Published in Nature on October 05, 2006
Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics (2007) 9.45
A whole-cell computational model predicts phenotype from genotype. Cell (2012) 5.98
A tunable synthetic mammalian oscillator. Nature (2009) 4.33
Growth control of the eukaryote cell: a systems biology study in yeast. J Biol (2007) 2.79
Predicting metabolic adaptation, body weight change, and energy intake in humans. Am J Physiol Endocrinol Metab (2009) 2.33
Sequencing studies in human genetics: design and interpretation. Nat Rev Genet (2013) 2.27
Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion. Proc Natl Acad Sci U S A (2010) 2.22
Rapid and sustained nuclear-cytoplasmic ERK oscillations induced by epidermal growth factor. Mol Syst Biol (2009) 2.10
Synthetic biology: promises and challenges. Mol Syst Biol (2007) 1.99
Stochastic reaction-diffusion kinetics in the microscopic limit. Proc Natl Acad Sci U S A (2010) 1.85
Multiscale cancer modeling. Annu Rev Biomed Eng (2011) 1.65
Coronary intraplaque hemorrhage evokes a novel atheroprotective macrophage phenotype. Am J Pathol (2009) 1.44
Tipping the balance: robustness of tip cell selection, migration and fusion in angiogenesis. PLoS Comput Biol (2009) 1.40
Reverse engineering and identification in systems biology: strategies, perspectives and challenges. J R Soc Interface (2013) 1.38
SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool. BMC Bioinformatics (2008) 1.30
Simulating non-small cell lung cancer with a multiscale agent-based model. Theor Biol Med Model (2007) 1.25
Nutritional systems biology modeling: from molecular mechanisms to physiology. PLoS Comput Biol (2009) 1.18
Hybridization kinetics is different inside cells. Proc Natl Acad Sci U S A (2009) 1.13
Simulation of genes and genomes forward in time. Curr Genomics (2010) 1.13
Personalized respiratory medicine: exploring the horizon, addressing the issues. Summary of a BRN-AJRCCM workshop held in Barcelona on June 12, 2014. Am J Respir Crit Care Med (2015) 1.12
OpenWorm: an open-science approach to modeling Caenorhabditis elegans. Front Comput Neurosci (2014) 1.10
Cross-scale, cross-pathway evaluation using an agent-based non-small cell lung cancer model. Bioinformatics (2009) 1.10
Simulating cancer growth with multiscale agent-based modeling. Semin Cancer Biol (2014) 1.09
Diverse metabolic model parameters generate similar methionine cycle dynamics. J Theor Biol (2007) 1.06
Cross-scale sensitivity analysis of a non-small cell lung cancer model: linking molecular signaling properties to cellular behavior. Biosystems (2008) 1.03
Oscillations by minimal bacterial suicide circuits reveal hidden facets of host-circuit physiology. PLoS One (2010) 1.02
Models of signalling networks - what cell biologists can gain from them and give to them. J Cell Sci (2013) 0.99
Goethe's dream. Challenges and opportunities for synthetic biology. EMBO Rep (2009) 0.97
A top-performing algorithm for the DREAM3 gene expression prediction challenge. PLoS One (2010) 0.97
The cycling hair follicle as an ideal systems biology research model. Exp Dermatol (2010) 0.95
Towards a multiscale model of colorectal cancer. World J Gastroenterol (2007) 0.95
Phosphorylation site dynamics of early T-cell receptor signaling. PLoS One (2014) 0.93
Data analysis and data mining: current issues in biomedical informatics. Methods Inf Med (2011) 0.93
Mathematical models light up plant signaling. Plant Cell (2014) 0.93
Receptor downregulation and desensitization enhance the information processing ability of signalling receptors. BMC Syst Biol (2007) 0.92
Self-organized partitioning of dynamically localized proteins in bacterial cell division. Mol Syst Biol (2011) 0.92
Engineering prokaryotic gene circuits. FEMS Microbiol Rev (2008) 0.91
Derivation, identification and validation of a computational model of a novel synthetic regulatory network in yeast. J Math Biol (2010) 0.90
Fluctuation and response in biology. Cell Mol Life Sci (2010) 0.90
A Method to Constrain Genome-Scale Models with 13C Labeling Data. PLoS Comput Biol (2015) 0.90
Dehydrogenation of the indoline-containing drug 4-chloro-N-(2-methyl-1-indolinyl)-3-sulfamoylbenzamide (indapamide) by CYP3A4: correlation with in silico predictions. Drug Metab Dispos (2008) 0.88
Inferring regulatory networks from experimental morphological phenotypes: a computational method reverse-engineers planarian regeneration. PLoS Comput Biol (2015) 0.88
A comprehensive, multi-scale dynamical model of ErbB receptor signal transduction in human mammary epithelial cells. PLoS One (2013) 0.88
A metabolic model of human erythrocytes: practical application of the E-Cell Simulation Environment. J Biomed Biotechnol (2010) 0.87
Gene networks and liar paradoxes. Bioessays (2009) 0.86
Investigation of the novel lead of melanocortin 1 receptor for pigmentary disorders. Evid Based Complement Alternat Med (2014) 0.86
Quantifying the effects of co-expressing EGFR and HER2 on HER activation and trafficking. Biochem Biophys Res Commun (2008) 0.86
Alzheimer's disease and type 2 diabetes mellitus: the cholinesterase connection? Lipids Health Dis (2006) 0.85
Robustness and stability of the gene regulatory network involved in DV boundary formation in the Drosophila wing. PLoS One (2007) 0.84
Integrative systems biology for data-driven knowledge discovery. Semin Nephrol (2010) 0.84
Web-based applications for building, managing and analysing kinetic models of biological systems. Brief Bioinform (2008) 0.82
In silico design for adenosine monophosphate-activated protein kinase agonist from traditional chinese medicine for treatment of metabolic syndromes. Evid Based Complement Alternat Med (2014) 0.81
Modeling biology spanning different scales: an open challenge. Biomed Res Int (2014) 0.81
Construction and analysis of the model of energy metabolism in E. coli. PLoS One (2013) 0.81
Approaches to in vitro tissue regeneration with application for human disease modeling and drug development. Drug Discov Today (2014) 0.81
toyLIFE: a computational framework to study the multi-level organisation of the genotype-phenotype map. Sci Rep (2014) 0.81
Can physiological stress alter population persistence? A model with conservation implications. Conserv Physiol (2013) 0.79
Integrated PK-PD and agent-based modeling in oncology. J Pharmacokinet Pharmacodyn (2015) 0.79
Synthetic biology outside the cell: linking computational tools to cell-free systems. Front Bioeng Biotechnol (2014) 0.78
Control of translation initiation: a model-based analysis from limited experimental data. J R Soc Interface (2009) 0.78
Dynamics of elongation factor 2 kinase regulation in cortical neurons in response to synaptic activity. J Neurosci (2015) 0.77
Simplification of stochastic chemical reaction models with fast and slow dynamics. J Biol Phys (2007) 0.77
Quantitative analysis of receptor tyrosine kinase-effector coupling at functionally relevant stimulus levels. J Biol Chem (2015) 0.77
Diffusion-limited attachment of large spherical particles to flexible membrane-immobilized receptors. Eur Biophys J (2015) 0.76
Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach. BMC Bioinformatics (2009) 0.76
Dissecting Leishmania infantum Energy Metabolism - A Systems Perspective. PLoS One (2015) 0.76
In silico models for dynamic connected cell cultures mimicking hepatocyte-endothelial cell-adipocyte interaction circle. PLoS One (2014) 0.75
Selection on Network Dynamics Drives Differential Rates of Protein Domain Evolution. PLoS Genet (2016) 0.75
Simulation of E. coli gene regulation including overlapping cell cycles, growth, division, time delays and noise. PLoS One (2013) 0.75
Constrained inference of protein interaction networks for invadopodium formation in cancer. IET Syst Biol (2016) 0.75
Computer Simulation, Visualization, and Image Processing of Cancer Data and Processes. Cancer Inform (2016) 0.75
In-silico experiments of zebrafish behaviour: modeling swimming in three dimensions. Sci Rep (2017) 0.75
On an infrastructure to support sharing and aggregating pre- and post-publication systems biology research data. Syst Synth Biol (2012) 0.75
A Generic Individual-Based Spatially Explicit Model as a Novel Tool for Investigating Insect-Plant Interactions: A Case Study of the Behavioural Ecology of Frugivorous Tephritidae. PLoS One (2016) 0.75
Reconstruction and visualization of large-scale volumetric models of neocortical circuits for physically-plausible in silico optical studies. BMC Bioinformatics (2017) 0.75
Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol (2002) 9.74
Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases. Nat Biotechnol (2007) 8.88
Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotechnol (2004) 7.02
The FoldX web server: an online force field. Nucleic Acids Res (2005) 6.30
Transcriptome complexity in a genome-reduced bacterium. Science (2009) 4.64
Correlation of mRNA and protein in complex biological samples. FEBS Lett (2009) 4.38
Proteome organization in a genome-reduced bacterium. Science (2009) 3.97
Impact of genome reduction on bacterial metabolism and its regulation. Science (2009) 3.45
Evolvability and hierarchy in rewired bacterial gene networks. Nature (2008) 3.43
Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol (2005) 3.28
Structure-based assembly of protein complexes in yeast. Science (2004) 2.89
Exploring the sequence determinants of amyloid structure using position-specific scoring matrices. Nat Methods (2010) 2.74
Sequence determinants of amyloid fibril formation. Proc Natl Acad Sci U S A (2003) 2.71
SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs. Nucleic Acids Res (2005) 2.69
Noise in transcription negative feedback loops: simulation and experimental analysis. Mol Syst Biol (2006) 2.69
De novo designed peptide-based amyloid fibrils. Proc Natl Acad Sci U S A (2002) 2.59
Control of Drosophila gastrulation by apical localization of adherens junctions and RhoGEF2. Science (2007) 2.51
How protein stability and new functions trade off. PLoS Comput Biol (2008) 2.41
Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases. Nature (2008) 2.37
Prediction of water and metal binding sites and their affinities by using the Fold-X force field. Proc Natl Acad Sci U S A (2005) 2.31
Quantification of mRNA and protein and integration with protein turnover in a bacterium. Mol Syst Biol (2011) 2.31
The stability effects of protein mutations appear to be universally distributed. J Mol Biol (2007) 2.25
Protein aggregation and amyloidosis: confusion of the kinds? Curr Opin Struct Biol (2006) 2.10
A comparative study of the relationship between protein structure and beta-aggregation in globular and intrinsically disordered proteins. J Mol Biol (2004) 2.05
Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets. J Mol Biol (2005) 2.04
Analysis and description of HOLTIN service provision for AECG monitoring in complex indoor environments. Sensors (Basel) (2013) 2.02
Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins. Protein Sci (2005) 1.91
How evolutionary pressure against protein aggregation shaped chaperone specificity. J Mol Biol (2005) 1.91
Computer-aided design of a PDZ domain to recognize new target sequences. Nat Struct Biol (2002) 1.89
Short amino acid stretches can mediate amyloid formation in globular proteins: the Src homology 3 (SH3) case. Proc Natl Acad Sci U S A (2004) 1.83
Recognizing and defining true Ras binding domains I: biochemical analysis. J Mol Biol (2005) 1.76
Computer design of obligate heterodimer meganucleases allows efficient cutting of custom DNA sequences. Nucleic Acids Res (2008) 1.74
Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network. Genome Res (2009) 1.68
Specificity and evolvability in eukaryotic protein interaction networks. PLoS Comput Biol (2006) 1.64
Strand-specific deep sequencing of the transcriptome. Genome Res (2010) 1.58
A graphical interface for the FoldX forcefield. Bioinformatics (2011) 1.50
Engineering gene networks to emulate Drosophila embryonic pattern formation. PLoS Biol (2005) 1.48
Designed tumor necrosis factor-related apoptosis-inducing ligand variants initiating apoptosis exclusively via the DR5 receptor. Proc Natl Acad Sci U S A (2006) 1.45
Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. Mol Syst Biol (2012) 1.44
A detailed thermodynamic analysis of ras/effector complex interfaces. J Mol Biol (2004) 1.42
The amyloid stretch hypothesis: recruiting proteins toward the dark side. Proc Natl Acad Sci U S A (2005) 1.41
Energy estimation in protein design. Curr Opin Struct Biol (2002) 1.39
Bacterial transcriptomics: what is beyond the RNA horiz-ome? Nat Rev Microbiol (2011) 1.39
PepX: a structural database of non-redundant protein-peptide complexes. Nucleic Acids Res (2009) 1.35
Towards cellular systems in 4D. Cell (2005) 1.33
Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and energy calculations. J Mol Biol (2005) 1.33
Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution. PLoS Genet (2013) 1.32
Analyzing protein interaction networks using structural information. Annu Rev Biochem (2008) 1.32
Design of a wearable device for ECG continuous monitoring using wireless technology. Conf Proc IEEE Eng Med Biol Soc (2004) 1.28
Calculation of mutational free energy changes in transition states for protein folding. Biophys J (2003) 1.27
Space as the final frontier in stochastic simulations of biological systems. FEBS Lett (2005) 1.25
Predicted effects of missense mutations on native-state stability account for phenotypic outcome in phenylketonuria, a paradigm of misfolding diseases. Am J Hum Genet (2007) 1.24
Engineering signal transduction pathways. Cell (2010) 1.21
Computational design of peptide ligands. Trends Biotechnol (2011) 1.19
Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus. Nucleic Acids Res (2010) 1.19
Unspecific hydrophobic stabilization of folding transition states. Proc Natl Acad Sci U S A (2002) 1.16
Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: the Pax6 example. Nucleic Acids Res (2010) 1.16
Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants. Nucleic Acids Res (2011) 1.15
Computer modelling in combination with in vitro studies reveals similar binding affinities of Drosophila Crumbs for the PDZ domains of Stardust and DmPar-6. Eur J Cell Biol (2006) 1.15
Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions. PLoS Comput Biol (2005) 1.15
Advancing cell biology through proteomics in space and time (PROSPECTS). Mol Cell Proteomics (2012) 1.15
The multiple-specificity landscape of modular peptide recognition domains. Mol Syst Biol (2011) 1.14
Cell type-specific importance of ras-c-raf complex association rate constants for MAPK signaling. Sci Signal (2009) 1.12
Personalized respiratory medicine: exploring the horizon, addressing the issues. Summary of a BRN-AJRCCM workshop held in Barcelona on June 12, 2014. Am J Respir Crit Care Med (2015) 1.12
Structures in systems biology. Curr Opin Struct Biol (2007) 1.11
Analysis of disease-linked rhodopsin mutations based on structure, function, and protein stability calculations. J Mol Biol (2010) 1.10
Human epidermal stem cell function is regulated by circadian oscillations. Cell Stem Cell (2013) 1.09
The ubiquitin domain superfold: structure-based sequence alignments and characterization of binding epitopes. J Mol Biol (2005) 1.08
Conformational strain in the hydrophobic core and its implications for protein folding and design. Nat Struct Biol (2002) 1.06
Localized transfection on arrays of magnetic beads coated with PCR products. Nat Methods (2005) 1.06
Quantifying information transfer by protein domains: analysis of the Fyn SH2 domain structure. BMC Struct Biol (2008) 1.05
Transcription start site associated RNAs in bacteria. Mol Syst Biol (2012) 1.04
Strategies for protein synthetic biology. Nucleic Acids Res (2010) 1.04
Sequence dependence of amyloid fibril formation: insights from molecular dynamics simulations. J Mol Biol (2005) 1.04
Reconstruction of protein backbones from the BriX collection of canonical protein fragments. PLoS Comput Biol (2008) 1.04
Protein-peptide interactions adopt the same structural motifs as monomeric protein folds. Structure (2009) 1.04
Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm. PLoS Comput Biol (2008) 1.02
Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering. Proc Natl Acad Sci U S A (2008) 1.01
High frequency of germline succinate dehydrogenase mutations in sporadic cervical paragangliomas in northern Spain: mitochondrial succinate dehydrogenase structure-function relationships and clinical-pathological correlations. J Clin Endocrinol Metab (2007) 1.01
DR4-selective tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) variants obtained by structure-based design. J Biol Chem (2008) 1.01
Insights into the origin of the tendency of the PI3-SH3 domain to form amyloid fibrils. J Mol Biol (2002) 1.00
BriX: a database of protein building blocks for structural analysis, modeling and design. Nucleic Acids Res (2010) 0.98
The tryptophan switch: changing ligand-binding specificity from type I to type II in SH3 domains. J Mol Biol (2004) 0.96
Structural and functional protein network analyses predict novel signaling functions for rhodopsin. Mol Syst Biol (2011) 0.95
Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling. Mol Syst Biol (2013) 0.95
Amyloid toxicity is independent of polypeptide sequence, length and chirality. J Mol Biol (2007) 0.95
Synthetic biology: challenges ahead. Bioinformatics (2006) 0.95
Combinatorial approaches: a new tool to search for highly structured beta-hairpin peptides. Proc Natl Acad Sci U S A (2002) 0.95
Building blocks for protein interaction devices. Nucleic Acids Res (2010) 0.94
Integration of protein abundance and structure data reveals competition in the ErbB signaling network. Sci Signal (2013) 0.94
A genome-wide Ras-effector interaction network. J Mol Biol (2007) 0.94
A thermodynamic and kinetic analysis of the folding pathway of an SH3 domain entropically stabilised by a redesigned hydrophobic core. J Mol Biol (2003) 0.94
In situ overlap and sequence synthesis during DNA assembly. ACS Synth Biol (2013) 0.93
Hacking the code of amyloid formation: the amyloid stretch hypothesis. Prion (2007) 0.93