Publications from CB

[Extracted from DiVA, the publication database at KTH.]

Aurell, E.; Mahmoudi, H. (2012):

Dynamic mean-field and cavity methods for diluted Ising systems.

Physical Review E. Statistical, Nonlinear, and Soft Matter Physics 85: 031119 [Details]

Aurell, E.; Ekeberg, M. (2012):

Inverse Ising Inference Using All the Data.

Physical Review Letters 108: 090201 [Details]

Aurell, E.; Mejia-Monasterio, C.; Muratore-Ginanneschi, P. (2012):

Boundary layers in stochastic thermodynamics.

Physical Review E. Statistical, Nonlinear, and Soft Matter Physics 85: 020103 [Details]

Auffarth, B. (2012):

Machine Learning Techniques with Specific Application to the Early Olfactory System.

Doctoral thesis, comprehensive summary [Details]

Lansner, A.; Diesmann, M. (2012):

Virtues, pitfalls, and methodology of neuronal network modeling and simulations on supercomputers.

Chapter in book [Details]

Benjaminsson, S.; Silverstein, D.; Herman, P.; Lansner, A. (2012):

Visualization of Output from Large-Scale Brain Simulations.

Report [Details]

Krishnamurthy, P.; Gilad, S.; Lansner, A. (2012):

A cortical attractor network with Martinotti cells driven by facilitating synapses.

PLoS ONE : [Details]

Lindeberg, T. (2012):

Scale invariant feature transform.

Scholarpedia : [Details]

Tigerholm, J. (2012):

Mechanisms of excitability in the central and peripheral nervous systems - Implications for epilepsy and chronic pain.

Doctoral thesis, comprehensive summary [Details]

Lundqvist, M.; Herman, P.; Lansner, A. (2012):

Variability of spike firing during theta-coupled replay of memories in a simulated attractor network.

Brain Research 1434: 152-161 [Details]

Lindeberg, T. (2012):

Scale selection.

Chapter in book [Details]

Linde, O.; Lindeberg, T. (2012):

Composed Complex-Cue Histograms - An Investigation of the Information Content in Receptive Field Based Image Descriptors for Object Recognition.

Computer Vision and Image Understanding 116: 538-560 [Details]

Iglesias, M.; Reilly, S.; Emanuelsson, O.; Sennblad, B.; Najafabadi, M.; Folkersen, L.; Mälarstig, A.; Lagergren, J.; Eriksson, P.; Hamsten, A.; Odeberg, J. (2012):

Combined Chromatin and Expression Analysis Reveals Specific Regulatory Mechanisms within Cytokine Genes in the Macrophage Early Immune Response.

PLoS ONE 7: e32306 [Details]

Fouquier D´Hérouel, A. (2011):

On diverse biophysical aspects of genetics - from the action of regulators to the characterization of transcripts.

Doctoral thesis, comprehensive summary [Details]

Fouquier d'Hérouel, A.; Wessner, F.; Halpern, D.; Ly-Vu, J.; Kennedy, S.; Serror, P.; Aurell, E.; 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-U88 [Details]

Herman, P.; Lansner, A. (2011):

Odor recognition framework for evaluating olfactory codes.

[Conference paper] [Details]

Benjaminsson, S.; Lansner, A. (2011):

Adaptive sensor drift counteraction by a modular neural network.

Other [Details]

Tofigh, A.; Hallett, M.; Lagergren, J. (2011):

Simultaneous Identification of Duplications and Lateral Gene Transfers.

IEEE/ACM Transactions on Computational Biology & Bioinformatics 8: 517-535 [Details]

Brocke, E.; Djurfeldt, M. (2011):

Efficient spike communication in the MUSIC multi-simulation framework.

[Conference paper] CNS*2011, Stockholm, July 23-28; Twentieth Annual Computational Neuroscience Meeting [Details]

Brandi, M.; Brocke, E.; Talukdar, H.; Hanke, M.; Bhalla, U.; Hällgren-Kotaleski, J.; Djurfeldt, M. (2011):

Connecting MOOSE and NeuroRD through MUSIC - towards a communication framework for multi-scale modeling.

[Conference paper] Computational Neuroscience, Stockholm, Sweden, 23-28 July 2011; Twentieth Annual Computational Neuroscience Meeting [Details]

Lindahl, M.; Hellgren Kotaleski, J. (2011):

Short term plasticity within the basal ganglia - a systems level computational investigation.

BMC neuroscience (Online) 12: P145 [Details]

Fino, E.; Paille, V.; Du, K.; Morera Herreras, T.; Hellgren Kotaleski, J.; Venance, L. (2011):

GABA operates as a Hebbian/anti-Hebbian switch for spike-timing-dependent plasticity .

[Conference paper] Neuroscience 2011, Washington, DC, November 12-16, 2011; [Details]

Klaus, A.; Planert, H.; Hjorth, J.; Berke, J.; Silberberg, G.; Hellgren Kotaleski, J. (2011):

Striatal fast-spiking interneurons - from firing patterns to postsynaptic impact.

Frontiers in Systems Neuroscience 5: 57 [Details]

Lindén, H.; Tetzlaff, T.; Potjans, T.; Pettersen, K.; Grün, S.; Diesmann, M.; Einevoll, G. (2011):

Modeling the spatial reach of the LFP.

Neuron 72: 859-872 [Details]

Aurell, E.; Mahmoudi, H. (2011):

Three Lemmas on Dynamic Cavity Method.

Communications in Theoretical Physics 56: 157-162 [Details]

Tigerholm, J.; Fransén, E. (2011):

Reversing Nerve Cell Pathology by Optimizing Modulatory Action on Target Ion Channels.

Biophysical Journal 101: 1871-1879 [Details]

Benjaminsson, S.; Lansner, A. (2011):

Extreme scaling of brain simulation on JUGENE.

Report [Details]

Harischandra, N. (2011):

Computer Simulation of the Neural Control of Locomotion in the Cat and the Salamander.

Doctoral thesis, comprehensive summary [Details]

Nazem, A.; Kootstra, G.; Kragic, D.; Djurfeldt, M. (2011):

Interfacing a parallel simulation of a neuronal network to robotic hardware using MUSIC, with application to real-time figure-ground segregation..

BMC neuroscience (Online) 12: 78-78 [Details]

Nazem, A.; Kootstra, G.; Kragic, D.; Djurfeldt, M. (2011):

Parallel implementation of a biologically inspired model of figure-ground segregation - Application to real-time data using MUSIC.

Frontiers in Neuroinformatics : [Details]

Auffarth, B.; Kaplan, B.; Anders, L. (2011):

Map formation in the olfactory bulb by axon guidance of olfactory neurons.

Frontiers in Systems Neuroscience 5: [Details]

Harischandra, N.; Knuesel, J.; Kozlov, A.; Bicanski, A.; Cabelguen, J.; Ijspeert, A.; Ekeberg, Ö. (2011):

Sensory feedback plays a significant role in generating walking gait and in gait transition in salamanders - a simulation study.

Frontiers in Neurorobotics 5: 3:1-3:13 [Details]

Lindeberg, T. (2011):

Generalized Gaussian Scale-Space Axiomatics Comprising Linear Scale-Space, Affine Scale-Space and Spatio-Temporal Scale-Space.

Journal of Mathematical Imaging and Vision 40: 36-81 [Details]

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

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

Frontiers in Systems Neuroscience 5: 13 [Details]

Petersson, M.; Yoshida, M.; Fransén, E. (2011):

Low-frequency summation of synaptically activated transient receptor potential channel-mediated depolarizations.

European Journal of Neuroscience 34: 578-593 [Details]

Aurell, E.; Mejia-Monasterio, C.; Muratore-Ginanneschi, P. (2011):

Optimal Protocols and Optimal Transport in Stochastic Thermodynamics.

Physical Review Letters 106: 250601 [Details]

Bruederle, D.; Petrovici, M.; Vogginger, B.; Ehrlich, M.; Pfeil, T.; Millner, S.; Gruebl, A.; Wendt, K.; Mueller, E.; Schwartz, M.; de Oliveira, D.; Jeltsch, S.; Fieres, J.; Schilling, M.; Mueller, P.; Breitwieser, O.; Petkov, V.; Muller, L.; Davison, A.; Krishnamurthy, P.; Kremkow, J.; Lundqvist, M.; Muller, E.; Partzsch, J.; Scholze, S.; Zuehl, L.; Mayr, C.; Destexhe, A.; Diesmann, M.; Potjans, T.; Lansner, A.; Schueffny, R.; Schemmel, J.; Meier, K. (2011):

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

Biological cybernetics 104: 263-296 [Details]

Zeng, H.; Aurell, E.; Alava, M.; Mahmoudi, H. (2011):

Network inference using asynchronously updated kinetic Ising model.

Physical Review E 83: 041135 [Details]

Silverstein, D.; Lansner, A. (2011):

Is attentional blink a byproduct of neocortical attractors?.

FRONTIERS IN COMPUTATIONAL NEUROSCIENCE 5: 13 [Details]

Aurell, E.; Mahmoudi, H. (2011):

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

JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT : P04014 [Details]

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

SUMOylation Mediates the Nuclear Translocation and Signaling of the IGF-1 Receptor.

Science Signaling 3: [Details]

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

Bounds on Threshold of Regular Random k-SAT.

Lecture Notes in Computer Science 6175: 264-277 [Details]

Planert, H.; Szydlowski, S.; Hjorth, J.; Grillner, S.; Silberberg, G. (2010):

Dynamics of Synaptic Transmission between Fast-Spiking Interneurons and Striatal Projection Neurons of the Direct and Indirect Pathways.

Journal of Neuroscience 30: 3499-3507 [Details]

Frygelius, J.; Arvestad, L.; Wedell, A.; Tohonen, V. (2010):

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

Evolution & Development 12: 329-342 [Details]

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

Bistable, Irregular Firing and Population Oscillations in a Modular Attractor Memory Network.

PloS Computational Biology 6: e1000803 [Details]

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

Classification of DNA sequences using Bloom filters.

Bioinformatics 26: 1595-1600 [Details]

Petersson, M. (2010):

Beyond AMPA and NMDA: Slow synaptic mGlu/TRPC currents - Implications for dendritic integration.

Licentiate thesis, comprehensive summary [Details]

Cervenka, S.; Varrone, A.; Fransén, E.; Halldin, C.; Farde, L. (2010):

PET Studies of D2-Receptor Binding in Striatal and Extrastriatal Brain Regions - Biochemical Support In Vivo for Separate Dopaminergic Systems in Humans.

Synapse 64: 478-485 [Details]

Hällgren Kotaleski, J.; Blackwell, K. (2010):

Modelling the molecular mechanisms of synaptic plasticity using systems biology approaches.

Nature Reviews Neuroscience 11: 239-251 [Details]

Holme, P.; Kim, B.; Fodor, V. (2010):

Heterogeneous attachment strategies optimize the topology of dynamic wireless networks.

European Physical Journal B 73: 597-604 [Details]

More