Michael Stumpf

I hold the Chair of Theoretical Systems Biology, and work on a range of topics in theoretical and statistical systems biology, systems medicine, statistical bioinformatics, dynamical systems and networks, and evolutionary theory. My main interests are all related to reverse engineering the structure, dynamics and evolutionary history of biological systems, in particular those processes which enable cells to respond to and interact with their environment. Biological applications include bacterial and fungal host-pathogen interactions, analysis and design of microbial systems, and cellular decision making processes in eukaryotic (including human) stem cell systems.

I originally studied theoretical physics in Tübingen, Göttingen and Oxford. I completed my DPhil in Statistical Physics in Oxford in 1999 and moved straight into Biology. I spent three years as a Wellcome Trust Research Training Fellow in Mathematical Biology in the Department of Zoology in Oxford. In 2002 I took up a Wellcome Trust Career Development Fellowship and moved to the Department of Biology at UCL in London. Since October 2003 I have been based at the Centre for Bioinformatics at Imperial College London.

From October 2004 until December 2007 I was an EMBO Young Investigator. Between March 2006 and February 2009 I was on the BBSRC Engineering and Biological Systems Research Committee. Since October 2008 I have served on the BBSRC Training and Awards Committee. In October 2009 I was awarded a Royal Society Wolfson Research Merit Award.

I am course director of the MSc in Bioinformatics at Imperial College London and am involved with the 3rd year undergraduate option in Systems Biology.


Research Interests

The research in the Theoretical Systems Biology Group uses mathematical, statistical and computational methods to explore functional, evolutionary and statistical problems in systems biology. The methods we use can be applied widely in evolutionary biology, systems biology and bioinformatics, and beyond.

Our research covers several different areas, which include:

  • Development of inferential procedures for model selection and parameter estimation in complex dynamical systems
  • Bayesian reverse engineering of biological systems using statistical, comparative and text-mining approaches
  • Inference-based modelling of signalling and regulatory networks in bacteria, pathogenic fungi and mammalian systems
  • Multi-scale modelling of signal transduction and decision making processes in immunology, haematopoiesis and stem-cell biology more generally.
  • Identification of molecular mechanisms underlying disease and drug response mechanisms.
  • Stochastic processes and statistical inference in the evolutionary analysis of biological networks
  • Sampling properties of random networks
  • Mathematical and statistical properties of complex stochastic systems and networks
  • Bayesian analysis of gene regulation

Our work involves extensive computer simulations as well as analytical approaches. We are also interested in analyzing real data and work closely together with both experimental and clinical scientists.


Selected Publications

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

Mishto M, Liepe J, Textoris-Taube K, Keller C, Henklein P, Weberruß M, Dahlmann B, Enenkel C, Voigt A, Kuckelkorn U, Stumpf MP, Kloetzel PM.

Eur J Immunol. 2014 Sep 17. doi: 10.1002/eji.201444902. [Epub ahead of print]

PMID:
25231383
[PubMed - as supplied by publisher]

Overlapping genes: a window on gene evolvability.

Huvet M, Stumpf MP.

BMC Genomics. 2014 Aug 27;15:721. doi: 10.1186/1471-2164-15-721.

PMID:
25159814
[PubMed - in process]

Free PMC Article

Approximate Bayesian inference for complex ecosystems.

Stumpf MP.

F1000Prime Rep. 2014 Jul 17;6:60. doi: 10.12703/P6-60. eCollection 2014. Review.

PMID:
25152812
[PubMed]

Free PMC Article

Modelling proteasome and proteasome regulator activities.

Liepe J, Holzhütter HG, Kloetzel PM, Stumpf MP, Mishto M.

Biomolecules. 2014 Jun 20;4(2):585-99. doi: 10.3390/biom4020585.

PMID:
24970232
[PubMed]

Free PMC Article

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

Mc Mahon SS, Sim A, Filippi S, Johnson R, Liepe J, Smith D, Stumpf MP.

Semin Cell Dev Biol. 2014 Nov;35C:98-108. doi: 10.1016/j.semcdb.2014.06.011. Epub 2014 Jun 19. Review.

PMID:
24953199
[PubMed - as supplied by publisher]

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

Michailovici I, Harrington HA, Azogui HH, Yahalom-Ronen Y, Plotnikov A, Ching S, Stumpf MP, Klein OD, Seger R, Tzahor E.

Development. 2014 Jul;141(13):2611-20. doi: 10.1242/dev.107078. Epub 2014 Jun 12.

PMID:
24924195
[PubMed - indexed for MEDLINE]

Model selection in systems biology depends on experimental design.

Silk D, Kirk PD, Barnes CP, Toni T, Stumpf MP.

PLoS Comput Biol. 2014 Jun 12;10(6):e1003650. doi: 10.1371/journal.pcbi.1003650. eCollection 2014 Jun.

PMID:
24922483
[PubMed - in process]

Free PMC Article

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

MacLean AL, Filippi S, Stumpf MP.

Proc Natl Acad Sci U S A. 2014 Mar 11;111(10):3883-8. doi: 10.1073/pnas.1317072111. Epub 2014 Feb 24.

PMID:
24567385
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Liepe J, Kirk P, Filippi S, Toni T, Barnes CP, Stumpf MP.

Nat Protoc. 2014 Feb;9(2):439-56. doi: 10.1038/nprot.2014.025. Epub 2014 Jan 23.

PMID:
24457334
[PubMed - indexed for MEDLINE]

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

Schumacher J, Behrends V, Pan Z, Brown DR, Heydenreich F, Lewis MR, Bennett MH, Razzaghi B, Komorowski M, Barahona M, Stumpf MP, Wigneshweraraj S, Bundy JG, Buck M.

MBio. 2013 Nov 19;4(6):e00881-13. doi: 10.1128/mBio.00881-13.

PMID:
24255125
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Jetka T, Charzyńska A, Gambin A, Stumpf MP, Komorowski M.

Bioinformatics. 2014 Jan 1;30(1):137-8. doi: 10.1093/bioinformatics/btt631. Epub 2013 Nov 4.

PMID:
24191070
[PubMed - indexed for MEDLINE]

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

Silk D, Filippi S, Stumpf MP.

Stat Appl Genet Mol Biol. 2013 Oct 1;12(5):603-18. doi: 10.1515/sagmb-2012-0043.

PMID:
24025688
[PubMed - indexed for MEDLINE]

Balancing the robustness and predictive performance of biomarkers.

Kirk P, Witkover A, Bangham CR, Richardson S, Lewin AM, Stumpf MP.

J Comput Biol. 2013 Dec;20(12):979-89. doi: 10.1089/cmb.2013.0018. Epub 2013 Aug 2.

PMID:
23909374
[PubMed - indexed for MEDLINE]

A general moment expansion method for stochastic kinetic models.

Ale A, Kirk P, Stumpf MP.

J Chem Phys. 2013 May 7;138(17):174101. doi: 10.1063/1.4802475.

PMID:
23656108
[PubMed - indexed for MEDLINE]

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

Harrington HA, Feliu E, Wiuf C, Stumpf MP.

Biophys J. 2013 Apr 16;104(8):1824-31. doi: 10.1016/j.bpj.2013.02.028.

PMID:
23601329
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Komorowski M, Miękisz J, Stumpf MP.

Biophys J. 2013 Apr 16;104(8):1783-93. doi: 10.1016/j.bpj.2013.02.027.

PMID:
23601325
[PubMed - indexed for MEDLINE]

Free PMC Article

Graphical modelling of molecular networks underlying sporadic inclusion body myositis.

Thorne T, Fratta P, Hanna MG, Cortese A, Plagnol V, Fisher EM, Stumpf MP.

Mol Biosyst. 2013 Jul;9(7):1736-42. doi: 10.1039/c3mb25497f. Epub 2013 Apr 17.

PMID:
23595110
[PubMed - indexed for MEDLINE]

Model selection in systems and synthetic biology.

Kirk P, Thorne T, Stumpf MP.

Curr Opin Biotechnol. 2013 Aug;24(4):767-74. doi: 10.1016/j.copbio.2013.03.012. Epub 2013 Apr 8. Review.

PMID:
23578462
[PubMed - indexed for MEDLINE]

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

Filippi S, Barnes CP, Cornebise J, Stumpf MP.

Stat Appl Genet Mol Biol. 2013 Mar 26;12(1):87-107. doi: 10.1515/sagmb-2012-0069.

PMID:
23502346
[PubMed - indexed for MEDLINE]

Maximizing the information content of experiments in systems biology.

Liepe J, Filippi S, Komorowski M, Stumpf MP.

PLoS Comput Biol. 2013;9(1):e1002888. doi: 10.1371/journal.pcbi.1002888. Epub 2013 Jan 31.

PMID:
23382663
[PubMed - indexed for MEDLINE]

Free PMC Article

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

MacLean AL, Lo Celso C, Stumpf MP.

J R Soc Interface. 2013 Jan 24;10(81):20120968. doi: 10.1098/rsif.2012.0968. Print 2013 Apr 6.

PMID:
23349436
[PubMed - indexed for MEDLINE]

Free PMC Article

Bayesian design strategies for synthetic biology.

Barnes CP, Silk D, Stumpf MP.

Interface Focus. 2011 Dec 6;1(6):895-908. doi: 10.1098/rsfs.2011.0056. Epub 2011 Oct 5.

PMID:
23226588
[PubMed]

Free PMC Article

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

Taylor HB, Liepe J, Barthen C, Bugeon L, Huvet M, Kirk PD, Brown SB, Lamb JR, Stumpf MP, Dallman MJ.

Immunol Cell Biol. 2013 Jan;91(1):60-9. doi: 10.1038/icb.2012.57. Epub 2012 Nov 20.

PMID:
23165607
[PubMed - indexed for MEDLINE]

Free PMC Article

Inference of temporally varying Bayesian networks.

Thorne T, Stumpf MP.

Bioinformatics. 2012 Dec 15;28(24):3298-305. doi: 10.1093/bioinformatics/bts614. Epub 2012 Oct 16.

PMID:
23074260
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Roy A, Cowan G, Mead AJ, Filippi S, Bohn G, Chaidos A, Tunstall O, Chan JK, Choolani M, Bennett P, Kumar S, Atkinson D, Wyatt-Ashmead J, Hu M, Stumpf MP, Goudevenou K, O’Connor D, Chou ST, Weiss MJ, Karadimitris A, Jacobsen SE, Vyas P, Roberts I.

Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17579-84. doi: 10.1073/pnas.1211405109. Epub 2012 Oct 8.

PMID:
23045701
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Harrington HA, Ho KL, Thorne T, Stumpf MP.

Proc Natl Acad Sci U S A. 2012 Sep 25;109(39):15746-51. Epub 2012 Sep 11.

PMID:
22967512
[PubMed]

Free PMC Article

Evolutionary characteristics of bacterial two-component systems.

Sheng X, Huvet M, Pinney JW, Stumpf MP.

Adv Exp Med Biol. 2012;751:121-37. doi: 10.1007/978-1-4614-3567-9_6.

PMID:
22821456
[PubMed - indexed for MEDLINE]

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

Toni T, Ozaki Y, Kirk P, Kuroda S, Stumpf MP.

Mol Biosyst. 2012 Jul 6;8(7):1921-9. doi: 10.1039/c2mb05493k. Epub 2012 May 3.

PMID:
22555461
[PubMed - indexed for MEDLINE]

Graph spectral analysis of protein interaction network evolution.

Thorne T, Stumpf MP.

J R Soc Interface. 2012 Oct 7;9(75):2653-66. doi: 10.1098/rsif.2012.0220. Epub 2012 May 2.

PMID:
22552917
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Harrington HA, Komorowski M, Beguerisse-Díaz M, Ratto GM, Stumpf MP.

Phys Biol. 2012 Jun;9(3):036001. doi: 10.1088/1478-3975/9/3/036001. Epub 2012 May 3.

PMID:
22551942
[PubMed - indexed for MEDLINE]

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

Komorowski M, Zurauskiene J, Stumpf MP.

Bioinformatics. 2012 Mar 1;28(5):731-3. doi: 10.1093/bioinformatics/btr714.

PMID:
22378710
[PubMed - indexed for MEDLINE]

Free Article

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

Liepe J, Taylor H, Barnes CP, Huvet M, Bugeon L, Thorne T, Lamb JR, Dallman MJ, Stumpf MP.

Integr Biol (Camb). 2012 Mar;4(3):335-45. doi: 10.1039/c2ib00175f. Epub 2012 Feb 10.

PMID:
22327539
[PubMed - indexed for MEDLINE]

Mathematics. Critical truths about power laws.

Stumpf MP, Porter MA.

Science. 2012 Feb 10;335(6069):665-6. doi: 10.1126/science.1216142. No abstract available.

PMID:
22323807
[PubMed]

The degree distribution of networks: statistical model selection.

Kelly WP, Ingram PJ, Stumpf MP.

Methods Mol Biol. 2012;804:245-62. doi: 10.1007/978-1-61779-361-5_13.

PMID:
22144157
[PubMed - indexed for MEDLINE]

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

Harmston N, Filsell W, Stumpf MP.

Bioinformatics. 2012 Jan 15;28(2):254-60. doi: 10.1093/bioinformatics/btr640. Epub 2011 Nov 30.

PMID:
22135416
[PubMed - indexed for MEDLINE]

Free Article

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

Tang Y, Sheng X, Stumpf MP.

Mol Biosyst. 2011 Dec;7(12):3280-6. doi: 10.1039/c1mb05325f. Epub 2011 Oct 14.

PMID:
22002096
[PubMed - indexed for MEDLINE]

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

Kirk PD, Witkover A, Courtney A, Lewin AM, Wait R, Stumpf MP, Richardson S, Taylor GP, Bangham CR.

Retrovirology. 2011 Oct 12;8:81. doi: 10.1186/1742-4690-8-81.

PMID:
21992623
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Silk D, Kirk PD, Barnes CP, Toni T, Rose A, Moon S, Dallman MJ, Stumpf MP.

Nat Commun. 2011 Oct 4;2:489. doi: 10.1038/ncomms1496.

PMID:
21971504
[PubMed - indexed for MEDLINE]

Free PMC Article

Bayesian design of synthetic biological systems.

Barnes CP, Silk D, Sheng X, Stumpf MP.

Proc Natl Acad Sci U S A. 2011 Sep 13;108(37):15190-5. doi: 10.1073/pnas.1017972108. Epub 2011 Aug 29.

PMID:
21876136
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Kelly WP, Stumpf MP.

Bull Math Biol. 2012 Feb;74(2):356-74. doi: 10.1007/s11538-011-9680-2. Epub 2011 Aug 26.

PMID:
21870201
[PubMed - indexed for MEDLINE]

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

Toni T, Jovanovic G, Huvet M, Buck M, Stumpf MP.

BMC Syst Biol. 2011 May 12;5:69. doi: 10.1186/1752-0509-5-69.

PMID:
21569396
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Komorowski M, Costa MJ, Rand DA, Stumpf MP.

Proc Natl Acad Sci U S A. 2011 May 24;108(21):8645-50. doi: 10.1073/pnas.1015814108. Epub 2011 May 6.

PMID:
21551095
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Erguler K, Stumpf MP.

Mol Biosyst. 2011 May;7(5):1593-602. doi: 10.1039/c0mb00107d. Epub 2011 Mar 4.

PMID:
21380410
[PubMed - indexed for MEDLINE]

GPU accelerated biochemical network simulation.

Zhou Y, Liepe J, Sheng X, Stumpf MP, Barnes C.

Bioinformatics. 2011 Mar 15;27(6):874-6. doi: 10.1093/bioinformatics/btr015. Epub 2011 Jan 11.

PMID:
21224286
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Thorne TW, Ho HL, Huvet M, Haynes K, Stumpf MP.

Fungal Genet Biol. 2011 May;48(5):504-11. doi: 10.1016/j.fgb.2010.12.005. Epub 2010 Dec 28.

PMID:
21193057
[PubMed - indexed for MEDLINE]

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

Harmston N, Filsell W, Stumpf MP.

Hum Genomics. 2010 Oct;5(1):17-29. Review.

PMID:
21106487
[PubMed - indexed for MEDLINE]

Free PMC Article

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

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

Mol Biol Evol. 2011 Mar;28(3):1141-55. doi: 10.1093/molbev/msq301. Epub 2010 Nov 8.

PMID:
21059793
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Lèbre S, Becq J, Devaux F, Stumpf MP, Lelandais G.

BMC Syst Biol. 2010 Sep 22;4:130. doi: 10.1186/1752-0509-4-130.

PMID:
20860793
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Kelly WP, Stumpf MP.

BMC Bioinformatics. 2010 Sep 20;11:470. doi: 10.1186/1471-2105-11-470.

PMID:
20854660
[PubMed - indexed for MEDLINE]

Free PMC Article

Parameter inference and model selection in signaling pathway models.

Toni T, Stumpf MP.

Methods Mol Biol. 2010;673:283-95. doi: 10.1007/978-1-60761-842-3_18. Review.

PMID:
20835806
[PubMed - indexed for MEDLINE]

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

Joly N, Engl C, Jovanovic G, Huvet M, Toni T, Sheng X, Stumpf MP, Buck M.

FEMS Microbiol Rev. 2010 Sep;34(5):797-827. doi: 10.1111/j.1574-6976.2010.00240.x. Epub 2010 Jun 9. Review.

PMID:
20636484
[PubMed - indexed for MEDLINE]

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

Liepe J, Barnes C, Cule E, Erguler K, Kirk P, Toni T, Stumpf MP.

Bioinformatics. 2010 Jul 15;26(14):1797-9. doi: 10.1093/bioinformatics/btq278.

PMID:
20591907
[PubMed - indexed for MEDLINE]

Free PMC Article

Incomplete and noisy network data as a percolation process.

Stumpf MP, Wiuf C.

J R Soc Interface. 2010 Oct 6;7(51):1411-9. doi: 10.1098/rsif.2010.0044. Epub 2010 Apr 8.

PMID:
20378609
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Toni T, Stumpf MP.

Bioinformatics. 2010 Jan 1;26(1):104-10. doi: 10.1093/bioinformatics/btp619. Epub 2009 Oct 29.

PMID:
19880371
[PubMed - indexed for MEDLINE]

Free PMC Article

The ABC of reverse engineering biological signalling systems.

Secrier M, Toni T, Stumpf MP.

Mol Biosyst. 2009 Dec;5(12):1925-35. doi: 10.1039/b908951a. Epub 2009 Sep 24.

PMID:
19798456
[PubMed - indexed for MEDLINE]

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

Huvet M, Toni T, Tan H, Jovanovic G, Engl C, Buck M, Stumpf MP.

Biochem Soc Trans. 2009 Aug;37(Pt 4):762-7. doi: 10.1042/BST0370762.

PMID:
19614590
[PubMed - indexed for MEDLINE]

Evolution of pathogenicity and sexual reproduction in eight Candida genomes.

Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S, Munro CA, Rheinbay E, Grabherr M, Forche A, Reedy JL, Agrafioti I, Arnaud MB, Bates S, Brown AJ, Brunke S, Costanzo MC, Fitzpatrick DA, de Groot PW, Harris D, Hoyer LL, Hube B, Klis FM, Kodira C, Lennard N, Logue ME, Martin R, Neiman AM, Nikolaou E, Quail MA, Quinn J, Santos MC, Schmitzberger FF, Sherlock G, Shah P, Silverstein KA, Skrzypek MS, Soll D, Staggs R, Stansfield I, Stumpf MP, Sudbery PE, Srikantha T, Zeng Q, Berman J, Berriman M, Heitman J, Gow NA, Lorenz MC, Birren BW, Kellis M, Cuomo CA.

Nature. 2009 Jun 4;459(7247):657-62. doi: 10.1038/nature08064.

PMID:
19465905
[PubMed - indexed for MEDLINE]

Free PMC Article

Evolving proteins at Darwin’s bicentenary.

Pinney JW, Stumpf MP.

Genome Biol. 2009;10(4):307. doi: 10.1186/gb-2009-10-4-307. Epub 2009 Apr 17.

PMID:
19435482
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Kirk PD, Stumpf MP.

Bioinformatics. 2009 May 15;25(10):1300-6. doi: 10.1093/bioinformatics/btp139. Epub 2009 Mar 16.

PMID:
19289448
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Toni T, Welch D, Strelkowa N, Ipsen A, Stumpf MP.

J R Soc Interface. 2009 Feb 6;6(31):187-202.

PMID:
19205079
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Ingram PJ, Stumpf MP, Stark J.

PLoS Comput Biol. 2008 Oct;4(10):e1000192. doi: 10.1371/journal.pcbi.1000192. Epub 2008 Oct 10.

PMID:
18846201
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Erguler K, Stumpf MP.

Math Biosci. 2008 Nov;216(1):90-9. doi: 10.1016/j.mbs.2008.08.012.

PMID:
18805431
[PubMed - indexed for MEDLINE]

Estimating the size of the human interactome.

Stumpf MP, Thorne T, de Silva E, Stewart R, An HJ, Lappe M, Wiuf C.

Proc Natl Acad Sci U S A. 2008 May 13;105(19):6959-64. doi: 10.1073/pnas.0708078105. Epub 2008 May 12.

PMID:
18474861
[PubMed - indexed for MEDLINE]

Free PMC Article

Parameter inference for biochemical systems that undergo a Hopf bifurcation.

Kirk PD, Toni T, Stumpf MP.

Biophys J. 2008 Jul;95(2):540-9. doi: 10.1529/biophysj.107.126086. Epub 2008 May 2.

PMID:
18456830
[PubMed - indexed for MEDLINE]

Free PMC Article

Generating confidence intervals on biological networks.

Thorne T, Stumpf MP.

BMC Bioinformatics. 2007 Nov 30;8:467.

PMID:
18053130
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Stumpf MP, Kelly WP, Thorne T, Wiuf C.

Trends Ecol Evol. 2007 Jul;22(7):366-73. Epub 2007 May 1. Review.

PMID:
17475365
[PubMed - indexed for MEDLINE]

SNPSTR: a database of compound microsatellite-SNP markers.

Agrafioti I, Stumpf MP.

Nucleic Acids Res. 2007 Jan;35(Database issue):D71-5.

PMID:
17202172
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Stumpf MP, Robertson BD, Duncan K, Young DB.

Prog Drug Res. 2007;64:1, 3-20. Review.

PMID:
17195469
[PubMed - indexed for MEDLINE]

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

de Silva E, Thorne T, Ingram P, Agrafioti I, Swire J, Wiuf C, Stumpf MP.

BMC Biol. 2006 Nov 3;4:39.

PMID:
17081312
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Thomas MG, Stumpf MP, Härke H.

Proc Biol Sci. 2006 Oct 22;273(1601):2651-7.

PMID:
17002951
[PubMed - indexed for MEDLINE]

Free PMC Article

Complex networks and simple models in biology.

de Silva E, Stumpf MP.

J R Soc Interface. 2005 Dec 22;2(5):419-30. Review.

PMID:
16849202
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Jovanovic G, Lloyd LJ, Stumpf MP, Mayhew AJ, Buck M.

J Biol Chem. 2006 Jul 28;281(30):21147-61. Epub 2006 May 17.

PMID:
16709570
[PubMed - indexed for MEDLINE]

Free Article

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

Stumpf MP, Wilkinson-Herbots HM.

Trends Ecol Evol. 2004 Apr;19(4):166-8.

PMID:
16701249
[PubMed]

A likelihood approach to analysis of network data.

Wiuf C, Brameier M, Hagberg O, Stumpf MP.

Proc Natl Acad Sci U S A. 2006 May 16;103(20):7566-70. Epub 2006 May 8.

PMID:
16682633
[PubMed - indexed for MEDLINE]

Free PMC Article

Network motifs: structure does not determine function.

Ingram PJ, Stumpf MP, Stark J.

BMC Genomics. 2006 May 5;7:108.

PMID:
16677373
[PubMed - indexed for MEDLINE]

Free PMC Article

Sampling properties of random graphs: the degree distribution.

Stumpf MP, Wiuf C.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Sep;72(3 Pt 2):036118. Epub 2005 Sep 19.

PMID:
16241526
[PubMed]

Ecology. Making sense of evolution in an uncertain world.

Jansen VA, Stumpf MP.

Science. 2005 Sep 23;309(5743):2005-7. No abstract available.

PMID:
16179463
[PubMed - indexed for MEDLINE]

Recombination hotspots as a point process.

De Iorio M, de Silva E, Stumpf MP.

Philos Trans R Soc Lond B Biol Sci. 2005 Aug 29;360(1460):1597-603.

PMID:
16096109
[PubMed - indexed for MEDLINE]

Free PMC Article

Introduction: genetic variation and human health.

Stumpf MP, Goldstein DB, Wood NW.

Philos Trans R Soc Lond B Biol Sci. 2005 Aug 29;360(1460):1539-41. No abstract available.

PMID:
16096101
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Both M, Csukai M, Stumpf MP, Spanu PD.

Plant Cell. 2005 Jul;17(7):2107-22. Epub 2005 Jun 10.

PMID:
15951491
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Kauppi L, Stumpf MP, Jeffreys AJ.

Genomics. 2005 Jul;86(1):13-24.

PMID:
15885980
[PubMed - indexed for MEDLINE]

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

Agrafioti I, Swire J, Abbott J, Huntley D, Butcher S, Stumpf MP.

BMC Evol Biol. 2005 Mar 18;5:23.

PMID:
15777474
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Stumpf MP, Wiuf C, May RM.

Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4221-4. Epub 2005 Mar 14.

PMID:
15767579
[PubMed]

Free PMC Article

The extent and importance of intragenic recombination.

de Silva E, Kelley LA, Stumpf MP.

Hum Genomics. 2004 Nov;1(6):410-20.

PMID:
15606996
[PubMed - indexed for MEDLINE]

Free PMC Article

HIV and the CCR5-Delta32 resistance allele.

de Silva E, Stumpf MP.

FEMS Microbiol Lett. 2004 Dec 1;241(1):1-12. Review.

PMID:
15556703
[PubMed - indexed for MEDLINE]

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

Stumpf MP.

Eur J Hum Genet. 2004 Jun;12(6):469-77.

PMID:
15026785
[PubMed - indexed for MEDLINE]

Free Article

Estimating recombination rates from population-genetic data.

Stumpf MP, McVean GA.

Nat Rev Genet. 2003 Dec;4(12):959-68. Review.

PMID:
14631356
[PubMed - indexed for MEDLINE]

Some notes on the combinatorial properties of haplotype tagging.

Wiuf C, Laidlaw Z, Stumpf MP.

Math Biosci. 2003 Oct;185(2):205-16.

PMID:
12941537
[PubMed - indexed for MEDLINE]

A Y chromosome census of the British Isles.

Capelli C, Redhead N, Abernethy JK, Gratrix F, Wilson JF, Moen T, Hervig T, Richards M, Stumpf MP, Underhill PA, Bradshaw P, Shaha A, Thomas MG, Bradman N, Goldstein DB.

Curr Biol. 2003 May 27;13(11):979-84.

PMID:
12781138
[PubMed - indexed for MEDLINE]

Free Article

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

Mead S, Stumpf MP, Whitfield J, Beck JA, Poulter M, Campbell T, Uphill JB, Goldstein D, Alpers M, Fisher EM, Collinge J.

Science. 2003 Apr 25;300(5619):640-3. Epub 2003 Apr 10.

PMID:
12690204
[PubMed - indexed for MEDLINE]

Free Article

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

Stumpf MP, Goldstein DB.

Curr Biol. 2003 Jan 8;13(1):1-8.

PMID:
12526738
[PubMed - indexed for MEDLINE]

Free Article

Herpes viruses hedge their bets.

Stumpf MP, Laidlaw Z, Jansen VA.

Proc Natl Acad Sci U S A. 2002 Nov 12;99(23):15234-7. Epub 2002 Oct 30.

PMID:
12409612
[PubMed - indexed for MEDLINE]

Free PMC Article

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

Stumpf MP, Pybus OG.

FEMS Microbiol Lett. 2002 Sep 10;214(2):143-52. Review.

PMID:
12351222
[PubMed - indexed for MEDLINE]

Haplotype diversity and the block structure of linkage disequilibrium.

Stumpf MP.

Trends Genet. 2002 May;18(5):226-8.

PMID:
12047937
[PubMed - indexed for MEDLINE]

Population genomics: ageing by association.

Pletcher SD, Stumpf MP.

Curr Biol. 2002 Apr 30;12(9):R328-30.

PMID:
12007435
[PubMed - indexed for MEDLINE]

Free Article

Theoretical models of sheep BSE reveal possibilities.

Krebs JR, May RM, Stumpf MP.

Nature. 2002 Jan 10;415(6868):115. No abstract available.

PMID:
11805805
[PubMed - indexed for MEDLINE]

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

Stumpf MP, Zitzmann N.

Proc Biol Sci. 2001 Oct 7;268(1480):1993-9.

PMID:
11571045
[PubMed - indexed for MEDLINE]

Free PMC Article

Genealogical and evolutionary inference with the human Y chromosome.

Stumpf MP, Goldstein DB.

Science. 2001 Mar 2;291(5509):1738-42. Review.

PMID:
11249819
[PubMed - indexed for MEDLINE]

Ecology. Species-area relations in tropical forests.

May RM, Stumpf MP.

Science. 2000 Dec 15;290(5499):2084-6.

PMID:
11187834
[PubMed - indexed for MEDLINE]

A predominantly indigenous paternal heritage for the Austronesian-speaking peoples of insular Southeast Asia and Oceania.

Capelli C, Wilson JF, Richards M, Stumpf MP, Gratrix F, Oppenheimer S, Underhill P, Pascali VL, Ko TM, Goldstein DB.

Am J Hum Genet. 2001 Feb;68(2):432-43. Epub 2001 Jan 22.

PMID:
11170891
[PubMed - indexed for MEDLINE]

Free PMC Article

Mapping the parameters of prion-induced neuropathology.

Stumpf MP, Krakauer DC.

Proc Natl Acad Sci U S A. 2000 Sep 12;97(19):10573-7.

PMID:
10962032
[PubMed - indexed for MEDLINE]

Free PMC Article