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List of works by Michael Stumpf

A Comprehensive Evaluation of Nasal and Bronchial Cytokines and Chemokines Following Experimental Rhinovirus Infection in Allergic Asthma: Increased Interferons (IFN-γ and IFN-λ) and Type 2 Inflammation (IL-5 and IL-13)

scientific article

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

scientific article published on 18 September 2019

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

scientific article published on 01 November 2019

A Y chromosome census of the British Isles

scientific article (publication date: 27 May 2003)

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

scientific article

A general moment expansion method for stochastic kinetic models.

scientific article published in May 2013

A graph theoretical approach to data fusion

scientific article

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

scientific article published on 20 October 2016

A likelihood approach to analysis of network data

scientific article

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

scientific article

Accurate Reconstruction of Cell and Particle Tracks from 3D Live Imaging Data

scientific article

Allelic histories: positive selection on a HIV-resistance allele

scientific article published in April 2004

An information-theoretic framework for deciphering pleiotropic and noisy biochemical signaling

scientific article published in Nature Communications

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

scientific article

Approximate Bayesian inference for complex ecosystems

scientific article

Assessing coverage of protein interaction data using capture-recapture models ⬇️

scientific article published on August 26, 2011

Author Correction: Julia for biologists

scientific article published in 2023

Balancing selection at the prion protein gene consistent with prehistoric kurulike epidemics

scientific article

Balancing the robustness and predictive performance of biomarkers.

scientific article published on 2 August 2013

Bayesian design of synthetic biological systems

scientific article

Bayesian design strategies for synthetic biology ⬇️

scientific article published on October 5, 2011

Biology challenging statistics

scientific article published on 30 August 2018

Biosimulation in Drug Development.

scientific article published in September 2008

Calibrating spatio-temporal models of leukocyte dynamics against in vivo live-imaging data using approximate Bayesian computation

scientific article

Cellular compartments cause multistability and allow cells to process more information

scientific article

Cellular population dynamics control the robustness of the stem cell niche.

scientific article published on 9 October 2015

Coalescent models for developmental biology and the spatio-temporal dynamics of growing tissues

scientific article

Collocation based training of neural ordinary differential equations

scientific article published in 2021

Comparative analysis of the Saccharomyces cerevisiae and Caenorhabditis elegans protein interaction networks

scientific article

Complex networks and simple models in biology.

scientific article published on December 2005

Concise Review: Stem Cell Population Biology: Insights from Hematopoiesis.

scientific article published on 27 September 2016

Considerate approaches to constructing summary statistics for ABC model selection

Construction of quasipotentials for stochastic dynamical systems: An optimization approach

scientific article published on 01 August 2018

Control mechanisms for stochastic biochemical systems via computation of reachable sets

scientific article published on 23 August 2017

Decomposing noise in biochemical signaling systems highlights the role of protein degradation

scientific article

Demography, recombination hotspot intensity, and the block structure of linkage disequilibrium

scientific article

Designing attractive models via automated identification of chaotic and oscillatory dynamical regimes

scientific article published on 04 October 2011

Ecology. Making sense of evolution in an uncertain world.

scientific article published in September 2005

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

scientific article

Epithelial-Mesenchymal Transition in Metastatic Cancer Cell Populations Affects Tumor Dormancy in a Simple Mathematical Model

scientific article published on 9 December 2014

Estimating recombination rates from population-genetic data

scientific article

Estimating the size of the human interactome

scientific article

Evidence for an apartheid-like social structure in early Anglo-Saxon England

scientific article

Evolution at the system level: the natural history of protein interaction networks

scientific article published on May 2007

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

scientific article

Evolutionary characteristics of bacterial two-component systems

scientific article published in January 2012

Evolving proteins at Darwin's bicentenary

scientific article published on 17 April 2009

Exactly solvable models of stochastic gene expression

scientific article published on 01 April 2020

Extracellular proteasome-osteopontin circuit regulates cell migration with implications in multiple sclerosis

scientific article published on 09 March 2017

Extrinsic Noise and Heavy-Tailed Laws in Gene Expression

scientific article published on 01 March 2020

Feedback mechanisms control coexistence in a stem cell model of acute myeloid leukaemia.

scientific article published on 27 April 2016

From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli

scientific article

GPU accelerated biochemical network simulation

scientific article

Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data

scientific article

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

scientific article published on September 2017

Gene Regulatory Networks from Single Cell Data for Exploring Cell Fate Decisions

scientific article published on 01 January 2019

Gene expression profiles of Blumeria graminis indicate dynamic changes to primary metabolism during development of an obligate biotrophic pathogen.

scientific article published on 10 June 2005

Generating confidence intervals on biological networks

scientific article

Goldstein-Kac telegraph processes with random speeds: Path probabilities, likelihoods, and reported Lévy flights

scientific article published on 15 April 2015

GpABC: a Julia package for approximate Bayesian computation with Gaussian process emulation

scientific article published on 05 February 2020

Graph spectral analysis of protein interaction network evolution

scientific article published on 2 May 2012

Graphical modelling of molecular networks underlying sporadic inclusion body myositis.

scientific article published on 17 April 2013

Great cities look small. ⬇️

scientific article published on August 2015

HIV and the CCR5-Delta32 resistance allele

scientific article

Haplotype diversity and SNP frequency dependence in the description of genetic variation

scientific article published on 01 June 2004

Haplotype diversity and the block structure of linkage disequilibrium

scientific article published on 01 May 2002

Herpes viruses hedge their bets

scientific article

How to deal with parameters for whole-cell modelling.

scientific article published on 2 August 2017

HyperGraphs.jl: representing higher-order relationships in Julia

scientific article published in 2022

Incomplete and noisy network data as a percolation process

scientific article

Induction and function of the phage shock protein extracytoplasmic stress response in Escherichia coli.

scientific article

Inference of random walk models to describe leukocyte migration

scientific article

Inference of temporally varying Bayesian networks

scientific article published on 16 October 2012

Inferring extrinsic noise from single-cell gene expression data using approximate Bayesian computation

scientific article

Information processing by simple molecular motifs and susceptibility to noise

scientific article published on September 2015

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

scientific article

Integration versus apartheid in post-Roman Britain: a response to Pattison.

scientific article published on 29 July 2008

Julia for biologists

scientific article published in 2023

Localized breakdown in linkage disequilibrium does not always predict sperm crossover hot spots in the human MHC class II region

scientific article published on 01 July 2005

MEANS: python package for Moment Expansion Approximation, iNference and Simulation.

scientific article

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

scientific article published on 09 June 2010

Mathematical and Statistical Techniques for Systems Medicine: The Wnt Signaling Pathway as a Case Study

scientific article published on January 2016

Mathematical modeling reveals the functional implications of the different nuclear shuttling rates of Erk1 and Erk2.

scientific article published on 3 May 2012

Mathematics. Critical truths about power laws

scientific article published in February 2012

Maximizing the information content of experiments in systems biology

scientific article

Model of Host-Pathogen Interaction Dynamics Links In Vivo Optical Imaging and Immune Responses

scientific article

Model selection in systems and synthetic biology

scientific article published on 08 April 2013

Model selection in systems biology depends on experimental design

scientific article

Model-based evolutionary analysis: the natural history of phage-shock stress response.

scientific article

Modelling proteasome and proteasome regulator activities.

scientific article

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

scientific article published on 21 October 2020

Multivariate moment closure techniques for stochastic kinetic models.

scientific article published in September 2015

Network motifs: structure does not determine function

scientific article

Neuroscience of birdsong

Nitrogen and carbon status are integrated at the transcriptional level by the nitrogen regulator NtrC in vivo

scientific article published on 19 November 2013

Noise and the molecular processes underlying cell fate decision-making

scientific article published on 12 November 2020

Non-equilibrium statistical physics, transitory epigenetic landscapes, and cell fate decision dynamics

scientific article published on 01 November 2020

Nonidentifiability of the source of intrinsic noise in gene expression from single-burst data

scientific article

Nuclear to cytoplasmic shuttling of ERK promotes differentiation of muscle stem/progenitor cells.

scientific article

On optimality of kernels for approximate Bayesian computation using sequential Monte Carlo

scientific article published on 26 March 2013

Optimizing threshold-schedules for sequential approximate Bayesian computation: applications to molecular systems.

scientific article

Overlapping genes: a window on gene evolvability

scientific article

P38 and JNK have opposing effects on persistence of in vivo leukocyte migration in zebrafish.

scientific article

PEITH(Θ) - Perfecting Experiments with Information Theory in Python with GPU support

scientific article published on 7 December 2017

Parameter inference and model selection in signaling pathway models

scientific article published on January 2010

Parameter inference for biochemical systems that undergo a Hopf bifurcation

scientific article

Parameter inference in dynamical systems with co-dimension 1 bifurcations

scientific article published on 30 October 2019

Parameter-free model discrimination criterion based on steady-state coplanarity.

scientific article

Parametric and non-parametric gradient matching for network inference: a comparison

scientific article published on 25 January 2019

Perturbation of fetal liver hematopoietic stem and progenitor cell development by trisomy 21

scientific article

Phosphorelay of non-orthodox two component systems functions through a bi-molecular mechanism in vivo: the case of ArcB.

scientific article published in May 2015

Plasma proteome analysis in HTLV-1-associated myelopathy/tropical spastic paraparesis.

scientific article

Population dynamics of normal and leukaemia stem cells in the haematopoietic stem cell niche show distinct regimes where leukaemia will be controlled.

scientific article published on 24 January 2013

Population genomics: ageing by association

scientific article published on 01 April 2002

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

scientific article published on March 4, 2011

Prediction of putative protein interactions through evolutionary analysis of osmotic stress response in the model yeast Saccharomyces cerevisae

article

Proteasome isoforms exhibit only quantitative differences in cleavage and epitope generation

scientific article published on 20 November 2014

Protein degradation rate is the dominant mechanism accounting for the differences in protein abundance of basal p53 in a human breast and colorectal cancer cell line

scientific article

Proteolytic dynamics of human 20S thymoproteasome

scientific article published on 26 March 2019

Quantifying Dynamic Regulation in Metabolic Pathways with Nonparametric Flux Inference

scientific article published on 19 April 2019

Quantitative time-resolved analysis reveals intricate, differential regulation of standard- and immuno-proteasomes

scientific article

Recombination hotspots as a point process.

scientific article published on August 2005

Reconciling Epigenetic Memory and Transcriptional Responsiveness

scientific article published in April 2017

Robustness of MEK-ERK Dynamics and Origins of Cell-to-Cell Variability in MAPK Signaling.

scientific article published on June 2016

SYSBIONS: nested sampling for systems biology

scientific article

Sampling properties of random graphs: the degree distribution.

scientific article

Sensitivity, robustness, and identifiability in stochastic chemical kinetics models.

scientific article

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

scientific article

Single Cell Phenotyping Reveals Heterogeneity among Haematopoietic Stem Cells Following Infection.

scientific article published on 22 August 2017

Some notes on the combinatorial properties of haplotype tagging.

scientific article published in October 2003

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

scientific article

Statistical interpretation of the interplay between noise and chaos in the stochastic logistic map.

scientific article published in November 2008

Stem Cell Differentiation as a Non-Markov Stochastic Process.

scientific article published on September 2017

StochDecomp--Matlab package for noise decomposition in stochastic biochemical systems

scientific article

StochSens--Matlab package for sensitivity analysis of stochastic chemical systems

scientific article published in March 2012

Subnets of scale-free networks are not scale-free: sampling properties of networks

scientific article

Systematic tracking of altered haematopoiesis during sporozoite-mediated malaria development reveals multiple response points

scientific article

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

scientific article published on 13 July 2016

The ABC of reverse engineering biological signalling systems

scientific article published on 24 September 2009

The chemical Langevin equation for biochemical systems in dynamic environments

scientific article published in 2022

The degree distribution of networks: statistical model selection

scientific article published in January 2012

The ecology in the hematopoietic stem cell niche determines the clinical outcome in chronic myeloid leukemia. ⬇️

scientific article published on 24 February 2014

The effects of incomplete protein interaction data on structural and evolutionary inferences

scientific article

The evolution of the phage shock protein response system: interplay between protein function, genomic organization, and system function ⬇️

scientific article published on November 8, 2010

The extent and importance of intragenic recombination.

scientific article published on November 2004

The roles of contact residue disorder and domain composition in characterizing protein-ligand binding specificity and promiscuity

scientific article published on 14 October 2011

Theoretical models of sheep BSE reveal possibilities

scientific article published in January 2002

Three plasma biomarkers of HTLV-1-associated myelopathy/tropical spastic paraparesis.

scientific article

Topological sensitivity analysis for systems biology

scientific article

Transition state characteristics during cell differentiation

scientific article published on 20 September 2018

Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins

scientific article

Turing pattern design principles and their robustness

scientific article published in 2021

What the papers say: text mining for genomics and systems biology

scientific article

Which species is it? Species-driven gene name disambiguation using random walks over a mixture of adjacency matrices

scientific article

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