Algebraic Biology 2007

Schedule:

July 1: Arrival, registration.
July 2: Conference opening. Plenary sessions. Tutorial sessions.
July 3: Plenary sessions. Tutorial sessions.
July 4: Plenary sessions. Tutorial session. Conference dinner. Closing.
July 5: Departure.

Monday, July 2.

07:30	The AB bus leaves from Sommerhaus Linz to Arcotel.
07:45	The AB bus leaves from Arcotel to Hagenberg.
08:15-08:30	Opening.
	Session 1. Chair: Bruno Buchberger
08:30-09:30	Invited Talk. Algebraic Systems Biology: Theses and Hypotheses.
	Bud Mishra
09:30-10:00	Algorithmic Algebraic Model Checking IV: Characterization of Metabolic Networks.
	Venkatesh Mysore and Bud Mishra.
10:00-10:15	Coffee break.
	Session 2.Chair: René Vestergaard
10:15-10:45	Translating Time-course Gene Expression Profiles into Semi-Algebraic Hybrid Automata via Dimension Reduction.
	Alberto Casagrande, Kevin Casey, Rachele Falchi, Carla Piazza, Benedetto Ruperti, Giannina Vizzotto, Bud Mishra.
10:45-11:15	On Proving the Absence of Oscillations in Models of Genetic Circuits.
	François Boulier, Marc Lefranc, François Lemaire, Pierre-Emmanuel Morant, Asli Ürgüplü.
11:15-11:45	Attenuation Regulation as a Term Rewriting System.
	Eugene Asarin, Thierry Cachat, Alexander Seliverstov, Tayssir Touili, Vassily Lyubetsky.
11:45-13:15	Lunch break.
	Session 3. Chair: Manfred Minimair
13:15-13:45	Glucose-Insulin Control of Type1 Diabetic Patients in H₂/H_∞ Space via Computer Algebra.
	Levente Kovács, Belá Paláncz.
13:45-14:15	Exact Parameter Determination for Parkinson's Disease Diagnosis with PET Using an Algebraic Approach.
	Hiroshi Yoshida, Koji Nakagawa, Hirokazu Anai, Katsuhisa Horimoto.
14:15-14:30	Coffee break.
	Session 4 (Tutorials). Chair: Bruno Buchberger
14:30-15:10	Quantified Constraint Solving and Biology.
	Hoon Hong.
15:10-15:50	Inference of Protein-Protein Interactions by Using Co-evolutionary Information.
	Tetsuya Sato, Yoshihiro Yamanishi, Katsuhisa Horimoto, Minoru Kanehisa, Hiroyuki Toh.
15:50-16:05	Coffee break.
	Session 5 (Tutorials). Chair: Carolyn Talcott
16:05-16:45	A Short Survey of Automated Reasoning.
	John Harrison.
16:45-17:25	Inference of Complex Regulatory Network for the Cell Cycle System in Saccharomyces cerevisiae.
	Sachiyo Aburatani.
18:00-20:00	Reception.
20:15	The school/AB bus leaves from Hagenberg to Linz

Tuesday, July 3.

07:45	The AB bus leaves from Sommerhaus Linz to Arcotel.
08:00	The AB bus leaves from Arcotel to Hagenberg.
	Session 6. Chair: Katsuhisa Horimoto.
08:30-09:30	Invited Talk. Discrete Models of Biochemical Networks: The Toric Variety of Nested Canalyzing Functions. (Slides)
	Abdul S. Jarrah, Reinhard Laubenbacher.
09:30-10:00	Efficient Haplotype Inference with Pseudo-Boolean Optimization.
	Ana Graça, João Marques-Silva, Inês Lynce, Arlindo L. Oliveira.
10:00-10:15	Coffee break.
	Session 7. Chair: Hiroshi Yoshida
10:15-10:45	An Algebraic Algorithm for the Identification of Glass Networks with Periodic Orbits along Cyclic Attractors.
	Igor Zinovik, Daniel Kroening and Yury Chebiryak.
10:45-11:15	Analyzing Biological Pathways using SAT-based Approaches.
	Ashish Tiwari, Carolyn Talcott, Merrill Knapp, Patrick Lincoln, Keith Laderoute.
11:15-11:45	Relating Attractors and Singular Steady States in the Logical Analysis of Bioregulatory Networks
	Heike Siebert, Alexander Bockmayr.
11:45-13:15	Lunch break.
	Session 8. Chair: François Boulier
13:15-13:45	Cascaded Games.
	Jittisak Senachak, Mun'delanji Vestergaard, René Vestergaard.
13:45-14:15	On Differential Algebraic Decision Methods for the Estimation of Anaerobic Digestion Models.
	Elena Chorukova, Sette Diop, Ivan Simeonov.
14:15-14:30	Coffee break.
	Session 9 (Tutorials). Chair: Hiroyuki Toh
14:30-15:10	Manifestation and Exploitation of Invariants in Bioinformatics.
	Limsoon Wong.
15:10-15:50	Towards a Statistical Definition of a Species in Terms of Probabilities of Conspecificity, with Examples Drawn from the Study of African Plio-Pleistocene Hominids. (Slides)
	Francis Thackeray.
15:50-16:05	Coffee break.
	Session 10 (Tutorials). Chair: Hoon Hong
16:05-16:45	New combinatorial results for words over four letters.
	Veikko Keränen.
17:00	The AB bus leaves from Hagenberg to Linz.

Wednesday, July 4.

07:45	The AB bus leaves from Sommerhaus Linz to Arcotel.
08:00	The AB bus leaves from Arcotel to Hagenberg.
	Session 11. Chair: Hoon Hong
08:30-09:30	Invited Talk. Membrane Computing as a Framework for Bio-Modeling (An Informal Glimpse).
	Gheorghe Păun.
09:30-10:00	Protein Structure Prediction using Residual Dipolar Couplings.
	Ioannis Z. Emiris, Sotirios I. Pantos.
10:00-10:15	Coffee break.
	Session 12. Chair: Thierry Cachat
10:15-10:45	A Stochastic Pi-Calculus for Concurrent Objects.
	Céline Kuttler, Cédric Lhoussaine, Joachim Niehren.
10:45-11:15	Modeling Static Biological Compartments with Beta-Binders. (Slides)
	Maria Luisa Guerriero, Corrado Priami, Alessandro Romanel.
11:15-11:45	Deducing Interactions in Partially Unspecified Biological Systems. (Slides)
	Paolo Baldan, Andrea Bracciali, Linda Brodo, Roberto Bruni.
11:45-13:15	Lunch break.
	Session 13. Chair: Ruriko Yoshida
13:15-13:45	Reduction of Algebraic Parametric Systems by Rectification of their Affine Expanded Lie Symmetries.
	Alexandre Sedoglavic.
13:45-14:15	Prefix Reversals on Binary and Ternary Strings.
	Cor Hurkens, Leo van Iersel, Judith Keijsper, Leen Stougie, John Tromp, Steven Kelk.
14:15-14:45	Toric Ideals of Phylogenetic Invariants for the General Group-Based Model on Claw Trees K_1,n. (Slides)
	Sonja Petrović, Julia Chifman.
14:45-15:00	Coffee break.
	Session 14 (Tutorials). Chair: Katsuhisa Horimoto
15:00-15:40	A Systematic Treatment of Growth Terms Appearing in Continuum Mechanics Formulations for Biological Materials. (Slides)
	Hans Irschik.
15:40-16:20	Harmonicity vs. Frustration in Protein Folding and Function.
	Nobuhiro Go.
16:20-17:00	Concavity in Biological Morphometric. (Slides, program)
	Gautam Dasgupta.
17:30	The school/AB bus leaves from Hagenberg to Linz.
19:00-22:00	Conference dinner.