Published in Bioinformatics on March 22, 2004
Mapping complex disease traits with global gene expression. Nat Rev Genet (2009) 7.44
A methodology for the structural and functional analysis of signaling and regulatory networks. BMC Bioinformatics (2006) 3.55
Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations. Proc Natl Acad Sci U S A (2005) 2.71
Ranked prediction of p53 targets using hidden variable dynamic modeling. Genome Biol (2006) 1.78
Computationally derived points of fragility of a human cascade are consistent with current therapeutic strategies. PLoS Comput Biol (2007) 1.33
Untangling the signalling wires. Nat Cell Biol (2007) 1.25
Inference of gene regulatory networks using time-series data: a survey. Curr Genomics (2009) 1.24
Quantitative inference of dynamic regulatory pathways via microarray data. BMC Bioinformatics (2005) 1.20
Experimental design for efficient identification of gene regulatory networks using sparse Bayesian models. BMC Syst Biol (2007) 1.15
Reconstructing nonlinear dynamic models of gene regulation using stochastic sampling. BMC Bioinformatics (2009) 1.07
Silence on the relevant literature and errors in implementation. Nat Biotechnol (2015) 1.07
Noise management by molecular networks. PLoS Comput Biol (2009) 1.05
A network analysis of the human T-cell activation gene network identifies JAGGED1 as a therapeutic target for autoimmune diseases. PLoS One (2007) 1.03
T cells translate individual, quantal activation into collective, analog cytokine responses via time-integrated feedbacks. Elife (2014) 1.02
Systems interface biology. J R Soc Interface (2006) 1.01
Inferring time-varying network topologies from gene expression data. EURASIP J Bioinform Syst Biol (2007) 0.88
Reconstruction of extended Petri nets from time series data and its application to signal transduction and to gene regulatory networks. BMC Syst Biol (2011) 0.87
Least-squares methods for identifying biochemical regulatory networks from noisy measurements. BMC Bioinformatics (2007) 0.86
Metabolic network discovery through reverse engineering of metabolome data. Metabolomics (2009) 0.86
Iterative experiment design guides the characterization of a light-inducible gene expression circuit. Proc Natl Acad Sci U S A (2015) 0.85
Plato's cave algorithm: inferring functional signaling networks from early gene expression shadows. PLoS Comput Biol (2010) 0.84
Comparisons of robustness and sensitivity between cancer and normal cells by microarray data. Cancer Inform (2008) 0.83
Exact reconstruction of gene regulatory networks using compressive sensing. BMC Bioinformatics (2014) 0.83
Cutting the wires: modularization of cellular networks for experimental design. Biophys J (2014) 0.83
Reverse engineering validation using a benchmark synthetic gene circuit in human cells. ACS Synth Biol (2013) 0.81
Identification of crosstalk between phosphoprotein signaling pathways in RAW 264.7 macrophage cells. PLoS Comput Biol (2010) 0.81
A dynamic time order network for time-series gene expression data analysis. BMC Syst Biol (2012) 0.80
Visualizing and manipulating temporal signaling dynamics with fluorescence-based tools. Sci Signal (2014) 0.80
Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering. BMC Bioinformatics (2009) 0.80
Integrating Bayesian variable selection with Modular Response Analysis to infer biochemical network topology. BMC Syst Biol (2013) 0.79
Optimization-based inference for temporally evolving networks with applications in biology. J Comput Biol (2012) 0.78
Gene regulatory network modeling using literature curated and high throughput data. Syst Synth Biol (2012) 0.77
Inferring cell-scale signalling networks via compressive sensing. PLoS One (2014) 0.76
Sparsity as cellular objective to infer directed metabolic networks from steady-state metabolome data: a theoretical analysis. PLoS One (2013) 0.76
Inferring sparse networks for noisy transient processes. Sci Rep (2016) 0.75
In silico model-based inference: an emerging approach for inverse problems in engineering better medicines. Curr Opin Chem Eng (2015) 0.75
Nonlinear dynamic trans/cis regulatory circuit for gene transcription via microarray data. Gene Regul Syst Bio (2007) 0.75
Discriminating direct and indirect connectivities in biological networks. Proc Natl Acad Sci U S A (2015) 0.75
A data-driven modeling approach to identify disease-specific multi-organ networks driving physiological dysregulation. PLoS Comput Biol (2017) 0.75
Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades. J Cell Biol (2004) 5.02
Untangling the wires: a strategy to trace functional interactions in signaling and gene networks. Proc Natl Acad Sci U S A (2002) 3.18
Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses. Mol Syst Biol (2007) 2.56
Cross-talk between mitogenic Ras/MAPK and survival PI3K/Akt pathways: a fine balance. Biochem Soc Trans (2012) 1.92
Quantitative analysis of signaling networks. Prog Biophys Mol Biol (2004) 1.89
Effects of sequestration on signal transduction cascades. FEBS J (2006) 1.84
Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics. Cell (2010) 1.82
Systems-level interactions between insulin-EGF networks amplify mitogenic signaling. Mol Syst Biol (2009) 1.77
Scaffolding protein Grb2-associated binder 1 sustains epidermal growth factor-induced mitogenic and survival signaling by multiple positive feedback loops. J Biol Chem (2006) 1.75
A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks. BMC Bioinformatics (2006) 1.53
Long-range signaling by phosphoprotein waves arising from bistability in protein kinase cascades. Mol Syst Biol (2006) 1.49
Signaling through receptors and scaffolds: independent interactions reduce combinatorial complexity. Biophys J (2005) 1.44
Modular response analysis of cellular regulatory networks. J Theor Biol (2002) 1.43
Systems biology-embedded target validation: improving efficacy in drug discovery. Wiley Interdiscip Rev Syst Biol Med (2013) 1.41
Temperature dependence of the epidermal growth factor receptor signaling network can be accounted for by a kinetic model. Biochemistry (2002) 1.38
Oscillatory dynamics arising from competitive inhibition and multisite phosphorylation. J Theor Biol (2006) 1.36
When ubiquitination meets phosphorylation: a systems biology perspective of EGFR/MAPK signalling. Cell Commun Signal (2013) 1.36
Anti-A beta 1-11 antibody binds to different beta-amyloid species, inhibits fibril formation, and disaggregates preformed fibrils but not the most toxic oligomers. J Biol Chem (2007) 1.30
Trading the micro-world of combinatorial complexity for the macro-world of protein interaction domains. Biosystems (2005) 1.26
Untangling the signalling wires. Nat Cell Biol (2007) 1.25
Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise. BMC Syst Biol (2012) 1.25
Bistability from double phosphorylation in signal transduction. Kinetic and structural requirements. FEBS J (2006) 1.21
Prolactin-stimulated activation of ERK1/2 mitogen-activated protein kinases is controlled by PI3-kinase/Rac/PAK signaling pathway in breast cancer cells. Cell Signal (2011) 1.21
PI3K/Akt-sensitive MEK-independent compensatory circuit of ERK activation in ER-positive PI3K-mutant T47D breast cancer cells. Cell Signal (2010) 1.18
Crosstalk and signaling switches in mitogen-activated protein kinase cascades. Front Physiol (2012) 1.16
Signaling cascades as cellular devices for spatial computations. J Math Biol (2008) 1.07
A dynamic model of the hypoxia-inducible factor 1α (HIF-1α) network. J Cell Sci (2013) 1.03
Immunogenicity, efficacy, safety, and mechanism of action of epitope vaccine (Lu AF20513) for Alzheimer's disease: prelude to a clinical trial. J Neurosci (2013) 1.02
Control analysis for autonomously oscillating biochemical networks. Biophys J (2002) 1.01
Positional information generated by spatially distributed signaling cascades. PLoS Comput Biol (2009) 1.00
Switches, excitable responses and oscillations in the Ring1B/Bmi1 ubiquitination system. PLoS Comput Biol (2011) 1.00
Multistrip Western blotting to increase quantitative data output. Electrophoresis (2007) 0.97
Inference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracy. J Theor Biol (2005) 0.95
Toggle switches, pulses and oscillations are intrinsic properties of the Src activation/deactivation cycle. FEBS J (2009) 0.95
Refinement of a DNA based Alzheimer's disease epitope vaccine in rabbits. Hum Vaccin Immunother (2013) 0.94
Endocytosis and signalling: a meeting with mathematics. Mol Oncol (2009) 0.92
Pseudophosphatase STYX modulates cell-fate decisions and cell migration by spatiotemporal regulation of ERK1/2. Proc Natl Acad Sci U S A (2013) 0.89
Complexity of receptor tyrosine kinase signal processing. Cold Spring Harb Perspect Biol (2013) 0.89
Molecular dynamics simulations reveal that Tyr-317 phosphorylation reduces Shc binding affinity for phosphotyrosyl residues of epidermal growth factor receptor. Biophys J (2009) 0.89
Signalling over a distance: gradient patterns and phosphorylation waves within single cells. Biochem Soc Trans (2010) 0.88
Tyr-317 phosphorylation increases Shc structural rigidity and reduces coupling of domain motions remote from the phosphorylation site as revealed by molecular dynamics simulations. J Biol Chem (2003) 0.88
It takes two to tango--signalling by dimeric Raf kinases. Mol Biosyst (2013) 0.88
Control of spatially heterogeneous and time-varying cellular reaction networks: a new summation law. J Theor Biol (2003) 0.86
The topology design principles that determine the spatiotemporal dynamics of G-protein cascades. Mol Biosyst (2012) 0.81
Signalling by protein phosphatases and drug development: a systems-centred view. FEBS J (2012) 0.81
Competing to coordinate cell fate decisions: the MST2-Raf-1 signaling device. Cell Cycle (2015) 0.81
Control of the G-protein cascade dynamics by GDP dissociation inhibitors. Mol Biosyst (2013) 0.81
Immunization with a plant-produced colorectal cancer antigen. Cancer Immunol Immunother (2003) 0.80
Versatility of cooperative transcriptional activation: a thermodynamical modeling analysis for greater-than-additive and less-than-additive effects. PLoS One (2012) 0.79
Integrating Bayesian variable selection with Modular Response Analysis to infer biochemical network topology. BMC Syst Biol (2013) 0.79
MST2-RASSF protein-protein interactions through SARAH domains. Brief Bioinform (2015) 0.79
Mammalian protein expression noise: scaling principles and the implications for knockdown experiments. Mol Biosyst (2012) 0.78
Catching transcriptional regulation by thermostatistical modeling. Phys Biol (2012) 0.78
Protein-protein interactions generate hidden feedback and feed-forward loops to trigger bistable switches, oscillations and biphasic dose-responses. Mol Biosyst (2015) 0.77
A dynamic model of the hypoxia-inducible factor 1a (HIF-1a) network. J Cell Sci (2015) 0.77
Species differential regulation of COX2 can be described by an NFκB-dependent logic AND gate. Cell Mol Life Sci (2015) 0.77
Modular interaction strengths in regulatory networks; an example. Mol Biol Rep (2002) 0.76
Frequency modulation of ERK activation dynamics rewires cell fate. Mol Syst Biol (2016) 0.76
Systems medicine: opportunities and challenges for systems biology approaches. FEBS J (2013) 0.76
Feedforward regulation of mRNA stability by prolonged extracellular signal-regulated kinase activity. FEBS J (2015) 0.76
Formation of intracellular concentration landscapes by multisite protein modification. Biophys J (2010) 0.75
Multistrip Western blotting: a tool for comparative quantitative analysis of multiple proteins. Methods Mol Biol (2015) 0.75
The International Consortium on Systems Biology of Receptor Tyrosine Kinase Regulatory Networks. Syst Biol (Stevenage) (2005) 0.75
Detection of the active components of calf thymus nuclear proteins (TNP), histones that are binding with high affinity to HIV-1 envelope proteins and CD4 molecules. Curr HIV Res (2008) 0.75