Published in Nucleic Acids Res on June 22, 2012
Single molecule fluorescence approaches shed light on intracellular RNAs. Chem Rev (2014) 0.94
In vivo single-molecule kinetics of activation and subsequent activity of the arabinose promoter. Nucleic Acids Res (2013) 0.83
In vivo kinetics of segregation and polar retention of MS2-GFP-RNA complexes in Escherichia coli. Biophys J (2014) 0.82
Dissecting the stochastic transcription initiation process in live Escherichia coli. DNA Res (2016) 0.78
Effects of rate-limiting steps in transcription initiation on genetic filter motifs. PLoS One (2013) 0.77
In silico analysis of division times of Escherichia coli populations as a function of the partitioning scheme of non-functional proteins. In Silico Biol (2015) 0.77
Effects of multimerization on the temporal variability of protein complex abundance. BMC Syst Biol (2013) 0.76
Precision of Readout at the hunchback Gene: Analyzing Short Transcription Time Traces in Living Fly Embryos. PLoS Comput Biol (2016) 0.75
In vivo transcription kinetics of a synthetic gene uninvolved in stress-response pathways in stressed Escherichia coli cells. PLoS One (2014) 0.75
Application of an E. coli signal sequence as a versatile inclusion body tag. Microb Cell Fact (2017) 0.75
Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements. PLoS Comput Biol (2016) 0.75
Illuminating Messengers: An Update and Outlook on RNA Visualization in Bacteria. Front Microbiol (2017) 0.75
Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods (2001) 414.27
Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. Proc Natl Acad Sci U S A (1992) 35.45
Stochastic gene expression in a single cell. Science (2002) 34.54
A synthetic oscillatory network of transcriptional regulators. Nature (2000) 24.58
Construction of a genetic toggle switch in Escherichia coli. Nature (2000) 24.02
A monomeric red fluorescent protein. Proc Natl Acad Sci U S A (2002) 21.56
Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet (2005) 14.39
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
Engineering stability in gene networks by autoregulation. Nature (2000) 12.88
Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics (1998) 12.21
Mechanism and control of transcription initiation in prokaryotes. Annu Rev Biochem (1985) 11.99
Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science (2010) 11.37
Real-time kinetics of gene activity in individual bacteria. Cell (2005) 11.08
Probing gene expression in live cells, one protein molecule at a time. Science (2006) 7.21
Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. EMBO J (2001) 7.03
The regulation of bacterial transcription initiation. Nat Rev Microbiol (2004) 5.94
Aging and death in an organism that reproduces by morphologically symmetric division. PLoS Biol (2005) 5.83
Rate-limiting steps in RNA chain initiation. Proc Natl Acad Sci U S A (1980) 5.71
Mechanisms underlying expression of Tn10 encoded tetracycline resistance. Annu Rev Microbiol (1994) 4.69
Basic mechanisms of transcript elongation and its regulation. Annu Rev Biochem (1997) 4.63
Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system. Nat Struct Biol (2000) 3.90
Asymmetric segregation of protein aggregates is associated with cellular aging and rejuvenation. Proc Natl Acad Sci U S A (2008) 3.56
Spatial organization of the flow of genetic information in bacteria. Nature (2010) 3.43
Interdependence of translation, transcription and mRNA degradation in the lacZ gene. J Mol Biol (1992) 3.38
A multifunctional gene (tetR) controls Tn10-encoded tetracycline resistance. J Bacteriol (1982) 3.19
RNA polymerase-promoter interactions: the comings and goings of RNA polymerase. J Bacteriol (1998) 3.16
Sequencing and analysis of the Bacillus subtilis lytRABC divergon: a regulatory unit encompassing the structural genes of the N-acetylmuramoyl-L-alanine amidase and its modifier. J Gen Microbiol (1992) 2.93
Use of the tetracycline promoter for the tightly regulated production of a murine antibody fragment in Escherichia coli. Gene (1994) 2.85
A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells. Cell (2007) 2.83
Absolute and relative QPCR quantification of plasmid copy number in Escherichia coli. J Biotechnol (2006) 2.78
General properties of transcriptional time series in Escherichia coli. Nat Genet (2011) 2.76
Kinetics of open complex formation between Escherichia coli RNA polymerase and the lac UV5 promoter. Evidence for a sequential mechanism involving three steps. Biochemistry (1985) 2.71
RNA dynamics in live Escherichia coli cells. Proc Natl Acad Sci U S A (2004) 2.57
Single-molecule approach to molecular biology in living bacterial cells. Annu Rev Biophys (2008) 2.52
Mechanism of bacterial transcription initiation: RNA polymerase - promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis. J Mol Biol (2011) 2.50
Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression. Proc Natl Acad Sci U S A (2009) 2.45
Control of expression of the Tn10-encoded tetracycline resistance operon. II. Interaction of RNA polymerase and TET repressor with the tet operon regulatory region. J Mol Biol (1984) 2.39
Translation-independent localization of mRNA in E. coli. Science (2011) 2.34
Non-genetic heterogeneity from stochastic partitioning at cell division. Nat Genet (2010) 2.32
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
Tetracyclines: antibiotic action, uptake, and resistance mechanisms. Arch Microbiol (1996) 1.99
The RNA binding site of bacteriophage MS2 coat protein. EMBO J (1993) 1.96
Effects of carriage and expression of the Tn10 tetracycline-resistance operon on the fitness of Escherichia coli K12. Mol Biol Evol (1989) 1.87
Construction of a single-copy promoter vector and its use in analysis of regulation of the transposon Tn10 tetracycline resistance determinant. J Bacteriol (1984) 1.85
Evidence for more than one mechanism of plasmid-determined tetracycline resistance in Escherichia coli. J Gen Microbiol (1980) 1.80
Ribosomal protection proteins and their mechanism of tetracycline resistance. Antimicrob Agents Chemother (2003) 1.70
Synthetic biology: integrated gene circuits. Science (2011) 1.66
The flap domain is required for pause RNA hairpin inhibition of catalysis by RNA polymerase and can modulate intrinsic termination. Mol Cell (2003) 1.62
Aureomycin; a product of the continuing search for new antibiotics. Ann N Y Acad Sci (1948) 1.61
Real-time RNA profiling within a single bacterium. Proc Natl Acad Sci U S A (2005) 1.56
Evidence that tetracycline analogs whose primary target is not the bacterial ribosome cause lysis of Escherichia coli. Antimicrob Agents Chemother (1992) 1.53
Tuning and controlling gene expression noise in synthetic gene networks. Nucleic Acids Res (2010) 1.52
Studies of RNA chain initiation by Escherichia coli RNA polymerase bound to T7 DNA. Direct analysis of the kinetics and extent of RNA chain initiation at T7 promoter A1. J Biol Chem (1979) 1.41
Random partitioning of molecules at cell division. Proc Natl Acad Sci U S A (2011) 1.34
Dissecting the functional program of Escherichia coli promoters: the combined mode of action of Lac repressor and AraC activator. Nucleic Acids Res (2001) 1.23
Segmentation of cDNA microarray images by kernel density estimation. J Biomed Inform (2008) 1.03
Thermodynamic analysis of tetracycline-mediated induction of Tet repressor by a quantitative methylation protection assay. Anal Biochem (1995) 1.02
A new experimental approach for studying the association between RNA polymerase and the tet promoter of pBR322. Nucleic Acids Res (1984) 1.01
In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate-limiting steps. BMC Syst Biol (2011) 0.97
A recombinant Escherichia coli sensor strain for the detection of tetracyclines. Anal Chem (1998) 0.93
Asymmetric disposal of individual protein aggregates in Escherichia coli, one aggregate at a time. J Bacteriol (2012) 0.91
Probabilistic RNA partitioning generates transient increases in the normalized variance of RNA numbers in synchronized populations of Escherichia coli. Mol Biosyst (2011) 0.90
Comparison of promoter-specific events during transcription initiation in mycobacteria. Microbiology (2010) 0.87
Stochastic simulations of the tetracycline operon. BMC Syst Biol (2011) 0.87
Tet repressor residues indirectly recognizing anhydrotetracycline. Eur J Biochem (2004) 0.84
Absolute and relative real-time PCR in the quantification of tst gene expression among methicillin-resistant Staphylococcus aureus: evaluation by two mathematical models. Lett Appl Microbiol (2007) 0.83
An interacting multiple model filter-based autofocus strategy for confocal time-lapse microscopy. J Microsc (2011) 0.82
Effects of Mg(2+) on in vivo transcriptional dynamics of the lar promoter. Biosystems (2011) 0.80
A novel Tn10 tetracycline regulon system controlling expression of the bacteriophage T3 gene encoding S-adenosyl-L-methionine hydrolase. Gene (1994) 0.78
Cell-to-cell diversity in protein levels of a gene driven by a tetracycline inducible promoter. BMC Mol Biol (2011) 0.76
High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity. Nat Biotechnol (2010) 3.21
CGH-Plotter: MATLAB toolbox for CGH-data analysis. Bioinformatics (2003) 2.28
In silico microdissection of microarray data from heterogeneous cell populations. BMC Bioinformatics (2005) 2.26
Robust detection of periodic time series measured from biological systems. BMC Bioinformatics (2005) 2.14
Gene expression dynamics in the macrophage exhibit criticality. Proc Natl Acad Sci U S A (2008) 1.95
The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma. J Clin Invest (2013) 1.76
Software for quantification of labeled bacteria from digital microscope images by automated image analysis. Biotechniques (2005) 1.76
Computational framework for simulating fluorescence microscope images with cell populations. IEEE Trans Med Imaging (2007) 1.69
Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks. Signal Processing (2006) 1.61
Global gene expression profile of human cord blood-derived CD133+ cells. Stem Cells (2005) 1.42
Robust quantification of in vitro angiogenesis through image analysis. IEEE Trans Med Imaging (2005) 1.36
Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data. BMC Bioinformatics (2007) 1.24
A novel strategy for microarray quality control using Bayesian networks. Bioinformatics (2003) 1.23
Bright field microscopy as an alternative to whole cell fluorescence in automated analysis of macrophage images. PLoS One (2009) 1.19
Critical networks exhibit maximal information diversity in structure-dynamics relationships. Phys Rev Lett (2008) 1.12
Simulation of microarray data with realistic characteristics. BMC Bioinformatics (2006) 1.12
Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images. BMC Bioinformatics (2010) 1.10
Effects of transcriptional pausing on gene expression dynamics. PLoS Comput Biol (2010) 1.06
Differential gene expression in adipose stem cells cultured in allogeneic human serum versus fetal bovine serum. Tissue Eng Part A (2010) 1.05
Analysis of signaling pathways in 90 cancer cell lines by protein lysate array. J Proteome Res (2007) 1.04
Stochastic differential equation model for cerebellar granule cell excitability. PLoS Comput Biol (2008) 1.04
Mutual information in random Boolean models of regulatory networks. Phys Rev E Stat Nonlin Soft Matter Phys (2008) 1.04
Simulating fluorescent microscope images of cell populations. Conf Proc IEEE Eng Med Biol Soc (2005) 1.01
Simulation tools for biochemical networks: evaluation of performance and usability. Bioinformatics (2004) 1.01
Studying genetic regulatory networks at the molecular level: delayed reaction stochastic models. J Theor Biol (2007) 1.01
In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate-limiting steps. BMC Syst Biol (2011) 0.97
Transcriptome and small RNA deep sequencing reveals deregulation of miRNA biogenesis in human glioma. J Pathol (2013) 0.96
SGN Sim, a stochastic genetic networks simulator. Bioinformatics (2007) 0.96
Mytoe: automatic analysis of mitochondrial dynamics. Bioinformatics (2012) 0.94
Segmentation of folds in tissue section images. Conf Proc IEEE Eng Med Biol Soc (2007) 0.93
Information diversity in structure and dynamics of simulated neuronal networks. Front Comput Neurosci (2011) 0.92
Asymmetric disposal of individual protein aggregates in Escherichia coli, one aggregate at a time. J Bacteriol (2012) 0.91
Delayed stochastic model of transcription at the single nucleotide level. J Comput Biol (2009) 0.90
Probabilistic RNA partitioning generates transient increases in the normalized variance of RNA numbers in synchronized populations of Escherichia coli. Mol Biosyst (2011) 0.90
Effects of the promoter open complex formation on gene expression dynamics. Phys Rev E Stat Nonlin Soft Matter Phys (2010) 0.90
Cell segmentation by multi-resolution analysis and maximum likelihood estimation (MAMLE). BMC Bioinformatics (2013) 0.89
Characterization of aberrant pathways across human cancers. BMC Syst Biol (2013) 0.89
A K-means segmentation method for finding 2-D object areas based on 3-D image stacks obtained by confocal microscopy. Conf Proc IEEE Eng Med Biol Soc (2007) 0.88
A systems biological approach to identify key transcription factors and their genomic neighborhoods in human sarcomas. Chin J Cancer (2011) 0.86
Regulation of mean and noise of the in vivo kinetics of transcription under the control of the lac/ara-1 promoter. FEBS Lett (2012) 0.86
Computational methods for estimation of cell cycle phase distributions of yeast cells. EURASIP J Bioinform Syst Biol (2007) 0.86
Transcriptional profiling reflects shared and unique characters for CD34+ and CD133+ cells. Stem Cells Dev (2006) 0.85
A beta-mixture model for dimensionality reduction, sample classification and analysis. BMC Bioinformatics (2011) 0.84
Extraction of the number of peroxisomes in yeast cells by automated image analysis. Conf Proc IEEE Eng Med Biol Soc (2006) 0.84
Cancer systems biology: signal processing for cancer research. Chin J Cancer (2011) 0.84
CellAging: a tool to study segregation and partitioning in division in cell lineages of Escherichia coli. Bioinformatics (2013) 0.84
Stochastic sequence-level model of coupled transcription and translation in prokaryotes. BMC Bioinformatics (2011) 0.83
In vivo single-molecule kinetics of activation and subsequent activity of the arabinose promoter. Nucleic Acids Res (2013) 0.83
A joint finite mixture model for clustering genes from independent Gaussian and beta distributed data. BMC Bioinformatics (2009) 0.83
Evaluating the performance of microarray segmentation algorithms. Bioinformatics (2006) 0.83
Effects of temperature on the dynamics of the LacI-TetR-CI repressilator. Mol Biosyst (2013) 0.82
NanoMiner - integrative human transcriptomics data resource for nanoparticle research. PLoS One (2013) 0.82
Stability of functions in Boolean models of gene regulatory networks. Chaos (2005) 0.82
Genome wide study of NF-Y type CCAAT boxes in unidirectional and bidirectional promoters in human and mouse. J Theor Biol (2011) 0.81
Quantification of vesicles in differentiating human SH-SY5Y neuroblastoma cells by automated image analysis. Neurosci Lett (2005) 0.81
An integrated study of aberrant gene copy number and gene expression in GIST and LMS. Technol Cancer Res Treat (2010) 0.81
Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network. PLoS One (2010) 0.81
Tracking perturbations in Boolean networks with spectral methods. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 0.81
Information propagation within the Genetic Network of Saccharomyces cerevisiae. BMC Syst Biol (2010) 0.81
Tuning cell differentiation patterns and single cell dynamics by regulating proteins' functionalities in a toggle switch. J Theor Biol (2009) 0.81
Automated quantification of lymph node size and number in surgical specimens of stage II colorectal cancer. Conf Proc IEEE Eng Med Biol Soc (2005) 0.81
Quantifying local structure effects in network dynamics. Phys Rev E Stat Nonlin Soft Matter Phys (2008) 0.81
Effects of Mg(2+) on in vivo transcriptional dynamics of the lar promoter. Biosystems (2011) 0.80
Dynamical effects of transcriptional pause-prone sites. Comput Biol Chem (2010) 0.80
Comparison and optimization of transient transfection methods at human astrocytoma cell line 1321N1. Anal Biochem (2011) 0.80
NF-Y influences directionality of transcription from the bidirectional Mrps12/Sarsm promoter in both mouse and human cells. Biochim Biophys Acta (2009) 0.80
Three-dimensional digital image analysis of immunostained neurons in thick tissue sections. Conf Proc IEEE Eng Med Biol Soc (2006) 0.79
Robustness and information propagation in attractors of Random Boolean Networks. PLoS One (2012) 0.79
Kinetics of the cellular intake of a gene expression inducer at high concentrations. Mol Biosyst (2015) 0.79
Robustness of the division symmetry in Escherichia coli and functional consequences of symmetry breaking. Phys Biol (2014) 0.79
Differential gene expression in non-malignant tumour microenvironment is associated with outcome in follicular lymphoma patients treated with rituximab and CHOP. Br J Haematol (2006) 0.79
Unsupervised analysis uncovers changes in histopathologic diagnosis in supervised genomic studies. Technol Cancer Res Treat (2006) 0.79