Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks

Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems: Fig. 1.

(2015) A. Raue et al.   BIOINFORMATICS

SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks

(2015) Andreas Dräger et al.   BMC Systems Biology

Robust and efficient parameter estimation in dynamic models of biological systems

(2015) Attila Gábor et al.   BMC Systems Biology

A consensus approach for estimating the predictive accuracy of dynamic models in biology

(2015) Alejandro F. Villaverde et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Predicting network functions with nested patterns

(2014) Mathias Ganter et al.   Nature Communications

Computational modelling of the regulation of Insulin signalling by oxidative stress

(2013) Graham R Smith et al.   BMC Systems Biology

High-dimensional Bayesian parameter estimation: Case study for a model of JAK2/STAT5 signaling

(2013) S. Hug et al.   MATHEMATICAL BIOSCIENCES

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Emerging landscape of oncogenic signatures across human cancers

(2013) Giovanni Ciriello et al.   NATURE GENETICS

Computational solutions for omics data

(2013) Bonnie Berger et al.   NATURE REVIEWS GENETICS

Lessons Learned from Quantitative Dynamical Modeling in Systems Biology

(2013) Andreas Raue et al.   PLoS One

Systematic Construction of Kinetic Models from Genome-Scale Metabolic Networks

(2013) Natalie J. Stanford et al.   PLoS One

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

(2012) Rui Chen et al.   CELL

Inverse problems from biomedicine

(2012) James Lu et al.   JOURNAL OF MATHEMATICAL BIOLOGY

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

State–time spectrum of signal transduction logic models

(2012) Aidan MacNamara et al.   PHYSICAL BIOLOGY

AMIGO, a toolbox for advanced model identification in systems biology using global optimization

(2011) E. Balsa-Canto et al.   BIOINFORMATICS

Riemann manifold Langevin and Hamiltonian Monte Carlo methods

(2011) Mark Girolami et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

SABIO-RK--database for biochemical reaction kinetics

(2011) U. Wittig et al.   NUCLEIC ACIDS RESEARCH

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

(2010) Chen Li et al.   BMC Systems Biology

Reactome: a database of reactions, pathways and biological processes

(2010) D. Croft et al.   NUCLEIC ACIDS RESEARCH

Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network

(2009) Clemens Kühn et al.   BMC Systems Biology

BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009

(2008) A. Chang et al.   NUCLEIC ACIDS RESEARCH