Multi-model and network inference based on ensemble estimates: avoiding the madness of crowds

Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data

(2020) Aditya Pratapa et al.   NATURE METHODS

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

A Comprehensive Network Atlas Reveals That Turing Patterns Are Common but Not Robust

(2019) Natalie S. Scholes et al.   Cell Systems

Mechanistic models versus machine learning, a fight worth fighting for the biological community?

(2018) Ruth E. Baker et al.   Biology Letters

Next-Generation Machine Learning for Biological Networks

(2018) Diogo M. Camacho et al.   CELL

How to deal with parameters for whole-cell modelling

(2017) Ann C. Babtie et al.   Journal of the Royal Society Interface

Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures

(2017) Thalia E. Chan et al.   Cell Systems

A computational method for the investigation of multistable systems and its application to genetic switches

(2016) Miriam Leon et al.   BMC Systems Biology

Biophysically Motivated Regulatory Network Inference: Progress and Prospects

(2016) Tarmo Äijö et al.   HUMAN HEREDITY

Crowdsourcing biomedical research: leveraging communities as innovation engines

(2016) Julio Saez-Rodriguez et al.   NATURE REVIEWS GENETICS

Modular Parameter Identification of Biomolecular Networks

(2016) Moritz Lang et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING

Model averaging and muddled multimodel inferences

(2015) Brian S. Cade   ECOLOGY

Diversity techniques improve the performance of the best imbalance learning ensembles

(2015) José F. Díez-Pastor et al.   INFORMATION SCIENCES

Quantitative and logic modelling of molecular and gene networks

(2015) Nicolas Le Novère   NATURE REVIEWS GENETICS

Systems biology (un)certainties

(2015) P. D. W. Kirk et al.   SCIENCE

Bayesian computation: a summary of the current state, and samples backwards and forwards

(2015) Peter J. Green et al.   STATISTICS AND COMPUTING

Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models

(2015) Jonathan R. Karr et al.   PLoS Computational Biology

Improving Collective Estimations Using Resistance to Social Influence

(2015) Gabriel Madirolas et al.   PLoS Computational Biology

Comparison of approaches for parameter identifiability analysis of biological systems

(2014) A. Raue et al.   BIOINFORMATICS

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach

(2014) Pablo Meyer et al.   BMC Systems Biology

Topological sensitivity analysis for systems biology

(2014) Ann C. Babtie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Information theory and signal transduction systems: From molecular information processing to network inference

(2014) Siobhan S. Mc Mahon et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Model Selection in Systems Biology Depends on Experimental Design

(2014) Daniel Silk et al.   PLoS Computational Biology

Topological augmentation to infer hidden processes in biological systems

(2013) Mikael Sunnåker et al.   BIOINFORMATICS

Near-optimal experimental design for model selection in systems biology

(2013) Alberto Giovanni Busetto et al.   BIOINFORMATICS

Model selection in systems and synthetic biology

(2013) Paul Kirk et al.   CURRENT OPINION IN BIOTECHNOLOGY

Maximizing the Information Content of Experiments in Systems Biology

(2013) Juliane Liepe et al.   PLoS Computational Biology

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

(2012) Gábor Szederkényi et al.   BMC Systems Biology

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Graph spectral analysis of protein interaction network evolution

(2012) T. Thorne et al.   Journal of the Royal Society Interface

Elucidating the in vivo phosphorylation dynamics of the ERK MAP kinase using quantitative proteomics data and Bayesian model selection

(2012) Tina Toni 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

Bayesian design of synthetic biological systems

(2011) C. P. Barnes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How to infer gene networks from expression profiles, revisited

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

Statistical inference of the time-varying structure of gene-regulation networks

(2010) Sophie Lèbre et al.   BMC Systems Biology

Incomplete and noisy network data as a percolation process

(2010) M. P. H. Stumpf et al.   Journal of the Royal Society Interface

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

(2009) Tina Toni et al.   BIOINFORMATICS

Defining Network Topologies that Can Achieve Biochemical Adaptation

(2009) Wenzhe Ma et al.   CELL

Mapping global sensitivity of cellular network dynamics: sensitivity heat maps and a global summation law

(2008) D.A Rand   Journal of the Royal Society Interface

Estimating the size of the human interactome

(2008) M. P. H. Stumpf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA