Published in PLoS Comput Biol on February 01, 2008
Dynamical modeling and multi-experiment fitting with PottersWheel. Bioinformatics (2008) 2.22
Sloppy models, parameter uncertainty, and the role of experimental design. Mol Biosyst (2010) 2.12
Optimal experimental design for parameter estimation of a cell signaling model. PLoS Comput Biol (2009) 1.47
Laser capture microdissection and protein microarray analysis of human non-small cell lung cancer: differential epidermal growth factor receptor (EGPR) phosphorylation events associated with mutated EGFR compared with wild type. Mol Cell Proteomics (2008) 1.44
Maximizing the information content of experiments in systems biology. PLoS Comput Biol (2013) 1.43
An iterative identification procedure for dynamic modeling of biochemical networks. BMC Syst Biol (2010) 1.41
Reverse engineering and identification in systems biology: strategies, perspectives and challenges. J R Soc Interface (2013) 1.38
Emerging concepts in biomarker discovery; the US-Japan Workshop on Immunological Molecular Markers in Oncology. J Transl Med (2009) 1.31
Pairing computation with experimentation: a powerful coupling for understanding T cell signalling. Nat Rev Immunol (2010) 1.25
Discriminating between rival biochemical network models: three approaches to optimal experiment design. BMC Syst Biol (2010) 1.22
An evolutionary firefly algorithm for the estimation of nonlinear biological model parameters. PLoS One (2013) 1.18
A model invalidation-based approach for elucidating biological signalling pathways, applied to the chemotaxis pathway in R. sphaeroides. BMC Syst Biol (2009) 1.04
Perspectives on tissue interactions in development and disease. Curr Mol Med (2010) 1.00
Optimal design of stimulus experiments for robust discrimination of biochemical reaction networks. Bioinformatics (2012) 0.95
In-vivo real-time control of protein expression from endogenous and synthetic gene networks. PLoS Comput Biol (2014) 0.94
Signaling network prediction by the Ontology Fingerprint enhanced Bayesian network. BMC Syst Biol (2012) 0.90
Robust and efficient parameter estimation in dynamic models of biological systems. BMC Syst Biol (2015) 0.89
Combining test statistics and models in bootstrapped model rejection: it is a balancing act. BMC Syst Biol (2014) 0.89
Parameter identifiability and sensitivity analysis predict targets for enhancement of STAT1 activity in pancreatic cancer and stellate cells. PLoS Comput Biol (2012) 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
Simultaneous model discrimination and parameter estimation in dynamic models of cellular systems. BMC Syst Biol (2013) 0.83
Experimental design schemes for learning Boolean network models. Bioinformatics (2014) 0.81
Multiple model-informed open-loop control of uncertain intracellular signaling dynamics. PLoS Comput Biol (2014) 0.81
Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering. BMC Bioinformatics (2009) 0.80
Systems Pharmacology of the NGF Signaling Through p75 and TrkA Receptors. CPT Pharmacometrics Syst Pharmacol (2014) 0.79
An integrated stochastic model of "inside-out" integrin activation and selective T-lymphocyte recruitment. Langmuir (2012) 0.79
Bridging Mechanistic and Phenomenological Models of Complex Biological Systems. PLoS Comput Biol (2016) 0.78
Nonparametric simulation of signal transduction networks with semi-synchronized update. PLoS One (2012) 0.78
Efficient Optimization of Stimuli for Model-Based Design of Experiments to Resolve Dynamical Uncertainty. PLoS Comput Biol (2015) 0.77
A Bayesian active learning strategy for sequential experimental design in systems biology. BMC Syst Biol (2014) 0.77
The Limitations of Model-Based Experimental Design and Parameter Estimation in Sloppy Systems. PLoS Comput Biol (2016) 0.75
Predicting Drug Combination Index and Simulating the Network-Regulation Dynamics by Mathematical Modeling of Drug-Targeted EGFR-ERK Signaling Pathway. Sci Rep (2017) 0.75
Untangling the ErbB signalling network. Nat Rev Mol Cell Biol (2001) 28.05
Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell (2006) 20.92
Systems biology: a brief overview. Science (2002) 14.69
Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nat Biotechnol (2002) 6.68
A comprehensive pathway map of epidermal growth factor receptor signaling. Mol Syst Biol (2005) 5.68
The EGF receptor family as targets for cancer therapy. Oncogene (2000) 5.44
Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules. Mol Cell Proteomics (2005) 4.33
Quantification of short term signaling by the epidermal growth factor receptor. J Biol Chem (1999) 4.19
A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat Biotechnol (2003) 3.54
Mechanistic studies of the dual phosphorylation of mitogen-activated protein kinase. J Biol Chem (1997) 3.09
Computational modeling of the EGF-receptor system: a paradigm for systems biology. Trends Cell Biol (2003) 2.85
Linking data to models: data regression. Nat Rev Mol Cell Biol (2006) 2.78
Neuregulins and their receptors: a versatile signaling module in organogenesis and oncogenesis. Neuron (1997) 2.33
A benchmark for methods in reverse engineering and model discrimination: problem formulation and solutions. Genome Res (2004) 2.06
Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments. Brief Bioinform (2006) 1.96
Control of MAPK signalling: from complexity to what really matters. Oncogene (2005) 1.82
Optimal experimental design in an epidermal growth factor receptor signalling and down-regulation model. IET Syst Biol (2007) 1.62
Akaike's Information Criterion and Recent Developments in Information Complexity. J Math Psychol (2000) 1.61
Systems biology--an engineering perspective. J Biotechnol (2007) 1.22
Experimental design for analysis of complex kinetics using surface plasmon resonance. Methods (2000) 1.13
Investigating the dynamic behavior of biochemical networks using model families. Bioinformatics (2004) 1.08
Optimal dynamic experiments for bioreactor model discrimination. Appl Microbiol Biotechnol (1995) 1.04
New targets and challenges in the molecular therapeutics of cancer. Br J Clin Pharmacol (2006) 0.97
Current challenges in quantitative modeling of epidermal growth factor signaling. FEBS Lett (2005) 0.94
Application of model discriminating experimental design for modeling and development of a fermentative fed-batch L-valine production process. Biotechnol Bioeng (2005) 0.89
Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat Biotechnol (2002) 8.37
Refinement and standardization of synthetic biological parts and devices. Nat Biotechnol (2008) 6.26
Engineering BioBrick vectors from BioBrick parts. J Biol Eng (2008) 5.98
Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell (2005) 5.71
Regulated cell-to-cell variation in a cell-fate decision system. Nature (2005) 5.68
Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc Natl Acad Sci U S A (2007) 4.80
Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules. Mol Cell Proteomics (2005) 4.33
Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma. Proc Natl Acad Sci U S A (2007) 3.63
Amplifying genetic logic gates. Science (2013) 3.33
Synthetic genomics | options for governance. Biosecur Bioterror (2007) 3.26
Subsystem identification through dimensionality reduction of large-scale gene expression data. Genome Res (2003) 3.06
Effects of HER2 overexpression on cell signaling networks governing proliferation and migration. Mol Syst Biol (2006) 3.01
Refactoring bacteriophage T7. Mol Syst Biol (2005) 3.01
14-3-3sigma controls mitotic translation to facilitate cytokinesis. Nature (2007) 2.98
Computational design of antibody-affinity improvement beyond in vivo maturation. Nat Biotechnol (2007) 2.92
Measuring the activity of BioBrick promoters using an in vivo reference standard. J Biol Eng (2009) 2.79
De novo determination of peptide structure with solid-state magic-angle spinning NMR spectroscopy. Proc Natl Acad Sci U S A (2002) 2.66
Precise and reliable gene expression via standard transcription and translation initiation elements. Nat Methods (2013) 2.61
The bromodomain protein Brd4 insulates chromatin from DNA damage signalling. Nature (2013) 2.46
Oncogenic EGFR signaling networks in glioma. Sci Signal (2009) 2.38
Sloppy models, parameter uncertainty, and the role of experimental design. Mol Biosyst (2010) 2.12
Rational cytokine design for increased lifetime and enhanced potency using pH-activated "histidine switching". Nat Biotechnol (2002) 2.09
Determination of cell fate selection during phage lambda infection. Proc Natl Acad Sci U S A (2008) 2.05
Rewritable digital data storage in live cells via engineered control of recombination directionality. Proc Natl Acad Sci U S A (2012) 2.03
Quantitative estimation of activity and quality for collections of functional genetic elements. Nat Methods (2013) 2.03
Androgen receptor phosphorylation. Regulation and identification of the phosphorylation sites. J Biol Chem (2002) 2.01
A post-synaptic scaffold at the origin of the animal kingdom. PLoS One (2007) 1.96
DNA synthesis and biological security. Nat Biotechnol (2007) 1.91
Engineering life: building a fab for biology. Sci Am (2006) 1.80
Modeling HER2 effects on cell behavior from mass spectrometry phosphotyrosine data. PLoS Comput Biol (2006) 1.74
Temporal dynamics of tyrosine phosphorylation in insulin signaling. Diabetes (2006) 1.68
Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control. Proc Natl Acad Sci U S A (2010) 1.65
Phosphoproteomic analysis of rat liver by high capacity IMAC and LC-MS/MS. J Proteome Res (2006) 1.61
Modeling formalisms in Systems Biology. AMB Express (2011) 1.61
Phosphoproteomic approaches to elucidate cellular signaling networks. Curr Opin Biotechnol (2006) 1.60
Progress in computational protein design. Curr Opin Biotechnol (2007) 1.59
Collecting and organizing systematic sets of protein data. Nat Rev Mol Cell Biol (2006) 1.58
Mcl-1 integrates the opposing actions of signaling pathways that mediate survival and apoptosis. Mol Cell Biol (2009) 1.56
Quantitative analysis of phosphotyrosine signaling networks triggered by CD3 and CD28 costimulation in Jurkat cells. J Immunol (2006) 1.55
Proteomic identification of 14-3-3zeta as a mitogen-activated protein kinase-activated protein kinase 2 substrate: role in dimer formation and ligand binding. Mol Cell Biol (2003) 1.53
Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Proc Natl Acad Sci U S A (2013) 1.53
Quantitative phosphoproteomics by mass spectrometry: past, present, and future. Proteomics (2008) 1.50
Synergistic drug-cytokine induction of hepatocellular death as an in vitro approach for the study of inflammation-associated idiosyncratic drug hepatotoxicity. Toxicol Appl Pharmacol (2009) 1.49
Global phosphoproteome of HT-29 human colon adenocarcinoma cells. J Proteome Res (2005) 1.46
Combination antibody treatment down-regulates epidermal growth factor receptor by inhibiting endosomal recycling. Proc Natl Acad Sci U S A (2010) 1.46
HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. J Am Chem Soc (2008) 1.43
Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance. J Virol (2010) 1.39
Distinct mechanisms act in concert to mediate cell cycle arrest. Proc Natl Acad Sci U S A (2009) 1.37
Interdisciplinary research and education at the biology-engineering-computer science interface: a perspective. Drug Discov Today (2005) 1.32
Aglycosylated immunoglobulin G1 variants productively engage activating Fc receptors. Proc Natl Acad Sci U S A (2008) 1.31
Large-scale discovery of ERK2 substrates identifies ERK-mediated transcriptional regulation by ETV3. Sci Signal (2011) 1.27
Molecular characterization of EGFR and EGFRvIII signaling networks in human glioblastoma tumor xenografts. Mol Cell Proteomics (2012) 1.25
Selection of horseradish peroxidase variants with enhanced enantioselectivity by yeast surface display. Chem Biol (2007) 1.23
CUB-domain-containing protein 1 (CDCP1) activates Src to promote melanoma metastasis. Proc Natl Acad Sci U S A (2011) 1.20
Tapasin is a facilitator, not an editor, of class I MHC peptide binding. J Immunol (2003) 1.19
Mechanical injury and cytokines cause loss of cartilage integrity and upregulate proteins associated with catabolism, immunity, inflammation, and repair. Mol Cell Proteomics (2009) 1.19
Phosphoproteomics: unraveling the signaling web. Mol Cell (2008) 1.18
Measurement and modeling of intrinsic transcription terminators. Nucleic Acids Res (2013) 1.18
Rational approaches to improving selectivity in drug design. J Med Chem (2012) 1.16
Manual validation of peptide sequence and sites of tyrosine phosphorylation from MS/MS spectra. Methods Mol Biol (2009) 1.16
Analysis of MHC class II antigen processing by quantitation of peptides that constitute nested sets. J Immunol (2002) 1.16
A survey of enabling technologies in synthetic biology. J Biol Eng (2013) 1.14
PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies. Mol Cell Proteomics (2010) 1.13
Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis. Chem Biol Drug Des (2007) 1.12
Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range. Proc Natl Acad Sci U S A (2011) 1.11
Phosphotyrosine signaling analysis of site-specific mutations on EGFRvIII identifies determinants governing glioblastoma cell growth. Mol Biosyst (2010) 1.11
Accurate solution of multi-region continuum biomolecule electrostatic problems using the linearized Poisson-Boltzmann equation with curved boundary elements. J Comput Chem (2009) 1.09
Signal transduction. Decoding NF-kappaB signaling. Science (2002) 1.07
Uncovering therapeutic targets for glioblastoma: a systems biology approach. Cell Cycle (2007) 1.07
One-step cloning and chromosomal integration of DNA. ACS Synth Biol (2013) 1.04
The Per2 negative feedback loop sets the period in the mammalian circadian clock mechanism. PLoS Comput Biol (2007) 1.02
A coarse-grained molecular model for glycosaminoglycans: application to chondroitin, chondroitin sulfate, and hyaluronic acid. Biophys J (2005) 1.02
Regulation and specificity of S-nitrosylation and denitrosylation. ACS Chem Biol (2006) 1.01
Qualitatively different T cell phenotypic responses to IL-2 versus IL-15 are unified by identical dependences on receptor signal strength and duration. J Immunol (2013) 1.01
Optimal drug cocktail design: methods for targeting molecular ensembles and insights from theoretical model systems. J Chem Inf Model (2008) 1.01
A computational method for the analysis and prediction of protein:phosphopeptide-binding sites. Protein Sci (2004) 1.00
Action-at-a-distance interactions enhance protein binding affinity. Protein Sci (2005) 1.00
Symmetric signaling by an asymmetric 1 erythropoietin: 2 erythropoietin receptor complex. Mol Cell (2009) 1.00
MIST: Maximum Information Spanning Trees for dimension reduction of biological data sets. Bioinformatics (2009) 0.99
Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease. Proteins (2008) 0.99
Engineered cell-cell communication via DNA messaging. J Biol Eng (2012) 0.99
Defining Cdk5 ligand chemical space with small molecule inhibitors of tau phosphorylation. Chem Biol (2005) 0.98
Limitations of quantitative gene regulation models: a case study. Genome Res (2003) 0.96
Quantitative phosphoproteomic analysis of T cell receptor signaling in diabetes prone and resistant mice. J Proteome Res (2010) 0.96
Rational design of new binding specificity by simultaneous mutagenesis of calmodulin and a target peptide. Biochemistry (2006) 0.96
MCAM: multiple clustering analysis methodology for deriving hypotheses and insights from high-throughput proteomic datasets. PLoS Comput Biol (2011) 0.95
Additivity in the analysis and design of HIV protease inhibitors. J Med Chem (2009) 0.95
Design of improved protein inhibitors of HIV-1 cell entry: Optimization of electrostatic interactions at the binding interface. Proteins (2005) 0.94
Gemini, a bifunctional enzymatic and fluorescent reporter of gene expression. PLoS One (2009) 0.94
A developmentally regulated translational control pathway establishes the meiotic chromosome segregation pattern. Genes Dev (2013) 0.94
Proteomic analysis of cellular signaling. Expert Rev Proteomics (2004) 0.94
An accurate surface formulation for biomolecule electrostatics in non-ionic solutions. Conf Proc IEEE Eng Med Biol Soc (2005) 0.93
Quantification of isomers from a mixture of twelve heparin and heparan sulfate disaccharides using tandem mass spectrometry. Rapid Commun Mass Spectrom (2005) 0.92
An integrated comparative phosphoproteomic and bioinformatic approach reveals a novel class of MPM-2 motifs upregulated in EGFRvIII-expressing glioblastoma cells. Mol Biosyst (2008) 0.92
Efficient calculation of molecular configurational entropies using an information theoretic approximation. J Phys Chem B (2012) 0.92
Computer aided manual validation of mass spectrometry-based proteomic data. Methods (2013) 0.91
Epidermal growth factor receptor downregulation by small heterodimeric binding proteins. Protein Eng Des Sel (2011) 0.91
Optimal charges in lead progression: a structure-based neuraminidase case study. J Med Chem (2006) 0.91