In theory, there is no difference between theory and practice. But, in practice, there is.
-- Jan L.A. van de Snepscheut
(If you have really sharp eyes you might see something. Thanks Earl :-))
Books
Web-Administration
- last modified 06/02/2007
Research
interests
Further
interests
ITSL 2008 Information Theory and Statistical Learning
July 14-15, 2008, Las Vegas, Nevada (USA).
Co-Chair of ITSL 2008.
ICSB 2007 The 8th International Conference on Systems Biology 2007
October 1-6, 2007, Long Beach, California (USA).
Scientific Review committee of ICSB 2007.
October 14-17, 2007, Harvard Medical School, Massachusetts (USA).
Session Chair of IEEE BIBE 2007.
Submission deadline: March 20, 2007.
June 25-28, 2007, Las Vegas, Nevada (USA).
Co-Chair of MLMTA'07.
(in conjunction with BIOCOMP'06)
Extended submission deadline: March 06, 2006.
Organizer of the workshop.
Submission deadline: February 10, 2006
Different data sets are provided including clinical, microarray, proteomics and SNP data concerning the Chronic Fatigue Syndrome (CFS).
Find some useful information about the different data sets on Earl Glynn's homepage.
Publications
(Sorted lists of my publications can be found here.)
Thesis
Aktive Computation in offenen Systemen.
Lerndynamiken in biologischen Systemen: Vom Netzwerk zum Organisms
Ph.D. Thesis - Theoretical Physics
Universität Bremen (Germany) (2003).
Quantenmechanik eines nicht abgeschlossenen Zwei-Niveau-Systems
Diploma Thesis - Theoretical Physics
Universität Siegen (Germany) (1998).
Proceedings (Editor)
Aktive Computation in offenen Systemen.
Lerndynamiken in biologischen Systemen: Vom Netzwerk zum Organismus
ISBN: 3-89820-790-0
Mensch & Buch Verlag, Berlin (2004).
Proceedings (Associate Editor)
Articles
Revealing Complex Diseases by Detecting Dynamical Disorder
In preparation (2007).
Statistical Analysis of the Transcriptional Regulatory Network of Saccharomyces cerevisiae
In preparation (2007).
Topological Classification of Protein Structures by Knot Polynomials
In preparation (2007).
Harnessing naturally randomized transcription to infer regulatory relationships among genes
Submitted (2007).
The Chronic Fatigue Syndrome: A Comparative Pathway Analysis
Journal of Computational Biology, 14(7) (2007) 961-972.
A Comparative Analysis of Multidimensional Features of Objects Resembling Sets of Graphs
Applied Mathematics and Computation, accepted (2007).
Nonlinear Time Series Prediction based on a Power-Law Noise Model
International Journal of Modern Physics C, accepted (2007).
Structural Similarity of Directed Universal Hierarchical Graphs: A low Computational Complexity Approach
Applied Mathematics and Computation, accepted (2007).
A Topological Algorithm for Identification of Structural Domains of Proteins
BMC Bioinformatics, (2007) 8-237.
Information Theoretic Measures of UHG Graphs with Low Computational Complexity
Applied Mathematics and Computation, 190(2) (2007) 1783-1794.
Comparing large graphs efficiently by margins of feature vectors
Applied Mathematics and Computation, 188(2) (2007) 1699-1710.
Detecting Pathological Pathways of the Chronic Fatigue Syndrome by the Comparison of Networks
Critical Assessment of Microarray Data Analysis (CAMDA) (2006), accepted (to appear in 2007).
Topolocial Mappings between Graphs, Trees and Generalized Trees
Applied Mathematics and Computation, 186(2) (2007) 1326-1333.
Algorithmic Computation of Knot Polynomials of Secondary Structure Elemtents of Proteins
Journal of Computational Biology, 13(8) (2006) 1503-1512.
A Heterosynaptic Learning Rule for Neural Networks
International Journal of Modern Physics C 17(10) (2006) 1501-1520.
preprint
Influence of Prior Information on the Reconstruction of the Yeast Cell Cycle from Microarray Data
BIOCOMP'06 - The 2006 International Conference on Bioinformatics and Computational Biology, Arabnia, H.A. and Valafar, H. (Eds.) (2006) 477-482.
Theoretical Bounds for the Number of inferable Edges in sparse Random Networks
BIOCOMP'06 - The 2006 International Conference on Bioinformatics and Computational Biology, Arabnia, H.A. and Valafar, H. (Eds.) (2006) 472-476.
Perspectives of Graph Mining Techniques
Rostocker Informatik Berichte 30(2) (2006) 47-56.
A Similarity Measure for Graphs with low Computational Complexity
Applied Mathematics and Computation 182(1) (2006) 447-459.
Influence of the neural network topology on the learning dynamics
Neurocomputing 69(10-12), 1179-1182 (2006).
A Novel Stochastic Learning Rule for Neural Networks
Advances in Neural Networks - Third International Symposium on Neural Networks, Lecture Notes in Computer Science (LNCS), 414-423 (2006).
Measuring the Structural Similarity of Web-based Documents: A novel Approach
International Journal of Computational Intelligence 3:1 (2006) 1-7.
Ranking Genes from DNA Microarray Data of cervical cancer by a local Tree Comparison
International Journal of Biomedical Sciences 1:1 (2006) 17--22.
First Studies of the Influence of Single Gene Perturbations on the Inference of Genetic Networks
VIII. International Conference on Enformatika, Systems Sciences and Engineering, Krakow, Poland, International Academy of Sciences: Enformatika 10 (2005) 65--69.
Influence of Noise on the Inference of Dynamic Bayesian Networks from Short Time Series
VIII. International Conference on Enformatika, Systems Sciences and Engineering, Krakow, Poland, International Academy of Sciences: Enformatika 10 (2005), 70--74.
Towards Clustering of Web-based Document Structures
VIII. International Conference on Enformatika, Systems Sciences and Engineering, Krakow, Poland, International Academy of Sciences: Enformatika 10 (2005), 304--309.
Protein graph partitioning by mutually maximization of cycle distributions
VI. International Conference on Enformatika, Systems Sciences and Engineering, Budapest, Hungary, International Academy of Sciences: Enformatika 8 (2005) 88-92.
A systems approach to gene ranking from DNA Microarray Data of cervical cancer
VI. International Conference on Enformatika, Systems Sciences and Engineering, Budapest, Hungary, International Academy of Sciences: Enformatika 8 (2005) 82-87.
Application of a similarity measure for graphs to web-based document structures
VI. International Conference on Enformatika, Systems Sciences and Engineering, Budapest, Hungary, International Academy of Sciences: Enformatika 8 (2005) 77-81.
A Systems Biology approach for the classification of DNA Microarray Data
(2005), accepted.
Stochastic Sznajd model in open community
International Journal of Modern Physics C, 16(11) (2005) 1693--1700.
Classification of large graphs by a local tree decomposition
Proceedings of the 2005 International Conference on Data Mining (DMIN'05), Editors: H.R. Arabnia, A. Scime (2005) 200--207.
Active Learning in Recurrent Neural Networks Facilitated by a Hebb-like Learning Rule with Memory.
Neural Information Processing - Letters and Reviews 9(2) (2005) 31--40.
A neurobiologically motivated model for self-organized learning
MICAI 2005: Advances in Artificial Intelligence, Lecture Notes in Computes Science (LNCS), Lecture Notes in Artificial Intelligence, Vol. 3789 Alexander Gelbukh and Hugo Terashima (Eds.) (2005) 415--424.
Self-Reinforcement Learning: A neurobiologically motivated Model
Annual Conference on Artificial & Computational Intelligence for Decision, Control and Automation in Engineering and Industrial Applications - International Conference on Machine Intelligence (ACIDCA-ICMI) (2005) 335--342.
Self-organized annealing in laterally inhibited neural networks shows power law decay
Neural Information Processing - Letters and Reviews, 7(3) (2005) 29-38.
A novel stochastic Hebb-like learning rule for neural networks
cond-mat/0307666 (2003).
A constrained HMM-based approach to the estimation of perceptual switching dynamics in Pigeons
Neurocomputing 38-40, 1495-1501 (2001).
Extracting the Dynamics of Perceptual Switching from Noisy Behaviour: An Application of Hidden Markov Modeling to Pecking Data from Pigeons
Journal of Physiology (Paris) 94 No 5-6 555-567 (2000).
Autonomous robots and neuroethology: Emergence of behavior from a sense
of curiosity.
In U. Rückert A. Löffler, F.
Mondada, editor, Experiments with the Mini-Robot Khepera, Proceedings of
the 1st Int. Khepera Workshop, pages 89-98, Paderborn.
HNI-Verlagsschriftenreihe, Bd. 64. (1999).
Conferences
Annotating Genes with unknown Function by a Systems Approach
The 8th International Conference on Systems Biology (ICSB 2007), Long Beach, California, USA (2007).
Structural Analysis of Graphs by using Information theoretic Functionals
Colourings, Independence and Domination (CID), 12th Workshop on Graph Theory, Karpacz, Poland (2007).
FDR Controlled Topological Core of the Transcriptional Regulatory Network of Saccharomyces cerevisiae
Research in Computational Molecular Biology (RECOMB), California, USA (2007).
Inferring gene networks from microarray data by closed-loop optimization
DIMACS Workshop on Dialogue on Reverse Engineering Assessment and Methods (DREAM), New York, USA (2006).
An Attempt to Categorize the Servity of the Chronic Fatigue Syndrome Disease using Affective Disorder Pathways
Critical Assessment of Microarray Data Analysis (CAMDA) (2006).
Gene ranking based on generalized tree alignment from DNA Microarray Data
German Conference on Bioinformatics (GCB'05), University of Hamburg, Center for Bioinformatics, Germany (2005).
A graph theoretical approach for the Identification of Protein Domains
Intelligent Systems for Molecular Biology (ISMB), University of Michigan, Detroit, Michigan, USA (2005).
Applications of graph similiarity measures for generalized trees
40th Czech and Slovak Conference on Graph Theory and Combinatorics (GRAPHS 2005), Budmerice, Slovakia (2005).
Identification of protein domains
LSRD, Life Sciences Institute, Kansas City , Missouri, USA (2005).
Identifying the domains of a protein by a graph theoretical approach
Pacific Symposium on Biocomputing (PSB), Hawaii, USA (2005).
A stochastic Hebb-like learning rule for neural networks
Verhandlungen der Deutschen Physikalischen Gesellschaft (DPG) DY 46.57
Statistical Physics in biological Systems, Dresden, Germany (2003).
Hebb-like learning rule based on the principle of extremal optimization
Dynamic Days Europe , Heidelberg, Germany (2002).
Active Computation: On-line learning in the action-perception-cycle
Concepts for Complex Adaptive Systems, HWK, Germany (2002).
Aktive Computation in offenen Systemen
Verhandlungen der Deutschen Physikalischen Gesellschaft (DPG) DY 42.3,
Statistical Physics far from equilibrium I, Regensburg, Germany (2002).
A constrained HMM-based approach to the estimation of perceptual switching dynamics in Pigeons
Computational Neuroscience (CNS), Brugge, Belgium (2000).
A Stochastic Model for the Estimation of Perceptual Switching Events in Pigeons
FENS, Brighton, UK (2000).
Extracting the Dynamics of Perceptual Switching from Noisy Behaviour: An Application of Hidden Markov Modeling to Pecking Data from Pigeons
Aspects of Neural Dynamics, HWK , Germany (2000).
Unpublished
Perception (2001).
Professional Affiliations
Institute:
General Contact:
University of Washington
Storey Lab
Department of Biostatistics
Department of Genome Sciences
Phone:
+001-206-685-0265
Fax:
+001-816-926-4668
E-Mail
Postal Adress:
1705 NE Pacific St, Box 357730
Seattle, WA 98195-5065
USA
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