Michael Stumpf

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

Evgeny Tankhilevich, Jonathan Ish-Horowicz, Tara Hameed, Elisabeth Roesch, Istvan Kleijn, Michael PH Stumpf, Fei He

Journal article  |  2020  |  Bioinformatics

MOTIVATION: Approximate Bayesian computation (ABC) is an important framework within which to infer the structure and parameters of..

Exactly solvable models of stochastic gene expression

Lucy Ham, David Schnoerr, Rowan D Brackston, Michael PH Stumpf

Journal article  |  2020  |  The Journal of Chemical Physics

Stochastic models are key to understanding the intricate dynamics of gene expression. However, the simplest models that only accou..

Extrinsic Noise and Heavy-Tailed Laws in Gene Expression.

Lucy Ham, Rowan D Brackston, Michael PH Stumpf

Journal article  |  2020  |  Physical Review Letters

Noise in gene expression is one of the hallmarks of life at the molecular scale. Here we derive analytical solutions to a set of m..

Exactly solvable models of stochastic gene expression

Lucy Ham, David Schnoerr, Rowan Brackston, Michael Stumpf

Journal article  |  2020

Stochastic models are key to understanding the intricate dynamics of gene expression. But the simplest models which only account f..

Multi-Model and Network Inference Based on Ensemble Estimates: Avoiding the Madness of Crowds

Michael PH Stumpf

Journal article  |  2019

Abstract Recent progress in theoretical systems biology, applied mathematics and computational statistics allows us to compare qua..

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

Natalie S Scholes, David Schnoerr, Mark Isalan, Michael PH Stumpf

Journal article  |  2019  |  Cell Systems

Parameter inference in dynamical systems with co-dimension 1 bifurcations

Elisabeth Roesch, Michael PH Stumpf

Journal article  |  2019  |  Royal Society Open Science

Dynamical systems with intricate behaviour are all-pervasive in biology. Many of the most interesting biological processes indicat..

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

Natalie S Scholes, David Schnoerr, Mark Isalan, Michael PH Stumpf

Journal article  |  2019  |  Cell Systems

Turing patterns (TPs) underlie many fundamental developmental processes, but they operate over narrow parameter ranges, raising th..

Quantifying Dynamic Regulation in Metabolic Pathways with Nonparametric Flux Inference.

Fei He, Michael PH Stumpf

Journal article  |  2019  |  Biophysical Journal

One of the central tasks in systems biology is to understand how cells regulate their metabolism. Hierarchical regulation analysis..

Proteolytic dynamics of human 20S thymoproteasome.

Ulrike Kuckelkorn, Sabine Stübler, Kathrin Textoris-Taube, Christiane Kilian, Agathe Niewienda, Petra Henklein, Katharina Janek, Michael PH Stumpf, Michele Mishto, Juliane Liepe

Journal article  |  2019  |  Journal of Biological Chemistry

An efficient immunosurveillance of CD8+ T cells in the periphery depends on positive/negative selection of thymocytes and thus on ..

Extrinsic noise and heavy-tailed laws in gene expression

Lucy Ham, Rowan Brackston, Michael PH Stumpf

Journal article  |  2019

Abstract Noise in gene expression is one of the hallmarks of life at the molecular scale. Here we derive analytical solutions to a..

Parameter inference in dynamical systems with co-dimension 1 bifurcations

Elisabeth Roesch, Michael PH Stumpf

Journal article  |  2019

Abstract Dynamical systems with intricate behaviour are all-pervasive in biology. Many of the most interesting biological processe..

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

Leander Dony, Fei He, Michael PH Stumpf

Journal article  |  2019  |  BMC Bioinformatics

BACKGROUND: Reverse engineering of gene regulatory networks from time series gene-expression data is a challenging problem, not on..

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

Thalia E Chan, Michael PH Stumpf, Ann C Babtie

Journal article  |  2019  |  Methods in molecular biology (Clifton, N.J.)

Single cell experimental techniques now allow us to quantify gene expression in up to thousands of individual cells. These data re..

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

Tomasz Jetka, Karol Nienałtowski, Sarah Filippi, Michael PH Stumpf, Michał Komorowski

Journal article  |  2018  |  Nature Communications

Many components of signaling pathways are functionally pleiotropic, and signaling responses are marked with substantial cell-to-ce..

Transition state characteristics during cell differentiation.

Rowan D Brackston, Eszter Lakatos, Michael PH Stumpf

Journal article  |  2018  |  PLOS Computational Biology

Models describing the process of stem-cell differentiation are plentiful, and may offer insights into the underlying mechanisms an..

Biology challenging statistics.

Michael PH Stumpf

Journal article  |  2018  |  Statistical Applications in Genetics and Molecular Biology

Construction of quasipotentials for stochastic dynamical systems: An optimization approach.

RD Brackston, A Wynn, MPH Stumpf

Journal article  |  2018  |  Physical Review E

The construction of effective and informative landscapes for stochastic dynamical systems has proven a long-standing and complex p..

Signalling pathways drive heterogeneity of ground state pluripotency

Kirsten McEwen, Sarah Linnett, Harry Leitch, Prashant Srivastava, Lara Al-Zouabi, Tien-Chi Huang, Maxime Rotival, Alessandro Sardini, Thalia Chan, Sarah Filippi, Michael PH Stumpf, Enrico Petretto, Petra Hajkova

Journal article  |  2018

Abstract Pluripotent stem cells (PSCs) can self-renew indefinitely while maintaining the ability to generate all cell types of the..

PEITH(Θ): perfecting experiments with information theory in Python with GPU support.

Leander Dony, Jonas Mackerodt, Scott Ward, Sarah Filippi, Michael PH Stumpf, Juliane Liepe

Journal article  |  2018  |  Bioinformatics

Motivation: Different experiments provide differing levels of information about a biological system. This makes it difficult, a pr..

Empirical Bayes Meets Information Theoretical Network Reconstruction from Single Cell Data

Thalia Chan, Ananth Pallaseni, Ann Babtie, Kirsten McEwen, Michael PH Stumpf

Journal article  |  2018

Abstract Gene expression is controlled by networks of transcription factors and regulators, but the structure of these networks is..

Transition State Characteristics During Cell Differentiation

Rowan Brackston, Eszter Lakatos, Michael PH Stumpf

Journal article  |  2018

Abstract Models describing the process of stem-cell differentiation are plentiful, and may offer insights into the underlying mech..

Single Cell Phenotyping Reveals Heterogeneity Among Hematopoietic Stem Cells Following Infection.

Adam L MacLean, Maia A Smith, Juliane Liepe, Aaron Sim, Reema Khorshed, Narges M Rashidi, Nico Scherf, Axel Krinner, Ingo Roeder, Cristina Lo Celso, Michael PH Stumpf

Journal article  |  2017  |  STEM CELLS

The hematopoietic stem cell (HSC) niche provides essential microenvironmental cues for the production and maintenance of HSCs with..

Stem Cell Differentiation as a Non-Markov Stochastic Process.

Patrick S Stumpf, Rosanna CG Smith, Michael Lenz, Andreas Schuppert, Franz-Josef Müller, Ann Babtie, Thalia E Chan, Michael PH Stumpf, Colin P Please, Sam D Howison, Fumio Arai, Ben D MacArthur

Journal article  |  2017  |  Cell Systems

Pluripotent stem cells can self-renew in culture and differentiate along all somatic lineages in vivo. While much is known about t..

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

Thalia E Chan, Michael PH Stumpf, Ann C Babtie

Journal article  |  2017  |  Cell Systems

While single-cell gene expression experiments present new challenges for data processing, the cell-to-cell variability observed al..

Control mechanisms for stochastic biochemical systems via computation of reachable sets

Eszter Lakatos, Michael PH Stumpf

Journal article  |  2017  |  Royal Society Open Science

How to deal with parameters for whole-cell modelling

Ann C Babtie, Michael PH Stumpf

Journal article  |  2017  |  Journal of The Royal Society Interface

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).

Trevor T Hansel, Tanushree Tunstall, Maria-Belen Trujillo-Torralbo, Betty Shamji, Ajerico Del-Rosario, Jaideep Dhariwal, Paul DW Kirk, Michael PH Stumpf, Jens Koopmann, Aurica Telcian, Julia Aniscenko, Leila Gogsadze, Eteri Bakhsoliani, Luminita Stanciu, Nathan Bartlett, Michael Edwards, Ross Walton, Patrick Mallia, Toby M Hunt, Trevor L Hunt, et al.

Journal article  |  2017  |  EBioMedicine

BACKGROUND: Rhinovirus infection is a major cause of asthma exacerbations. OBJECTIVES: We studied nasal and bronchial mucosal infl..

Reconciling Epigenetic Memory and Transcriptional Responsiveness.

Amanda G Fisher, Michael PH Stumpf, Matthias Merkenschlager

Journal article  |  2017  |  Cell Systems

The molecular basis of cellular memory is important but poorly understood. Using estimates of histone dynamics, Martin Howard and ..

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

Chiara Dianzani, Elena Bellavista, Juliane Liepe, Claudia Verderio, Morena Martucci, Aurelia Santoro, Annalisa Chiocchetti, Casimiro Luca Gigliotti, Elena Boggio, Benedetta Ferrara, Loredana Riganti, Christin Keller, Katharina Janek, Agathe Niewienda, Chiara Fenoglio, Melissa Sorosina, Roberto Cantello, Peter M Kloetzel, Michael PH Stumpf, Friedemann Paul, et al.

Journal article  |  2017  |  Scientific Reports

Osteopontin is a pleiotropic cytokine that is involved in several diseases including multiple sclerosis. Secreted osteopontin is c..

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

Adam L MacLean, Cristina Lo Celso, Michael PH Stumpf

Journal article  |  2017  |  STEM CELLS

Stem cells are fundamental to human life and offer great therapeutic potential, yet their biology remains incompletely-or in cases..

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

Angelique Ale, Valerie F Crepin, James W Collins, Nicholas Constantinou, Maryam Habibzay, Ann C Babtie, Gad Frankel, Michael PH Stumpf

Journal article  |  2017  |  Infection and Immunity

Tracking disease progression in vivo is essential for the development of treatments against bacterial infection. Optical imaging h..

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

Juliane Liepe, Fabio Marino, John Sidney, Anita Jeko, Daniel E Bunting, Alessandro Sette, Peter M Kloetzel, Michael PH Stumpf, Albert JR Heck, Michele Mishto

Journal article  |  2016  |  Science

The proteasome generates the epitopes presented on human leukocyte antigen (HLA) class I molecules that elicit CD8+ T cell respons..

Gene regulatory network inference from single-cell data using multivariate information measures

Thalia Chan, Michael PH Stumpf, Ann Babtie

Journal article  |  2016

Abstract While single-cell gene expression experiments present new challenges for data processing, the cell-to-cell variability ob..

Single Cell Phenotyping Reveals Heterogeneity among Haematopoietic Stem Cells Following Infection

Adam MacLean, Maia Smith, Juliane Liepe, Aaron Sim, Reema Khorshed, Narges Rashidi, Nico Scherf, Axel Krinner, Ingo Roeder, Cristina Lo Celso, Michael PH Stumpf

Journal article  |  2016

Abstract The haematopoietic stem cell (HSC) niche provides essential micro-environmental cues for the production and maintenance o..

Control mechanisms for stochastic biochemical systems via computation of reachable sets

Eszter Lakatos, Michael PH Stumpf

Journal article  |  2016

Abstract Controlling the behaviour of cells by rationally guiding molecular processes is an overarching aim of much of synthetic b..

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

Sisi Fan, Quentin Geissmann, Eszter Lakatos, Saulius Lukauskas, Angelique Ale, Ann C Babtie, Paul DW Kirk, Michael PH Stumpf

Journal article  |  2016  |  Bioinformatics

MOTIVATION: Many biochemical systems require stochastic descriptions. Unfortunately these can only be solved for the simplest case..

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

Helen Weavers, Juliane Liepe, Aaron Sim, Will Wood, Paul Martin, Michael PH Stumpf

Journal article  |  2016  |  Current Biology

In the acute inflammatory phase following tissue damage, cells of the innate immune system are rapidly recruited to sites of injur..

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

Helena L Crowell, Adam L MacLean, Michael PH Stumpf

Journal article  |  2016  |  Journal of Theoretical Biology

Haematopoietic stem cell dynamics regulate healthy blood cell production and are disrupted during leukaemia. Competition models of..

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

Juliane Liepe, Aaron Sim, Helen Weavers, Laura Ward, Paul Martin, Michael PH Stumpf

Journal article  |  2016  |  Cell Systems

Spatial structures often constrain the 3D movement of cells or particles in vivo, yet this information is obscured when microscopy..

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

Sarah Filippi, Chris P Barnes, Paul DW Kirk, Takamasa Kudo, Katsuyuki Kunida, Siobhan S McMahon, Takaho Tsuchiya, Takumi Wada, Shinya Kuroda, Michael PH Stumpf

Journal article  |  2016  |  Cell Reports

Cellular signaling processes can exhibit pronounced cell-to-cell variability in genetically identical cells. This affects how indi..

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

Maria L Vainieri, Andrew M Blagborough, Adam L MacLean, Myriam LR Haltalli, Nicola Ruivo, Helen A Fletcher, Michael PH Stumpf, Robert E Sinden, Cristina Lo Celso

Journal article  |  2016  |  Open Biology

Haematopoiesis is the complex developmental process that maintains the turnover of all blood cell lineages. It critically depends ..

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

Patrick Smadbeck, Michael PH Stumpf

Journal article  |  2016  |  Journal of The Royal Society Interface

Development is a process that needs to be tightly coordinated in both space and time. Cell tracking and lineage tracing have becom..

A graph theoretical approach to data fusion.

Justina Žurauskienė, Paul DW Kirk, Michael PH Stumpf

Journal article  |  2016  |  Statistical Applications in Genetics and Molecular Biology

The rapid development of high throughput experimental techniques has resulted in a growing diversity of genomic datasets being pro..

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

Adam L MacLean, Heather A Harrington, Michael PH Stumpf, Helen M Byrne

Journal article  |  2016  |  Methods in molecular biology (Clifton, N.J.)

The last decade has seen an explosion in models that describe phenomena in systems medicine. Such models are especially useful for..

SYSTEMS BIOLOGY. Systems biology (un)certainties.

PDW Kirk, AC Babtie, MPH Stumpf

Journal article  |  2015  |  Science

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

Adam L MacLean, Paul DW Kirk, Michael PH Stumpf

Journal article  |  2015  |  Biology Open

Within populations of cells, fate decisions are controlled by an indeterminate combination of cell-intrinsic and cell-extrinsic fa..

Inference of random walk models to describe leukocyte migration.

Phoebe JM Jones, Aaron Sim, Harriet B Taylor, Laurence Bugeon, Magaret J Dallman, Bernard Pereira, Michael PH Stumpf, Juliane Liepe

Journal article  |  2015  |  Physical Biology

While the majority of cells in an organism are static and remain relatively immobile in their tissue, migrating cells occur common..

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

Juliane Liepe, Hermann-Georg Holzhütter, Elena Bellavista, Peter M Kloetzel, Michael PH Stumpf, Michele Mishto

Journal article  |  2015  |  eLife

Proteasomal protein degradation is a key determinant of protein half-life and hence of cellular processes ranging from basic metab..

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

J Liepe, HG Holzhütter, E Bellavista, PM Kloetzel, MPH Stumpf, M Mishto

Journal article  |  2015  |  eLife

Multivariate moment closure techniques for stochastic kinetic models.

Eszter Lakatos, Angelique Ale, Paul DW Kirk, Michael PH Stumpf

Journal article  |  2015  |  The Journal of Chemical Physics

Stochastic effects dominate many chemical and biochemical processes. Their analysis, however, can be computationally prohibitively..

Information processing by simple molecular motifs and susceptibility to noise.

Siobhan S Mc Mahon, Oleg Lenive, Sarah Filippi, Michael PH Stumpf

Journal article  |  2015  |  Journal of The Royal Society Interface

Biological organisms rely on their ability to sense and respond appropriately to their environment. The molecular mechanisms that ..

Great cities look small.

Aaron Sim, Sophia N Yaliraki, Mauricio Barahona, Michael PH Stumpf

Journal article  |  2015  |  Journal of The Royal Society Interface

Great cities connect people; failed cities isolate people. Despite the fundamental importance of physical, face-to-face social tie..

Information Processing by Simple Molecular Motifs and Susceptibility to Noise

Siobhan McMahon, Oleg Lenive, Sarah Filippi, Michael Stumpf

Journal article  |  2015

Biological organisms rely on their ability to sense and respond appropriately to their environment. The molecular mechanisms that ..

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

Patrick Smadbeck, Michael PH Stumpf

Journal article  |  2015

Development is a process that needs to tightly coordinated in both space and time. Cell tracking and lineage tracing have become i..

Cellular Population Dynamics Control the Robustness of the Stem Cell Niche

Adam MacLean, Paul Kirk, Michael PH Stumpf

Journal article  |  2015

Within populations of cells, fate decisions are controlled by an indeterminate combination of cell-intrinsic and cell-extrinsic fa..

Origins of cell-to-cell variability, kinetic proof-reading and the robustness of MAPK signal transduction

Sarah Filippi, Chris Barnes, Paul Kirk, Takamasa Kudo, Siobhan McMahon, Takaho Tsuchiya, Takumi Wada, Shinya Kuroda, Michael Stumpf

Journal article  |  2015

Cellular signalling processes can exhibit pronounced cell-to-cell variability in genetically identical cells. This affects how ind..

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

Goran Jovanovic, Xia Sheng, Angelique Ale, Elisenda Feliu, Heather A Harrington, Paul Kirk, Carsten Wiuf, Martin Buck, Michael PH Stumpf

Journal article  |  2015  |  Molecular BioSystems

Two-component systems play a central part in bacterial signal transduction. Phosphorelay mechanisms have been linked to more robus..

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

Aaron Sim, Juliane Liepe, Michael PH Stumpf

Journal article  |  2015  |  Physical Review E

The Goldstein-Kac telegraph process describes the one-dimensional motion of particles with constant speed undergoing random change..

SYSBIONS: nested sampling for systems biology.

Rob Johnson, Paul Kirk, Michael PH Stumpf

Journal article  |  2015  |  Bioinformatics

MOTIVATION: Model selection is a fundamental part of the scientific process in systems biology. Given a set of competing hypothese..

Topological sensitivity analysis for systems biology.

Ann C Babtie, Paul Kirk, Michael PH Stumpf

Journal article  |  2014  |  Proceedings of the National Academy of Sciences

Mathematical models of natural systems are abstractions of much more complicated processes. Developing informative and realistic m..

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

Adam L MacLean, Heather A Harrington, Michael PH Stumpf, Marc DH Hansen

Journal article  |  2014  |  Biomedicines

Signaling from the c-Met receptor tyrosine kinase is associated with progression and metastasis of epithelial tumors. c-Met, the r..

Proteasome isoforms exhibit only quantitative differences in cleavage and epitope generation.

Michele Mishto, Juliane Liepe, Kathrin Textoris-Taube, Christin Keller, Petra Henklein, Marion Weberruß, Burkhardt Dahlmann, Cordula Enenkel, Antje Voigt, Ulrike Kuckelkorn, Michael PH Stumpf, Peter M Kloetzel

Journal article  |  2014  |  European Journal of Immunology

Immunoproteasomes are considered to be optimised to process Ags and to alter the peptide repertoire by generating a qualitatively ..

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

Siobhan S Mc Mahon, Aaron Sim, Sarah Filippi, Robert Johnson, Juliane Liepe, Dominic Smith, Michael PH Stumpf

Journal article  |  2014  |  Seminars in Cell & Developmental Biology

Sensing and responding to the environment are two essential functions that all biological organisms need to master for survival an..

Overlapping genes: a window on gene evolvability.

Maxime Huvet, Michael PH Stumpf

Journal article  |  2014  |  BMC Genomics

BACKGROUND: The forces underlying genome architecture and organization are still only poorly understood in detail. Overlapping gen..

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

Inbal Michailovici, Heather A Harrington, Hadar Hay Azogui, Yfat Yahalom-Ronen, Alexander Plotnikov, Saunders Ching, Michael PH Stumpf, Ophir D Klein, Rony Seger, Eldad Tzahor

Journal article  |  2014  |  Development

The transition between the proliferation and differentiation of progenitor cells is a key step in organogenesis, and alterations i..

Derivative processes for modelling metabolic fluxes.

Justina Zurauskienė, Paul Kirk, Thomas Thorne, John Pinney, Michael Stumpf

Journal article  |  2014  |  Bioinformatics

MOTIVATION: One of the challenging questions in modelling biological systems is to characterize the functional forms of the proces..

Modelling proteasome and proteasome regulator activities.

Juliane Liepe, Herman-Georg Holzhütter, Peter M Kloetzel, Michael PH Stumpf, Michele Mishto

Journal article  |  2014  |  Biomolecules

Proteasomes are key proteases involved in a variety of processes ranging from the clearance of damaged proteins to the presentatio..

Model selection in systems biology depends on experimental design.

Daniel Silk, Paul DW Kirk, Chris P Barnes, Tina Toni, Michael PH Stumpf

Journal article  |  2014  |  PLoS Computational Biology

Experimental design attempts to maximise the information available for modelling tasks. An optimal experiment allows the inferred ..

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

Adam L MacLean, Sarah Filippi, Michael PH Stumpf

Journal article  |  2014  |  Proceedings of the National Academy of Sciences

Chronic myeloid leukemia (CML) is a blood disease that disrupts normal function of the hematopoietic system. Despite the great pro..

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

Juliane Liepe, Paul Kirk, Sarah Filippi, Tina Toni, Chris P Barnes, Michael PH Stumpf

Journal article  |  2014  |  Nature Protocols

As modeling becomes a more widespread practice in the life sciences and biomedical sciences, researchers need reliable tools to ca..

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

Tomasz Jetka, Agata Charzyńska, Anna Gambin, Michael PH Stumpf, Michał Komorowski

Journal article  |  2014  |  Bioinformatics

MOTIVATION: Stochasticity is an indispensable aspect of biochemical processes at the cellular level. Studies on how the noise ente..

Approximate Bayesian inference for complex ecosystems.

Michael PH Stumpf

Journal article  |  2014  |  F1000Prime Reports

Mathematical models have been central to ecology for nearly a century. Simple models of population dynamics have allowed us to und..

Balancing the robustness and predictive performance of biomarkers.

Paul Kirk, Aviva Witkover, Charles RM Bangham, Sylvia Richardson, Alexandra M Lewin, Michael PH Stumpf

Journal article  |  2013  |  Journal of Computational Biology

Recent studies have highlighted the importance of assessing the robustness of putative biomarkers identified from experimental dat..

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

Jörg Schumacher, Volker Behrends, Zhensheng Pan, Dan R Brown, Franziska Heydenreich, Matthew R Lewis, Mark H Bennett, Banafsheh Razzaghi, Michal Komorowski, Mauricio Barahona, Michael PH Stumpf, Sivaramesh Wigneshweraraj, Jacob G Bundy, Martin Buck

Journal article  |  2013  |  mBio

UNLABELLED: Nitrogen regulation in Escherichia coli is a model system for gene regulation in bacteria. Growth on glutamine as a so..

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

Daniel Silk, Sarah Filippi, Michael PH Stumpf

Journal article  |  2013  |  Statistical Applications in Genetics and Molecular Biology

The likelihood-free sequential Approximate Bayesian Computation (ABC) algorithms are increasingly popular inference tools for comp..

Model selection in systems and synthetic biology.

Paul Kirk, Thomas Thorne, Michael PH Stumpf

Journal article  |  2013  |  Current Opinion in Biotechnology

Developing mechanistic models has become an integral aspect of systems biology, as has the need to differentiate between alternati..

Graphical modelling of molecular networks underlying sporadic inclusion body myositis.

Thomas Thorne, Pietro Fratta, Michael G Hanna, Andrea Cortese, Vincent Plagnol, Elizabeth M Fisher, Michael PH Stumpf

Journal article  |  2013  |  Molecular BioSystems

Here we present a novel statistical methodology that allows us to analyze gene expression data that have been collected from a num..

A general moment expansion method for stochastic kinetic models.

Angelique Ale, Paul Kirk, Michael PH Stumpf

Journal article  |  2013  |  The Journal of Chemical Physics

Moment approximation methods are gaining increasing attention for their use in the approximation of the stochastic kinetics of che..

Cellular compartments cause multistability and allow cells to process more information.

Heather A Harrington, Elisenda Feliu, Carsten Wiuf, Michael PH Stumpf

Journal article  |  2013  |  Biophysical Journal

Many biological, physical, and social interactions have a particular dependence on where they take place; e.g., in living cells, p..

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

Michał Komorowski, Jacek Miękisz, Michael PH Stumpf

Journal article  |  2013  |  Biophysical Journal

Stochasticity is an essential aspect of biochemical processes at the cellular level. We now know that living cells take advantage ..

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

Adam L MacLean, Cristina Lo Celso, Michael PH Stumpf

Journal article  |  2013  |  Journal of The Royal Society Interface

Haematopoietic stem cells (HSCs) are responsible for maintaining immune cells, red blood cells and platelets throughout life. HSCs..

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

Sarah Filippi, Chris P Barnes, Julien Cornebise, Michael PH Stumpf

Journal article  |  2013  |  Statistical Applications in Genetics and Molecular Biology

Approximate Bayesian computation (ABC) has gained popularity over the past few years for the analysis of complex models arising in..

Clinical drug resistance linked to interconvertible phenotypic and functional states of tumor-propagating cells in multiple myeloma.

Aristeidis Chaidos, Chris P Barnes, Gillian Cowan, Philippa C May, Valeria Melo, Evdoxia Hatjiharissi, Maria Papaioannou, Heather Harrington, Helen Doolittle, Evangelos Terpos, Meletios Dimopoulos, Saad Abdalla, Helen Yarranton, Kikkeri Naresh, Letizia Foroni, Alistair Reid, Amin Rahemtulla, Michael Stumpf, Irene Roberts, Anastasios Karadimitris

Journal article  |  2013  |  Blood

The phenotype and function of cells enriched in tumor-propagating activity and their relationship to the phenotypic architecture i..

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

Harriet B Taylor, Juliane Liepe, Charlotte Barthen, Laurence Bugeon, Maxime Huvet, Paul DW Kirk, Simon B Brown, Jonathan R Lamb, Michael PH Stumpf, Margaret J Dallman

Journal article  |  2013  |  Immunology & Cell Biology

The recruitment and migration of macrophages and neutrophils is an important process during the early stages of the innate immune ..

Maximizing the information content of experiments in systems biology.

Juliane Liepe, Sarah Filippi, Michał Komorowski, Michael PH Stumpf

Journal article  |  2013  |  PLoS Computational Biology

Our understanding of most biological systems is in its infancy. Learning their structure and intricacies is fraught with challenge..

Inference of temporally varying Bayesian networks.

Thomas Thorne, Michael PH Stumpf

Journal article  |  2012  |  Bioinformatics

MOTIVATION: When analysing gene expression time series data, an often overlooked but crucial aspect of the model is that the regul..

Graph spectral analysis of protein interaction network evolution.

Thomas Thorne, Michael PH Stumpf

Journal article  |  2012  |  Journal of The Royal Society Interface

We present an analysis of protein interaction network data via the comparison of models of network evolution to the observed data...

Combinatorial stresses kill pathogenic Candida species.

Despoina Kaloriti, Anna Tillmann, Emily Cook, Mette Jacobsen, Tao You, Megan Lenardon, Lauren Ames, Mauricio Barahona, Komelapriya Chandrasekaran, George Coghill, Daniel Goodman, Neil AR Gow, Celso Grebogi, Hsueh-Lui Ho, Piers Ingram, Andrew McDonagh, Alessandro PS de Moura, Wei Pang, Melanie Puttnam, Elahe Radmaneshfar, et al.

Journal article  |  2012  |  Medical Mycology

Pathogenic microbes exist in dynamic niches and have evolved robust adaptive responses to promote survival in their hosts. The maj..

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

Heather A Harrington, Kenneth L Ho, Thomas Thorne, Michael PH Stumpf

Journal article  |  2012  |  Proceedings of the National Academy of Sciences

We introduce a procedure for deciding when a mass-action model is incompatible with observed steady-state data that does not requi..

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

Tina Toni, Yu-ichi Ozaki, Paul Kirk, Shinya Kuroda, Michael PH Stumpf

Journal article  |  2012  |  Molecular BioSystems

Ever since reversible protein phosphorylation was discovered, it has been clear that it plays a key role in the regulation of cell..

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

Heather A Harrington, Michał Komorowski, Mariano Beguerisse-Díaz, Gian Michele Ratto, Michael PH Stumpf

Journal article  |  2012  |  Physical Biology

The mitogen-activated protein kinase (MAPK) family of proteins is involved in regulating cellular fates such as proliferation, dif..

A systems biology analysis of long and short-term memories of osmotic stress adaptation in fungi.

Tao You, Piers Ingram, Mette D Jacobsen, Emily Cook, Andrew McDonagh, Thomas Thorne, Megan D Lenardon, Alessandro PS de Moura, M Carmen Romano, Marco Thiel, Michael Stumpf, Neil AR Gow, Ken Haynes, Celso Grebogi, Jaroslav Stark, Alistair JP Brown

Journal article  |  2012  |  BMC Research Notes

BACKGROUND: Saccharomyces cerevisiae senses hyperosmotic conditions via the HOG signaling network that activates the stress-activa..

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

Juliane Liepe, Harriet Taylor, Chris P Barnes, Maxime Huvet, Laurence Bugeon, Thomas Thorne, Jonathan R Lamb, Margaret J Dallman, Michael PH Stumpf

Journal article  |  2012  |  Integrative Biology

In vivo studies allow us to investigate biological processes at the level of the organism. But not all aspects of in vivo systems ..

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

Michal Komorowski, Justina Zurauskiene, Michael PH Stumpf

Journal article  |  2012  |  Bioinformatics

MOTIVATION: The growing interest in the role of stochasticity in biochemical systems drives the demand for tools to analyse stocha..

Mathematics. Critical truths about power laws.

Michael PH Stumpf, Mason A Porter

Journal article  |  2012  |  Science

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

WP Kelly, MPH Stumpf

Journal article  |  2012  |  Bulletin of Mathematical Biology

Protein interaction networks comprise thousands of individual binary links between distinct proteins. Whilst these data have attra..

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

Nathan Harmston, Wendy Filsell, Michael PH Stumpf

Journal article  |  2012  |  Bioinformatics

MOTIVATION: The scientific literature contains a wealth of information about biological systems. Manual curation lacks the scalabi..

The degree distribution of networks: statistical model selection.

William P Kelly, Piers J Ingram, Michael PH Stumpf

Journal article  |  2012  |  Methods in molecular biology (Clifton, N.J.)

The degree distribution has been viewed as an important characteristic of network data. Many biological networks have been labelle..

Evolutionary characteristics of bacterial two-component systems.

Xia Sheng, Maxime Huvet, John W Pinney, Michael PH Stumpf

Journal article  |  2012  |  Advances in experimental medicine and biology

The evolution of biological systems is influenced by a number of factors and forces that have acted in different combinations at d..

Bayesian design strategies for synthetic biology.

Chris P Barnes, Daniel Silk, Michael PH Stumpf

Journal article  |  2011  |  Interface Focus

We discuss how statistical inference techniques can be applied in the context of designing novel biological systems. Bayesian tech..

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

Yurong Tang, Xia Sheng, Michael PH Stumpf

Journal article  |  2011  |  Molecular BioSystems

Most protein chains interact with only one ligand but a small number of protein chains can bind several ligands, and many examples..

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

Paul DW Kirk, Aviva Witkover, Alan Courtney, Alexandra M Lewin, Robin Wait, Michael PH Stumpf, Sylvia Richardson, Graham P Taylor, Charles RM Bangham

Journal article  |  2011  |  Retrovirology

BACKGROUND: Human T lymphotropic virus Type 1 (HTLV-1) causes a chronic inflammatory disease of the central nervous system known a..

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

Daniel Silk, Paul DW Kirk, Chris P Barnes, Tina Toni, Anna Rose, Simon Moon, Margaret J Dallman, Michael PH Stumpf

Journal article  |  2011  |  Nature Communications

Chaos and oscillations continue to capture the interest of both the scientific and public domains. Yet despite the importance of t..

Bayesian design of synthetic biological systems.

Chris P Barnes, Daniel Silk, Xia Sheng, Michael PH Stumpf

Journal article  |  2011  |  Proceedings of the National Academy of Sciences

Here we introduce a new design framework for synthetic biology that exploits the advantages of Bayesian model selection. We will a..

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

Michał Komorowski, Maria J Costa, David A Rand, Michael PH Stumpf

Journal article  |  2011  |  Proceedings of the National Academy of Sciences

We present a novel and simple method to numerically calculate Fisher information matrices for stochastic chemical kinetics models...

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

Tina Toni, Goran Jovanovic, Maxime Huvet, Martin Buck, Michael PH Stumpf

Journal article  |  2011  |  BMC Systems Biology

BACKGROUND: Bacteria have evolved a rich set of mechanisms for sensing and adapting to adverse conditions in their environment. Th..

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

Thomas W Thorne, Hsueh-Lui Ho, Maxime Huvet, Ken Haynes, Michael PH Stumpf

Journal article  |  2011  |  Fungal Genetics and Biology

The osmotic stress response signalling pathway of the model yeast Saccharomyces cerevisae is crucial for the survival of cells und..

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

Kamil Erguler, Michael PH Stumpf

Journal article  |  2011  |  Molecular BioSystems

The size and complexity of cellular systems make building predictive models an extremely difficult task. In principle dynamical ti..

GPU accelerated biochemical network simulation.

Yanxiang Zhou, Juliane Liepe, Xia Sheng, Michael PH Stumpf, Chris Barnes

Journal article  |  2011  |  Bioinformatics

MOTIVATION: Mathematical modelling is central to systems and synthetic biology. Using simulations to calculate statistics or to ex..

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

M Huvet, T Toni, X Sheng, T Thorne, G Jovanovic, C Engl, M Buck, JW Pinney, MPH Stumpf

Journal article  |  2011  |  Molecular Biology and Evolution

Sensing the environment and responding appropriately to it are key capabilities for the survival of an organism. All extant organi..

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

Paul Kirk, Aviva Witkover, Alan Courtney, Alexandra M Lewin, Robin Wait, Michael P Stumpf, Sylvia Richardson, Graham P Taylor, Charles R Bangham

Journal article  |  2011  |  Retrovirology

Incomplete and noisy network data as a percolation process.

Michael PH Stumpf, Carsten Wiuf

Journal article  |  2010  |  Journal of The Royal Society Interface

We discuss the ramifications of noisy and incomplete observations of network data on the existence of a giant connected component ..

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

Nathan Harmston, Wendy Filsell, Michael PH Stumpf

Journal article  |  2010  |  Human Genomics

Keeping up with the rapidly growing literature has become virtually impossible for most scientists. This can have dire consequence..

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

Sophie Lèbre, Jennifer Becq, Frédéric Devaux, Michael PH Stumpf, Gaëlle Lelandais

Journal article  |  2010  |  BMC Systems Biology

BACKGROUND: Biological networks are highly dynamic in response to environmental and physiological cues. This variability is in con..

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

William P Kelly, Michael PH Stumpf

Journal article  |  2010  |  BMC Bioinformatics

BACKGROUND: Phylogenies capture the evolutionary ancestry linking extant species. Correlations and similarities among a set of spe..

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

Nicolas Joly, Christoph Engl, Goran Jovanovic, Maxime Huvet, Tina Toni, Xia Sheng, Michael PH Stumpf, Martin Buck

Journal article  |  2010  |  FEMS Microbiology Reviews

The bacterial phage shock protein (Psp) response functions to help cells manage the impacts of agents impairing cell membrane func..

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

Juliane Liepe, Chris Barnes, Erika Cule, Kamil Erguler, Paul Kirk, Tina Toni, Michael PH Stumpf

Journal article  |  2010  |  Bioinformatics

MOTIVATION: The growing field of systems biology has driven demand for flexible tools to model and simulate biological systems. Tw..

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

Tina Toni, Michael PH Stumpf

Journal article  |  2010  |  Bioinformatics

MOTIVATION: Computer simulations have become an important tool across the biomedical sciences and beyond. For many important probl..

An organizing region in metamorphosing hydrozoan planula larvae--stimulation of axis formation in both larval and in adult tissue.

Melanie Stumpf, Britta Will, Karola Wittig, Jennifer Kasper, Benjamin Fischer, Jurgen Schmich, Stefanie Seipp, Thomas Leitz

Journal article  |  2010  |  The International Journal of Developmental Biology

A novel wingless gene was isolated from the marine colonial hydroid Hydractinia echinata. Alignments and Bayesian inference analys..

Parameter inference and model selection in signaling pathway models.

Tina Toni, Michael PH Stumpf

Journal article  |  2010  |  Methods in molecular biology (Clifton, N.J.)

To support and guide an extensive experimental research into systems biology of signaling pathways, increasingly more mechanistic ..

The ABC of reverse engineering biological signalling systems.

Maria Secrier, Tina Toni, Michael PH Stumpf

Journal article  |  2009  |  Molecular BioSystems

Modelling biological systems would be straightforward if we knew the structure of the model and the parameters governing their dyn..

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

Maxime Huvet, Tina Toni, Hui Tan, Goran Jovanovic, Christoph Engl, Martin Buck, Michael PH Stumpf

Journal article  |  2009  |  Biochemical Society Transactions

The evolution of proteins is inseparably linked to their function. Because most biological processes involve a number of different..

Evolution of pathogenicity and sexual reproduction in eight Candida genomes.

Geraldine Butler, Matthew D Rasmussen, Michael F Lin, Manuel AS Santos, Sharadha Sakthikumar, Carol A Munro, Esther Rheinbay, Manfred Grabherr, Anja Forche, Jennifer L Reedy, Ino Agrafioti, Martha B Arnaud, Steven Bates, Alistair JP Brown, Sascha Brunke, Maria C Costanzo, David A Fitzpatrick, Piet WJ de Groot, David Harris, Lois L Hoyer, et al.

Journal article  |  2009  |  Nature

Candida species are the most common cause of opportunistic fungal infection worldwide. Here we report the genome sequences of six ..

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

Paul DW Kirk, Michael PH Stumpf

Journal article  |  2009  |  Bioinformatics

MOTIVATION: Although widely accepted that high-throughput biological data are typically highly noisy, the effects that this uncert..

Phylogenetic diversity of stress signalling pathways in fungi.

Elissavet Nikolaou, Ino Agrafioti, Michael Stumpf, Janet Quinn, Ian Stansfield, Alistair JP Brown

Journal article  |  2009  |  BMC Evolutionary Biology

BACKGROUND: Microbes must sense environmental stresses, transduce these signals and mount protective responses to survive in hosti..

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

Tina Toni, David Welch, Natalja Strelkowa, Andreas Ipsen, Michael PH Stumpf

Journal article  |  2009  |  Journal of The Royal Society Interface

Approximate Bayesian computation (ABC) methods can be used to evaluate posterior distributions without having to calculate likelih..

Neuroscience of birdsong.

Michael Stumpf

Journal article  |  2009  |  Human Genomics

Evolving proteins at Darwin's bicentenary.

John W Pinney, Michael PH Stumpf

Conference Proceedings  |  2009  |  Genome Biology

A report of the Biochemical Society/Wellcome Trust meeting 'Protein Evolution - Sequences, Structures and Systems', Hinxton, UK, 2..

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

Kamil Erguler, Michael PH Stumpf

Journal article  |  2008  |  Mathematical Biosciences

A recurring problem in population biology--as well as other stochastic dynamical systems in biology, the physical and social scien..

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

Mark G Thomas, Michael PH Stumpf, Heinrich Härke

Journal article  |  2008  |  Proceedings of the Royal Society B: Biological Sciences

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

Piers J Ingram, Michael PH Stumpf, Jaroslav Stark

Journal article  |  2008  |  PLoS Computational Biology

Over the last few years, experimental data on the fluctuations in gene activity between individual cells and within the same cell ..

Protein-protein interactions: from global to local analyses.

Wp Kelly, Mph Stumpf

Journal article  |  2008  |  Current Opinion in Biotechnology

For the increasing number of species with complete genome sequences, the task of elucidating their complete proteomes and interact..

Parameter inference for biochemical systems that undergo a Hopf bifurcation.

Paul DW Kirk, Tina Toni, Michael PH Stumpf

Journal article  |  2008  |  Biophysical Journal

The increasingly widespread use of parametric mathematical models to describe biological systems means that the ability to infer m..

Estimating the size of the human interactome.

Michael PH Stumpf, Thomas Thorne, Eric de Silva, Ronald Stewart, Hyeong Jun An, Michael Lappe, Carsten Wiuf

Journal article  |  2008  |  Proceedings of the National Academy of Sciences

After the completion of the human and other genome projects it emerged that the number of genes in organisms as diverse as fruit f..

Systems biology and its potential role in radiobiology.

Ludwig Feinendegen, Philip Hahnfeldt, Eric E Schadt, Michael Stumpf, Eberhard O Voit

Journal article  |  2008  |  Radiation and Environmental Biophysics

About a century ago, Conrad Röentgen discovered X-rays, and Henri Becquerel discovered a new phenomenon, which Marie and Pierre Cu..

Biosimulation in Drug Development.

Michael PH Stumpf

Journal article  |  2008  |  Human Genomics

Generating confidence intervals on biological networks.

Thomas Thorne, Michael PH Stumpf

Journal article  |  2007  |  BMC Bioinformatics

BACKGROUND: In the analysis of networks we frequently require the statistical significance of some network statistic, such as meas..

Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H. pylori and P. falciparum.

Oliver Ratmann, Ole Jørgensen, Trevor Hinkley, Michael Stumpf, Sylvia Richardson, Carsten Wiuf

Journal article  |  2007  |  PLoS Computational Biology

Gene duplication with subsequent interaction divergence is one of the primary driving forces in the evolution of genetic systems. ..

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

Michael PH Stumpf, William P Kelly, Thomas Thorne, Carsten Wiuf

Journal article  |  2007  |  Trends in Ecology & Evolution

Recent work leading to new insights into the molecular architecture underlying complex cellular phenotypes enables researchers to ..

SNPSTR: a database of compound microsatellite-SNP markers.

I Agrafioti, MPH Stumpf

Journal article  |  2007  |  Nucleic Acids Research

There has been widespread and growing interest in genetic markers suitable for drawing population genetic inferences about past de..

Systems biology and its impact on anti-infective drug development.

Michael P Stumpf, Brian D Robertson, Ken Duncan, Douglas B Young

Journal article  |  2007  |  Progress in drug research. Fortschritte der Arzneimittelforschung. Progres des recherches pharmaceutiques

Systems biology offers the potential for more effective selection of novel targets for anti-infective drugs. In contrast to conven..

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

Eric de Silva, Thomas Thorne, Piers Ingram, Ino Agrafioti, Jonathan Swire, Carsten Wiuf, Michael PH Stumpf

Journal article  |  2006  |  BMC Biology

BACKGROUND: Present protein interaction network data sets include only interactions among subsets of the proteins in an organism. ..

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

Mark G Thomas, Michael PH Stumpf, Heinrich Härke

Journal article  |  2006  |  Proceedings of the Royal Society B: Biological Sciences

The role of migration in the Anglo-Saxon transition in England remains controversial. Archaeological and historical evidence is in..

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

Goran Jovanovic, Louise J Lloyd, Michael PH Stumpf, Antony J Mayhew, Martin Buck

Journal article  |  2006  |  Journal of Biological Chemistry

The phage shock protein (Psp) F regulon response in Escherichia coli is thought to be induced by impaired inner membrane integrity..

A likelihood approach to analysis of network data.

Carsten Wiuf, Markus Brameier, Oskar Hagberg, Michael PH Stumpf

Journal article  |  2006  |  Proceedings of the National Academy of Sciences

Biological, sociological, and technological network data are often analyzed by using simple summary statistics, such as the observ..

Network motifs: structure does not determine function.

Piers J Ingram, Michael PH Stumpf, Jaroslav Stark

Journal article  |  2006  |  BMC Genomics

BACKGROUND: A number of publications have recently examined the occurrence and properties of the feed-forward motif in a variety o..

Complex networks and simple models in biology.

Eric de Silva, Michael PH Stumpf

Journal article  |  2005  |  Journal of The Royal Society Interface

The analysis of molecular networks, such as transcriptional, metabolic and protein interaction networks, has progressed substantia..

Ecology. Making sense of evolution in an uncertain world.

Vincent AA Jansen, Michael PH Stumpf

Journal article  |  2005  |  Science

Sampling properties of random graphs: the degree distribution.

Michael PH Stumpf, Carsten Wiuf

Journal article  |  2005  |  Physical Review E

We discuss two sampling schemes for selecting random subnets from a network, random sampling and connectivity dependent sampling, ..

Recombination hotspots as a point process.

Maria De Iorio, Eric de Silva, Michael PH Stumpf

Journal article  |  2005  |  Philosophical Transactions of the Royal Society B: Biological Sciences

The variation of the recombination rate along chromosomal DNA is one of the important determinants of the patterns of linkage dise..

Introduction: genetic variation and human health.

MPH Stumpf, DB Goldstein, NW Wood

Journal article  |  2005  |  Philosophical Transactions of the Royal Society B: Biological Sciences

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

Maike Both, Michael Csukai, Michael PH Stumpf, Pietro D Spanu

Journal article  |  2005  |  The Plant Cell

cDNA microarrays of Blumeria graminis f sp hordei transcript profiles during the asexual development cycle reveal the dynamics of ..

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

Liisa Kauppi, Michael PH Stumpf, Alec J Jeffreys

Journal article  |  2005  |  Genomics

To investigate the relationship between meiotic crossover hot spots and block-like linkage disequilibrium (LD), we have extended o..

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

Michael PH Stumpf, Carsten Wiuf, Robert M May

Journal article  |  2005  |  Proceedings of the National Academy of Sciences

Most studies of networks have only looked at small subsets of the true network. Here, we discuss the sampling properties of a netw..

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

Ino Agrafioti, Jonathan Swire, James Abbott, Derek Huntley, Sarah Butcher, Michael PH Stumpf

Journal article  |  2005  |  BMC Evolutionary Biology

BACKGROUND: Protein interaction networks aim to summarize the complex interplay of proteins in an organism. Early studies suggeste..

HIV and the CCR5-Delta32 resistance allele.

Eric de Silva, Michael PH Stumpf

Journal article  |  2004  |  FEMS Microbiology Letters

The combination of molecular biology, epidemiology, virology, evolutionary and population genetics has enabled us to understand th..

The extent and importance of intragenic recombination.

Eric de Silva, Lawrence A Kelley, Michael PH Stumpf

Journal article  |  2004  |  Human Genomics

We have studied the recombination rate behaviour of a set of 140 genes which were investigated for their potential importance in i..

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

Michael PH Stumpf

Journal article  |  2004  |  European Journal of Human Genetics

Haplotype diversity is controlled by a variety of processes, including mutation, recombination, marker ascertainment and demograph..

Allelic histories: positive selection on a HIV-resistance allele.

Michael PH Stumpf, Hilde M Wilkinson-Herbots

Journal article  |  2004  |  Trends in Ecology & Evolution

The CCR5-Delta32 allele crucially determines the course of HIV infection and appears to be highly protective against the disease. ..

Estimating recombination rates from population-genetic data.

Michael PH Stumpf, Gilean AT McVean

Journal article  |  2003  |  Nature Reviews Genetics

Obtaining an accurate measure of how recombination rates vary across the genome has implications for understanding the molecular b..

Some notes on the combinatorial properties of haplotype tagging

C Wiuf, Z Laidlaw, MPH Stumpf

Journal article  |  2003  |  Mathematical Biosciences

A Y chromosome census of the British Isles.

Cristian Capelli, Nicola Redhead, Julia K Abernethy, Fiona Gratrix, James F Wilson, Torolf Moen, Tor Hervig, Martin Richards, Michael PH Stumpf, Peter A Underhill, Paul Bradshaw, Alom Shaha, Mark G Thomas, Neal Bradman, David B Goldstein

Journal article  |  2003  |  Current Biology

The degree of population replacement in the British Isles associated with cultural changes has been extensively debated. Recent wo..

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

Simon Mead, Michael PH Stumpf, Jerome Whitfield, Jonathan A Beck, Mark Poulter, Tracy Campbell, James B Uphill, David Goldstein, Michael Alpers, Elizabeth MC Fisher, John Collinge

Journal article  |  2003  |  Science

Kuru is an acquired prion disease largely restricted to the Fore linguistic group of the Papua New Guinea Highlands, which was tra..

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

Michael PH Stumpf, David B Goldstein

Journal article  |  2003  |  Current Biology

BACKGROUND: Effective gene mapping based on genetic association data will require detailed knowledge of patterns of linkage disequ..

Herpes viruses hedge their bets

MPH Stumpf, Z Laidlaw, VAA Jansen

Journal article  |  2002  |  Proceedings of the National Academy of Sciences

Genetic diversity and models of viral evolution for the hepatitis C virus.

MPH Stumpf, OG Pybus

Journal article  |  2002  |  FEMS Microbiology Letters

In this review we discuss the application of theoretical frameworks to the interpretation of viral gene sequence data, with partic..

Haplotype diversity and the block structure of linkage disequilibrium.

Michael PH Stumpf

Journal article  |  2002  |  Trends in Genetics

Several recent studies indicate that patterns of linkage disequilibrium in the human genome cannot be reconciled with a uniform di..

Population genomics: ageing by association.

Scott D Pletcher, Michael PH Stumpf

Journal article  |  2002  |  Current Biology

Mutations in the gene Klotho lead to premature ageing in mice. Recent work on human genetic variation has identified an associatio..

Theoretical models of sheep BSE reveal possibilities.

John R Krebs, Robert M May, Michael PH Stumpf

Journal article  |  2002  |  Nature

RNA replication kinetics, genetic polymorphism and selection in the case of the hepatitis C virus.

MP Stumpf, N Zitzmann

Journal article  |  2001  |  Proceedings of the Royal Society of London. Series B: Biological Sciences

We show in a simple theoretical quasispecies model that the replication dynamics of hepatitis C virus and a related model-system, ..

Genealogical and evolutionary inference with the human Y chromosome.

MP Stumpf, DB Goldstein

Journal article  |  2001  |  Science

Population genetics has emerged as a powerful tool for unraveling human history. In addition to the study of mitochondrial and aut..

Ecology. Species-area relations in tropical forests.

RM May, MP Stumpf

Journal article  |  2000  |  Science

A power law called the species-area relationship describes the finding that the number of species is proportional to the size of t..

Mapping the parameters of prion-induced neuropathology.

MP Stumpf, DC Krakauer

Journal article  |  2000  |  Proceedings of the National Academy of Sciences

We present a theoretical framework that enables us to dissect out the parametric dependencies of the pathogenesis of prion disease..

Repeated Decision Stumping Distils Simple Rules from Single Cell Data

Ivan A Croydon Veleslavov, Michael PH Stumpf

Journal article

AbstractHere we introduce repeated decision stumping, to distill simple models from single cell data. We develop decision trees of..