Published in Mol Syst Biol on August 01, 2006
Nature, nurture, or chance: stochastic gene expression and its consequences. Cell (2008) 12.13
The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol (2009) 6.58
Fundamental limits on the suppression of molecular fluctuations. Nature (2010) 2.75
Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression. Proc Natl Acad Sci U S A (2009) 2.45
Colored extrinsic fluctuations and stochastic gene expression. Mol Syst Biol (2008) 2.32
Quantification of mRNA and protein and integration with protein turnover in a bacterium. Mol Syst Biol (2011) 2.31
Adaptive response of a gene network to environmental changes by fitness-induced attractor selection. PLoS One (2006) 2.30
Non-genetic cell-to-cell variability and the consequences for pharmacology. Curr Opin Chem Biol (2009) 2.05
Noise propagation and signaling sensitivity in biological networks: a role for positive feedback. PLoS Comput Biol (2007) 1.94
The role of incoherent microRNA-mediated feedforward loops in noise buffering. PLoS Comput Biol (2011) 1.84
Intron length increases oscillatory periods of gene expression in animal cells. Genes Dev (2008) 1.63
Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression. Genome Res (2011) 1.62
Tuning and controlling gene expression noise in synthetic gene networks. Nucleic Acids Res (2010) 1.52
Impact of gene expression noise on organismal fitness and the efficacy of natural selection. Proc Natl Acad Sci U S A (2011) 1.46
Intron delays and transcriptional timing during development. Dev Cell (2008) 1.43
Recurrent design patterns in the feedback regulation of the mammalian signalling network. Mol Syst Biol (2008) 1.41
A Stochastic Model of the Yeast Cell Cycle Reveals Roles for Feedback Regulation in Limiting Cellular Variability. PLoS Comput Biol (2016) 1.39
Counter-intuitive stochastic behavior of simple gene circuits with negative feedback. Biophys J (2010) 1.22
Rate of environmental change determines stress response specificity. Proc Natl Acad Sci U S A (2013) 1.21
Optimal feedback strength for noise suppression in autoregulatory gene networks. Biophys J (2009) 1.21
Strong negative self regulation of prokaryotic transcription factors increases the intrinsic noise of protein expression. BMC Syst Biol (2008) 1.15
Antiviral response dictated by choreographed cascade of transcription factors. J Immunol (2010) 1.10
Bimodal gene expression in noncooperative regulatory systems. Proc Natl Acad Sci U S A (2010) 1.09
miR-451 regulates dendritic cell cytokine responses to influenza infection. J Immunol (2012) 1.08
Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli. BMC Syst Biol (2011) 1.07
Dose response relationship in anti-stress gene regulatory networks. PLoS Comput Biol (2006) 1.07
Culture history and population heterogeneity as determinants of bacterial adaptation: the adaptomics of a single environmental transition. Microbiol Mol Biol Rev (2012) 1.07
Noise management by molecular networks. PLoS Comput Biol (2009) 1.05
Stochastic analysis of the SOS response in Escherichia coli. PLoS One (2009) 0.97
Gene autoregulation via intronic microRNAs and its functions. BMC Syst Biol (2012) 0.96
Transcriptional autoregulatory loops are highly conserved in vertebrate evolution. PLoS One (2008) 0.95
Engineering prokaryotic gene circuits. FEMS Microbiol Rev (2008) 0.91
The magnitude and colour of noise in genetic negative feedback systems. Nucleic Acids Res (2012) 0.91
Quantifying intrinsic and extrinsic variability in stochastic gene expression models. PLoS One (2013) 0.91
Stochastic noise and synchronisation during dictyostelium aggregation make cAMP oscillations robust. PLoS Comput Biol (2007) 0.90
Combined model of intrinsic and extrinsic variability for computational network design with application to synthetic biology. PLoS Comput Biol (2013) 0.89
The negative feedback-loop between the oncomir Mir-24-1 and menin modulates the Men1 tumorigenesis by mimicking the "Knudson's second hit". PLoS One (2012) 0.89
Decoy receptors block TRAIL sensitivity at a supracellular level: the role of stromal cells in controlling tumour TRAIL sensitivity. Oncogene (2015) 0.88
A novel non-overlapping bi-clustering algorithm for network generation using living cell array data. Bioinformatics (2007) 0.88
A synthetic biology approach to understanding cellular information processing. ACS Synth Biol (2012) 0.87
Stochastic simulations of the tetracycline operon. BMC Syst Biol (2011) 0.87
Design and implementation of a biomolecular concentration tracker. ACS Synth Biol (2014) 0.85
Transcription factor binding kinetics constrain noise suppression via negative feedback. Nat Commun (2013) 0.85
Synthetic mammalian transgene negative autoregulation. Mol Syst Biol (2013) 0.85
A reconfigurable NAND/NOR genetic logic gate. BMC Syst Biol (2012) 0.85
Kinetics in signal transduction pathways involving promiscuous oligomerizing receptors can be determined by receptor specificity: apoptosis induction by TRAIL. Mol Cell Proteomics (2012) 0.85
Phenotypic impact of regulatory noise in cellular stress-response pathways. Syst Synth Biol (2010) 0.84
Multicellular computing using conjugation for wiring. PLoS One (2013) 0.84
Advances and computational tools towards predictable design in biological engineering. Comput Math Methods Med (2014) 0.84
Modeling suggests that gene circuit architecture controls phenotypic variability in a bacterial persistence network. BMC Syst Biol (2012) 0.84
Delay-induced transient increase and heterogeneity in gene expression in negatively auto-regulated gene circuits. PLoS One (2008) 0.84
Cellular noise suppression by the regulator of G protein signaling Sst2. Mol Cell (2014) 0.84
Quantifying negative feedback regulation by micro-RNAs. Phys Biol (2011) 0.83
Frequency domain analysis reveals external periodic fluctuations can generate sustained p53 oscillation. PLoS One (2011) 0.82
Noise propagation in gene regulation networks involving interlinked positive and negative feedback loops. PLoS One (2012) 0.82
Consequences of mRNA transport on stochastic variability in protein levels. Biophys J (2012) 0.82
Transcription factor competition allows embryonic stem cells to distinguish authentic signals from noise. Cell Syst (2015) 0.82
Using topology to tame the complex biochemistry of genetic networks. Philos Trans A Math Phys Eng Sci (2012) 0.81
Interplay between intrinsic noise and the stochasticity of the cell cycle in bacterial colonies. Biophys J (2010) 0.81
Phenotypic Variability in Synthetic Biology Applications: Dealing with Noise in Microbial Gene Expression. Front Microbiol (2016) 0.80
Modelling the effects of cell-to-cell variability on the output of interconnected gene networks in bacterial populations. BMC Syst Biol (2015) 0.80
Increasing the efficiency of bacterial transcription simulations: when to exclude the genome without loss of accuracy. BMC Bioinformatics (2008) 0.80
Functional roles of slow enzyme conformational changes in network dynamics. Biophys J (2012) 0.80
Defining biological networks for noise buffering and signaling sensitivity using approximate Bayesian computation. ScientificWorldJournal (2014) 0.80
Linearization through distortion: a new facet of negative feedback in signalling. Mol Syst Biol (2009) 0.79
A GFP-lacZ bicistronic reporter system for promoter analysis in environmental gram-negative bacteria. PLoS One (2012) 0.79
Noise modulation in retinoic acid signaling sharpens segmental boundaries of gene expression in the embryonic zebrafish hindbrain. Elife (2016) 0.79
Quantitative analysis of cellular metabolic dissipative, self-organized structures. Int J Mol Sci (2010) 0.78
Post-translational regulation enables robust p53 regulation. BMC Syst Biol (2013) 0.78
A simple negative interaction in the positive transcriptional feedback of a single gene is sufficient to produce reliable oscillations. PLoS One (2011) 0.78
Quantitative, non-disruptive monitoring of transcription in single cells with a broad-host range GFP-luxCDABE dual reporter system. PLoS One (2012) 0.78
Small regulatory RNA-induced growth rate heterogeneity of Bacillus subtilis. PLoS Genet (2015) 0.77
Delays induce novel stochastic effects in negative feedback gene circuits. Biophys J (2014) 0.77
Design of regulation and dynamics in simple biochemical pathways. J Math Biol (2010) 0.77
Addressing biological uncertainties in engineering gene circuits. Integr Biol (Camb) (2015) 0.77
Estimation of the source-by-source effect of autorepression on genetic noise. Biophys J (2008) 0.76
Semi-adaptive response and noise attenuation in bone morphogenetic protein signalling. J R Soc Interface (2015) 0.76
Is the Cell Nucleus a Necessary Component in Precise Temporal Patterning? PLoS One (2015) 0.75
Stochastic effects as a force to increase the complexity of signaling networks. Sci Rep (2013) 0.75
Build to understand: synthetic approaches to biology. Integr Biol (Camb) (2015) 0.75
A Metabolic Widget Adjusts the Phosphoenolpyruvate-Dependent Fructose Influx in Pseudomonas putida. mSystems (2016) 0.75
Transcription factor levels enable metabolic diversification of single cells of environmental bacteria. ISME J (2015) 0.75
Determining the Limitations and Benefits of Noise in Gene Regulation and Signal Transduction through Single Cell, Microscopy-Based Analysis. J Mol Biol (2017) 0.75
Stochastic timing in gene expression for simple regulatory strategies. Nucleic Acids Res (2017) 0.75
Ultrasensitive Negative Feedback Control: A Natural Approach for the Design of Synthetic Controllers. PLoS One (2016) 0.75
Stochastic gene expression in a single cell. Science (2002) 34.54
Construction of a genetic toggle switch in Escherichia coli. Nature (2000) 24.02
Partitioning of lipid-modified monomeric GFPs into membrane microdomains of live cells. Science (2002) 18.89
Regulation of noise in the expression of a single gene. Nat Genet (2002) 14.93
Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res (1997) 13.15
Noise in eukaryotic gene expression. Nature (2003) 13.01
Engineering stability in gene networks by autoregulation. Nature (2000) 12.88
Control of stochasticity in eukaryotic gene expression. Science (2004) 12.85
Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc Natl Acad Sci U S A (2002) 11.46
Summing up the noise in gene networks. Nature (2004) 9.62
Noise propagation in gene networks. Science (2005) 8.19
Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. Biophys J (2001) 7.52
Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. EMBO J (2001) 7.03
Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis (1997) 6.82
New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Appl Environ Microbiol (1998) 6.61
RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol (2000) 6.36
Mechanisms underlying expression of Tn10 encoded tetracycline resistance. Annu Rev Microbiol (1994) 4.69
From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. Bioessays (1998) 4.42
Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Proc Natl Acad Sci U S A (2005) 4.11
Gene network shaping of inherent noise spectra. Nature (2006) 3.25
Comparison of classical and autogenous systems of regulation in inducible operons. Nature (1974) 3.19
Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases. Syst Biol (Stevenage) (2004) 3.18
Stochastic reaction-diffusion simulation with MesoRD. Bioinformatics (2005) 2.96
Structural requirements of tetracycline-Tet repressor interaction: determination of equilibrium binding constants for tetracycline analogs with the Tet repressor. Antimicrob Agents Chemother (1991) 2.12
Frequency domain analysis of noise in autoregulated gene circuits. Proc Natl Acad Sci U S A (2003) 2.10
SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks. Syst Biol (Stevenage) (2004) 2.03
DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise. Curr Opin Genet Dev (2005) 2.03
Tethering sigma70 to RNA polymerase reveals high in vivo activity of sigma factors and sigma70-dependent pausing at promoter-distal locations. Genes Dev (2003) 1.64
Evidence that tetracycline analogs whose primary target is not the bacterial ribosome cause lysis of Escherichia coli. Antimicrob Agents Chemother (1992) 1.53
Cytoplasmic RNA Polymerase in Escherichia coli. J Bacteriol (2001) 1.19
Thermodynamic analysis of tetracycline-mediated induction of Tet repressor by a quantitative methylation protection assay. Anal Biochem (1995) 1.02
Noise-induced cooperative behavior in a multicell system. Bioinformatics (2005) 1.00
Combinations of the alpha-helix-turn-alpha-helix motif of TetR with respective residues from LacI or 434Cro: DNA recognition, inducer binding, and urea-dependent denaturation. Biochemistry (1997) 1.00
STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res (2005) 10.44
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
From in vivo to in silico biology and back. Nature (2006) 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
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
FlhA provides the adaptor for coordinated delivery of late flagella building blocks to the type III secretion system. Proc Natl Acad Sci U S A (2010) 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
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
Cell type-specific importance of ras-c-raf complex association rate constants for MAPK signaling. Sci Signal (2009) 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
Sequence dependence of amyloid fibril formation: insights from molecular dynamics simulations. J Mol Biol (2005) 1.04
Strategies for protein synthetic biology. Nucleic Acids Res (2010) 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
Structural basis for the molecular evolution of SRP-GTPase activation by protein. Nat Struct Mol Biol (2011) 0.96
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
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
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