Published in PLoS Biol on October 04, 2005
Network 'small-world-ness': a quantitative method for determining canonical network equivalence. PLoS One (2008) 4.01
Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling. PLoS Biol (2006) 3.53
Nonrandom connectivity of the epileptic dentate gyrus predicts a major role for neuronal hubs in seizures. Proc Natl Acad Sci U S A (2008) 2.56
Robustness and modular design of the Drosophila segment polarity network. Mol Syst Biol (2006) 2.06
Functional motifs in biochemical reaction networks. Annu Rev Phys Chem (2010) 2.04
Network motifs: structure does not determine function. BMC Genomics (2006) 2.01
Noise propagation and signaling sensitivity in biological networks: a role for positive feedback. PLoS Comput Biol (2007) 1.94
Bistability and oscillations in the Huang-Ferrell model of MAPK signaling. PLoS Comput Biol (2007) 1.93
Dynamics and design principles of a basic regulatory architecture controlling metabolic pathways. PLoS Biol (2008) 1.86
Network inference, analysis, and modeling in systems biology. Plant Cell (2007) 1.27
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Memory switches in chemical reaction space. PLoS Comput Biol (2008) 1.13
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Non-transcriptional regulatory processes shape transcriptional network dynamics. Nat Rev Microbiol (2011) 1.04
Modeling protein network evolution under genome duplication and domain shuffling. BMC Syst Biol (2007) 1.03
Motifs, control, and stability. PLoS Biol (2005) 1.02
Capturing cell-fate decisions from the molecular signatures of a receptor-dependent signaling response. Mol Syst Biol (2007) 1.02
Regulatory architecture determines optimal regulation of gene expression in metabolic pathways. Proc Natl Acad Sci U S A (2012) 1.01
Systems interface biology. J R Soc Interface (2006) 1.01
Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae. BMC Bioinformatics (2006) 0.96
Specialized or flexible feed-forward loop motifs: a question of topology. BMC Syst Biol (2009) 0.95
Digital clocks: simple Boolean models can quantitatively describe circadian systems. J R Soc Interface (2012) 0.94
Pervasive robustness in biological systems. Nat Rev Genet (2015) 0.91
Investigations into the relationship between feedback loops and functional importance of a signal transduction network based on Boolean network modeling. BMC Bioinformatics (2007) 0.91
The Regulatory Network of Pseudomonas aeruginosa. Microb Inform Exp (2011) 0.91
The effect of negative feedback loops on the dynamics of boolean networks. Biophys J (2008) 0.88
Algorithmic and analytical methods in network biology. Wiley Interdiscip Rev Syst Biol Med (2010) 0.87
Colored motifs reveal computational building blocks in the C. elegans brain. PLoS One (2011) 0.87
Functions of bifans in context of multiple regulatory motifs in signaling networks. Biophys J (2008) 0.87
Stability and structural constraints of random brain networks with excitatory and inhibitory neural populations. J Comput Neurosci (2008) 0.87
Control of complex networks requires both structure and dynamics. Sci Rep (2016) 0.85
Network motifs provide signatures that characterize metabolism. Mol Biosyst (2013) 0.85
Heterochronic evolution reveals modular timing changes in budding yeast transcriptomes. Genome Biol (2010) 0.85
Mutational robustness of gene regulatory networks. PLoS One (2012) 0.84
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On the contributions of topological features to transcriptional regulatory network robustness. BMC Bioinformatics (2012) 0.84
Computational analyses of synergism in small molecular network motifs. PLoS Comput Biol (2014) 0.84
Structurally robust biological networks. BMC Syst Biol (2011) 0.84
Ground state robustness as an evolutionary design principle in signaling networks. PLoS One (2009) 0.84
A Statistical Approach Reveals Designs for the Most Robust Stochastic Gene Oscillators. ACS Synth Biol (2016) 0.84
Evolvability of feed-forward loop architecture biases its abundance in transcription networks. BMC Syst Biol (2012) 0.83
Associative memory model with long-tail-distributed Hebbian synaptic connections. Front Comput Neurosci (2013) 0.82
Slicing, sampling, and distance-dependent effects affect network measures in simulated cortical circuit structures. Front Neuroanat (2014) 0.82
Sequential logic model deciphers dynamic transcriptional control of gene expressions. PLoS One (2007) 0.82
Transcription factor competition allows embryonic stem cells to distinguish authentic signals from noise. Cell Syst (2015) 0.82
Failure tolerance of motif structure in biological networks. PLoS One (2011) 0.81
Scale-free topology of the CA3 hippocampal network: a novel method to analyze functional neuronal assemblies. Biophys J (2010) 0.81
Evolutionary conservation and network structure characterize genes of phenotypic relevance for mitosis in human. PLoS One (2012) 0.81
Function does not follow form in gene regulatory circuits. Sci Rep (2015) 0.81
Rapid reorganization of the transcriptional regulatory network after genome duplication in yeast. Proc Biol Sci (2009) 0.81
Investigating the validity of current network analysis on static conglomerate networks by protein network stratification. BMC Bioinformatics (2010) 0.81
Motif Participation by Genes in E. coli Transcriptional Networks. Front Physiol (2012) 0.80
PANET: a GPU-based tool for fast parallel analysis of robustness dynamics and feed-forward/feedback loop structures in large-scale biological networks. PLoS One (2014) 0.80
Spatiotemporal network motif reveals the biological traits of developmental gene regulatory networks in Drosophila melanogaster. BMC Syst Biol (2012) 0.80
Stability from structure: metabolic networks are unlike other biological networks. EURASIP J Bioinform Syst Biol (2009) 0.80
Activating and inhibiting connections in biological network dynamics. Biol Direct (2008) 0.80
Dense neuron clustering explains connectivity statistics in cortical microcircuits. PLoS One (2014) 0.79
Differential dynamic properties of scleroderma fibroblasts in response to perturbation of environmental stimuli. PLoS One (2008) 0.79
Dynamical pathway analysis. BMC Syst Biol (2008) 0.79
Structural properties of the MAPK pathway topologies in PC12 cells. J Math Biol (2012) 0.78
Cellular automata simulation of topological effects on the dynamics of feed-forward motifs. J Biol Eng (2008) 0.78
Transcriptional robustness and protein interactions are associated in yeast. BMC Syst Biol (2011) 0.78
Gap Junctional Blockade Stochastically Induces Different Species-Specific Head Anatomies in Genetically Wild-Type Girardia dorotocephala Flatworms. Int J Mol Sci (2015) 0.78
Social insect colony as a biological regulatory system: modelling information flow in dominance networks. J R Soc Interface (2014) 0.78
Modularity and stability in ecological communities. Nat Commun (2016) 0.78
Quantifying the dynamics of coupled networks of switches and oscillators. PLoS One (2012) 0.77
Determinative developmental cell lineages are robust to cell deaths. PLoS Genet (2014) 0.77
An analytical approach to network motif detection in samples of networks with pairwise different vertex labels. Comput Math Methods Med (2012) 0.76
A top-down approach to mechanistic biological modeling: application to the single-chain antibody folding pathway. Biophys J (2008) 0.76
The Integration of the Glutamatergic and the White Matter Hypotheses of Schizophrenia's Etiology. Curr Neuropharmacol (2012) 0.76
Identifying emerging motif in growing networks. PLoS One (2014) 0.76
Dynamics of regulatory networks in gastrin-treated adenocarcinoma cells. PLoS One (2014) 0.76
Differential gene expression regulated by oscillatory transcription factors. PLoS One (2012) 0.76
A developmental systems perspective on epistasis: computational exploration of mutational interactions in model developmental regulatory networks. PLoS One (2009) 0.76
A choice motif. Elife (2016) 0.75
Transcriptional Network Growing Models Using Motif-Based Preferential Attachment. Front Bioeng Biotechnol (2015) 0.75
Noise Decomposition Principle in a Coherent Feed-Forward Transcriptional Regulatory Loop. Front Physiol (2016) 0.75
Time-Delayed Models of Gene Regulatory Networks. Comput Math Methods Med (2015) 0.75
Optimality and thermodynamics determine the evolution of transcriptional regulatory networks. Mol Biosyst (2011) 0.75
Systems Modeling at Multiple Levels of Regulation: Linking Systems and Genetic Networks to Spatially Explicit Plant Populations. Plants (Basel) (2013) 0.75
Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res (2003) 103.76
Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52
Network biology: understanding the cell's functional organization. Nat Rev Genet (2004) 36.62
Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell (2000) 36.09
Network motifs: simple building blocks of complex networks. Science (2002) 35.80
Stochastic gene expression in a single cell. Science (2002) 34.54
Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21
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A synthetic oscillatory network of transcriptional regulators. Nature (2000) 24.58
Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet (2002) 19.57
The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation. Science (2002) 13.86
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Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32
Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A (2003) 9.03
Superfamilies of evolved and designed networks. Science (2004) 8.12
Highly nonrandom features of synaptic connectivity in local cortical circuits. PLoS Biol (2005) 7.81
Multistability in the lactose utilization network of Escherichia coli. Nature (2004) 7.71
Robustness of cellular functions. Cell (2004) 6.65
Combinatorial synthesis of genetic networks. Science (2002) 5.91
The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. J Mol Biol (2003) 5.20
Motifs in brain networks. PLoS Biol (2004) 3.40
Subgraphs in random networks. Phys Rev E Stat Nonlin Soft Matter Phys (2003) 2.65
Design of genetic networks with specified functions by evolution in silico. Proc Natl Acad Sci U S A (2004) 2.60
Motifs, modules and games in bacteria. Curr Opin Microbiol (2003) 2.58
Design principles for elementary gene circuits: Elements, methods, and examples. Chaos (2001) 2.25
Surviving heat shock: control strategies for robustness and performance. Proc Natl Acad Sci U S A (2005) 2.12
A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli. Mol Syst Biol (2005) 1.97
Topological generalizations of network motifs. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 1.78
Networks, dynamics, and modularity. Phys Rev Lett (2004) 1.49
Control motifs for intracellular regulatory networks. Annu Rev Biomed Eng (2001) 1.13
Regulatory modules that generate biphasic signal response in biological systems. Syst Biol (Stevenage) (2004) 0.99
The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation. Science (2002) 13.86
Models of eukaryotic gradient sensing: application to chemotaxis of amoebae and neutrophils. Biophys J (2002) 3.93
MAPK-mediated bimodal gene expression and adaptive gradient sensing in yeast. Nature (2007) 3.23
Chromosome alignment and segregation regulated by ubiquitination of survivin. Science (2005) 3.09
PIP3-independent activation of TorC2 and PKB at the cell's leading edge mediates chemotaxis. Curr Biol (2008) 3.06
Information transduction capacity of noisy biochemical signaling networks. Science (2011) 2.95
A microfluidic chemostat for experiments with bacterial and yeast cells. Nat Methods (2005) 2.91
Cells navigate with a local-excitation, global-inhibition-biased excitable network. Proc Natl Acad Sci U S A (2010) 2.54
PLA2 and PI3K/PTEN pathways act in parallel to mediate chemotaxis. Dev Cell (2007) 2.53
Chemoattractant-induced phosphatidylinositol 3,4,5-trisphosphate accumulation is spatially amplified and adapts, independent of the actin cytoskeleton. Proc Natl Acad Sci U S A (2004) 2.52
Nanoscale cues regulate the structure and function of macroscopic cardiac tissue constructs. Proc Natl Acad Sci U S A (2009) 2.25
Matrix nanotopography as a regulator of cell function. J Cell Biol (2012) 2.20
A homeostatic model of IkappaB metabolism to control constitutive NF-kappaB activity. Mol Syst Biol (2007) 2.13
Interactions between myosin and actin crosslinkers control cytokinesis contractility dynamics and mechanics. Curr Biol (2008) 2.09
Transient IkappaB kinase activity mediates temporal NF-kappaB dynamics in response to a wide range of tumor necrosis factor-alpha doses. J Biol Chem (2005) 2.08
Microengineered platforms for cell mechanobiology. Annu Rev Biomed Eng (2009) 2.02
Two complementary, local excitation, global inhibition mechanisms acting in parallel can explain the chemoattractant-induced regulation of PI(3,4,5)P3 response in dictyostelium cells. Biophys J (2004) 1.91
Mechanosensing through cooperative interactions between myosin II and the actin crosslinker cortexillin I. Curr Biol (2009) 1.86
Comment on "Oscillations in NF-kappaB signaling control the dynamics of gene expression". Science (2005) 1.79
Understanding NF-kappaB signaling via mathematical modeling. Mol Syst Biol (2008) 1.79
Chemoattractant signaling in dictyostelium discoideum. Annu Rev Cell Dev Biol (2004) 1.77
Hypoxia-inducible factor-dependent breast cancer-mesenchymal stem cell bidirectional signaling promotes metastasis. J Clin Invest (2012) 1.71
Mitosis-specific mechanosensing and contractile-protein redistribution control cell shape. Curr Biol (2006) 1.70
Modeling the cell's guidance system. Sci STKE (2002) 1.68
Nucleocytoplasmic shuttling of a GATA transcription factor functions as a development timer. Science (2014) 1.64
Optimal noise filtering in the chemotactic response of Escherichia coli. PLoS Comput Biol (2006) 1.61
Mechanosensitivity of fibroblast cell shape and movement to anisotropic substratum topography gradients. Biomaterials (2009) 1.53
Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations. Bioinformatics (2003) 1.53
Self-organization in high-density bacterial colonies: efficient crowd control. PLoS Biol (2007) 1.52
Use of MR cell tracking to evaluate targeting of glial precursor cells to inflammatory tissue by exploiting the very late antigen-4 docking receptor. Radiology (2012) 1.51
Chaperone-mediated autophagy targets hypoxia-inducible factor-1α (HIF-1α) for lysosomal degradation. J Biol Chem (2013) 1.48
A microfluidics-based turning assay reveals complex growth cone responses to integrated gradients of substrate-bound ECM molecules and diffusible guidance cues. Lab Chip (2008) 1.46
GSK-3 kinases enhance calcineurin signaling by phosphorylation of RCNs. Genes Dev (2003) 1.46
An information-theoretic characterization of the optimal gradient sensing response of cells. PLoS Comput Biol (2007) 1.45
Synergistic effect of HIF-1alpha gene therapy and HIF-1-activated bone marrow-derived angiogenic cells in a mouse model of limb ischemia. Proc Natl Acad Sci U S A (2009) 1.43
Human cerebrospinal fluid regulates proliferation and migration of stem cells through insulin-like growth factor-1. Stem Cells Dev (2015) 1.42
Diverse sensitivity thresholds in dynamic signaling responses by social amoebae. Sci Signal (2012) 1.41
Guided Cell Migration on Microtextured Substrates with Variable Local Density and Anisotropy. Adv Funct Mater (2009) 1.39
Signaling diversity of PKA achieved via a Ca2+-cAMP-PKA oscillatory circuit. Nat Chem Biol (2010) 1.35
An excitable signal integrator couples to an idling cytoskeletal oscillator to drive cell migration. Nat Cell Biol (2013) 1.34
A 3D Monte Carlo analysis of the role of dyadic space geometry in spark generation. Biophys J (2005) 1.34
Molecular mechanisms of cellular mechanosensing. Nat Mater (2013) 1.34
Multiple signaling pathways regulate yeast cell death during the response to mating pheromones. Mol Biol Cell (2006) 1.29
High content cell screening in a microfluidic device. Mol Cell Proteomics (2008) 1.29
Regulation of brain tumor dispersal by NKCC1 through a novel role in focal adhesion regulation. PLoS Biol (2012) 1.29
Oscillatory phosphorylation of yeast Fus3 MAP kinase controls periodic gene expression and morphogenesis. Curr Biol (2008) 1.27
Negative autoregulation by FAS mediates robust fetal erythropoiesis. PLoS Biol (2007) 1.25
Understanding the cooperative interaction between myosin II and actin cross-linkers mediated by actin filaments during mechanosensation. Biophys J (2012) 1.25
Fine temporal control of the medium gas content and acidity and on-chip generation of series of oxygen concentrations for cell cultures. Lab Chip (2009) 1.25
Modeling cellular deformations using the level set formalism. BMC Syst Biol (2008) 1.25
Engineering neuronal growth cones to promote axon regeneration over inhibitory molecules. Proc Natl Acad Sci U S A (2011) 1.24
Visualization of JNK activity dynamics with a genetically encoded fluorescent biosensor. Proc Natl Acad Sci U S A (2010) 1.20
Lab-on-a-chip devices as an emerging platform for stem cell biology. Lab Chip (2010) 1.20
Synergistically enhanced osteogenic differentiation of human mesenchymal stem cells by culture on nanostructured surfaces with induction media. Biomacromolecules (2010) 1.18
Subcellular-resolution delivery of a cytokine through precisely manipulated nanowires. Nat Nanotechnol (2010) 1.18
A nontranscriptional role for HIF-1α as a direct inhibitor of DNA replication. Sci Signal (2013) 1.17
Cell motility of neural stem cells is reduced after SPIO-labeling, which is mitigated after exocytosis. Magn Reson Med (2012) 1.16
Quantifying robustness of biochemical network models. BMC Bioinformatics (2002) 1.16
Enhanced sensitivity to IGF-II signaling links loss of imprinting of IGF2 to increased cell proliferation and tumor risk. Proc Natl Acad Sci U S A (2007) 1.15
14-3-3 coordinates microtubules, Rac, and myosin II to control cell mechanics and cytokinesis. Curr Biol (2010) 1.14
Synthetic spatially graded Rac activation drives cell polarization and movement. Proc Natl Acad Sci U S A (2012) 1.14
Robust and sensitive control of a quorum-sensing circuit by two interlocked feedback loops. Mol Syst Biol (2008) 1.14
Interaction of motility, directional sensing, and polarity modules recreates the behaviors of chemotaxing cells. PLoS Comput Biol (2013) 1.10
The systems biology of glycosylation. Chembiochem (2004) 1.09
Local excitation, global inhibition mechanism for gradient sensing: an interactive applet. Sci STKE (2004) 1.08
Nanopatterned cardiac cell patches promote stem cell niche formation and myocardial regeneration. Integr Biol (Camb) (2012) 1.08
Matrix rigidity controls endothelial differentiation and morphogenesis of cardiac precursors. Sci Signal (2012) 1.08
Automated characterization of cell shape changes during amoeboid motility by skeletonization. BMC Syst Biol (2010) 1.08
Systems biology. How information theory handles cell signaling and uncertainty. Science (2012) 1.08
Lineage mapping the pre-implantation mouse embryo by two-photon microscopy, new insights into the segregation of cell fates. Dev Biol (2011) 1.07
Biomimetic nanopatterns as enabling tools for analysis and control of live cells. Adv Mater (2010) 1.07
Control of stem cell fate and function by engineering physical microenvironments. Integr Biol (Camb) (2012) 1.04
A mechanosensory system governs myosin II accumulation in dividing cells. Mol Biol Cell (2012) 1.04
Deconvolution of the cellular force-generating subsystems that govern cytokinesis furrow ingression. PLoS Comput Biol (2012) 1.04
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Modelling cell polarization driven by synthetic spatially graded Rac activation. PLoS Comput Biol (2012) 1.03
A mechanosensory system controls cell shape changes during mitosis. Cell Cycle (2007) 0.99
Coordination of chromosome alignment and mitotic progression by the chromosome-based Ran signal. Cell Cycle (2007) 0.98
Analysis of pairwise cell interactions using an integrated dielectrophoretic-microfluidic system. Mol Syst Biol (2008) 0.98
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Positive feedback may cause the biphasic response observed in the chemoattractant-induced response of Dictyostelium cells. Syst Control Lett (2006) 0.97
Ergosterol regulates sterol regulatory element binding protein (SREBP) cleavage in fission yeast. J Biol Chem (2010) 0.96
Spatial regulation improves antiparallel microtubule overlap during mitotic spindle assembly. Biophys J (2007) 0.95
Marginal zone B cells regulate antigen-specific T cell responses during infection. J Immunol (2012) 0.94
Mesenchymal stem cells from human fat engineered to secrete BMP4 are nononcogenic, suppress brain cancer, and prolong survival. Clin Cancer Res (2014) 0.93
Oscillatory signaling processes: the how, the why and the where. Curr Opin Genet Dev (2010) 0.92
A cell-based model for quorum sensing in heterogeneous bacterial colonies. PLoS Comput Biol (2010) 0.92
Physical transfer of membrane and cytoplasmic components as a general mechanism of cell-cell communication. J Cell Sci (2009) 0.91
Dynacortin facilitates polarization of chemotaxing cells. BMC Biol (2007) 0.91
Mitotic membrane helps to focus and stabilize the mitotic spindle. Biophys J (2010) 0.91
Control analysis of bacterial chemotaxis signaling. Methods Enzymol (2007) 0.91
The application of information theory to biochemical signaling systems. Phys Biol (2012) 0.90
Using a microfluidic device for high-content analysis of cell signaling. Sci Signal (2009) 0.88
Separation anxiety: stress, tension and cytokinesis. Exp Cell Res (2012) 0.88
Computational model and microfluidic platform for the investigation of paracrine and autocrine signaling in mouse embryonic stem cells. Mol Biosyst (2009) 0.88
Scp160-dependent mRNA trafficking mediates pheromone gradient sensing and chemotropism in yeast. Cell Rep (2012) 0.87
A new link between epigenetic progenitor lesions in cancer and the dynamics of signal transduction. Cell Cycle (2009) 0.87
Superimposed topographic and chemical cues synergistically guide neurite outgrowth. Lab Chip (2013) 0.86
A method for determining the robustness of bio-molecular oscillator models. BMC Syst Biol (2009) 0.84