Published in Biophys J on April 16, 2013
Simplifying biochemical models with intermediate species. J R Soc Interface (2013) 0.99
Parameter-free methods distinguish Wnt pathway models and guide design of experiments. Proc Natl Acad Sci U S A (2015) 0.93
Nuclear to cytoplasmic shuttling of ERK promotes differentiation of muscle stem/progenitor cells. Development (2014) 0.92
Catalytic constants enable the emergence of bistability in dual phosphorylation. J R Soc Interface (2014) 0.80
Long-term dynamics of multisite phosphorylation. Mol Biol Cell (2016) 0.79
Finding the positive feedback loops underlying multi-stationarity. BMC Syst Biol (2015) 0.78
Robustness of MEK-ERK Dynamics and Origins of Cell-to-Cell Variability in MAPK Signaling. Cell Rep (2016) 0.77
The effect of site-to-site variability in ultrasensitive dose responses. J Math Biol (2016) 0.75
The role of the Hes1 crosstalk hub in Notch-Wnt interactions of the intestinal crypt. PLoS Comput Biol (2017) 0.75
Core signalling motif displaying multistability through multi-state enzymes. J R Soc Interface (2016) 0.75
Spatial Control of Biochemical Modification Cascades and Pathways. Biophys J (2015) 0.75
An amplified sensitivity arising from covalent modification in biological systems. Proc Natl Acad Sci U S A (1981) 10.04
Multistability in the lactose utilization network of Escherichia coli. Nature (2004) 7.71
Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades. J Cell Biol (2004) 5.02
Cellular decision making and biological noise: from microbes to mammals. Cell (2011) 4.44
Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm. PLoS Comput Biol (2010) 3.65
Signalling ballet in space and time. Nat Rev Mol Cell Biol (2010) 3.32
Mechanistic studies of the dual phosphorylation of mitogen-activated protein kinase. J Biol Chem (1997) 3.09
Information transduction capacity of noisy biochemical signaling networks. Science (2011) 2.95
Dynamics of the Ras/ERK MAPK cascade as monitored by fluorescent probes. J Biol Chem (2006) 2.73
Ultrasensitivity in biochemical systems controlled by covalent modification. Interplay between zero-order and multistep effects. J Biol Chem (1984) 2.59
Unlimited multistability in multisite phosphorylation systems. Nature (2009) 2.57
Cell fate decisions are specified by the dynamic ERK interactome. Nat Cell Biol (2009) 2.23
Rapid and sustained nuclear-cytoplasmic ERK oscillations induced by epidermal growth factor. Mol Syst Biol (2009) 2.10
Bistability and oscillations in the Huang-Ferrell model of MAPK signaling. PLoS Comput Biol (2007) 1.93
A mechanism for the evolution of phosphorylation sites. Cell (2011) 1.47
Dynamic regulation of ERK2 nuclear translocation and mobility in living cells. J Cell Sci (2006) 1.44
On the number of steady states in a multiple futile cycle. J Math Biol (2007) 1.39
ERK nuclear translocation is dimerization-independent but controlled by the rate of phosphorylation. J Biol Chem (2009) 1.31
Spatial positive feedback at the onset of mitosis. Cell (2012) 1.26
Enzyme-sharing as a cause of multi-stationarity in signalling systems. J R Soc Interface (2011) 1.12
Four-dimensional dynamics of MAPK information processing systems. Wiley Interdiscip Rev Syst Biol Med (2010) 1.06
Mathematical modeling reveals the functional implications of the different nuclear shuttling rates of Erk1 and Erk2. Phys Biol (2012) 0.87
Sensitivity control through attenuation of signal transfer efficiency by negative regulation of cellular signalling. Nat Commun (2012) 0.87
Sensitivity analysis predicts that the ERK-pMEK interaction regulates ERK nuclear translocation. IET Syst Biol (2009) 0.87
Trafficking motifs as the basis for two-compartment signaling systems to form multiple stable states. Biophys J (2011) 0.85
Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems. J R Soc Interface (2009) 6.08
Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature (2009) 5.90
Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Res (2006) 4.70
Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science (2003) 4.48
Diagnostic and prognostic microRNAs in stage II colon cancer. Cancer Res (2008) 4.20
Subnets of scale-free networks are not scale-free: sampling properties of networks. Proc Natl Acad Sci U S A (2005) 3.75
Estimating the size of the human interactome. Proc Natl Acad Sci U S A (2008) 3.66
Balancing selection at the prion protein gene consistent with prehistoric kurulike epidemics. Science (2003) 3.59
Monitoring endangered freshwater biodiversity using environmental DNA. Mol Ecol (2011) 3.45
Identification of endogenous retroviral reading frames in the human genome. Retrovirology (2004) 2.58
Simulation-based model selection for dynamical systems in systems and population biology. Bioinformatics (2009) 2.27
Assessing the fidelity of ancient DNA sequences amplified from nuclear genes. Genetics (2005) 2.21
Common variants at VRK2 and TCF4 conferring risk of schizophrenia. Hum Mol Genet (2011) 2.21
Network motifs: structure does not determine function. BMC Genomics (2006) 2.01
Frequent occurrence of uniparental disomy in colorectal cancer. Carcinogenesis (2006) 1.99
Model criticism based on likelihood-free inference, with an application to protein network evolution. Proc Natl Acad Sci U S A (2009) 1.89
A Y chromosome census of the British Isles. Curr Biol (2003) 1.84
ABC-SysBio--approximate Bayesian computation in Python with GPU support. Bioinformatics (2010) 1.76
Long-term persistence of bacterial DNA. Curr Biol (2004) 1.70
Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data. Bioinformatics (2009) 1.68
SOX4 expression in bladder carcinoma: clinical aspects and in vitro functional characterization. Cancer Res (2006) 1.66
Managing membrane stress: the phage shock protein (Psp) response, from molecular mechanisms to physiology. FEMS Microbiol Rev (2010) 1.65
A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays. BMC Bioinformatics (2007) 1.65
Comprehensive genome methylation analysis in bladder cancer: identification and validation of novel methylated genes and application of these as urinary tumor markers. Clin Cancer Res (2011) 1.46
Perturbation of fetal liver hematopoietic stem and progenitor cell development by trisomy 21. Proc Natl Acad Sci U S A (2012) 1.46
Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments. Genetics (2006) 1.44
Maximizing the information content of experiments in systems biology. PLoS Comput Biol (2013) 1.43
Sensitivity, robustness, and identifiability in stochastic chemical kinetics models. Proc Natl Acad Sci U S A (2011) 1.43
Induction and function of the phage shock protein extracytoplasmic stress response in Escherichia coli. J Biol Chem (2006) 1.37
The effects of incomplete protein interaction data on structural and evolutionary inferences. BMC Biol (2006) 1.36
Practical limits for reverse engineering of dynamical systems: a statistical analysis of sensitivity and parameter inferability in systems biology models. Mol Biosyst (2011) 1.35
High-density single nucleotide polymorphism array defines novel stage and location-dependent allelic imbalances in human bladder tumors. Cancer Res (2005) 1.34
Development of a hypoxia gene expression classifier with predictive impact for hypoxic modification of radiotherapy in head and neck cancer. Cancer Res (2011) 1.33
Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H. pylori and P. falciparum. PLoS Comput Biol (2007) 1.33
Genotyping and annotation of Affymetrix SNP arrays. Nucleic Acids Res (2006) 1.31
Simulating haplotype blocks in the human genome. Bioinformatics (2003) 1.31
Model selection in systems and synthetic biology. Curr Opin Biotechnol (2013) 1.30
Ab initio identification of human microRNAs based on structure motifs. BMC Bioinformatics (2007) 1.27
Role of activating fibroblast growth factor receptor 3 mutations in the development of bladder tumors. Clin Cancer Res (2005) 1.25
The ABC of reverse engineering biological signalling systems. Mol Biosyst (2009) 1.24
An algebraic approach to signaling cascades with N layers. Bull Math Biol (2011) 1.23
Haplotype diversity and the block structure of linkage disequilibrium. Trends Genet (2002) 1.23
Comparative analysis of the Saccharomyces cerevisiae and Caenorhabditis elegans protein interaction networks. BMC Evol Biol (2005) 1.23
Statistical inference of the time-varying structure of gene-regulation networks. BMC Syst Biol (2010) 1.22
Genome-wide scans using archived neonatal dried blood spot samples. BMC Genomics (2009) 1.20
Complex networks and simple models in biology. J R Soc Interface (2005) 1.19
Decomposing noise in biochemical signaling systems highlights the role of protein degradation. Biophys J (2013) 1.18
GPU accelerated biochemical network simulation. Bioinformatics (2011) 1.15
Estimation of tumor heterogeneity using CGH array data. BMC Bioinformatics (2009) 1.14
A general moment expansion method for stochastic kinetic models. J Chem Phys (2013) 1.13
Importance sampling for the infinite sites model. Stat Appl Genet Mol Biol (2008) 1.13
Enzyme-sharing as a cause of multi-stationarity in signalling systems. J R Soc Interface (2011) 1.12
Sampling properties of random graphs: the degree distribution. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 1.11
Gene expression profiles of Blumeria graminis indicate dynamic changes to primary metabolism during development of an obligate biotrophic pathogen. Plant Cell (2005) 1.11
Evidence for an apartheid-like social structure in early Anglo-Saxon England. Proc Biol Sci (2006) 1.10
Co-clustering and visualization of gene expression data and gene ontology terms for Saccharomyces cerevisiae using self-organizing maps. J Biomed Inform (2006) 1.07
A likelihood approach to analysis of network data. Proc Natl Acad Sci U S A (2006) 1.07
Evolution at the system level: the natural history of protein interaction networks. Trends Ecol Evol (2007) 1.07
Quality assessment of DNA derived from up to 30 years old formalin fixed paraffin embedded (FFPE) tissue for PCR-based methylation analysis using SMART-MSP and MS-HRM. BMC Cancer (2009) 1.06
Bayesian design of synthetic biological systems. Proc Natl Acad Sci U S A (2011) 1.05
Germline mutation in RNASEL predicts increased risk of head and neck, uterine cervix and breast cancer. PLoS One (2008) 1.04
Localized breakdown in linkage disequilibrium does not always predict sperm crossover hot spots in the human MHC class II region. Genomics (2005) 1.03
Gene expression classifier predicts for hypoxic modification of radiotherapy with nimorazole in squamous cell carcinomas of the head and neck. Radiother Oncol (2011) 1.02
HIV and the CCR5-Delta32 resistance allele. FEMS Microbiol Lett (2004) 1.02
A bimodular mechanism of calcium control in eukaryotes. Nature (2012) 1.02
Clonal evolution in t(14;18)-positive follicular lymphoma, evidence for multiple common pathways, and frequent parallel clonal evolution. Clin Cancer Res (2008) 1.01
Variable elimination in post-translational modification reaction networks with mass-action kinetics. J Math Biol (2012) 1.00
Designing attractive models via automated identification of chaotic and oscillatory dynamical regimes. Nat Commun (2011) 1.00
Simplifying biochemical models with intermediate species. J R Soc Interface (2013) 0.99
Nonidentifiability of the source of intrinsic noise in gene expression from single-burst data. PLoS Comput Biol (2008) 0.99
Parameter inference for biochemical systems that undergo a Hopf bifurcation. Biophys J (2008) 0.99
Bayesian design strategies for synthetic biology. Interface Focus (2011) 0.99
Tumor heterogeneity in neoplasms of breast, colon, and skin. BMC Res Notes (2010) 0.97
The association between genetic variants in hMLH1 and hMSH2 and the development of sporadic colorectal cancer in the Danish population. BMC Med Genet (2008) 0.97
Omics-based profiling of carcinoma of the breast and matched regional lymph node metastasis. Proteomics (2008) 0.95
Elucidating the in vivo phosphorylation dynamics of the ERK MAP kinase using quantitative proteomics data and Bayesian model selection. Mol Biosyst (2012) 0.95
Graph spectral analysis of protein interaction network evolution. J R Soc Interface (2012) 0.94
Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis. BMC Genomics (2011) 0.94
Optimizing threshold-schedules for sequential approximate Bayesian computation: applications to molecular systems. Stat Appl Genet Mol Biol (2013) 0.93
Plasma proteome analysis in HTLV-1-associated myelopathy/tropical spastic paraparesis. Retrovirology (2011) 0.91
On optimality of kernels for approximate Bayesian computation using sequential Monte Carlo. Stat Appl Genet Mol Biol (2013) 0.91
Generating confidence intervals on biological networks. BMC Bioinformatics (2007) 0.91
The genealogy, site frequency spectrum and ages of two nested mutant alleles. Theor Popul Biol (2009) 0.91
Proteasome isoforms exhibit only quantitative differences in cleavage and epitope generation. Eur J Immunol (2014) 0.91
Understanding protein-protein interactions using local structural features. J Mol Biol (2013) 0.90
Short tandem repeats in human exons: a target for disease mutations. BMC Genomics (2008) 0.90
Phosphorelays provide tunable signal processing capabilities for the cell. PLoS Comput Biol (2013) 0.90
Increased cell motility and invasion upon knockdown of lipolysis stimulated lipoprotein receptor (LSR) in SW780 bladder cancer cells. BMC Med Genomics (2008) 0.89
Parameter-free model discrimination criterion based on steady-state coplanarity. Proc Natl Acad Sci U S A (2012) 0.88
Modelling the contribution of family history and variation in single nucleotide polymorphisms to risk of schizophrenia: a Danish national birth cohort-based study. Schizophr Res (2011) 0.87
Mathematical modeling reveals the functional implications of the different nuclear shuttling rates of Erk1 and Erk2. Phys Biol (2012) 0.87
Population dynamics of normal and leukaemia stem cells in the haematopoietic stem cell niche show distinct regimes where leukaemia will be controlled. J R Soc Interface (2013) 0.87
Recombination hotspots as a point process. Philos Trans R Soc Lond B Biol Sci (2005) 0.87
Nitrogen and carbon status are integrated at the transcriptional level by the nitrogen regulator NtrC in vivo. MBio (2013) 0.87
A computational method to preclude multistationarity in networks of interacting species. Bioinformatics (2013) 0.86
The extent and importance of intragenic recombination. Hum Genomics (2004) 0.86
Exact analysis of intrinsic qualitative features of phosphorelays using mathematical models. J Theor Biol (2012) 0.85