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Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015

BMC bioinformatics 2016年第3期17 Suppl 3卷 95页

作者： Katie Wilkins Mehedi Hassan Margherita Francescatto Jakob Jespersen R. Gonzalo Parra Bart Cuypers Dan DeBlasio Alexander Junge Anupama Jigisha Farzana Rahman Griet Laenen Sander Willems Lieven Thorrez Yves Moreau Nagarajan Raju Sonia Pankaj Chothani C. Ramakrishnan Masakazu Sekijima M. Michael Gromiha Paddy J Slator Nigel J Burroughs Przemysław Szałaj Zhonghui Tang Paul Michalski Oskar Luo Xingwang Li Yijun Ruan Dariusz Plewczynski Giulia Fiscon Emanuel Weitschek Massimo Ciccozzi Paola Bertolazzi Giovanni Felici Pieter Meysman Manu Vanaerschot Maya Berg Hideo Imamura Jean-Claude Dujardin Kris Laukens Westa Domanova James R. Krycer Rima Chaudhuri Pengyi Yang Fatemeh Vafaee Daniel J. Fazakerley Sean J. Humphrey David E. James Zdenka Kuncic Plant Pathology and Plant-Microbe Biology Section School of Integrative Plant Science Cornell University Ithaca USA Graduate Field of Computational Biology Cornell University Ithaca USA School of Computing & Mathematics University of South Wales Cardiff UK Department of Genome Biology for Neurodegenerative Diseases German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association ᅟ Germany Department of Surgery Massachusetts General Hospital The Broad Institute of MIT and Harvard Boston USA Department of Systems Biology Technical University of Denmark Kemitorvet Denmark Protein Physiology Lab Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Buenos Aires Argentina Molecular Parasitology Unit (MPU) Institute of Tropical Medicine Antwerp Belgium Advanced Database Research and Modeling (ADReM) research group University of Antwerp Antwerpen Belgium Department of Computer Science University of Arizona Tucson USA Department of Veterinary Clinical and Animal Sciences Center for non-coding RNA in Technology and Health University of Copenhagen Copenhagen Denmark University College Dublin Dublin Ireland Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems Signal Processing and Data Analytics KU Leuven Leuven Belgium Minds Medical IT Department Leuven Belgium Scientific Institute of Public Health (WIV-ISP) Platform of Biotechnology and Molecular Biology (PBB) Brussels Belgium Department of Development and Regeneration @ Kulak KU Leuven Kortrijk Belgium Department of Biotechnology Bhupat and Jyoti Metha School of Biosciences Indian Institute of Technology Madras Chennai India Philips Research North America Briarcliff Manor USA Global Scientific Information and Computing Center (GSIC) Tokyo Institute of Technology Tokyo Japan Systems Biology Centre University of Warwick Senate House Coventry UK Systems Biology Doctoral Training Centre University of Warwick Senate House Coventry UK Center for B

A1 Highlights from the eleventh ISCB Student Council Symposium 2015 Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman O1 Prioritizing a drug’s targets using both gene expression and structural similarity Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau O2 Organism specific protein-RNA recognition: A computational analysis of protein-RNA complex structures from different organisms Nagarajan Raju, Sonia Pankaj Chothani, C. Ramakrishnan, Masakazu Sekijima; M. Michael Gromiha O3 Detection of Heterogeneity in Single Particle Tracking Trajectories Paddy J Slator, Nigel J Burroughs O4 3D-NOME: 3D NucleOme Multiscale Engine for data-driven modeling of three-dimensional genome architecture Przemysław Szałaj, Zhonghui Tang, Paul Michalski, Oskar Luo, Xingwang Li, Yijun Ruan, Dariusz Plewczynski O5 A novel feature selection method to extract multiple adjacent solutions for viral genomic sequences classification Giulia Fiscon, Emanuel Weitschek, Massimo Ciccozzi, Paola Bertolazzi, Giovanni Felici O6 A Systems Biology Compendium for Leishmania donovani Bart Cuypers, Pieter Meysman, Manu Vanaerschot, Maya Berg, Hideo Imamura, Jean-Claude Dujardin, Kris Laukens O7 Unravelling signal coordination from large scale phosphorylation kinetic data Westa Domanova, James R. Krycer, Rima Chaudhuri, Pengyi Yang, Fatemeh Vafaee, Daniel J. Fazakerley, Sean J. Humphrey, David E. James, Zdenka Kuncic

关键词： Visceral Leishmaniasis Feature Selection Method Frequent Itemset Mining Leishmania Donovani Student Council

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Statistical validation of event predictors: A comparative study based on the field of seizure prediction

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Physical Review E 2011年第6期83卷 066704-066704页

作者： Hinnerk Feldwisch-Drentrup Andreas Schulze-Bonhage Jens Timmer Björn Schelter Bernstein Center Freiburg (BCF) University of Freiburg Freiburg Germany Freiburg Center for Data Analysis and Modeling (FDM) University of Freiburg Freiburg Germany Department of Neurobiology and Biophysics Faculty of Biology University of Freiburg Freiburg Germany Freiburg Institute for Advanced Studies University of Freiburg Freiburg Germany Department of Physics University of Freiburg Freiburg Germany Epilepsy Center University Hospital of Freiburg Freiburg Germany Department of Clinical and Experimental Medicine Linköping University Linköping Sweden Institute for Complex Systems and Mathematical Biology SUPA University of Aberdeen Aberdeen United Kingdom

The prediction of events is of substantial interest in many research areas. To evaluate the performance of prediction methods, the statistical validation of these methods is of utmost importance. Here, we compare an analytical validation method to numerical approaches that are based on Monte Carlo simulations. The comparison is performed in the field of the prediction of epileptic seizures. In contrast to the analytical validation method, we found that for numerical validation methods insufficient but realistic sample sizes can lead to invalid high rates of false positive conclusions. Hence we outline necessary preconditions for sound statistical tests on above chance predictions.

关键词： Forecasting

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Observation of oscillation coupling ratios and the meridional flow

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Journal of physics: Conference Series 2011年第1期271卷

作者： A Schad M Roth J Timmer Freiburg Center for Data Analysis and Modeling University of Freiburg 79104 Freiburg Germany Kiepenheuer-Insitut für Sonnenphysik 79104 Freiburg Germany Freiburg Institute for Advanced Studies University of Freiburg 79104 Freiburg Germany

Measurements from local helioseismology indicate the existence of a meridional flow in the Sun with a strength up to 15 m/s near the solar surface. The flow profile at depths below ≈ 15 Mm are not accessible. We propose a method using global helioseismic measurements with the prospect to infer the meridional flow profile throughout the solar convection zone and show its performance on simulated data.

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Distinguishing Direct from Indirect Interactions in Oscillatory Networks with Multiple Time Scales

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Physical Review Letters 2010年第3期104卷 038701-038701页

作者： Jakob Nawrath M. Carmen Romano Marco Thiel István Z. Kiss Mahesh Wickramasinghe Jens Timmer Jürgen Kurths Björn Schelter Physics Department University of Freiburg Hermann-Herder Str. 3 79104 Freiburg Germany Center for Data Analysis and Modeling University of Freiburg Eckertstr. 1 79104 Freiburg Germany Institute for Complex Systems and Mathematical Biology University of Aberdeen Aberdeen AB24 3UE United Kingdom Institute of Medical Sciences Foresterhill University of Aberdeen Aberdeen AB25 2ZD United Kingdom Department of Chemistry Saint Louis University St. Louis Missouri 63103 USA Freiburg Institute for Advanced Studies Albertstr. 19 79104 Freiburg Germany Institute of Physics Humboldt University Berlin 12489 Berlin Germany Potsdam Institute for Climate Impact Research 14412 Potsdam Germany

We propose a method to infer the coupling structure in networks of nonlinear oscillatory systems with multiple time scales. The method of partial phase synchronization allows us to infer the coupling structure for coupled nonlinear oscillators with one well-defined time scale. The case of oscillators with multiple time scales has remained a challenge until now. Here, we introduce partial recurrence based synchronization analysis to tackle this challenge. We successfully apply the proposed method to model systems and experimental data from coupled electrochemical oscillators. The statistical significance of the results is evaluated based on a surrogate hypothesis test.

关键词： Time measurement

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Inferring direct directed-information flow from multivariate nonlinear time series

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Physical Review E 2009年第1期80卷 011138-011138页

作者： Michael Jachan Kathrin Henschel Jakob Nawrath Ariane Schad Jens Timmer Björn Schelter Center for Data Analysis and Modeling (FDM) University of Freiburg Eckerstrasse 1 D-79104 Freiburg Germany Department of Neurology University Hospital of Freiburg Breisacher Strasse 64 D-79098 Freiburg Germany Bernstein Center for Computational Neuroscience (BCCN) University of Freiburg Hansastrasse 9A D-79104 Freiburg Germany Department of Physics University of Freiburg Hermann Herder Strasse 3 D-79104 Freiburg Germany Freiburg Institute for Advanced Studies (FRIAS) University of Freiburg Albertstrasse 19 D-79104 Freiburg Germany

Estimating the functional topology of a network from multivariate observations is an important task in nonlinear dynamics. We introduce the nonparametric partial directed coherence that allows disentanglement of direct and indirect connections and their directions. We illustrate the performance of the nonparametric partial directed coherence by means of a simulation with data from synchronized nonlinear oscillators and apply it to real-world data from a patient suffering from essential tremor.

关键词： Condensed matter physics

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Estimating causal dependencies in networks of nonlinear stochastic dynamical systems

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Physical Review E 2009年第5期80卷 051128-051128页

作者： Linda Sommerlade Michael Eichler Michael Jachan Kathrin Henschel Jens Timmer Björn Schelter Department of Physics University of Freiburg Hermann-Herder-Str. 3 79104 Freiburg Germany Bernstein Center for Computational Neuroscience University of Freiburg Hansastr. 9A 79104 Freiburg Germany FDM Freiburg Center for Data Analysis and Modeling University of Freiburg Eckerstr. 1 79104 Freiburg Germany Department of Quantitative Economics Maastricht University P.O. Box 616 6200 MD Maastricht The Netherlands Freiburg Institute for Advanced Studies (FRIAS) University of Freiburg Albertstr. 19 79104 Freiburg Germany

The inference of causal interaction structures in multivariate systems enables a deeper understanding of the investigated network. Analyzing nonlinear systems using partial directed coherence requires high model orders of the underlying vector-autoregressive process. We present a method to overcome the drawbacks caused by the high model orders. We calculate the corresponding statistics and provide a significance level. The performance is illustrated by means of model systems and in an application to neurological data.

关键词： Stochastic systems

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Probabilistic forecasts of epileptic seizures and evaluation by the brier score

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4th European Conference of the International Federation for Medical and Biological Engineering, ECIFMBE 2008

作者： Jachan, M. Feldwisch Genannt Drentrup, H. Posdziech, F. Brandt, A. Altenmüller, D.-M. Schulze-Bonhage, A. Timmer, J. Schelter, B. Epilepsy Centre University of Freiburg Germany FDM Center for Data Analysis and Modeling University of Freiburg Germany BCCN Bernstein Center for Computational Neuroscience University of Freiburg Germany Department of Neurobiology and Biophysics University of Freiburg Germany FRIAS Freiburg Institute of Advanced Studies Germany

ISBN: (纸本)9783540892076

We present a probabilistic epileptic seizure predictor and an according method for its statistical evaluation. The probabilistic predictor is based on a combination of feature channels, which are derived from the intracranial electroencephalogram (EEG), by a logistic regression map. The evaluation is done by the Brier score, an established assessment method in meteorology, which quantifies the prediction error. From the prediction features, the weights of the logistic regression are learned in a training phase and in a test phase the Brier score is assessed. A test for significance of the probabilistic predictor, based on seizure time surrogates, is computed. For 3 of 5 patients we obtained significant predictive power with the mean phase coherence and with the dynamical similarity index we obtained for 2 of the 5 patients significant results. The concept of probabilistic prediction can be a valuable tool for the development of future seizure intervention systems. © 2009 Springer Berlin Heidelberg.

关键词： Electroencephalography

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Partial Phase Synchronization for Multivariate Synchronizing Systems

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Physical Review Letters 2006年第20期96卷 208103-208103页

作者： Björn Schelter Matthias Winterhalder Rainer Dahlhaus Jürgen Kurths Jens Timmer FDM Freiburg Center for Data Analysis and Modeling University of Freiburg Eckerstraße 1 79104 Freiburg Germany Bernstein Center for Computational Neuroscience Freiburg University of Freiburg Germany Physics Department University of Freiburg Hermann-Herder Straße 3 79104 Freiburg Germany Department of Applied Mathematics University of Heidelberg Im Neuenheimer Feld 294 69120 Heidelberg Germany Nonlinear Dynamics Group Institute of Physics University of Potsdam 14415 Potsdam Germany

Graphical models applying partial coherence to multivariate time series are a powerful tool to distinguish direct and indirect interdependencies in multivariate linear systems. We carry over the concept of graphical models and partialization analysis to phase signals of nonlinear synchronizing systems. This procedure leads to the partial phase synchronization index which generalizes a bivariate phase synchronization index to the multivariate case and reveals the coupling structure in multivariate synchronizing systems by differentiating direct and indirect interactions. This ensures that no false positive conclusions are drawn concerning the interaction structure in multivariate synchronizing systems. By application to the paradigmatic model of a coupled chaotic Roessler system, the power of the partial phase synchronization index is demonstrated.

关键词： Multivariable systems

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Mixing properties of the Rössler system and consequences for coherence and synchronization analysis

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Physical Review E 2005年第2期72卷 026213-026213页

作者： M. Peifer B. Schelter M. Winterhalder J. Timmer Institute of Physics University of Freiburg Hermann-Herder-Str. 3 79104 Freiburg Germany Freiburg Centre for Data Analysis and Modelling University of Freiburg Eckerstr. 1 79104 Freiburg Germany Bernstein Center for Computational Neuroscience University of Freiburg Hansastr. 9 79104 Freiburg Germany

Cross-spectral and synchronization analysis of two independent, identical chaotic Rössler systems suggest a coupling although there is no interaction. This spuriously detected interaction can either be explained by the absence of mixing or by finite size effects. To decide which alternative holds the phase dynamics is studied by a model of the fluctuations derived from the system’s equations. The basic assumption of the model is a diffusive character for the system which corresponds to mixing. Comparison of theoretical properties of the model with empirical properties of the Rössler system suggests that the system is mixing but the rate of mixing appears to be rather low.

关键词： Nonlinear systems

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Stability analysis of coupled map lattices at locally unstable fixed points

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The European Physical Journal B - Condensed Matter and Complex Systems 2005年第2期44卷 229-239页

作者： Atmanspacher, H. Filk, T. Scheingraber, H. Center for Interdisciplinary Plasma Science Max-Planck-Institut für extraterrestrische Physik Garching Germany Department of Theory and Data Analysis Institute for Frontier Areas of Psychology and Mental Health Freiburg Germany Institute of Physics University of Freiburg Freiburg Germany

Numerical simulations of coupled map lattices (CMLs) and other complex model systems show an enormous phenomenological variety that is difficult to classify and understand. It is therefore desirable to establish analytical tools for exploring fundamental features of CMLs, such as their stability properties. Since CMLs can be considered as graphs, we apply methods of spectral graph theory to analyze their stability at locally unstable fixed points for different updating rules, different coupling scenarios, and different types of neighborhoods. Numerical studies are found to be in excellent agreement with our theoretical results.

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