Detailed Conference Schedule

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 REGISTRATION
  Date: June 10, 2007
  Time: 11:00-17:00
 

 SESSION SuPMTutorial1: Robert Henson: Working with Large Biological Datasets in MATLAB, Mathworks [Abstract]
 Date: June 10, 2007
 Time: 13:00 - 13:45
 Location: Auditorium
 Chair: Heikki Huttunen, Tampere Univ. of Technology, Finland

  SESSION SuPMTutorial2: Christophe Roos: Demonstration of Integrator Platform, Medicel Oy [Abstract]
 Date: June 10, 2007
 Time: 13:45 - 14:30
 Location: Auditorium
 Chair: Heikki Huttunen, Tampere Univ. of Technology, Finland

14:30-15:00 Coffee break

 SESSION MoAMOral1: Gene Networks
 Date: June 11, 2007
 Time: 10:30 - 12:30
 Location: Auditorium
 Chair: Ilya Shmulevich, Institute for Systems Biology, United States

 10:30 

ROBUSTNESS OF INTERVENTION STRATEGIES FOR PROBABILISTIC BOOLEAN NETWORKS
Ranadip Pal, Aniruddha Datta, Edward Dougherty, Texas A&M University, United States
 

 10:50 

RECOVERING GENETIC REGULATORY NETWORKS BY INTEGRATING MULTIPLE DATA SOURCES
Wentao Zhao, Erchin Serpedin, Texas A&M University, United States; Edward Dougherty, Translational Genomic Research Institute, United States
 

 11:10 

UNCOVERING REGULATORY PATHWAYS WITH EXPRESSION QUANTITATIVE TRAIT LOCI
Andreas Beyer, BIOTEC, TU Dresden, Germany; Silpa Suthram, Trey Ideker, UCSD, United States
 

 11:30 

 A UNIVERSAL MINIMUM DESCRIPTION LENGTH-BASED ALGORITHM FOR INFERRING THE STRUCTURE OF GENETIC NETWORKS
John Dougherty, Ioan Tabus, Jaakko Astola, Tampere University of Technology, Finland
 

 11:50 

DISCOVERING CONDITION-DEPENDENT BAYESIAN NETWORKS FOR GENE REGULATION
Antti Ajanki, Janne Nikkilä, Samuel Kaski, Helsinki University of Technology, Finland
 

 12:10 

A BAYESIAN APPROACH FOR UNCOVERING GENE NETWORK MOTIFS
Yufang Yin, Yufei Huang, U. of Texas at San Antonio, United States; Viji Shanmugam, Marcel Brun, Jianping Hua, Edward Dougherty, Translational Genomics Research Institute, United States
 

 SESSION MoPMPlen2: Jorma Rissanen: Complexity and Information in Data, Tampere University of Technology [Abstract]
 Date: June 11, 2007
 Time: 14:00 - 15:00
 Location: Auditorium
 Chair: Ioan Tabus, Tampere University of Technology, Finland

 SESSION MoPMPost1: Poster 1
 Date: June 11, 2007
 Time: 15:30 - 17:30
 Location: Main Lobby
 Chair: Erchin Serpedin, Texas A&M University

P 1. TRANSCRIPTION FACTOR DISCOVERY USING SUPPORT VECTOR MACHINES AND HETEROGENEOUS DATA
Jose Barbe, Ahmed Tewfik, Arkady Khodursky, University of Minnesota, United States
 

P 2. COMPARISON OF AUTOREGRESSIVE MEASURES FOR DNA SEQUENCE SIMILARITY
Gail Rosen, Drexel University, United States
 

P 3. LINEAR PREDICTIVE CODING FOR ENHANCED MICROARRAY DATA CLUSTERING
Robert Istepanian, Ala Sungoor, Jean-Christophe Nebel, Kingston University, United Kingdom
 

P 4. CORRELATION MODEL FOR UNIFORM SCALAR QUANTIZERS WITH ARBITRARY REPRESENTATION LEVELS
Are Hjørungnes, University of Oslo, Norway; Pradeepa Yahampath, Mirek Pawlak, University of Manitoba, Canada
 

P 5. ROBUST FISHER'S TEST FOR PERIODICITY DETECTION IN NOISY BIOLOGICAL TIME SERIES
Miika Ahdesmäki, TUT, Finland; Harri Lähdesmäki, TUT, ISB, Finland; Olli Yli-Harja, TUT, Finland
 

P 6. IMPROVEMENT OF SPECTRAL ANALYSIS AS A GENOMIC ANALYSIS TOOL
Evan Santo, Cold Spring Harbor Laboratory, United States; Nevenka Dimitrova, Philips Research India, India
 

P 7. DISTRIBUTED ROBUST BICLUSTERING ALGORITHM FOR GENE EXPRESSION ANALYSIS
Alain Tchagang, Ahmed Tewfik, University of Minnesota, United States
 

P 8. BIDIRECTIONAL RELATIONSHIPS AND ATTRACTOR STRUCTURE OF BOOLEAN NETWORKS
Golnaz Vahedi, Ivan Ivanov, Edward Dougherty, Texas A&M University, United States
 

P 9. FINDING INCOMING GLOBAL STATES IN BOOLEAN NETWORKS
Tatsuya Akutsu, Morihiro Hayashida, Kyoto University, Japan; Shu-Qin Zhang, Wai-Ki Ching, The University of Hong Kong, China; Michael Ng, Hong Kong Baptist University, China
 

P 10. ESTIMATION OF NEURONAL SIGNALING MODEL PARAMETERS USING DETERMINISTIC AND STOCHASTIC IN SILICO TRAINING DATA: EVALUATION OF FOUR PARAMETER ESTIMATION METHODS
Antti Pettinen, Tiina Manninen, Olli Yli-Harja, Keijo Ruohonen, Marja-Leena Linne, Tampere University of Technology, Finland
 

P 11. THRESHOLD LOGIC GENE REGULATORY NETWORKS
Tejaswi Gowda, Samuel Leshner, Sarma Vrudhula, Arizona State University, United States; Seungchan Kim, Translational Genomics Research Institute, United States
 

P 12. MODELING THE KINETICS OF HYBRIDIZATION IN MICROARRAYS
Haris Vikalo, Babak Hassibi, Mihailo Stojnic, Caltech, United States; Arjang Hassibi, University of Texas at Austin, United States
 

P 13. DNA COPY NUMBER DETECTION AND SIGMA FILTER
Abdullah Alqallaf, Ahmed Tewfik, University of Minnesota, United States
 

 CONFERENCE BANQUET
  Date: June 11, 2007
  Time: 19:00-
 Location: TBA
 

 SESSION TuAMPlen3: Olli-Pekka Kallioniemi, VTT Technical Research Centre of Finland
 Date: June 12, 2007
 Time: 08:30 - 09:30
 Location: Auditorium
 Chair: Olli Yli-Harja, Tampere Univ. of Technology, Finland

 9:30-10:00 Coffee Break

 SESSION TuAMSpecial: Special Session:

• Ilya Shmulevich: Modeling and Inference of Transcriptional Regulatory Networks
• Mike Bittner: Will biomedical control be an engineering discipline?

 SESSION TuAMOral2: Signal processing methods in sequence analysis
 Date: June 12, 2007
 Time: 11:00 - 12:00
 Location: Auditorium
 Chair: Ciprian Doru Giurcaneanu, Tampere Univ. of Technology, Finland

 11:00 

 JOINTLY ENCODING PROTEIN SEQUENCES AND THEIR SECONDARY STRUCTURE INFORMATION
Andrea Hategan, Ioan Tabus, Tampere University of Technology, Finland
 

 11:20 

PROBABILISTIC FRAMEWORK FOR TRANSCRIPTION FACTOR BINDING PREDICTION
Harri Lähdesmäki, Ilya Shmulevich, Institute for Systems Biology, United States
 

 11:40 

ON DNA NUMERICAL REPRESENTATIONS FOR PERIOD-3 BASED EXON PREDICTION
Mahmood Akhtar, The University of New South Wales, Australia; Julien Epps, UNSW Asia, Singapore; Eliathamby Ambikairajah, The University of New South Wales, Australia
 

 12:00-13:00 Lunch Break

 SESSION TuPMPoster2: Poster 2
 Date: June 12, 2007
 Time: 13:00 - 15:00
 Location: Main Lobby
 Chair: Mauno Vihinen, University of Tampere

P 14. LEARNING CONTEXT-SPECIFIC GENE REGULATORY NETWORKS VIA IN-SILICO CONDITIONING
Seungchan Kim, Translational Genomics Research Institute, United States; Ina Roy, Siddharth Raghavan, Arizona State University, United States; Edward Dougherty, Texas A&M University, United States; Michael Bittner, Translational Genomics Research Institute, United States
 

P 15. ACCURATE QUANTIFICATION OF GENE EXPRESSION USING FUZZY CLUSTERING APPROACHES
Yu-Ping Wang, University of Missouri-Kansas City, United States
 

P 16. PRIORITIZING MOLECULAR SIGNATURES BY COMBINING ACGH AND GLOBAL GENE EXPRESSION PROFILING
Tae-Hoon Chung, Translational Genomics Research Institute, United States; Seungchan Kim, Translational Genomics Research Institute and Arizona State University, United States
 

P 17. DETECTION OF PERIODICITIES IN GENE SEQUENCES: A MAXIMUM LIKELIHOOD APPROACH
Raman Arora, William A. Sethares, University Of Wisconsin-Madison, United States
 

P 18. EFFECT OF PARAMETER VARIATIONS ON THE INFERENCE OF CONTEXT-SENSITIVE PROBABLISITIC BOOLEAN NETWORKS
Stephen Marshall, Le Yu, University of Strathclyde, United Kingdom; Yufei Xiao, Texas A&M University, United States; Edward Dougherty, Texas A&M/ TGEN, United States
 

P 19. HAPLOTYPE BLOCK PARTITIONING USING A NORMALIZED MAXIMUM LIKELIHOOD MODEL
Yinghua Yang, Ioan Tabus, Tampere University of Technology, Finland
 

P 20. IN SILICO SIMULATION OF EPIDERMAL GROWTH FACTOR SIGNALING IN PROSTATE CANCER CELLS
Takashi Nakakuki, Kaori Ide, Noriko Yumoto, Takeshi Nagashima, Mariko Hatakeyama, RIKEN GSC, Japan
 

P 21. STOCHASTIC COMPLEXITY FOR THE DETECTION OF PERIODICALLY EXPRESSED GENES
Ciprian Doru Giurcaneanu, Tampere University of Technology, Finland
 

P 22. A UNIVERSAL ALGORITHM FOR RANDOM-ACCESS COMPRESSION AND APPLICATIONS FOR ANNOTATED DNA SEQUENCES
Gergely Korodi, Ioan Tabus, Tampere University of Technology, Finland
 

P 23. IMMUNOME, IMMTREE AND IMMUNITY: DATABASES FOR SYSTEMS BIOLOGY OF IMMUNE SYSTEM
Csaba Ortutay, Markku Siermala, Kathryn Rannikko, Mauno Vihinen, Institute of Medical Technology, University of Tampere, Finland
 

P 24. DETECTION OF PATHOGENIC MUTATION PRONE LOCATIONS FROM PROTEIN SEQUENCES USING SOLVENT ACCESSIBILITY MEASUREMENTS
Miika Ahdesmäki, Tampere University of Technology, Finland; Janita Thusberg, University of Tampere, Finland; Heikki Huttunen, Tampere University of Technology, Finland; Mauno Vihinen, University of Tampere, Finland; Olli Yli-Harja, Tampere University of Technology, Finland
 

P 25. EXPLORING THE INTERRELATIONSHIP BETWEEN BIOREACTOR STABILITY AND CARBON BALANCE
Tommi Aho, Virpi Kivinen, Perttu Koskinen, Jaakko Puhakka, Olli Yli-Harja, Tampere University of Technology, Finland
 

P 26. INFERENCE OF BOOLEAN NETWORKS FROM TIME SERIES DATA WITH REALISTIC CHARACTERISTICS
Timo Erkkilä, Tomi Korpelainen, Olli Yli-Harja, Tampere University of Technology (TUT), Finland
 

 SESSION TuPMOral3: Statistical modeling and simulation
 Date: June 12, 2007
 Time: 15:00 - 16:00
 Location: Auditorium
 Chair: Annirudha Datta, Texas A&M University

 15:00 

PARAMETER ESTIMATION AND TUNING OF FIREFLY LUCIFERASE PATHWAY MODEL
Tiina Manninen, Tampere University of Technology, Finland; Andre Ribeiro, Jason Lloyd-Price, University of Calgary, Canada; Marja-Leena Linne, Keijo Ruohonen, Olli Yli-Harja, Tampere University of Technology, Finland; Stuart A. Kauffman, University of Calgary, Canada
 

 15:20 

RECIPROCAL RANK-BASED COMPARISON OF ORDERED GENE LISTS
Ronald Pearson, ProSanos Corporation, United States
 

 15:40 

MODELING G-PROTEIN INDUCED PROTEIN KINASE C ACTIVATION CASCADE: DETERMINISTIC AND STOCHASTIC SIMULATIONS
Eeva Mäkiraatikka, Antti Saarinen, Olli Yli-Harja, Marja-Leena Linne, Tampere Univ. of Technology, Finland
 

 16:00 

Closing and Coffee