Paul DW Kirk
Paul DW Kirk
Verified email at mrc-bsu.cam.ac.uk - Homepage
Title
Cited by
Cited by
Year
A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation
J Liepe, P Kirk, S Filippi, T Toni, CP Barnes, MPH Stumpf
Nature protocols 9 (2), 439-456, 2014
1682014
ABC-SysBio—approximate Bayesian computation in Python with GPU support
J Liepe, C Barnes, E Cule, K Erguler, P Kirk, T Toni, MPH Stumpf
Bioinformatics 26 (14), 1797-1799, 2010
1632010
Bayesian correlated clustering to integrate multiple datasets
P Kirk, JE Griffin, RS Savage, Z Ghahramani, DL Wild
Bioinformatics 28 (24), 3290-3297, 2012
1572012
Model selection in systems and synthetic biology
P Kirk, T Thorne, MPH Stumpf
Current opinion in biotechnology 24 (4), 767-774, 2013
1032013
Topological sensitivity analysis for systems biology
AC Babtie, P Kirk, MPH Stumpf
Proceedings of the National Academy of Sciences 111 (52), 18507-18512, 2014
842014
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
MP Menden, D Wang, MJ Mason, B Szalai, KC Bulusu, Y Guan, T Yu, ...
Nature communications 10 (1), 1-17, 2019
83*2019
Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data
PDW Kirk, MPH Stumpf
Bioinformatics 25 (10), 1300-1306, 2009
812009
Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach
P Meyer, T Cokelaer, D Chandran, KH Kim, PR Loh, G Tucker, M Lipson, ...
BMC systems biology 8 (1), 13, 2014
742014
A general moment expansion method for stochastic kinetic models
A Ale, P Kirk, MPH Stumpf
The Journal of chemical physics 138 (17), 174101, 2013
702013
Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements
EJ Cooke, RS Savage, PDW Kirk, R Darkins, DL Wild
BMC bioinformatics 12 (1), 399, 2011
662011
Systems biology (un) certainties
PDW Kirk, AC Babtie, MPH Stumpf
Science 350 (6259), 386-388, 2015
652015
Multivariate moment closure techniques for stochastic kinetic models
E Lakatos, A Ale, PDW Kirk, MPH Stumpf
The Journal of chemical physics 143 (9), 094107, 2015
562015
A comprehensive evaluation of nasal and bronchial cytokines and chemokines following experimental rhinovirus infection in allergic asthma: increased interferons (IFN-γ and IFN …
TT Hansel, T Tunstall, MB Trujillo-Torralbo, B Shamji, A Del-Rosario, ...
EBioMedicine 19, 128-138, 2017
552017
Model selection in systems biology depends on experimental design
D Silk, PDW Kirk, CP Barnes, T Toni, MPH Stumpf
PLoS Comput Biol 10 (6), e1003650, 2014
492014
Robustness of MEK-ERK dynamics and origins of cell-to-cell variability in MAPK signaling
S Filippi, CP Barnes, PDW Kirk, T Kudo, K Kunida, SS McMahon, ...
Cell reports 15 (11), 2524-2535, 2016
392016
Robustness of MEK-ERK dynamics and origins of cell-to-cell variability in MAPK signaling
S Filippi, CP Barnes, PDW Kirk, T Kudo, K Kunida, SS McMahon, ...
Cell reports 15 (11), 2524-2535, 2016
392016
Designing attractive models via automated identification of chaotic and oscillatory dynamical regimes
D Silk, PDW Kirk, CP Barnes, T Toni, A Rose, S Moon, MJ Dallman, ...
Nature communications 2 (1), 1-6, 2011
312011
Parameter inference for biochemical systems that undergo a Hopf bifurcation
PDW Kirk, T Toni, MPH Stumpf
Biophysical journal 95 (2), 540-549, 2008
312008
Elucidating the in vivo phosphorylation dynamics of the ERK MAP kinase using quantitative proteomics data and Bayesian model selection
T Toni, Y Ozaki, P Kirk, S Kuroda, MPH Stumpf
Molecular BioSystems 8 (7), 1921-1929, 2012
272012
SYSBIONS: nested sampling for systems biology
R Johnson, P Kirk, MPH Stumpf
Bioinformatics 31 (4), 604-605, 2015
212015
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