Reverse engineering and identification in systems biology: strategies, perspectives and challenges

Systems Biology, Synthetic Biology and Control Theory: A promising golden braid

(2013) José E.R. Cury et al.   ANNUAL REVIEWS IN CONTROL

Biostatistical approaches for the reconstruction of gene co-expression networks based on transcriptomic data

(2013) L. Lopez-Kleine et al.   Briefings in Functional Genomics

Properties of cell death models calibrated and compared using Bayesian approaches

(2013) H. Eydgahi et al.   Molecular Systems Biology

Robust Optimal Design of Experiments for Model Discrimination Using an Interactive Software Tool

(2013) Johannes Stegmaier et al.   PLoS One

Bayes' Theorem in the 21st Century

(2013) B. Efron   SCIENCE

Convergence in parameters and predictions using computational experimental design

(2013) D. R. Hagen et al.   Interface Focus

Maximizing the Information Content of Experiments in Systems Biology

(2013) Juliane Liepe et al.   PLoS Computational Biology

Reverse Engineering Cellular Networks with Information Theoretic Methods

(2013) Alejandro Villaverde et al.   Cells

Optimal design of stimulus experiments for robust discrimination of biochemical reaction networks

(2012) R. J. Flassig et al.   BIOINFORMATICS

Deterministic global optimization algorithm based on outer approximation for the parameter estimation of nonlinear dynamic biological systems

(2012) Anton Miró et al.   BMC BIOINFORMATICS

Inference of complex biological networks: distinguishability issues and optimization-based solutions

(2012) Gábor Szederkényi et al.   BMC Systems Biology

A cooperative strategy for parameter estimation in large scale systems biology models

(2012) Alejandro F Villaverde et al.   BMC Systems Biology

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Conclusions via unique predictions obtained despite unidentifiability - new definitions and a general method

(2012) Gunnar Cedersund   FEBS Journal

Engineering and control of biological systems: A new way to tackle complex diseases

(2012) Filippo Menolascina et al.   FEBS LETTERS

Detection of Long-Range Concerted Motions in Protein by a Distance Covariance

(2012) Amitava Roy et al.   Journal of Chemical Theory and Computation

Analysis of omics data with genome-scale models of metabolism

(2012) Daniel R. Hyduke et al.   Molecular BioSystems

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Using distance correlation and SS-ANOVA to assess associations of familial relationships, lifestyle factors, diseases, and mortality

(2012) J. Kong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-term model predictive control of gene expression at the population and single-cell levels

(2012) J. Uhlendorf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient Reverse-Engineering of a Developmental Gene Regulatory Network

(2012) Anton Crombach et al.   PLoS Computational Biology

Analysis, design and implementation of a novel scheme for in-vivo control of synthetic gene regulatory networks

(2011) Filippo Menolascina et al.   AUTOMATICA

Dynamic Bayesian networks in molecular plant science: inferring gene regulatory networks from multiple gene expression time series

(2011) Frank Dondelinger et al.   EUPHYTICA

Multi-scale modelling and simulation in systems biology

(2011) Joseph O. Dada et al.   Integrative Biology

Finding complex balanced and detailed balanced realizations of chemical reaction networks

(2011) Gábor Szederkényi et al.   JOURNAL OF MATHEMATICAL CHEMISTRY

Riemann manifold Langevin and Hamiltonian Monte Carlo methods

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

Design principles for robust biochemical reaction networks: What works, what cannot work, and what might almost work

(2011) Guy Shinar et al.   MATHEMATICAL BIOSCIENCES

Reply to Comment on “Sloppy models, parameter uncertainty, and the role of experimental design”

(2011) David R. Hagen et al.   Molecular BioSystems

Comment on “Sloppy models, parameter uncertainty, and the role of experimental design”

(2011) Ricky Chachra et al.   Molecular BioSystems

Practical limits for reverse engineering of dynamical systems: a statistical analysis of sensitivity and parameter inferability in systems biology models

(2011) Kamil Erguler et al.   Molecular BioSystems

In silico feedback for in vivo regulation of a gene expression circuit

(2011) Andreas Milias-Argeitis et al.   NATURE BIOTECHNOLOGY

Systems: What's In a Name?

(2011) Denis Noble   PHYSIOLOGY

Influence of Statistical Estimators of Mutual Information and Data Heterogeneity on the Inference of Gene Regulatory Networks

(2011) Ricardo de Matos Simoes et al.   PLoS One

Structural Identifiability of Systems Biology Models: A Critical Comparison of Methods

(2011) Oana-Teodora Chis et al.   PLoS One

Detecting Novel Associations in Large Data Sets

(2011) D. N. Reshef et al.   SCIENCE

Statistical analysis of nonlinear dynamical systems using differential geometric sampling methods

(2011) B. Calderhead et al.   Interface Focus

How to infer gene networks from expression profiles, revisited

(2011) C. A. Penfold et al.   Interface Focus

Automatic Design of Digital Synthetic Gene Circuits

(2011) Mario A. Marchisio et al.   PLoS Computational Biology

Characterization of diverse natural variants of CYP102A1 found within a species of Bacillus megaterium

(2011) Ji-Yeon Kang et al.   AMB Express

Brownian distance covariance

(2010) Gábor J. Székely et al.   Annals of Applied Statistics

Perspectives on system identification

(2010) Lennart Ljung   ANNUAL REVIEWS IN CONTROL

An optimal experimental design approach to model discrimination in dynamic biochemical systems

(2010) Dominik Skanda et al.   BIOINFORMATICS

TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach

(2010) Pietro Zoppoli et al.   BMC BIOINFORMATICS

Discriminating between rival biochemical network models: three approaches to optimal experiment design

(2010) Bence Mélykúti et al.   BMC Systems Biology

An iterative identification procedure for dynamic modeling of biochemical networks

(2010) Eva Balsa-Canto et al.   BMC Systems Biology

Engineering Static and Dynamic Control of Synthetic Pathways

(2010) William J. Holtz et al.   CELL

Model-based inference of biochemical parameters and dynamic properties of microbial signal transduction networks

(2010) Jörg Schaber et al.   CURRENT OPINION IN BIOTECHNOLOGY

A Survey on Methods for Modeling and Analyzing Integrated Biological Networks

(2010) N Tenazinha et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Maximin and Bayesian robust experimental design for measurement set selection in modelling biochemical regulatory systems

(2010) Fei He et al.   INTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL

Parameter identifiability of power-law biochemical system models

(2010) Sridharan Srinath et al.   JOURNAL OF BIOTECHNOLOGY

Reducing the allowable kinetic space by constructing ensemble of dynamic models with the same steady-state flux

(2010) Yikun Tan et al.   METABOLIC ENGINEERING

Sloppy models, parameter uncertainty, and the role of experimental design

(2010) Joshua F. Apgar et al.   Molecular BioSystems

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Advantages and limitations of current network inference methods

(2010) Riet De Smet et al.   NATURE REVIEWS MICROBIOLOGY

Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges

(2010) Robert J. Prill et al.   PLoS One

DREAM4: Combining Genetic and Dynamic Information to Identify Biological Networks and Dynamical Models

(2010) Alex Greenfield et al.   PLoS One

Revealing strengths and weaknesses of methods for gene network inference

(2010) D. Marbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Machine Science

(2010) J. Evans et al.   SCIENCE

Structural Sources of Robustness in Biochemical Reaction Networks

(2010) G. Shinar et al.   SCIENCE

Inferring Signaling Pathway Topologies from Multiple Perturbation Measurements of Specific Biochemical Species

(2010) T.-R. Xu et al.   Science Signaling

Multiple Equilibria in Complex Chemical Reaction Networks: Semiopen Mass Action Systems

(2010) Gheorghe Craciun et al.   SIAM JOURNAL ON APPLIED MATHEMATICS

Parameter Estimation and Model Selection in Computational Biology

(2010) Gabriele Lillacci et al.   PLoS Computational Biology

A divide-and-conquer approach to analyze underdetermined biochemical models

(2009) Oliver Kotte et al.   BIOINFORMATICS

Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood

(2009) A. Raue et al.   BIOINFORMATICS

Simulation-based model selection for dynamical systems in systems and population biology

(2009) Tina Toni et al.   BIOINFORMATICS

Exploring multiplicity conditions in enzymatic reaction networks

(2009) Irene Otero-Muras et al.   BIOTECHNOLOGY PROGRESS

Systematic identifiability testing for unambiguous mechanistic modeling – application to JAK-STAT, MAP kinase, and NF-κB signaling pathway models

(2009) Tom Quaiser et al.   BMC Systems Biology

A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches

(2009) Irene Cantone et al.   CELL

Systems biology: parameter estimation for biochemical models

(2009) Maksat Ashyraliyev et al.   FEBS Journal

Systems analysis of cellular networks under uncertainty

(2009) Hans-Michael Kaltenbach et al.   FEBS LETTERS

Inverse problems in systems biology

(2009) Heinz W Engl et al.   INVERSE PROBLEMS

Computing sparse and dense realizations of reaction kinetic systems

(2009) Gábor Szederkényi   JOURNAL OF MATHEMATICAL CHEMISTRY

Structural identifiability of polynomial and rational systems

(2009) Jana Němcová   MATHEMATICAL BIOSCIENCES

The ABC of reverse engineering biological signalling systems

(2009) Maria Secrier et al.   Molecular BioSystems

A tunable synthetic mammalian oscillator

(2009) Marcel Tigges et al.   NATURE

Sequences and consequences

(2009) S. Brenner   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Automation of Science

(2009) Ross D. King et al.   SCIENCE

Distilling Free-Form Natural Laws from Experimental Data

(2009) Michael Schmidt et al.   SCIENCE

Optimal Experimental Design for Parameter Estimation of a Cell Signaling Model

(2009) Samuel Bandara et al.   PLoS Computational Biology

Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information

(2008) Weijun Luo et al.   BMC BIOINFORMATICS

Optimization in computational systems biology

(2008) Julio R Banga   BMC Systems Biology

Parameter estimation and optimal experimental design

(2008) Julio R. Banga et al.   Essays in Biochemistry

Computational procedures for optimal experimental design in biological systems

(2008) E. Balsa-Canto et al.   IET Systems Biology

Stoichiometric modelling of cell metabolism

(2008) Francisco Llaneras et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

A review of recent advances in global optimization

(2008) C. A. Floudas et al.   JOURNAL OF GLOBAL OPTIMIZATION

Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems

(2008) T. Toni et al.   Journal of the Royal Society Interface

Model reduction and a priori kinetic parameter identifiability analysis using metabolome time series for metabolic reaction networks with linlog kinetics

(2008) I. Emrah Nikerel et al.   METABOLIC ENGINEERING

Reverse engineering the cell

(2008) Nicholas T. Ingolia et al.   NATURE

Metabolic gene regulation in a dynamically changing environment

(2008) Matthew R. Bennett et al.   NATURE

Design principles of biochemical oscillators

(2008) Béla Novák et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Stimulus Design for Model Selection and Validation in Cell Signaling

(2008) Joshua F. Apgar et al.   PLoS Computational Biology

Bayesian inference for differential equations

(2008) Mark Girolami   THEORETICAL COMPUTER SCIENCE

Bayesian inference for nonlinear multivariate diffusion models observed with error

(2007) A. Golightly et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS