Guidelines for visualizing and annotating rule-based models.

Programming biological models in Python using PySB. Mol Syst Biol (2013) 1.15

A framework for mapping, visualisation and automatic model creation of signal-transduction networks. Mol Syst Biol (2012) 1.07

Abstractions for DNA circuit design. J R Soc Interface (2011) 1.06

Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. Wiley Interdiscip Rev Syst Biol Med (2013) 1.04

Phosphorylation site dynamics of early T-cell receptor signaling. PLoS One (2014) 0.93

Toward a comprehensive language for biological systems. BMC Biol (2011) 0.92

Disease-enhancing antibodies improve the efficacy of bacterial toxin-neutralizing antibodies. Cell Host Microbe (2013) 0.90

A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn. J Immunol (2012) 0.89

Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling. BMC Syst Biol (2012) 0.88

The Process-Interaction-Model: a common representation of rule-based and logical models allows studying signal transduction on different levels of detail. BMC Bioinformatics (2012) 0.83

Modeling for (physical) biologists: an introduction to the rule-based approach. Phys Biol (2015) 0.81

Leveraging modeling approaches: reaction networks and rules. Adv Exp Med Biol (2012) 0.80

An Interaction Library for the FcεRI Signaling Network. Front Immunol (2014) 0.79

A predictive mathematical model of the DNA damage G2 checkpoint. J Theor Biol (2012) 0.78

Modeling the effect of APC truncation on destruction complex function in colorectal cancer cells. PLoS Comput Biol (2013) 0.78

NetworkViewer: visualizing biochemical reaction networks with embedded rendering of molecular interaction rules. BMC Syst Biol (2014) 0.78

Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. Bioinformatics (2015) 0.77

Computational analysis of an autophagy/translation switch based on mutual inhibition of MTORC1 and ULK1. PLoS One (2015) 0.77

The Pfam protein families database. Nucleic Acids Res (2009) 37.98

Mapping the protein universe. Science (1996) 13.72

RING domain E3 ubiquitin ligases. Annu Rev Biochem (2009) 12.55

Cell signaling by receptor tyrosine kinases. Cell (2010) 12.39

Assembly of cell regulatory systems through protein interaction domains. Science (2003) 10.59

Infrastructure for the life sciences: design and implementation of the UniProt website. BMC Bioinformatics (2009) 8.87

The Systems Biology Graphical Notation. Nat Biotechnol (2009) 8.53

Apoptosis: controlled demolition at the cellular level. Nat Rev Mol Cell Biol (2008) 8.30

Cell-signalling dynamics in time and space. Nat Rev Mol Cell Biol (2006) 7.25

Modelling cellular behaviour. Nature (2001) 5.85

Using process diagrams for the graphical representation of biological networks. Nat Biotechnol (2005) 5.75

Structure of an IkappaBalpha/NF-kappaB complex. Cell (1998) 5.67

Structural origins of high-affinity biotin binding to streptavidin. Science (1989) 5.37

An open-and-shut case? Recent insights into the activation of EGF/ErbB receptors. Mol Cell (2003) 5.06

Normal and oncogenic p21ras proteins bind to the amino-terminal regulatory domain of c-Raf-1. Nature (1993) 4.88

Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics (2008) 4.34

Protein posttranslational modifications: the chemistry of proteome diversifications. Angew Chem Int Ed Engl (2005) 4.10

Structures of complement component C3 provide insights into the function and evolution of immunity. Nature (2005) 4.01

Rules for modeling signal-transduction systems. Sci STKE (2006) 3.86

Human RAS superfamily proteins and related GTPases. Sci STKE (2004) 3.80

Rule-based modeling of biochemical systems with BioNetGen. Methods Mol Biol (2009) 3.47

The interaction of IgE with rat basophilic leukemia cells. II. Quantitative aspects of the binding reaction. J Exp Med (1974) 3.33

BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinformatics (2004) 3.32

Signalling ballet in space and time. Nat Rev Mol Cell Biol (2010) 3.32

Tyrosine phosphorylation: thirty years and counting. Curr Opin Cell Biol (2009) 3.31

An overview of the molecular mechanism of autophagy. Curr Top Microbiol Immunol (2009) 3.29

Automatic generation of cellular reaction networks with Moleculizer 1.0. Nat Biotechnol (2005) 3.26

Regulation of ubiquitin-binding proteins by monoubiquitination. Nat Cell Biol (2006) 2.99

Molecular interaction maps of bioregulatory networks: a general rubric for systems biology. Mol Biol Cell (2005) 2.82

DOG 1.0: illustrator of protein domain structures. Cell Res (2009) 2.77

Detailed simulations of cell biology with Smoldyn 2.1. PLoS Comput Biol (2010) 2.72

Structure and biology of complement protein C3, a connecting link between innate and acquired immunity. Immunol Rev (2001) 2.69

ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Res (2009) 2.59

Regulation of APC/C activators in mitosis and meiosis. Annu Rev Cell Dev Biol (2008) 2.46

Virtual Cell modelling and simulation software environment. IET Syst Biol (2008) 2.43

Antigen and Fc receptor signaling. The awesome power of the immunoreceptor tyrosine-based activation motif (ITAM). J Immunol (1995) 2.40

Internal coarse-graining of molecular systems. Proc Natl Acad Sci U S A (2009) 2.37

A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity. Biosystems (2005) 2.36

Efficient modeling, simulation and coarse-graining of biological complexity with NFsim. Nat Methods (2010) 2.24

Post-translational modifications in signal integration. Nat Struct Mol Biol (2010) 2.23

Cancer systems biology: a network modeling perspective. Carcinogenesis (2009) 2.22

The complexity of complexes in signal transduction. Biotechnol Bioeng (2003) 2.20

Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method. PLoS Comput Biol (2006) 2.13

The internal thioester and the covalent binding properties of the complement proteins C3 and C4. Protein Sci (1997) 2.12

Molecular machines or pleiomorphic ensembles: signaling complexes revisited. J Biol (2009) 2.07

The scaffold protein Ste5 directly controls a switch-like mating decision in yeast. Nature (2010) 1.90

Structure of the Fc fragment of human IgE bound to its high-affinity receptor Fc epsilonRI alpha. Nature (2000) 1.90

Investigation of early events in Fc epsilon RI-mediated signaling using a detailed mathematical model. J Immunol (2003) 1.78

Kinetic Monte Carlo method for rule-based modeling of biochemical networks. Phys Rev E Stat Nonlin Soft Matter Phys (2008) 1.76

Programming with models: modularity and abstraction provide powerful capabilities for systems biology. J R Soc Interface (2009) 1.69

Small molecule inhibition of phosphatidylinositol-3,4,5-triphosphate (PIP3) binding to pleckstrin homology domains. Proc Natl Acad Sci U S A (2010) 1.61

A comprehensive map of the mTOR signaling network. Mol Syst Biol (2010) 1.59

New insights on mast cell activation via the high affinity receptor for IgE. Adv Immunol (2008) 1.51

RuleMonkey: software for stochastic simulation of rule-based models. BMC Bioinformatics (2010) 1.49

The Src, Syk, and Tec family kinases: distinct types of molecular switches. Cell Signal (2010) 1.39

Specific dephosphorylation of the Lck tyrosine protein kinase at Tyr-394 by the SHP-1 protein-tyrosine phosphatase. J Biol Chem (2001) 1.29

Combinatorial complexity and dynamical restriction of network flows in signal transduction. Syst Biol (Stevenage) (2005) 1.27

Balance between acetylation and methylation of histone H3 lysine 9 on the E2F-responsive dihydrofolate reductase promoter. Mol Cell Biol (2003) 1.26

Integrated analysis of breast cancer cell lines reveals unique signaling pathways. Genome Biol (2009) 1.25

Efficient stochastic simulation of reaction-diffusion processes via direct compilation. Bioinformatics (2009) 1.23

Role of the histone domain in the autoinhibition and activation of the Ras activator Son of Sevenless. Proc Natl Acad Sci U S A (2010) 1.22

Aggregation of membrane proteins by cytosolic cross-linkers: theory and simulation of the LAT-Grb2-SOS1 system. Biophys J (2009) 1.19

Regulation of PTEN function as a PIP3 gatekeeper through membrane interaction. Cell Cycle (2006) 1.18

Simulation of large-scale rule-based models. Bioinformatics (2009) 1.18

Depicting combinatorial complexity with the molecular interaction map notation. Mol Syst Biol (2006) 1.17

The regulatory logic of the NF-kappaB signaling system. Cold Spring Harb Perspect Biol (2010) 1.13

Adaptable functionality of transcriptional feedback in bacterial two-component systems. PLoS Comput Biol (2010) 1.13

Modeling multivalent ligand-receptor interactions with steric constraints on configurations of cell-surface receptor aggregates. Biophys J (2010) 1.09

Rule-based spatial modeling with diffusing, geometrically constrained molecules. BMC Bioinformatics (2010) 1.07

Reciprocal regulation of SH3 and SH2 domain binding via tyrosine phosphorylation of a common site in CD3epsilon. J Immunol (2007) 1.05

Modeling the early signaling events mediated by FcepsilonRI. Mol Immunol (2002) 1.05

Structure-based kinetic models of modular signaling protein function: focus on Shp2. Biophys J (2007) 1.03

Computational models of tandem SRC homology 2 domain interactions and application to phosphoinositide 3-kinase. J Biol Chem (2008) 0.95

Scalable rule-based modelling of allosteric proteins and biochemical networks. PLoS Comput Biol (2010) 0.92

Depicting signaling cascades. Nat Biotechnol (2006) 0.90

ALC: automated reduction of rule-based models. BMC Syst Biol (2008) 0.89

Modelling the response of FOXO transcription factors to multiple post-translational modifications made by ageing-related signalling pathways. PLoS One (2010) 0.89

Intrinsic information carriers in combinatorial dynamical systems. Chaos (2010) 0.87

Hierarchical graphs for rule-based modeling of biochemical systems. BMC Bioinformatics (2011) 0.87

A bipolar clamp mechanism for activation of Jak-family protein tyrosine kinases. PLoS Comput Biol (2009) 0.87

GetBonNie for building, analyzing and sharing rule-based models. Bioinformatics (2009) 0.86

Rule-based modelling and simulation of biochemical systems with molecular finite automata. IET Syst Biol (2010) 0.86

A detailed mathematical model predicts that serial engagement of IgE-Fc epsilon RI complexes can enhance Syk activation in mast cells. J Immunol (2010) 0.83

Predicted functions of MdmX in fine-tuning the response of p53 to DNA damage. PLoS Comput Biol (2010) 0.83

Shaping the response: the role of FcεRI and Syk expression levels in mast cell signaling. IET Syst Biol (2010) 0.83

Network architecture of signaling from uncoupled helicase-polymerase to cell cycle checkpoints and trans-lesion DNA synthesis. Cell Cycle (2009) 0.82

Demographic history and rare allele sharing among human populations. Proc Natl Acad Sci U S A (2011) 7.36

Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing. Nature (2010) 5.27

A porous supramolecular architecture from a copper(II) coordination polymer with a 3D four-connected 8(6) net. Inorg Chem (2003) 5.16

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol (2011) 4.84

High-throughput, subpixel precision analysis of bacterial morphogenesis and intracellular spatio-temporal dynamics. Mol Microbiol (2011) 4.82

A structural mechanism of integrin alpha(IIb)beta(3) "inside-out" activation as regulated by its cytoplasmic face. Cell (2002) 4.57

From molecular noise to behavioural variability in a single bacterium. Nature (2004) 4.28

Rules for modeling signal-transduction systems. Sci STKE (2006) 3.86

Comparative and demographic analysis of orang-utan genomes. Nature (2011) 3.83

Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data. Proc Natl Acad Sci U S A (2011) 3.80

Rule-based modeling of biochemical systems with BioNetGen. Methods Mol Biol (2009) 3.47

Spatial organization of the flow of genetic information in bacteria. Nature (2010) 3.43

BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinformatics (2004) 3.32

Activated TCRs remain marked for internalization after dissociation from pMHC. Nat Immunol (2002) 3.01

Chromatin regulation by Brg1 underlies heart muscle development and disease. Nature (2010) 2.85

Structural and functional analysis of the middle segment of hsp90: implications for ATP hydrolysis and client protein and cochaperone interactions. Mol Cell (2003) 2.83

Global distribution of genomic diversity underscores rich complex history of continental human populations. Genome Res (2009) 2.76

A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity. Biosystems (2005) 2.36

Efficient modeling, simulation and coarse-graining of biological complexity with NFsim. Nat Methods (2010) 2.24

An Smc3 acetylation cycle is essential for establishment of sister chromatid cohesion. Mol Cell (2010) 2.23

Single-cell quantification of IL-2 response by effector and regulatory T cells reveals critical plasticity in immune response. Mol Syst Biol (2010) 2.21

The complexity of complexes in signal transduction. Biotechnol Bioeng (2003) 2.20

CD4+CD25+ regulatory T cells cure murine colitis: the role of IL-10, TGF-beta, and CTLA4. J Immunol (2003) 2.19

Molecular machines or pleiomorphic ensembles: signaling complexes revisited. J Biol (2009) 2.07

Mathematical and computational models of immune-receptor signalling. Nat Rev Immunol (2004) 2.06

Salmonella paratyphi A rates, Asia. Emerg Infect Dis (2005) 1.94

The distal carboxyl-terminal domains of ADAMTS13 are required for regulation of in vivo thrombus formation. Blood (2008) 1.93

Effect of antipsychotic medication alone vs combined with psychosocial intervention on outcomes of early-stage schizophrenia: A randomized, 1-year study. Arch Gen Psychiatry (2010) 1.89

Using independent open-to-closed transitions to simplify aggregated Markov models of ion channel gating kinetics. Proc Natl Acad Sci U S A (2005) 1.87

Design of gene circuits: lessons from bacteria. Nat Rev Genet (2004) 1.82

Modifying the DPClus algorithm for identifying protein complexes based on new topological structures. BMC Bioinformatics (2008) 1.81

Genome-wide association study in Chinese men identifies two new prostate cancer risk loci at 9q31.2 and 19q13.4. Nat Genet (2012) 1.78

Investigation of early events in Fc epsilon RI-mediated signaling using a detailed mathematical model. J Immunol (2003) 1.78

Kinetic Monte Carlo method for rule-based modeling of biochemical networks. Phys Rev E Stat Nonlin Soft Matter Phys (2008) 1.76

Cohesin's DNA exit gate is distinct from its entrance gate and is regulated by acetylation. Cell (2012) 1.75

Co-chaperone regulation of conformational switching in the Hsp90 ATPase cycle. J Biol Chem (2004) 1.71

Targets of balancing selection in the human genome. Mol Biol Evol (2009) 1.69

RodZ, a component of the bacterial core morphogenic apparatus. Proc Natl Acad Sci U S A (2009) 1.68

Polyspecificity of T cell and B cell receptor recognition. Semin Immunol (2007) 1.68

Series of 2D and 3D coordination polymers based on 1,2,3,4-benzenetetracarboxylate and N-donor ligands: synthesis, topological structures, and photoluminescent properties. Inorg Chem (2010) 1.68

Influence of neutral ligands on the structures of silver(I) sulfonates. Inorg Chem (2005) 1.66

Syntheses and characterization of six coordination polymers of zinc(II) and cobalt(II) with 1,3,5-benzenetricarboxylate anion and bis(imidazole) ligands. Inorg Chem (2007) 1.66

The noncoding RNA expression profile and the effect of lncRNA AK126698 on cisplatin resistance in non-small-cell lung cancer cell. PLoS One (2013) 1.65

Structural basis for recruitment of the ATPase activator Aha1 to the Hsp90 chaperone machinery. EMBO J (2004) 1.63

Quercetin activates AMP-activated protein kinase by reducing PP2C expression protecting old mouse brain against high cholesterol-induced neurotoxicity. J Pathol (2010) 1.62

Sloppiness, robustness, and evolvability in systems biology. Curr Opin Biotechnol (2008) 1.62

Fluorescent and photo-oxidizing TimeSTAMP tags track protein fates in light and electron microscopy. Nat Neurosci (2012) 1.60

Quantitative elucidation of a distinct spatial gradient-sensing mechanism in fibroblasts. J Cell Biol (2005) 1.58

Dynamic reciprocity of sodium and potassium channel expression in a macromolecular complex controls cardiac excitability and arrhythmia. Proc Natl Acad Sci U S A (2012) 1.58

Hsp90-dependent activation of protein kinases is regulated by chaperone-targeted dephosphorylation of Cdc37. Mol Cell (2008) 1.57

Real-time RNA profiling within a single bacterium. Proc Natl Acad Sci U S A (2005) 1.56

The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. Genome Res (2007) 1.56

What is the optimal value of the g-ratio for myelinated fibers in the rat CNS? A theoretical approach. PLoS One (2009) 1.55

Activation of the mouse heme oxygenase-1 gene by 15-deoxy-Delta(12,14)-prostaglandin J(2) is mediated by the stress response elements and transcription factor Nrf2. Antioxid Redox Signal (2002) 1.53

Genetic randomization reveals functional relationships among morphologic and tissue-quality traits that contribute to bone strength and fragility. Mamm Genome (2007) 1.52

The JNK signaling pathway is involved in sodium-selenite-induced apoptosis mediated by reactive oxygen in HepG2 cells. Cancer Biol Ther (2008) 1.50

T cell receptor binding kinetics required for T cell activation depend on the density of cognate ligand on the antigen-presenting cell. Proc Natl Acad Sci U S A (2005) 1.49

RuleMonkey: software for stochastic simulation of rule-based models. BMC Bioinformatics (2010) 1.49

A multi-algorithm, multi-timescale method for cell simulation. Bioinformatics (2004) 1.48

A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing. Genomics (2010) 1.47

Determination of Cd, Co, Ni and Pb in biological samples by microcolumn packed with black stone (Pierre noire) online coupled with ICP-OES. J Hazard Mater (2008) 1.46

Systematic quantification of negative feedback mechanisms in the extracellular signal-regulated kinase (ERK) signaling network. J Biol Chem (2010) 1.45

Kinetic analysis of platelet-derived growth factor receptor/phosphoinositide 3-kinase/Akt signaling in fibroblasts. J Biol Chem (2003) 1.43

Rapamycin affects tissue plasminogen activator and plasminogen activator inhibitor I expression: a potential prothrombotic mechanism of drug-eluting stents. Angiology (2011) 1.42

Deletion allele of the angiotensin-converting enzyme gene as a risk factor for pneumonia in elderly patients. Am J Med (2002) 1.41

Activation of volume-sensitive Cl(-) channel is involved in carboplatin-induced apoptosis in human lung adenocarcinoma cells. Cancer Biol Ther (2010) 1.41

PI3K-dependent cross-talk interactions converge with Ras as quantifiable inputs integrated by Erk. Mol Syst Biol (2009) 1.40

Flexible solid-state supercapacitors based on carbon nanoparticles/MnO2 nanorods hybrid structure. ACS Nano (2011) 1.39

Mechanisms of gradient sensing and chemotaxis: conserved pathways, diverse regulation. Cell Cycle (2006) 1.36

Chromatin remodeling in cardiovascular development and physiology. Circ Res (2011) 1.34

A novel alphaB-crystallin mutation associated with autosomal dominant congenital lamellar cataract. Invest Ophthalmol Vis Sci (2006) 1.34

Sloppy-model universality class and the Vandermonde matrix. Phys Rev Lett (2006) 1.33

Structural study of silver(I) sulfonate complexes with pyrazine derivatives. Inorg Chem (2007) 1.33

Electrophysiology and Pharmacology of the Corticothalamic Input to Lateral Thalamic Nuclei: an Intracellular Study in the Cat. Eur J Neurosci (1990) 1.31

Cerebral hemispherectomy in pediatric patients with epilepsy: comparison of three techniques by pathological substrate in 115 patients. J Neurosurg (2004) 1.29

Structural basis for recruitment of the ATPase activator Aha1 to the Hsp90 chaperone machinery. EMBO J (2004) 1.29

Cigarette smoke induces endoplasmic reticulum stress and the unfolded protein response in normal and malignant human lung cells. BMC Cancer (2008) 1.28

On imposing detailed balance in complex reaction mechanisms. Biophys J (2006) 1.28

Spatial analysis of 3' phosphoinositide signaling in living fibroblasts, III: influence of cell morphology and morphological Polarity. Biophys J (2005) 1.28

Hidden stochastic nature of a single bacterial motor. Phys Rev Lett (2006) 1.27

Interdependence of behavioural variability and response to small stimuli in bacteria. Nature (2010) 1.26

AEG-1/MTDH/LYRIC: signaling pathways, downstream genes, interacting proteins, and regulation of tumor angiogenesis. Adv Cancer Res (2013) 1.26

Sulfate ion encapsulation in caged supramolecular structures assembled by second-sphere coordination. Chem Commun (Camb) (2008) 1.25

Siomycin A targets brain tumor stem cells partially through a MELK-mediated pathway. Neuro Oncol (2011) 1.25