AUTHORS

TITLE

R. Alves, E. Villaprinyo, and A. Sorribas

Semi-Automated Reconstruction of Biological Circuits

I-C Chou, M. Vilela, J.S. Almeida, and E.O. Voit

Computational Identification of Dynamic Biological Networks: Inverse Modeling Approach and Parameter Estimation Strategies

P. Coelho, A. Salvador, M. Savageau

Global Tolerance of Biochemical Systems and the Design of Moiety-Transfer Cycles

M.P. David, A. Phillips, E. Mendoza, and L. Cardelli

Implementing Brane Calculus

A.W.M. Dress, C. Flamm, G. Fritzsch, S. Grunewald, M. Kruspe, S.J. Prohaska and P.F. Stadler

Noisy: Identification of Problematic Columns in Multiple Sequence Alignments

R. Fasani and M. Savageau

Global Nonlinear Root-Finding Using the Canonical S-system Form

J. Hormiga, J. Vera, I. Frias O. Wolkenhauer, and N.V. Torres-Darias

Growth and Ligninolytic System Production Dynamics of the Phanerochaete chrysosporium Fungus: A Modelling and Optimization Approach

M-F Lee and D. Fernandez

Patent Prosecution in Systems Biology Software

P-K Liu and F-S Wang

Multi-Objective Evolutionary Optimization for Inferring S-System Models of Biological Networks

A. Marin-Sanguino, N.V. Torres, E. Mendoza, and D. Oesterhelt

Model-Driven Optimization Based on Standard Formalisms

J. Pabico, E. Mojica, and J.R. Micor

Design of a Homogeneous Ensemble for Splice-Site Identification in Human Sequences

Z. Qi, G.W. Miller, and E.O. Voit

A Computational Model of Dopamine Metabolism and Parkinson's Disease

E. Rodriguez, R. del Rosario, A. Rudy, A. Vollmar, E. Mendoza

Cephalostatin 1-Induced Apoptosis in Leukemic Cells: From Petri Net Model to Kinetic Model

R. del Rosario, M.T. Echavez, M.T. de Paz, P.C. Zuniga, M.C.R. Bargo, C.O. Talaue, C. Arellano, J.M. Pasia, P.C. Naval, E.O. Voit, E. Mendoza

MADMan: A Benchmarking Framework for Parameter Estimation in Biochemical Systems Theory Models

R. Santos and E. Mendoza

EUCLIS: Towards a Digital Library–Based Common Information Space for Chronobiologists

K. Selvarajoo, M. Helmy, M. Tomita, and M. Tsuchiya

Inferring the Mechanistic Basis for the Dynamic Response of the MyD88-Dependent and –Independent Pathways

A. Sigal, R. Milo, A. Cohen, and U. Alon

Variability Dynamics of Protein Levels in Human Cells

F. Shiraishi and Y. Suzuki

Determination of Bottleneck Enzymes in a Metabolic Reaction System by Dynamic Sensitivity Analysis

A. Sioson and L. Heath

Programming Language Support in Simulating Semantic Multimodal Network Models

A. Sorribas, E. Villaprinyo, and R. Alves

Approximate Kinetic Formalisms for Modeling Metabolic Networks: Does Anything Work?

S. Veflingstad, D. Oesterheld, E.O. Voit

A Mathematical Model of Light-Induced ATP Synthesis in the Archaea Halobacterium salinarum

E. Villaprinyo, R. Alves, A. Sorribas, and A. Salvador

Gene Expression Levels in Saccharomyces cerevisiae Strongly Reflect Energetic Cost Rates of Gene Products

E. Villaprinyo, A. Salvador, R. Alves, A. Sorribas

Energetic Constraints in Adaptive Gene Expression Responses of Yeast Under Environmental Changes

G. Yagil

On the Structural Complexity of DNA Templates and Some Wider Implications