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Maximizing the information content of experiments in systems biology

PLoS computational biology, 2013-01, Vol.9 (1), p.e1002888-e1002888

2013

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Critical Truths About Power Laws

Science (American Association for the Advancement of Science), 2012-02, Vol.335 (6069), p.665-666

2012

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A large fraction of HLA class I ligands are proteasome-generated spliced peptides

Science (American Association for the Advancement of Science), 2016-10, Vol.354 (6310), p.354-358

2016

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Extrinsic Noise and Heavy-Tailed Laws in Gene Expression

Physical review letters, 2020-03, Vol.124 (10), p.108101-108101, Article 108101

2020

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Estimating the size of the human interactome

Proceedings of the National Academy of Sciences - PNAS, 2008-05, Vol.105 (19), p.6959-6964

2008

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Surveying membrane landscapes: a new look at the bacterial cell surface

Nature reviews. Microbiology, 2023-08, Vol.21 (8), p.502-518

2023

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

Journal of the Royal Society interface, 2009-02, Vol.6 (31), p.187-202

2009

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A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation

Nature protocols, 2014-02, Vol.9 (2), p.439-456

2014

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Transition state characteristics during cell differentiation

PLoS computational biology, 2018-09, Vol.14 (9), p.e1006405-e1006405

2018

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

Bioinformatics, 2010-01, Vol.26 (1), p.104-110

2010

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Sensitivity, robustness, and identifiability in stochastic chemical kinetics models

Proceedings of the National Academy of Sciences - PNAS, 2011-05, Vol.108 (21), p.8645-8650

2011

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

Cell systems, 2017-09, Vol.5 (3), p.251-267.e3

2017

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Model selection in systems and synthetic biology

Current opinion in biotechnology, 2013-08, Vol.24 (4), p.767-774

2013

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Topological sensitivity analysis for systems biology

Proceedings of the National Academy of Sciences - PNAS, 2014-12, Vol.111 (52), p.18507-18512

2014

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How to deal with parameters for whole-cell modelling

Journal of the Royal Society interface, 2017-08, Vol.14 (133), p.20170237

2017

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Managing membrane stress: the phage shock protein (Psp) response, from molecular mechanisms to physiology

FEMS microbiology reviews, 2010-09, Vol.34 (5), p.797-827

2010

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Systems Analysis of the Dynamic Inflammatory Response to Tissue Damage Reveals Spatiotemporal Properties of the Wound Attractant Gradient

Current biology, 2016-08, Vol.26 (15), p.1975-1989

2016

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Julia for biologists

Nature methods, 2023-05, Vol.20 (5), p.655-664

2023

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ABC-SysBio—approximate Bayesian computation in Python with GPU support

Bioinformatics, 2010-07, Vol.26 (14), p.1797-1799

2010

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Network motifs: structure does not determine function

BMC genomics, 2006-05, Vol.7 (1), p.108-108, Article 108

2006

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BondGraphs.jl: composable energy-based modelling in systems biology

Bioinformatics (Oxford, England), 2023-10, Vol.39 (10)

2023

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GPU accelerated biochemical network simulation

Bioinformatics, 2011-03, Vol.27 (6), p.874-876

2011

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Proteasome isoforms exhibit only quantitative differences in cleavage and epitope generation

European journal of immunology, 2014-12, Vol.44 (12), p.3508-3521

2014

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Turing pattern design principles and their robustness

Philosophical transactions of the Royal Society of London. Series A: Mathematical, physical, and engineering sciences, 2021-12, Vol.379 (2213), p.20200272

2021

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Cohesin couples transcriptional bursting probabilities of inducible enhancers and promoters

Nature communications, 2022-07, Vol.13 (1), p.4342-16, Article 4342

2022

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Maximizing the information content of experiments in systems biology

Critical Truths About Power Laws

A large fraction of HLA class I ligands are proteasome-generated spliced peptides

Extrinsic Noise and Heavy-Tailed Laws in Gene Expression

Estimating the size of the human interactome

Surveying membrane landscapes: a new look at the bacterial cell surface

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

A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation

Transition state characteristics during cell differentiation

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

Sensitivity, robustness, and identifiability in stochastic chemical kinetics models

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

Model selection in systems and synthetic biology

Topological sensitivity analysis for systems biology

How to deal with parameters for whole-cell modelling

Managing membrane stress: the phage shock protein (Psp) response, from molecular mechanisms to physiology

Systems Analysis of the Dynamic Inflammatory Response to Tissue Damage Reveals Spatiotemporal Properties of the Wound Attractant Gradient

Julia for biologists

ABC-SysBio—approximate Bayesian computation in Python with GPU support

Network motifs: structure does not determine function

BondGraphs.jl: composable energy-based modelling in systems biology

GPU accelerated biochemical network simulation

Proteasome isoforms exhibit only quantitative differences in cleavage and epitope generation

Turing pattern design principles and their robustness

Cohesin couples transcriptional bursting probabilities of inducible enhancers and promoters

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