Published in Nature on November 14, 2002
Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res (2003) 14.79
Universally sloppy parameter sensitivities in systems biology models. PLoS Comput Biol (2007) 7.89
Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol (2003) 7.32
The principles of collective animal behaviour. Philos Trans R Soc Lond B Biol Sci (2006) 6.90
Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals. Nat Immunol (2009) 3.60
Stochastic modelling for quantitative description of heterogeneous biological systems. Nat Rev Genet (2009) 3.27
Systems biology of stem cell fate and cellular reprogramming. Nat Rev Mol Cell Biol (2009) 2.93
Construction, visualisation, and clustering of transcription networks from microarray expression data. PLoS Comput Biol (2007) 2.73
Network visualization and analysis of gene expression data using BioLayout Express(3D). Nat Protoc (2009) 2.66
Design of genetic networks with specified functions by evolution in silico. Proc Natl Acad Sci U S A (2004) 2.60
Software for systems biology: from tools to integrated platforms. Nat Rev Genet (2011) 2.42
A tunable algorithm for collective decision-making. Proc Natl Acad Sci U S A (2006) 2.38
Systems vaccinology. Immunity (2010) 2.36
A logical model provides insights into T cell receptor signaling. PLoS Comput Biol (2007) 2.25
Efficient modeling, simulation and coarse-graining of biological complexity with NFsim. Nat Methods (2010) 2.24
MACSIMS: multiple alignment of complete sequences information management system. BMC Bioinformatics (2006) 2.23
Global analyses of human immune variation reveal baseline predictors of postvaccination responses. Cell (2014) 2.23
Modeling network dynamics: the lac operon, a case study. J Cell Biol (2003) 2.03
Deformation and failure of protein materials in physiologically extreme conditions and disease. Nat Mater (2009) 2.00
Computational imaging in cell biology. J Cell Biol (2003) 1.94
Bacterial adaptation through distributed sensing of metabolic fluxes. Mol Syst Biol (2010) 1.83
AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis. Plant Physiol (2009) 1.81
Iterative approach to model identification of biological networks. BMC Bioinformatics (2005) 1.80
Genomic analysis of metabolic pathway gene expression in mice. Genome Biol (2005) 1.79
Programming with models: modularity and abstraction provide powerful capabilities for systems biology. J R Soc Interface (2009) 1.69
Gene expression prediction by soft integration and the elastic net-best performance of the DREAM3 gene expression challenge. PLoS One (2010) 1.64
The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states. Proc Natl Acad Sci U S A (2005) 1.63
Optimal noise filtering in the chemotactic response of Escherichia coli. PLoS Comput Biol (2006) 1.61
Nanotechnology, nanotoxicology, and neuroscience. Prog Neurobiol (2008) 1.59
Computer modelling of epilepsy. Nat Rev Neurosci (2008) 1.52
In silico cancer modeling: is it ready for prime time? Nat Clin Pract Oncol (2008) 1.52
A survey of current software for network analysis in molecular biology. Hum Genomics (2010) 1.48
Optimal experimental design for parameter estimation of a cell signaling model. PLoS Comput Biol (2009) 1.47
Scaling theory of transport in complex biological networks. Proc Natl Acad Sci U S A (2007) 1.45
SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. Nucleic Acids Res (2009) 1.44
A review of imaging techniques for systems biology. BMC Syst Biol (2008) 1.42
The Biokinetic Spectrum for Temperature. PLoS One (2016) 1.40
Bayesian parameter inference for stochastic biochemical network models using particle Markov chain Monte Carlo. Interface Focus (2011) 1.38
Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics. Mol Syst Biol (2011) 1.35
The Cell Collective: toward an open and collaborative approach to systems biology. BMC Syst Biol (2012) 1.33
Computationally derived points of fragility of a human cascade are consistent with current therapeutic strategies. PLoS Comput Biol (2007) 1.33
Biochemical simulations: stochastic, approximate stochastic and hybrid approaches. Brief Bioinform (2009) 1.31
Computational systems biology: integration of sequence, structure, network, and dynamics. BMC Syst Biol (2011) 1.26
A systems biology perspective on Nrf2-mediated antioxidant response. Toxicol Appl Pharmacol (2009) 1.25
Thermodynamically feasible kinetic models of reaction networks. Biophys J (2007) 1.25
Personalizing medicine: a systems biology perspective. Mol Syst Biol (2009) 1.23
A survey of scholarly literature describing the field of bioinformatics education and bioinformatics educational research. CBE Life Sci Educ (2014) 1.22
Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach. PLoS Comput Biol (2006) 1.21
Directing experimental biology: a case study in mitochondrial biogenesis. PLoS Comput Biol (2009) 1.20
Inference of complex biological networks: distinguishability issues and optimization-based solutions. BMC Syst Biol (2011) 1.20
Hierarchies, multiple energy barriers, and robustness govern the fracture mechanics of alpha-helical and beta-sheet protein domains. Proc Natl Acad Sci U S A (2007) 1.20
Systems vaccinology: learning to compute the behavior of vaccine induced immunity. Wiley Interdiscip Rev Syst Biol Med (2011) 1.19
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes. BMC Bioinformatics (2006) 1.18
Modelling biological systems from molecules to dynamical networks. BMC Syst Biol (2012) 1.18
Systems biology approaches to new vaccine development. Curr Opin Immunol (2011) 1.17
The European Bioinformatics Institute's data resources 2014. Nucleic Acids Res (2013) 1.17
Image-derived, three-dimensional generative models of cellular organization. Cytometry A (2011) 1.16
Integrating systems biology models and biomedical ontologies. BMC Syst Biol (2011) 1.16
Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae. BMC Genomics (2008) 1.15
Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102. Nucleic Acids Res (2006) 1.14
Dynamic simulations on the arachidonic acid metabolic network. PLoS Comput Biol (2007) 1.14
When the optimal is not the best: parameter estimation in complex biological models. PLoS One (2010) 1.13
Microfluidic technologies for temporal perturbations of chemotaxis. Annu Rev Biomed Eng (2010) 1.12
Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria. Mol Syst Biol (2014) 1.12
Evaluating strategies to normalise biological replicates of Western blot data. PLoS One (2014) 1.10
OpenWorm: an open-science approach to modeling Caenorhabditis elegans. Front Comput Neurosci (2014) 1.10
Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions. Mol Syst Biol (2006) 1.10
Transcriptome and proteome exploration to model translation efficiency and protein stability in Lactococcus lactis. PLoS Comput Biol (2009) 1.10
Nested sampling for parameter inference in systems biology: application to an exemplar circadian model. BMC Syst Biol (2013) 1.09
The acute inflammatory response in trauma / hemorrhage and traumatic brain injury: current state and emerging prospects. Libyan J Med (2009) 1.08
pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer. Nucleic Acids Res (2006) 1.07
A scale-free systems theory of motivation and addiction. Neurosci Biobehav Rev (2007) 1.07
Bridging the gap between systems biology and medicine. Genome Med (2009) 1.07
Genetic Interaction Motif Finding by expectation maximization--a novel statistical model for inferring gene modules from synthetic lethality. BMC Bioinformatics (2005) 1.07
Rule-based spatial modeling with diffusing, geometrically constrained molecules. BMC Bioinformatics (2010) 1.07
Rule-based multi-level modeling of cell biological systems. BMC Syst Biol (2011) 1.06
A framework for evolutionary systems biology. BMC Syst Biol (2009) 1.05
ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists. BMC Syst Biol (2009) 1.05
A novel approach for biomarker selection and the integration of repeated measures experiments from two assays. BMC Bioinformatics (2012) 1.05
Systems biology: the next frontier for bioinformatics. Adv Bioinformatics (2011) 1.04
Leaf development: a cellular perspective. Front Plant Sci (2014) 1.04
Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. Wiley Interdiscip Rev Syst Biol Med (2013) 1.04
Topology of molecular interaction networks. BMC Syst Biol (2013) 1.03
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
Network analysis of human glaucomatous optic nerve head astrocytes. BMC Med Genomics (2009) 1.03
CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models. Cell Mol Bioeng (2010) 1.02
Quantitative microscopy and systems biology: seeing the whole picture. Histochem Cell Biol (2008) 1.02
The oncogenic RNA-binding protein Musashi1 is regulated by HuR via mRNA translation and stability in glioblastoma cells. Mol Cancer Res (2012) 1.02
Translational systems biology of inflammation and healing. Wound Repair Regen (2010) 1.02
Human embryonic stem cell derived hepatocyte-like cells as a tool for in vitro hazard assessment of chemical carcinogenicity. Toxicol Sci (2011) 1.02
Towards a systems biology approach to understanding seed dormancy and germination. Proc Biol Sci (2009) 1.02
Systematic reviews of animal models: methodology versus epistemology. Int J Med Sci (2013) 1.01
The future of whole-cell modeling. Curr Opin Biotechnol (2014) 1.01
Systems interface biology. J R Soc Interface (2006) 1.01
Overview of the gene regulation network and the bacteria biotope tasks in BioNLP'13 shared task. BMC Bioinformatics (2015) 1.01
Neurodegenerative diseases: Lessons from genome-wide screens in small model organisms. EMBO Mol Med (2009) 1.00
Signature pathways identified from gene expression profiles in the human uterine cervix before and after spontaneous term parturition. Am J Obstet Gynecol (2007) 1.00
Biological robustness: paradigms, mechanisms, and systems principles. Front Genet (2012) 0.99
Regulation Systems of Bacteria such as Escherichia coli in Response to Nutrient Limitation and Environmental Stresses. Metabolites (2013) 0.99
Multivariate models of inter-subject anatomical variability. Neuroimage (2010) 0.99