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Items: 1 to 50 of 143

1.

Quantifying Dynamic Regulation in Metabolic Pathways with Nonparametric Flux Inference.

He F, Stumpf MPH.

Biophys J. 2019 May 21;116(10):2035-2046. doi: 10.1016/j.bpj.2019.04.009. Epub 2019 Apr 19.

PMID:
31076100
2.

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

Chan TE, Stumpf MPH, Babtie AC.

Methods Mol Biol. 2019;1975:211-238. doi: 10.1007/978-1-4939-9224-9_10.

PMID:
31062312
3.

Proteolytic dynamics of human 20S thymoproteasome.

Kuckelkorn U, Stübler S, Textoris-Taube K, Kilian C, Niewienda A, Henklein P, Janek K, Stumpf MPH, Mishto M, Liepe J.

J Biol Chem. 2019 May 10;294(19):7740-7754. doi: 10.1074/jbc.RA118.007347. Epub 2019 Mar 26.

PMID:
30914481
4.

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

Dony L, He F, Stumpf MPH.

BMC Bioinformatics. 2019 Jan 25;20(1):52. doi: 10.1186/s12859-018-2590-7.

5.

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

Jetka T, Nienałtowski K, Filippi S, Stumpf MPH, Komorowski M.

Nat Commun. 2018 Nov 2;9(1):4591. doi: 10.1038/s41467-018-07085-1.

6.

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

Brackston RD, Wynn A, Stumpf MPH.

Phys Rev E. 2018 Aug;98(2-1):022136. doi: 10.1103/PhysRevE.98.022136.

7.

Transition state characteristics during cell differentiation.

Brackston RD, Lakatos E, Stumpf MPH.

PLoS Comput Biol. 2018 Sep 20;14(9):e1006405. doi: 10.1371/journal.pcbi.1006405. eCollection 2018 Sep.

8.

Biology challenging statistics.

Stumpf MPH.

Stat Appl Genet Mol Biol. 2018 Aug 30;17(4). pii: /j/sagmb.2018.17.issue-4/sagmb-2018-0048/sagmb-2018-0048.xml. doi: 10.1515/sagmb-2018-0048. No abstract available.

PMID:
30169328
9.

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

Dony L, Mackerodt J, Ward S, Filippi S, Stumpf MPH, Liepe J.

Bioinformatics. 2018 Apr 1;34(7):1249-1250. doi: 10.1093/bioinformatics/btx776.

10.

Stem Cell Differentiation as a Non-Markov Stochastic Process.

Stumpf PS, Smith RCG, Lenz M, Schuppert A, Müller FJ, Babtie A, Chan TE, Stumpf MPH, Please CP, Howison SD, Arai F, MacArthur BD.

Cell Syst. 2017 Sep 27;5(3):268-282.e7. doi: 10.1016/j.cels.2017.08.009.

11.

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

Chan TE, Stumpf MPH, Babtie AC.

Cell Syst. 2017 Sep 27;5(3):251-267.e3. doi: 10.1016/j.cels.2017.08.014.

12.

Control mechanisms for stochastic biochemical systems via computation of reachable sets.

Lakatos E, Stumpf MPH.

R Soc Open Sci. 2017 Aug 23;4(8):160790. doi: 10.1098/rsos.160790. eCollection 2017 Aug.

13.

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

MacLean AL, Smith MA, Liepe J, Sim A, Khorshed R, Rashidi NM, Scherf N, Krinner A, Roeder I, Lo Celso C, Stumpf MPH.

Stem Cells. 2017 Nov;35(11):2292-2304. doi: 10.1002/stem.2692. Epub 2017 Sep 24.

14.

How to deal with parameters for whole-cell modelling.

Babtie AC, Stumpf MPH.

J R Soc Interface. 2017 Aug;14(133). pii: 20170237. doi: 10.1098/rsif.2017.0237. Epub 2017 Aug 2. Review.

15.

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.

Lakatos E, Salehi-Reyhani A, Barclay M, Stumpf MPH, Klug DR.

PLoS One. 2017 May 10;12(5):e0177336. doi: 10.1371/journal.pone.0177336. eCollection 2017.

16.

Reconciling Epigenetic Memory and Transcriptional Responsiveness.

Fisher AG, Stumpf MPH, Merkenschlager M.

Cell Syst. 2017 Apr 26;4(4):373-374. doi: 10.1016/j.cels.2017.04.005.

17.

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).

Hansel TT, Tunstall T, Trujillo-Torralbo MB, Shamji B, Del-Rosario A, Dhariwal J, Kirk PDW, Stumpf MPH, Koopmann J, Telcian A, Aniscenko J, Gogsadze L, Bakhsoliani E, Stanciu L, Bartlett N, Edwards M, Walton R, Mallia P, Hunt TM, Hunt TL, Hunt DG, Westwick J, Edwards M, Kon OM, Jackson DJ, Johnston SL.

EBioMedicine. 2017 May;19:128-138. doi: 10.1016/j.ebiom.2017.03.033. Epub 2017 Mar 28.

18.

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

Dianzani C, Bellavista E, Liepe J, Verderio C, Martucci M, Santoro A, Chiocchetti A, Gigliotti CL, Boggio E, Ferrara B, Riganti L, Keller C, Janek K, Niewienda A, Fenoglio C, Sorosina M, Cantello R, Kloetzel PM, Stumpf MP, Paul F, Ruprecht K, Galimberti D, Martinelli Boneschi F, Comi C, Dianzani U, Mishto M.

Sci Rep. 2017 Mar 9;7:43718. doi: 10.1038/srep43718.

19.

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

Liepe J, Marino F, Sidney J, Jeko A, Bunting DE, Sette A, Kloetzel PM, Stumpf MP, Heck AJ, Mishto M.

Science. 2016 Oct 21;354(6310):354-358. Epub 2016 Oct 20.

20.

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

Ale A, Crepin VF, Collins JW, Constantinou N, Habibzay M, Babtie AC, Frankel G, Stumpf MPH.

Infect Immun. 2016 Dec 29;85(1). pii: e00606-16. doi: 10.1128/IAI.00606-16. Print 2017 Jan.

21.

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

MacLean AL, Lo Celso C, Stumpf MP.

Stem Cells. 2017 Jan;35(1):80-88. doi: 10.1002/stem.2508. Epub 2016 Oct 26. Review.

22.

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

Liepe J, Sim A, Weavers H, Ward L, Martin P, Stumpf MP.

Cell Syst. 2016 Jul;3(1):102-7. doi: 10.1016/j.cels.2016.06.002. Epub 2016 Jul 21.

23.

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

Weavers H, Liepe J, Sim A, Wood W, Martin P, Stumpf MPH.

Curr Biol. 2016 Aug 8;26(15):1975-1989. doi: 10.1016/j.cub.2016.06.012. Epub 2016 Jul 14.

24.

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

Vainieri ML, Blagborough AM, MacLean AL, Haltalli ML, Ruivo N, Fletcher HA, Stumpf MP, Sinden RE, Celso CL.

Open Biol. 2016 Jun;6(6). pii: 160038. doi: 10.1098/rsob.160038.

25.

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

Filippi S, Barnes CP, Kirk PD, Kudo T, Kunida K, McMahon SS, Tsuchiya T, Wada T, Kuroda S, Stumpf MP.

Cell Rep. 2016 Jun 14;15(11):2524-35. doi: 10.1016/j.celrep.2016.05.024. Epub 2016 Jun 2.

26.

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

Fan S, Geissmann Q, Lakatos E, Lukauskas S, Ale A, Babtie AC, Kirk PD, Stumpf MP.

Bioinformatics. 2016 Sep 15;32(18):2863-5. doi: 10.1093/bioinformatics/btw229. Epub 2016 May 5.

27.

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

Crowell HL, MacLean AL, Stumpf MP.

J Theor Biol. 2016 Jul 21;401:43-53. doi: 10.1016/j.jtbi.2016.04.002. Epub 2016 Apr 27.

28.

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

Smadbeck P, Stumpf MP.

J R Soc Interface. 2016 Apr;13(117). pii: 20160112. doi: 10.1098/rsif.2016.0112.

29.

A graph theoretical approach to data fusion.

Žurauskienė J, Kirk PD, Stumpf MP.

Stat Appl Genet Mol Biol. 2016 Apr;15(2):107-22. doi: 10.1515/sagmb-2016-0016.

30.

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

MacLean AL, Harrington HA, Stumpf MP, Byrne HM.

Methods Mol Biol. 2016;1386:405-39. doi: 10.1007/978-1-4939-3283-2_18. Review.

PMID:
26677193
31.

SYSTEMS BIOLOGY. Systems biology (un)certainties.

Kirk PD, Babtie AC, Stumpf MP.

Science. 2015 Oct 23;350(6259):386-8. doi: 10.1126/science.aac9505. No abstract available.

PMID:
26494748
32.

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

MacLean AL, Kirk PD, Stumpf MP.

Biol Open. 2015 Oct 9;4(11):1420-6. doi: 10.1242/bio.013714.

33.

Inference of random walk models to describe leukocyte migration.

Jones PJ, Sim A, Taylor HB, Bugeon L, Dallman MJ, Pereira B, Stumpf MP, Liepe J.

Phys Biol. 2015 Sep 25;12(6):066001. doi: 10.1088/1478-3975/12/6/066001.

34.

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

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

Elife. 2015 Sep 22;4:e07545. doi: 10.7554/eLife.07545.

35.

Multivariate moment closure techniques for stochastic kinetic models.

Lakatos E, Ale A, Kirk PD, Stumpf MP.

J Chem Phys. 2015 Sep 7;143(9):094107. doi: 10.1063/1.4929837.

36.

Information processing by simple molecular motifs and susceptibility to noise.

Mc Mahon SS, Lenive O, Filippi S, Stumpf MP.

J R Soc Interface. 2015 Sep 6;12(110):0597. doi: 10.1098/rsif.2015.0597.

37.

Great cities look small.

Sim A, Yaliraki SN, Barahona M, Stumpf MP.

J R Soc Interface. 2015 Aug 6;12(109):20150315. doi: 10.1098/rsif.2015.0315.

38.

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

Sim A, Liepe J, Stumpf MP.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Apr;91(4):042115. Epub 2015 Apr 15.

PMID:
25974447
39.

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

Jovanovic G, Sheng X, Ale A, Feliu E, Harrington HA, Kirk P, Wiuf C, Buck M, Stumpf MP.

Mol Biosyst. 2015 May;11(5):1348-59. doi: 10.1039/c4mb00720d.

PMID:
25797699
40.

Topological sensitivity analysis for systems biology.

Babtie AC, Kirk P, Stumpf MP.

Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18507-12. doi: 10.1073/pnas.1414026112. Epub 2014 Dec 15.

41.

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

MacLean AL, Harrington HA, Stumpf MPH, Hansen MDH.

Biomedicines. 2014 Dec 9;2(4):384-402. doi: 10.3390/biomedicines2040384.

42.

SYSBIONS: nested sampling for systems biology.

Johnson R, Kirk P, Stumpf MP.

Bioinformatics. 2015 Feb 15;31(4):604-5. doi: 10.1093/bioinformatics/btu675. Epub 2014 Oct 16.

43.

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 Dec;44(12):3508-21. doi: 10.1002/eji.201444902. Epub 2014 Nov 20.

44.

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.

45.

Approximate Bayesian inference for complex ecosystems.

Stumpf MP.

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

46.

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. Review.

47.

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;35:98-108. doi: 10.1016/j.semcdb.2014.06.011. Epub 2014 Jun 19. Review.

PMID:
24953199
48.

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.

49.

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.

50.

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.

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