Published in Mol Biosyst on June 17, 2010
Maximizing the information content of experiments in systems biology. PLoS Comput Biol (2013) 1.43
Reverse engineering and identification in systems biology: strategies, perspectives and challenges. J R Soc Interface (2013) 1.38
A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation. Nat Protoc (2014) 1.17
Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria. Mol Syst Biol (2014) 1.12
Genetic design automation: engineering fantasy or scientific renewal? Trends Biotechnol (2011) 1.08
An in-silico model of lipoprotein metabolism and kinetics for the evaluation of targets and biomarkers in the reverse cholesterol transport pathway. PLoS Comput Biol (2014) 1.03
Bayesian design strategies for synthetic biology. Interface Focus (2011) 0.99
Model selection in systems biology depends on experimental design. PLoS Comput Biol (2014) 0.96
Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model. BMC Syst Biol (2013) 0.93
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What can causal networks tell us about metabolic pathways? PLoS Comput Biol (2012) 0.88
Topological sensitivity analysis for systems biology. Proc Natl Acad Sci U S A (2014) 0.84
Optimal experiment selection for parameter estimation in biological differential equation models. BMC Bioinformatics (2012) 0.84
Mathematical and statistical modeling in cancer systems biology. Front Physiol (2012) 0.81
Modeling for (physical) biologists: an introduction to the rule-based approach. Phys Biol (2015) 0.81
Prediction uncertainty assessment of a systems biology model requires a sample of the full probability distribution of its parameters. PeerJ (2014) 0.78
Bridging Mechanistic and Phenomenological Models of Complex Biological Systems. PLoS Comput Biol (2016) 0.78
A generalised enzyme kinetic model for predicting the behaviour of complex biochemical systems. FEBS Open Bio (2015) 0.78
A Six-Stage Workflow for Robust Application of Systems Pharmacology. CPT Pharmacometrics Syst Pharmacol (2016) 0.77
A new framework for modeling decisions about changing information: The Piecewise Linear Ballistic Accumulator model. Cogn Psychol (2016) 0.77
Efficient Optimization of Stimuli for Model-Based Design of Experiments to Resolve Dynamical Uncertainty. PLoS Comput Biol (2015) 0.77
Threshold-free population analysis identifies larger DRG neurons to respond stronger to NGF stimulation. PLoS One (2012) 0.77
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Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems. Cell Syst (2016) 0.76
Multilevel modeling and value of information in clinical trial decision support. BMC Syst Biol (2014) 0.75
Strategies for individual phenotyping of linoleic and arachidonic acid metabolism using an oral glucose tolerance test. PLoS One (2015) 0.75
A novel cost function to estimate parameters of oscillatory biochemical systems. EURASIP J Bioinform Syst Biol (2012) 0.75
Studying Cellular Signal Transduction with OMIC Technologies. J Mol Biol (2015) 0.75
Identifiability, reducibility, and adaptability in allosteric macromolecules. J Gen Physiol (2017) 0.75
The Limitations of Model-Based Experimental Design and Parameter Estimation in Sloppy Systems. PLoS Comput Biol (2016) 0.75
A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A (2004) 44.81
Untangling the ErbB signalling network. Nat Rev Mol Cell Biol (2001) 28.05
HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science (1996) 21.81
Systems biology: a brief overview. Science (2002) 14.69
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Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc Natl Acad Sci U S A (1996) 8.33
Universally sloppy parameter sensitivities in systems biology models. PLoS Comput Biol (2007) 7.89
Emergency response to a smallpox attack: the case for mass vaccination. Proc Natl Acad Sci U S A (2002) 7.78
Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nat Biotechnol (2002) 6.68
The EGFR family and its ligands in human cancer. signalling mechanisms and therapeutic opportunities. Eur J Cancer (2001) 5.96
Parameter estimation in biochemical pathways: a comparison of global optimization methods. Genome Res (2003) 5.50
Systems biology in drug discovery. Nat Biotechnol (2004) 3.29
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
The EGF receptor family: spearheading a merger of signaling and therapeutics. Curr Opin Cell Biol (2007) 2.74
A hybrid approach for efficient and robust parameter estimation in biochemical pathways. Biosystems (2005) 2.43
The statistical mechanics of complex signaling networks: nerve growth factor signaling. Phys Biol (2004) 2.24
A benchmark for methods in reverse engineering and model discrimination: problem formulation and solutions. Genome Res (2004) 2.06
The neuregulin-I/ErbB signaling system in development and disease. Adv Anat Embryol Cell Biol (2007) 1.87
Iterative approach to model identification of biological networks. BMC Bioinformatics (2005) 1.80
Stimulus design for model selection and validation in cell signaling. PLoS Comput Biol (2008) 1.75
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
ErbB receptors and the development of the nervous system. Exp Cell Res (2008) 1.40
Insights into the behaviour of systems biology models from dynamic sensitivity and identifiability analysis: a case study of an NF-kappaB signalling pathway. Mol Biosyst (2006) 1.38
Sloppy-model universality class and the Vandermonde matrix. Phys Rev Lett (2006) 1.33
Designing and encoding models for synthetic biology. J R Soc Interface (2009) 1.23
Systems biology--an engineering perspective. J Biotechnol (2007) 1.22
A dual receptor crosstalk model of G-protein-coupled signal transduction. PLoS Comput Biol (2008) 1.20
A mathematical model of hepatitis C virus dynamics in patients with high baseline viral loads or advanced liver disease. Gastroenterology (2009) 1.11
Applying computational modeling to drug discovery and development. Drug Discov Today (2006) 1.08
Optimal sampling time selection for parameter estimation in dynamic pathway modeling. Biosystems (2004) 1.08
Investigating the dynamic behavior of biochemical networks using model families. Bioinformatics (2004) 1.08
Computational model for effects of ligand/receptor binding properties on interleukin-2 trafficking dynamics and T cell proliferation response. Biotechnol Prog (2000) 1.04
MIST: Maximum Information Spanning Trees for dimension reduction of biological data sets. Bioinformatics (2009) 0.99
Mathematical model of human growth hormone (hGH)-stimulated cell proliferation explains the efficacy of hGH variants as receptor agonists or antagonists. Biotechnol Prog (2004) 0.92
A kernel-based method to determine optimal sampling times for the simultaneous estimation of the parameters of rival mathematical models. J Comput Chem (2009) 0.92
Application of global sensitivity analysis to determine goals for design of experiments: an example study on antibody-producing cell cultures. Biotechnol Prog (2005) 0.89
Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat Biotechnol (2002) 8.37
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
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
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
De novo determination of peptide structure with solid-state magic-angle spinning NMR spectroscopy. Proc Natl Acad Sci U S A (2002) 2.66
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
Rational cytokine design for increased lifetime and enhanced potency using pH-activated "histidine switching". Nat Biotechnol (2002) 2.09
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
Stimulus design for model selection and validation in cell signaling. PLoS Comput Biol (2008) 1.75
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
Modeling formalisms in Systems Biology. AMB Express (2011) 1.61
Phosphoproteomic analysis of rat liver by high capacity IMAC and LC-MS/MS. J Proteome Res (2006) 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
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
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
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
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
Uncovering therapeutic targets for glioblastoma: a systems biology approach. Cell Cycle (2007) 1.07
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
Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease. Proteins (2008) 0.99
MIST: Maximum Information Spanning Trees for dimension reduction of biological data sets. Bioinformatics (2009) 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
A developmentally regulated translational control pathway establishes the meiotic chromosome segregation pattern. Genes Dev (2013) 0.94
Design of improved protein inhibitors of HIV-1 cell entry: Optimization of electrostatic interactions at the binding interface. Proteins (2005) 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
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
Quantification of isomers from a mixture of twelve heparin and heparan sulfate disaccharides using tandem mass spectrometry. Rapid Commun Mass Spectrom (2005) 0.92
Efficient calculation of molecular configurational entropies using an information theoretic approximation. J Phys Chem B (2012) 0.92
Quantifying oncogenic phosphotyrosine signaling networks through systems biology. Curr Opin Genet Dev (2010) 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
Computer aided manual validation of mass spectrometry-based proteomic data. Methods (2013) 0.91
Numerical integration techniques for curved-element discretizations of molecule-solvent interfaces. J Chem Phys (2007) 0.89
SENSITIVITY ANALYSIS FOR OSCILLATING DYNAMICAL SYSTEMS. SIAM J Sci Comput (2009) 0.89
Combined model of intrinsic and extrinsic variability for computational network design with application to synthetic biology. PLoS Comput Biol (2013) 0.89
Biological network design strategies: discovery through dynamic optimization. Mol Biosyst (2006) 0.89
Quantitative proteomic analysis of phosphotyrosine-mediated cellular signaling networks. Methods Mol Biol (2007) 0.87
Novel method for probing the specificity binding profile of ligands: applications to HIV protease. Chem Biol Drug Des (2008) 0.87
Using small molecules and chemical genetics to interrogate signaling networks. ACS Chem Biol (2010) 0.86
Rotamer optimization for protein design through MAP estimation and problem-size reduction. J Comput Chem (2009) 0.86
Toward quantitative phosphotyrosine profiling in vivo. Semin Cell Dev Biol (2012) 0.86
Phosphotyrosine profiling of NSCLC cells in response to EGF and HGF reveals network specific mediators of invasion. J Proteome Res (2013) 0.86
Quantitative methods for developing Fc mutants with extended half-lives. Biotechnol Bioeng (2005) 0.85
Osmotic pressure of aqueous chondroitin sulfate solution: a molecular modeling investigation. Biophys J (2005) 0.85
Evaluation of an inverse molecular design algorithm in a model binding site. Proteins (2009) 0.85
Delineation of lipopolysaccharide (LPS)-binding sites on hemoglobin: from in silico predictions to biophysical characterization. J Biol Chem (2011) 0.85
Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance. Chem Biol (2013) 0.84
Engineered bromodomains to explore the acetylproteome. Proteomics (2015) 0.84
Integrated data management and validation platform for phosphorylated tandem mass spectrometry data. Proteomics (2010) 0.82
Systematic placement of structural water molecules for improved scoring of protein-ligand interactions. Protein Eng Des Sel (2011) 0.82
Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble Enumeration. J Chem Theory Comput (2013) 0.82
Testing the substrate-envelope hypothesis with designed pairs of compounds. ACS Chem Biol (2013) 0.81
X-ray structural and simulation analysis of a protein mutant: the value of a combined approach. Proteins (2004) 0.81