Published in Cell on March 05, 2010
Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators. Nat Biotechnol (2012) 3.65
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics (2010) 3.42
Encoding and decoding cellular information through signaling dynamics. Cell (2013) 2.96
General properties of transcriptional time series in Escherichia coli. Nat Genet (2011) 2.76
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther (2013) 2.64
Resolution of gene regulatory conflicts caused by combinations of antibiotics. Mol Cell (2011) 1.65
Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole. Mol Syst Biol (2011) 1.51
Defining principles of combination drug mechanisms of action. Proc Natl Acad Sci U S A (2012) 1.19
Global cellular response to chemotherapy-induced apoptosis. Elife (2013) 1.19
Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization. Nat Protoc (2013) 1.18
Mechanism-independent method for predicting response to multidrug combinations in bacteria. Proc Natl Acad Sci U S A (2012) 1.17
Quantitative profiling of caspase-cleaved substrates reveals different drug-induced and cell-type patterns in apoptosis. Proc Natl Acad Sci U S A (2012) 1.02
CDA: combinatorial drug discovery using transcriptional response modules. PLoS One (2012) 1.01
Perturbation biology: inferring signaling networks in cellular systems. PLoS Comput Biol (2013) 1.00
Models of signalling networks - what cell biologists can gain from them and give to them. J Cell Sci (2013) 0.99
Pairwise network mechanisms in the host signaling response to coxsackievirus B3 infection. Proc Natl Acad Sci U S A (2010) 0.97
Efficient discovery of anti-inflammatory small-molecule combinations using evolutionary computing. Nat Chem Biol (2011) 0.97
High-throughput, single-cell NF-κB dynamics. Curr Opin Genet Dev (2010) 0.96
Dynamic proteomics of human protein level and localization across the cell cycle. PLoS One (2012) 0.92
Exploring drug combinations in genetic interaction network. BMC Bioinformatics (2012) 0.91
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The drug cocktail network. BMC Syst Biol (2012) 0.88
Metabolomic high-content nuclear magnetic resonance-based drug screening of a kinase inhibitor library. Nat Commun (2011) 0.88
Chemogenomics and orthology-based design of antibiotic combination therapies. Mol Syst Biol (2016) 0.85
Linear superposition and prediction of bacterial promoter activity dynamics in complex conditions. PLoS Comput Biol (2014) 0.83
Time-resolved in silico modeling of fine-tuned cAMP signaling in platelets: feedback loops, titrated phosphorylations and pharmacological modulation. BMC Syst Biol (2011) 0.83
A streamlined search technology for identification of synergistic drug combinations. Sci Rep (2015) 0.81
Multiscale models of cell signaling. Ann Biomed Eng (2012) 0.80
Paring down signaling complexity. Nat Biotechnol (2010) 0.78
Quantification of Interactions between Dynamic Cellular Network Functionalities by Cascaded Layering. PLoS Comput Biol (2015) 0.78
Pairwise interactions and the battle against combinatorics in multidrug therapies. Proc Natl Acad Sci U S A (2016) 0.78
Modeling the zebrafish segmentation clock's gene regulatory network constrained by expression data suggests evolutionary transitions between oscillating and nonoscillating transcription. Genetics (2014) 0.77
Drug discovery: engineering drug combinations. Nat Chem Biol (2010) 0.77
A dynamic plasma membrane proteome analysis of alcohol-induced liver cirrhosis. Proteome Sci (2012) 0.76
Epigenetic polypharmacology: from combination therapy to multitargeted drugs. Clin Epigenetics (2016) 0.76
TNF-insulin crosstalk at the transcription factor GATA6 is revealed by a model that links signaling and transcriptomic data tensors. Sci Signal (2016) 0.76
Dynamic proteomics reveals bimodal protein dynamics of cancer cells in response to HSP90 inhibitor. BMC Syst Biol (2017) 0.75
Systems Biology of Immunomodulation for Post-Stroke Neuroplasticity: Multimodal Implications of Pharmacotherapy and Neurorehabilitation. Front Neurol (2016) 0.75
Discovering anti-platelet drug combinations with an integrated model of activator-inhibitor relationships, activator-activator synergies and inhibitor-inhibitor synergies. PLoS Comput Biol (2015) 0.75
Rough set soft computing cancer classification and network: one stone, two birds. Cancer Inform (2010) 0.75
Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet (2002) 19.57
Gene regulation at the single-cell level. Science (2005) 11.52
Dynamics of the p53-Mdm2 feedback loop in individual cells. Nat Genet (2004) 8.30
Superfamilies of evolved and designed networks. Science (2004) 8.12
Negative autoregulation speeds the response times of transcription networks. J Mol Biol (2002) 6.32
Variability and memory of protein levels in human cells. Nature (2006) 6.15
Optimality and evolutionary tuning of the expression level of a protein. Nature (2005) 5.94
Oscillations and variability in the p53 system. Mol Syst Biol (2006) 4.59
Spontaneous evolution of modularity and network motifs. Proc Natl Acad Sci U S A (2005) 4.49
A module of negative feedback regulators defines growth factor signaling. Nat Genet (2007) 4.35
Just-in-time transcription program in metabolic pathways. Nat Genet (2004) 4.30
Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proc Natl Acad Sci U S A (2002) 4.20
A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods (2006) 3.95
Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc Natl Acad Sci U S A (2004) 3.60
The incoherent feedforward loop can provide fold-change detection in gene regulation. Mol Cell (2009) 3.38
Proteome half-life dynamics in living human cells. Science (2011) 3.34
Plasticity of the cis-regulatory input function of a gene. PLoS Biol (2006) 3.22
Adaptive prediction of environmental changes by microorganisms. Nature (2009) 3.19
Cell-to-cell spread of HIV permits ongoing replication despite antiretroviral therapy. Nature (2011) 3.08
Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins. Nat Methods (2006) 2.94
Alternating electric fields arrest cell proliferation in animal tumor models and human brain tumors. Proc Natl Acad Sci U S A (2007) 2.64
Disruption of cancer cell replication by alternating electric fields. Cancer Res (2004) 2.62
Diverse two-dimensional input functions control bacterial sugar genes. Mol Cell (2008) 2.60
The genetic code is nearly optimal for allowing additional information within protein-coding sequences. Genome Res (2007) 2.56
Dynamics and variability of ERK2 response to EGF in individual living cells. Mol Cell (2009) 2.42
Using a quantitative blueprint to reprogram the dynamics of the flagella gene network. Cell (2004) 2.41
Input output robustness in simple bacterial signaling systems. Proc Natl Acad Sci U S A (2007) 2.17
Cost of unneeded proteins in E. coli is reduced after several generations in exponential growth. Mol Cell (2010) 2.17
Response delays and the structure of transcription networks. J Mol Biol (2003) 2.15
The incoherent feed-forward loop can generate non-monotonic input functions for genes. Mol Syst Biol (2008) 2.13
Central carbon metabolism as a minimal biochemical walk between precursors for biomass and energy. Mol Cell (2010) 2.08
A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli. Mol Syst Biol (2005) 1.97
Environmental variability and modularity of bacterial metabolic networks. BMC Evol Biol (2007) 1.88
Precise temporal modulation in the response of the SOS DNA repair network in individual bacteria. PLoS Biol (2005) 1.84
Varying environments can speed up evolution. Proc Natl Acad Sci U S A (2007) 1.81
The mirror game as a paradigm for studying the dynamics of two people improvising motion together. Proc Natl Acad Sci U S A (2011) 1.76
Robust control of nitrogen assimilation by a bifunctional enzyme in E. coli. Mol Cell (2011) 1.70
Coarse-graining and self-dissimilarity of complex networks. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 1.67
Fold-change detection and scalar symmetry of sensory input fields. Proc Natl Acad Sci U S A (2010) 1.67
Search for computational modules in the C. elegans brain. BMC Biol (2004) 1.61
Environmental selection of the feed-forward loop circuit in gene-regulation networks. Phys Biol (2005) 1.59
Mode of regulation and the insulation of bacterial gene expression. Mol Cell (2012) 1.53
Clopidogrel plus aspirin versus warfarin in patients with stroke and aortic arch plaques. Stroke (2014) 1.49
Accurate prediction of gene feedback circuit behavior from component properties. Mol Syst Biol (2007) 1.45
The immune-body cytokine network defines a social architecture of cell interactions. Biol Direct (2006) 1.41
Mutation rules and the evolution of sparseness and modularity in biological systems. PLoS One (2013) 1.40
A fluctuation method to quantify in vivo fluorescence data. Biophys J (2006) 1.39
Coding limits on the number of transcription factors. BMC Genomics (2006) 1.38
Generation of a fluorescently labeled endogenous protein library in living human cells. Nat Protoc (2007) 1.36
Dynamic response diversity of NFAT isoforms in individual living cells. Mol Cell (2012) 1.28
Defined order of evolutionary adaptations: experimental evidence. Evolution (2008) 1.26
Promoters maintain their relative activity levels under different growth conditions. Mol Syst Biol (2013) 1.26
Cost-benefit theory and optimal design of gene regulation functions. Phys Biol (2007) 1.25
The utility of paradoxical components in biological circuits. Mol Cell (2013) 1.25
Invariant distribution of promoter activities in Escherichia coli. PLoS Comput Biol (2009) 1.24
Fourier analysis and systems identification of the p53 feedback loop. Proc Natl Acad Sci U S A (2010) 1.19
Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels. Mol Syst Biol (2012) 1.19
Facilitated variation: how evolution learns from past environments to generalize to new environments. PLoS Comput Biol (2008) 1.17
SnapShot: network motifs. Cell (2010) 1.16
Robustness in glyoxylate bypass regulation. PLoS Comput Biol (2009) 1.15
A genome-wide analysis of promoter-mediated phenotypic noise in Escherichia coli. PLoS Genet (2012) 1.14
Protein dynamics in individual human cells: experiment and theory. PLoS One (2009) 1.12
Design principles of cell circuits with paradoxical components. Proc Natl Acad Sci U S A (2012) 1.11
Optimal gene partition into operons correlates with gene functional order. Phys Biol (2006) 1.08
Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli. BMC Syst Biol (2011) 1.07
Extinctions in heterogeneous environments and the evolution of modularity. Evolution (2009) 1.04
Subgraphs and network motifs in geometric networks. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 1.02
Rules for biological regulation based on error minimization. Proc Natl Acad Sci U S A (2006) 1.01
Evolutionary tradeoffs between economy and effectiveness in biological homeostasis systems. PLoS Comput Biol (2013) 1.01
Antibodies targeting the catalytic zinc complex of activated matrix metalloproteinases show therapeutic potential. Nat Med (2011) 0.99
Promoter activity dynamics in the lag phase of Escherichia coli. BMC Syst Biol (2013) 0.99
Anatomy of T cell autoimmunity to myelin oligodendrocyte glycoprotein (MOG): prime role of MOG44F in selection and control of MOG-reactive T cells in H-2b mice. Eur J Immunol (2006) 0.98
An analytically solvable model for rapid evolution of modular structure. PLoS Comput Biol (2009) 0.94
The geometry of the Pareto front in biological phenotype space. Ecol Evol (2013) 0.92
Developmental bias in the evolution of phalanges. Proc Natl Acad Sci U S A (2013) 0.92
Dynamic proteomics of human protein level and localization across the cell cycle. PLoS One (2012) 0.92