A. (2011):

Is attentional blink a byproduct of neocortical attractors?.

Front Comput Neurosci: 5, 1-14

Lindeberg T. (2011):

Generalized Gaussian scale-space axiomatics comprising linear scale-space, affine scale-space and spatio-temporal scale-space.

J. Math. Imaging Vision: 40, 36-81

Fouquier d'Hérouel A., Birgersdotter A. and Werner M. (2010):

Fr-like ebna1 binding sites in the human genome.

Virology: 2, 524-529

Frygelius J., Arvestad L., Wedell A. and Töhönen V. (2010):

Evolution and human tissue expression of the Cres/Testatin subgroup genes, a reproductive tissue-specific subgroup of the type 2 cystatins.

Evolution and Development: 12, 329-342

Harischandra N., Cabelguen J.-M. and Ekeberg Ö. (2010):

A 3D musculo-mechanical model of the salamander for the study of different gaits and modes of locomotion.

Front. Neurorobot.: 4, 112

Ensterö M., Åkerborg O., Lundin D., Wang B., Furey T., Öhman M. and Lagergren J. (2010):

A computational screen for site selective a-to-i editing detects novel sites in neuron specific hu proteins..

BMC Bioinformatics: 11, 6

Aurell E., Ollion C. and Roudi Y. (2010):

Dynamics and performance of susceptibility propagation on synthetic data.

Eur. Phys. J. B: 77, 587-595

Aurell E., Ollion C. and Roudi Y. (2010):

Dynamics and performance of susceptibility propagation on synthetic data.

European Physics Journal B: 77, 587-595

Benjaminsson S., Fransson P. and Lansner A. (2010):

A novel model-free data analysis technique based on clustering in a mutual information space: application to resting-state fmri.

Front. Syst Neurosci.: 4, 1-8

Djurfeldt M., Hjorth J., Eppler J. M., Dudani N., Helias M., Potjans T. C., Bhalla U. S., Diesmann M., Kotaleski J. H. and Ekeberg Ö. (2010):

Run-time interoperability between neuronal network simulators based on the music framework.

Neuroinformatics: 8, 43-60

Sehat B., Tofigh A., Lin Y., Trocme E., Liljedahl U., Lagergren J. and Larsson O. (2010):

SUMOylation mediates the nuclear translocation and signaling of the IGF-1 receptor..

Sci Signal: 3, ra10

Stranneheim H., Käller M., Allander T., Andersson B., Arvestad L. and Lundeberg J. (2010):

Classification of DNA sequences using Bloom filters.

Bioinformatics: 26, 1595-1600

Lundqvist M., Compte A. and Lansner A. (2010):

Bistable, irregular firing and population oscillations in a modular attractor memory network.

PLOS Comput Biology: 6, 1-12

Chiel H. J., Ting L. H., Ekeberg Ö. and Hartmann M. J. (2009):

The brain in its body: Motor control and sensing in a biomechanical context.

J. Neurosci.: 29, 12807-12814

Halnes G., Ulfhielm E., Eklöf Ljunggren E., Hellgren Kotaleski J. and Rospars J. (2009):

Modelling and sensitivity analysis of the reactions involving receptor, g-protein and effector in vertebrate olfactory receptor neurons.

J. Comput. Neurosci.: in press

Book contributions

Lindeberg T. (2011):

Scale selection.

In: Encyclopedia of Computer Vision (in press). Springer.

Lansner A. and Lundqvist M. (2010):

Modeling coordination in the neocortex at the microcircuit and global network level.

In: Dynamic Coordination in the Brain: From Neurons to Mind. Strüngmann Forum Report, (edited by V. d Malsburg C., Phillips W. A. and Singer W.) volume 5 MIT Press , pages 83-99.

Mehta M., Buzsaki G., Kreiter A., Lansner A., Lücke J., Martin K., Moghaddam B., Moser M.-B., Nikolic D. and Sejnowski T. (2010):

Coordination in circuits.

In: Dynamic Coordination in the Brain: From Neurons to Mind, (edited by v. d Malsburg C., Phillips W. and Singer W.) volume 5 MIT Press , pages 133-148.

Alava M., Aurell E. and Zhou H. (2009):

Five challenges on the statistical mechanics appraoch to constraint satisfaction problems [in chinese].

In: 10000 Selected Problems in Science. Beijing: Science Press (Chinese Academy of Sciences) , pages 422-427.

Fransén E. (2008):

Mechanisms of graded persistent activity: Implications for epilepsy.

In: Computational Neuroscience in Epilepsy, (edited by Soltesz I. and Staley K.) Amsterdam: Elsevier.

Fransén E. (2008):

Entorhinal cortex cells.

In: Hippocampal Microcircuits, (edited by Cutsuridis, Graham, Cobb and Vida).

Lindeberg T. (2008):

Scale-space.

In: Encyclopedia of Computer Science and Engineering, (edited by Wah B.) Hoboken, New Jersey: John Wiley and Sons , pages 2495-2504.

Lansner A., Benjaminsson S. and Johansson C. (2008):

From ANN to biomimetic signal processing.

Studies in Computational Intelligence.

Johansson C. and Lansner A. (2006):

Attractor memory with self-organizing input.

In: LNCS. volume 3853 Springer Verlag , pages 265-280.

Lansner A. (2005):

Neural network models.

In: Encyclopedia of Nonlinear Science, (edited by Scott A.) New York: Routledge , pages 614-616.

Conferences

Fransén E. A. and Tigerholm J. (2010):

Involvement of a-type potassium channels in suppression of synchronized synaptic input.

volume 36 , pages 254.4.

Krishnamurthy S., Ardelius J., Aurell E., Dam M., Stadler R. and Wuhib F. (2010):

The accuracy of tree-based counting in dynamic networks.

PODC '10 Proceeding of the 29th ACM SIGACT-SIGOPS symposium on Principles of distributed computing..

Hertz J., Roudi Y., Thorning A., Tyrcha J., Aurell E. and Zeng H.-L. (2010):

Inferring network connectivity using kinetic ising models.

CNS 2010, San Antonio, TX, USA..

Schultheiss N. W., Fransén E. A. and Hasselmo M. E. (2010):

Intrinsic mechanisms contributing to persistent spiking of medial entorhinal neurons during high conductance states.

volume 36 , pages 101.18.

Tigerholm J. and Fransén E. (2010):

Hyperexcitable neural responses can be suppressed by modulatory substances targeting the a-type potassium channel.

volume 36 , pages 254.1.

Rathi V., Aurell E., Rasmussen L. and Skoglund M. (2010):

Bounds on thresholds related to maximum satisfiability of regular random formulas.

6th International symposium on turbo codes and iterative information processing..

Rathi V., Aurell E., Rasmussen L. and Skoglund M. (2010):

Bounds on threshold of regular random $k$-sat.

SAT 2010 - Thirteenth International Conference on Theory and Applications of Satisfiability Testing. July 11—July 14, 2010, Edinburgh, Scotland, UK.

Petersson M. E. and Fransén E. A. (2010):

Role of trpc channels in dendritic integration and subthreshold membrane potential plateaus.

volume 36 , pages 246.1.

Fransén E. A., Petersson M. E. and Yoshida M. (2009):

Mechanisms of mglur activated trp-current mediated potentials in entorhinal cortex neurons.

volume 35 , pages 323.15.

Hellgren Kotaleski J. (2009):

Modelling of motor systems including the dynamics in intracellular signaling networks involved in learning and synaptic plasticity.

British Neuroscience Association Meeting. Liverpool.

Evans R., Du K., Sheehan T., Hellgren Kotaleski J. and Blackwell K. (2009):

Effects of nmda receptor nr2 subunit on calcium concentration.

Soc. Neurosci. Abstr.. Society for Neuroscience Chicago October.

Sandström M., and Lansner A. (2009):

A bulb model implementing fuzzy coding of odour concentration.

Proc of 13th International Symposium on Olfaction and Electronic Nose (ISOEN '09). , pages 159-162.

Samuelsson E., Hill R. and Hellgren Kotaleski J. (2009):

Exploration of the lamprey pallidal neurons - a combined computational and experimental study.

CNS 2009. Berlin July.

Samuelsson E., Hill R. and Hellgren Kotaleski J. (2009):

The basal ganglia output stage in the lamprey - a combined experimental and modeling study.

2nd INCF Congress of Neuroinformatics. Pilsen September.

Tigerholm J. and Fransén E. (2009):

Ka channels suppress cellular responses to fast ripple activity - implications for epilepsy.

volume 10 (Suppl 1) , pages P226.

Klaus A., Hjorth J. and Hellgren Kotaleski J. (2009):

The influence of subthreshold membrane potential oscillations and gabaergic input on firing activity in striatal fast-spiking neurons.

CNS 2009. Berlin July.

Robertson B., Jones M., Samuelsson E., Hellgren Kotaleski J. and Grillner S. (2009):

The lamprey basal ganglia - a vertebrate blue-print.

Soc. Neurosci. Abstr.. Society for Neuroscience Chicago October.

Klaus A., Hjorth J. and Hellgren Kotaleski J. (2009):

The influence of stuttering properties for firing activity in pairs of electrically coupled striatal fast-spiking interneurons.

2nd INCF Congress of Neuroinformatics. Pilsen September.

Petersson M. E. and Fransén E. (2009):

Trpc channels activated by group I mGluR in entorhinal pyramidal neurons support integration of low frequency (< 10 hz) synaptic inputs.

volume 10 (Suppl 1) , pages P26.

Halnes G., Ulfhielm E., Hellgren Kotaleski J. and Rospars J.-P. (2008):

Modeling of the receptor, g-protein and effector reactions in vertebrate olfactory receptor neurons.

CNS 2008. Portland, Oregon July.

Technical Reports

Benjaminsson S. and Lansner A. (2011):

Extreme scaling of brain simulations on jugene.

Technical Report Technical Report FZJ-JSC-IB-2011-02 Forschungszentrum Jülich, Germany.

Ekeberg Ö. and Djurfeldt M. (2009):

Music - multi-simulation coordinator, users manual.

Technical report International Neuroinformatics Coordinating Facility (INCF).

Ekeberg Ö. and Djurfeldt M. (2008):

Music - multi-simulation coordinator: Request for comments.

Technical report International Neuroinformatics Coordinating Facility (INCF).

Djurfeldt M. and Lansner A. (2007):

Large-scale modeling of the nervous system.

Tech. rep. International Neuroinformatics Coordinating Facility (INCF).

Sandstrom M. (2007):

Early information processing in the vertebrate olfactory system - a computational study.

Licentiate degree thesis TRITA-CSC-A 2007:8 KTH, School of Computer Science and Communication Stockholm.

Djurfeldt M., Johansson C., Ekeberg Ö., Rehn M., Lundqvist M. and Lansner A. (2005):

Massively parallel simulation of brain-scale neuronal network models.

Technical Report TRITA-NA-P0513 KTH, School of Computer Science and Communication Stockholm.