Published in IEEE/ACM Trans Comput Biol Bioinform on October 19, 2006
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics (2006) 7.53
Modeling molecular regulatory networks with JigCell and PET. Methods Mol Biol (2009) 0.83
Web-based applications for building, managing and analysing kinetic models of biological systems. Brief Bioinform (2008) 0.82
Model aggregation: a building-block approach to creating large macromolecular regulatory networks. Bioinformatics (2009) 0.81
Model composition for macromolecular regulatory networks. IEEE/ACM Trans Comput Biol Bioinform (2010) 0.80
Integrative analysis of cell cycle control in budding yeast. Mol Biol Cell (2004) 4.77
Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts. Proc Natl Acad Sci U S A (2002) 4.58
Design principles of biochemical oscillators. Nat Rev Mol Cell Biol (2008) 4.55
Steady states and oscillations in the p53/Mdm2 network. Cell Cycle (2005) 2.45
A model for restriction point control of the mammalian cell cycle. J Theor Biol (2004) 1.86
Analysis of a generic model of eukaryotic cell-cycle regulation. Biophys J (2006) 1.86
Irreversible cell-cycle transitions are due to systems-level feedback. Nat Cell Biol (2007) 1.68
Modeling networks of coupled enzymatic reactions using the total quasi-steady state approximation. PLoS Comput Biol (2007) 1.58
A systematic review of studies on forecasting the dynamics of influenza outbreaks. Influenza Other Respir Viruses (2013) 1.56
Mathematical modeling as a tool for investigating cell cycle control networks. Methods (2007) 1.55
Endoplasmic reticulum stress, the unfolded protein response, autophagy, and the integrated regulation of breast cancer cell fate. Cancer Res (2012) 1.47
Exploring the roles of noise in the eukaryotic cell cycle. Proc Natl Acad Sci U S A (2009) 1.46
Stochastic exit from mitosis in budding yeast: model predictions and experimental observations. Cell Cycle (2011) 1.46
Bifurcation analysis of a model of the budding yeast cell cycle. Chaos (2004) 1.38
Exploring mechanisms of the DNA-damage response: p53 pulses and their possible relevance to apoptosis. Cell Cycle (2007) 1.37
A model of yeast cell-cycle regulation based on multisite phosphorylation. Mol Syst Biol (2010) 1.33
Mathematical model of the morphogenesis checkpoint in budding yeast. J Cell Biol (2003) 1.33
Bistability by multiple phosphorylation of regulatory proteins. Prog Biophys Mol Biol (2009) 1.28
Another turn for p53. Mol Syst Biol (2006) 1.19
A mathematical model for the reciprocal differentiation of T helper 17 cells and induced regulatory T cells. PLoS Comput Biol (2011) 1.18
the JigCell model builder and run manager. Bioinformatics (2004) 1.17
Dynamical modeling of syncytial mitotic cycles in Drosophila embryos. Mol Syst Biol (2007) 1.14
A quantitative study of the division cycle of Caulobacter crescentus stalked cells. PLoS Comput Biol (2007) 1.13
Antagonism and bistability in protein interaction networks. J Theor Biol (2007) 1.11
Computational analysis of dynamical responses to the intrinsic pathway of programmed cell death. Biophys J (2009) 1.11
A proposal for robust temperature compensation of circadian rhythms. Proc Natl Acad Sci U S A (2007) 1.11
Stochastic simulation of enzyme-catalyzed reactions with disparate timescales. Biophys J (2008) 1.10
Reverse engineering dynamic temporal models of biological processes and their relationships. Proc Natl Acad Sci U S A (2010) 1.09
Graphical models of residue coupling in protein families. IEEE/ACM Trans Comput Biol Bioinform (2008) 1.07
Photosynthetic acclimation is reflected in specific patterns of gene expression in drought-stressed loblolly pine. Plant Physiol (2003) 1.07
Parameter estimation for a mathematical model of the cell cycle in frog eggs. J Comput Biol (2005) 1.04
System-level feedbacks make the anaphase switch irreversible. Proc Natl Acad Sci U S A (2011) 1.03
Temporal controls of the asymmetric cell division cycle in Caulobacter crescentus. PLoS Comput Biol (2009) 1.03
Modelling the fission yeast cell cycle. Brief Funct Genomic Proteomic (2004) 1.02
Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation. Mol Syst Biol (2009) 1.01
Modeling the septation initiation network (SIN) in fission yeast cells. Curr Genet (2007) 1.01
Network topologies and dynamics leading to endotoxin tolerance and priming in innate immune cells. PLoS Comput Biol (2012) 1.00
Transcriptional response of Saccharomyces cerevisiae to desiccation and rehydration. Appl Environ Microbiol (2005) 1.00
Spatial controls for growth zone formation during the fission yeast cell cycle. Yeast (2008) 0.98
Endoplasmic reticulum stress, the unfolded protein response, and gene network modeling in antiestrogen resistant breast cancer. Horm Mol Biol Clin Investig (2011) 0.97
A simple theoretical framework for understanding heterogeneous differentiation of CD4+ T cells. BMC Syst Biol (2012) 0.97
Modeling temporal relationships in large scale clinical associations. J Am Med Inform Assoc (2012) 0.95
A hybrid model of mammalian cell cycle regulation. PLoS Comput Biol (2011) 0.95
Cycling without the cyclosome: modeling a yeast strain lacking the APC. Cell Cycle (2004) 0.93
Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model. BMC Syst Biol (2013) 0.93
Molecular mechanisms creating bistable switches at cell cycle transitions. Open Biol (2013) 0.92
Graphical models of protein-protein interaction specificity from correlated mutations and interaction data. Proteins (2009) 0.92
Monitoring p53's pulse. Nat Genet (2004) 0.91
Connecting the dots between PubMed abstracts. PLoS One (2012) 0.91
Regulated protein kinases and phosphatases in cell cycle decisions. Curr Opin Cell Biol (2010) 0.91
Oscillatory dynamics of cell cycle proteins in single yeast cells analyzed by imaging cytometry. PLoS One (2011) 0.90
Modeling the estrogen receptor to growth factor receptor signaling switch in human breast cancer cells. FEBS Lett (2013) 0.90
Modeling regulatory networks at Virginia Tech. OMICS (2003) 0.88
System-level feedbacks control cell cycle progression. FEBS Lett (2009) 0.88
Differential expression of heat shock protein genes in preconditioning for photosynthetic acclimation in water-stressed loblolly pine. Plant Physiol Biochem (2010) 0.88
Describing the relationship between cat bites and human depression using data from an electronic health record. PLoS One (2013) 0.87
Rewiring the exit from mitosis. Cell Cycle (2005) 0.86
A kinetic model of the cyclin E/Cdk2 developmental timer in Xenopus laevis embryos. Biophys Chem (2003) 0.86
Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle. J Chem Phys (2012) 0.85
Multistate Model Builder (MSMB): a flexible editor for compact biochemical models. BMC Syst Biol (2014) 0.85
Clustering mass spectrometry data using order statistics. Proteomics (2003) 0.85
Cell cycle control in bacteria and yeast: a case of convergent evolution? Cell Cycle (2006) 0.85
Studying the functional genomics of stress responses in loblolly pine with the Expresso microarray experiment management system. Comp Funct Genomics (2002) 0.85
Protein design by sampling an undirected graphical model of residue constraints. IEEE/ACM Trans Comput Biol Bioinform (2009) 0.84
Quantitative prediction of the effect of genetic variation using hidden Markov models. BMC Bioinformatics (2014) 0.83
Modeling molecular regulatory networks with JigCell and PET. Methods Mol Biol (2009) 0.83
A mathematical model of mitotic exit in budding yeast: the role of Polo kinase. PLoS One (2012) 0.82
Periodic forcing of a mathematical model of the eukaryotic cell cycle. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 0.82
Reverse engineering models of cell cycle regulation. Adv Exp Med Biol (2008) 0.82
Model aggregation: a building-block approach to creating large macromolecular regulatory networks. Bioinformatics (2009) 0.81
Potential role of a bistable histidine kinase switch in the asymmetric division cycle of Caulobacter crescentus. PLoS Comput Biol (2013) 0.81
Validation and estimation of parameters for a general probabilistic model of the PCR process. J Comput Biol (2007) 0.80
Model composition for macromolecular regulatory networks. IEEE/ACM Trans Comput Biol Bioinform (2010) 0.80
Stiffness detection and reduction in discrete stochastic simulation of biochemical systems. J Chem Phys (2011) 0.80
Analysis of the fitness effect of compensatory mutations. HFSP J (2008) 0.79
Synchronization of eukaryotic cells by periodic forcing. Phys Rev Lett (2006) 0.79
Minimal models for cell-cycle control based on competitive inhibition and multisite phosphorylations of Cdk substrates. Biophys J (2013) 0.78
Note on the computation of critical effective population sizes. J Comput Biol (2007) 0.78
Simultaneously segmenting multiple gene expression time courses by analyzing cluster dynamics. J Bioinform Comput Biol (2009) 0.78
Mathematical models of the transitions between endocrine therapy responsive and resistant states in breast cancer. J R Soc Interface (2014) 0.78
Measurement and modeling of transcriptional noise in the cell cycle regulatory network. Cell Cycle (2013) 0.77
Adaptive aggregation method for the Chemical Master Equation. Int J Comput Biol Drug Des (2009) 0.77
A Mathematical Framework for Understanding Four-Dimensional Heterogeneous Differentiation of CD4+ T Cells. Bull Math Biol (2015) 0.77
Top-down network analysis to drive bottom-up modeling of physiological processes. J Comput Biol (2013) 0.77