Published in Cytometry A on January 01, 2010
High-throughput, subpixel precision analysis of bacterial morphogenesis and intracellular spatio-temporal dynamics. Mol Microbiol (2011) 4.82
Pattern recognition software and techniques for biological image analysis. PLoS Comput Biol (2010) 2.22
Automatic extraction of nuclei centroids of mouse embryonic cells from fluorescence microscopy images. PLoS One (2012) 1.04
Sequestration-based bistability enables tuning of the switching boundaries and design of a latch. Mol Syst Biol (2012) 0.99
Robust Nucleus/Cell Detection and Segmentation in Digital Pathology and Microscopy Images: A Comprehensive Review. IEEE Rev Biomed Eng (2016) 0.99
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
Asymmetric disposal of individual protein aggregates in Escherichia coli, one aggregate at a time. J Bacteriol (2012) 0.91
Cell segmentation by multi-resolution analysis and maximum likelihood estimation (MAMLE). BMC Bioinformatics (2013) 0.89
Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments. PLoS Comput Biol (2016) 0.89
BactImAS: a platform for processing and analysis of bacterial time-lapse microscopy movies. BMC Bioinformatics (2014) 0.87
FogBank: a single cell segmentation across multiple cell lines and image modalities. BMC Bioinformatics (2014) 0.87
Survey statistics of automated segmentations applied to optical imaging of mammalian cells. BMC Bioinformatics (2015) 0.86
Adaptive Mixture Modelling Metropolis Methods for Bayesian Analysis of Non-linear State-Space Models. J Comput Graph Stat (2010) 0.86
Analysis of gene expression levels in individual bacterial cells without image segmentation. Biochem Biophys Res Commun (2012) 0.85
GoIFISH: a system for the quantification of single cell heterogeneity from IFISH images. Genome Biol (2014) 0.85
Extracting fluorescent reporter time courses of cell lineages from high-throughput microscopy at low temporal resolution. PLoS One (2011) 0.84
Image analysis in fluorescence microscopy: bacterial dynamics as a case study. Bioessays (2012) 0.83
Bayesian learning from marginal data in bionetwork models. Stat Appl Genet Mol Biol (2011) 0.81
CellAnimation: an open source MATLAB framework for microscopy assays. Bioinformatics (2011) 0.80
Improved and robust detection of cell nuclei from four dimensional fluorescence images. PLoS One (2014) 0.79
Model-controlled flooding with applications to image reconstruction and segmentation. J Electron Imaging (2012) 0.77
Adaptive imaging cytometry to estimate parameters of gene networks models in systems and synthetic biology. PLoS One (2014) 0.77
Single Cell Analysis of a Bacterial Sender-Receiver System. PLoS One (2016) 0.76
Robust cell tracking in epithelial tissues through identification of maximum common subgraphs. J R Soc Interface (2016) 0.75
Long-term tracking of budding yeast cells in brightfield microscopy: CellStar and the Evaluation Platform. J R Soc Interface (2017) 0.75
Image analysis driven single-cell analytics for systems microbiology. BMC Syst Biol (2017) 0.75
Fast automated yeast cell counting algorithm using bright-field and fluorescence microscopic images. Biol Proced Online (2013) 0.75
ViCAR: An Adaptive and Landmark-Free Registration of Time Lapse Image Data from Microfluidics Experiments. Front Genet (2017) 0.75
Stochastic gene expression in a single cell. Science (2002) 34.54
CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol (2006) 32.51
A synthetic oscillatory network of transcriptional regulators. Nature (2000) 24.58
Control of stochasticity in eukaryotic gene expression. Science (2004) 12.85
Gene regulation at the single-cell level. Science (2005) 11.52
Real-time kinetics of gene activity in individual bacteria. Cell (2005) 11.08
Automated cell lineage tracing in Caenorhabditis elegans. Proc Natl Acad Sci U S A (2006) 6.22
An excitable gene regulatory circuit induces transient cellular differentiation. Nature (2006) 6.03
Regulated cell-to-cell variation in a cell-fate decision system. Nature (2005) 5.68
Tunability and noise dependence in differentiation dynamics. Science (2007) 5.23
Imaging in systems biology. Cell (2007) 4.62
Gene regulatory networks for development. Proc Natl Acad Sci U S A (2005) 4.45
The effects of molecular noise and size control on variability in the budding yeast cell cycle. Nature (2007) 4.15
A bottom-up approach to gene regulation. Nature (2006) 4.03
Fluorescence-intensity distribution analysis and its application in biomolecular detection technology. Proc Natl Acad Sci U S A (1999) 4.01
Programmed population control by cell-cell communication and regulated killing. Nature (2004) 4.00
Resilient circadian oscillator revealed in individual cyanobacteria. Nature (2004) 3.84
Single-cell quantification of molecules and rates using open-source microscope-based cytometry. Nat Methods (2007) 3.77
Automated segmentation, classification, and tracking of cancer cell nuclei in time-lapse microscopy. IEEE Trans Biomed Eng (2006) 3.45
Gene network shaping of inherent noise spectra. Nature (2006) 3.25
Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins. Nat Methods (2006) 2.94
Transient-mediated fate determination in a transcriptional circuit of HIV. Nat Genet (2008) 2.91
Heritable stochastic switching revealed by single-cell genealogy. PLoS Biol (2007) 2.11
A microfluidic device for temporally controlled gene expression and long-term fluorescent imaging in unperturbed dividing yeast cells. PLoS One (2008) 1.90
Automated cell lineage construction: a rapid method to analyze clonal development established with murine neural progenitor cells. Cell Cycle (2006) 1.85
Stochastic gene expression out-of-steady-state in the cyanobacterial circadian clock. Nature (2007) 1.74
Dynamics of single-cell gene expression. Mol Syst Biol (2006) 1.69
A fluctuation method to quantify in vivo fluorescence data. Biophys J (2006) 1.39
Automated tracking of gene expression in individual cells and cell compartments. J R Soc Interface (2006) 1.30
Application of 2D and 3D DIAS to motion analysis of live cells in transmission and confocal microscopy imaging. Methods Mol Biol (2006) 0.92
Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature (2005) 19.56
Gene expression predictors of breast cancer outcomes. Lancet (2003) 6.99
Retracted A genomic strategy to refine prognosis in early-stage non-small-cell lung cancer. N Engl J Med (2006) 6.69
Retracted An integrated genomic-based approach to individualized treatment of patients with advanced-stage ovarian cancer. J Clin Oncol (2007) 5.77
High-Dimensional Sparse Factor Modeling: Applications in Gene Expression Genomics. J Am Stat Assoc (2008) 3.92
Gene expression phenotypic models that predict the activity of oncogenic pathways. Nat Genet (2003) 3.78
Long-term monitoring of bacteria undergoing programmed population control in a microchemostat. Science (2005) 3.54
Engineering microbial consortia: a new frontier in synthetic biology. Trends Biotechnol (2008) 3.26
Statistical mixture modeling for cell subtype identification in flow cytometry. Cytometry A (2008) 3.06
A synthetic Escherichia coli predator-prey ecosystem. Mol Syst Biol (2008) 2.92
A bistable Rb-E2F switch underlies the restriction point. Nat Cell Biol (2008) 2.91
Emergent bistability by a growth-modulating positive feedback circuit. Nat Chem Biol (2009) 2.86
Integrated modeling of clinical and gene expression information for personalized prediction of disease outcomes. Proc Natl Acad Sci U S A (2004) 2.74
Gene expression profiling and genetic markers in glioblastoma survival. Cancer Res (2005) 2.63
Understanding GPU Programming for Statistical Computation: Studies in Massively Parallel Massive Mixtures. J Comput Graph Stat (2010) 2.38
Patterns of gene expression that characterize long-term survival in advanced stage serous ovarian cancers. Clin Cancer Res (2005) 2.37
Gene expression phenotypes of atherosclerosis. Arterioscler Thromb Vasc Biol (2004) 2.23
A genomic strategy to elucidate modules of oncogenic pathway signaling networks. Mol Cell (2009) 2.22
Gene expression profiles of multiple breast cancer phenotypes and response to neoadjuvant chemotherapy. Clin Cancer Res (2006) 1.72
The genomic analysis of lactic acidosis and acidosis response in human cancers. PLoS Genet (2008) 1.60
Spatial Mixture Modelling for Unobserved Point Processes: Examples in Immunofluorescence Histology. Bayesian Anal (2009) 1.58
Genomic prediction of locoregional recurrence after mastectomy in breast cancer. J Clin Oncol (2006) 1.57
Towards integrated clinico-genomic models for personalized medicine: combining gene expression signatures and clinical factors in breast cancer outcomes prediction. Hum Mol Genet (2003) 1.51
Hierarchical modeling for rare event detection and cell subset alignment across flow cytometry samples. PLoS Comput Biol (2013) 1.35
Lactic acidosis triggers starvation response with paradoxical induction of TXNIP through MondoA. PLoS Genet (2010) 1.34
Distinctions in the specificity of E2F function revealed by gene expression signatures. Proc Natl Acad Sci U S A (2005) 1.34
Biology by design: reduction and synthesis of cellular components and behaviour. J R Soc Interface (2007) 1.33
Origin of bistability underlying mammalian cell cycle entry. Mol Syst Biol (2011) 1.32
Prediction of optimal versus suboptimal cytoreduction of advanced-stage serous ovarian cancer with the use of microarrays. Am J Obstet Gynecol (2004) 1.29
Prediction and uncertainty in the analysis of gene expression profiles. In Silico Biol (2002) 1.27
Optimality and robustness in quorum sensing (QS)-mediated regulation of a costly public good enzyme. Proc Natl Acad Sci U S A (2012) 1.27
Distinct gene expression phenotypes of cells lacking Rb and Rb family members. Cancer Res (2003) 1.26
Network calisthenics: control of E2F dynamics in cell cycle entry. Cell Cycle (2011) 1.25
Bayesian analysis of matrix normal graphical models. Biometrika (2009) 1.18
An integrative approach to characterize disease-specific pathways and their coordination: a case study in cancer. BMC Genomics (2008) 1.14
A synthetic biology challenge: making cells compute. Mol Biosyst (2007) 1.14
Noise reduction by diffusional dissipation in a minimal quorum sensing motif. PLoS Comput Biol (2008) 1.12
Optimal tuning of bacterial sensing potential. Mol Syst Biol (2009) 1.12
Temporal control of self-organized pattern formation without morphogen gradients in bacteria. Mol Syst Biol (2013) 1.11
Molecular evidence for arterial repair in atherosclerosis. Proc Natl Acad Sci U S A (2005) 1.09
Efficient Classification-Based Relabeling in Mixture Models. Am Stat (2011) 1.06
Spatiotemporal modulation of biodiversity in a synthetic chemical-mediated ecosystem. Nat Chem Biol (2009) 1.05
Gene expression profiling for prediction of clinical characteristics of breast cancer. Recent Prog Horm Res (2003) 1.04
A bayesian analysis strategy for cross-study translation of gene expression biomarkers. Stat Appl Genet Mol Biol (2009) 1.04
Viral-mediated noisy gene expression reveals biphasic E2f1 response to MYC. Mol Cell (2011) 1.03
Stochastic E2F activation and reconciliation of phenomenological cell-cycle models. PLoS Biol (2010) 1.03
Programming stress-induced altruistic death in engineered bacteria. Mol Syst Biol (2012) 1.03
Sensing and integration of Erk and PI3K signals by Myc. PLoS Comput Biol (2008) 1.03
Bayesian analysis of binary prediction tree models for retrospectively sampled outcomes. Biostatistics (2004) 1.02
Accelerated maximum likelihood parameter estimation for stochastic biochemical systems. BMC Bioinformatics (2012) 1.02
Oscillations by minimal bacterial suicide circuits reveal hidden facets of host-circuit physiology. PLoS One (2010) 1.02
A programmable microenvironment for cellular studies via microfluidics-generated double emulsions. Biomaterials (2013) 0.99
Noise-limited frequency signal transmission in gene circuits. Biophys J (2007) 0.99
Engineering microbial systems to explore ecological and evolutionary dynamics. Curr Opin Biotechnol (2012) 0.99
Prognostic index score and clinical prediction model of local regional recurrence after mastectomy in breast cancer patients. Int J Radiat Oncol Biol Phys (2006) 0.97
Cross-study projections of genomic biomarkers: an evaluation in cancer genomics. PLoS One (2009) 0.96
The inoculum effect and band-pass bacterial response to periodic antibiotic treatment. Mol Syst Biol (2012) 0.96
Gene expression phenotypes of oncogenic signaling pathways. Cell Cycle (2003) 0.95
Hierarchical Bayesian mixture modelling for antigen-specific T-cell subtyping in combinatorially encoded flow cytometry studies. Stat Appl Genet Mol Biol (2013) 0.95
Engineering multicellular systems by cell-cell communication. Curr Opin Biotechnol (2009) 0.92
Optimization of a highly standardized carboxyfluorescein succinimidyl ester flow cytometry panel and gating strategy design using discriminative information measure evaluation. Cytometry A (2010) 0.92
Decoding biological principles using gene circuits. Mol Biosyst (2009) 0.90
Programmed Allee effect in bacteria causes a tradeoff between population spread and survival. Proc Natl Acad Sci U S A (2014) 0.89
Programmed cell death in bacteria and implications for antibiotic therapy. Trends Microbiol (2013) 0.89
Signal discrimination by differential regulation of protein stability in quorum sensing. J Mol Biol (2008) 0.88
Retraction: A genomic strategy to refine prognosis in early-stage non-small-cell lung cancer. N Engl J Med 2006;355:570-80. N Engl J Med (2011) 0.87
Bayesian Weibull tree models for survival analysis of clinico-genomic data. Stat Methodol (2008) 0.87
A synthetic biology approach to understanding cellular information processing. ACS Synth Biol (2012) 0.87
Selection Sampling from Large Data Sets for Targeted Inference in Mixture Modeling. Bayesian Anal (2010) 0.87
FOXO transcription factors control E2F1 transcriptional specificity and apoptotic function. Cancer Res (2013) 0.87
Computation of steady-state probability distributions in stochastic models of cellular networks. PLoS Comput Biol (2011) 0.86
Adaptive Mixture Modelling Metropolis Methods for Bayesian Analysis of Non-linear State-Space Models. J Comput Graph Stat (2010) 0.86
Proliferation behavior of E. coli in a three-dimensional in vitro tumor model. Integr Biol (Camb) (2011) 0.86
Synthetic biology: Division of logic labour. Nature (2011) 0.85
Productive work and employment for persons with traumatic brain injury: what have we learned after 20 years? J Head Trauma Rehabil (2005) 0.85
Tension and robustness in multitasking cellular networks. PLoS Comput Biol (2012) 0.82
Bayesian learning from marginal data in bionetwork models. Stat Appl Genet Mol Biol (2011) 0.81
A brave new synthetic world. A report of the first meeting on 'Frontiers in Synthetic Biology', Boston, USA, 1-2 December 2008. Genome Biol (2009) 0.80
Evolving sensitivity. ACS Chem Biol (2006) 0.80
Programming microbial population dynamics by engineered cell-cell communication. Biotechnol J (2011) 0.80
Engineered cell-cell communication and its applications. Adv Biochem Eng Biotechnol (2014) 0.80
Generic metric to quantify quorum sensing activation dynamics. ACS Synth Biol (2013) 0.79
AN INTEGRATIVE ANALYSIS OF CANCER GENE EXPRESSION STUDIES USING BAYESIAN LATENT FACTOR MODELING. Ann Appl Stat (2009) 0.79
Bayesian Learning in Sparse Graphical Factor Models via Variational Mean-Field Annealing. J Mach Learn Res (2010) 0.78
Cell biology. Cells listen to their inner voice. Science (2014) 0.78
Model-controlled flooding with applications to image reconstruction and segmentation. J Electron Imaging (2012) 0.77
Addressing biological uncertainties in engineering gene circuits. Integr Biol (Camb) (2015) 0.77
DIG--a system for gene annotation and functional discovery. Bioinformatics (2005) 0.77
Quantitative analysis of the spatiotemporal dynamics of a synthetic predator-prey ecosystem. Methods Mol Biol (2012) 0.76
A whole more than the sum of its synthetic parts. ACS Chem Biol (2008) 0.76
Of cardiovascular illness and diversity of biological response. Trends Cardiovasc Med (2008) 0.76
Modeling spatiotemporal dynamics of bacterial populations. Methods Mol Biol (2012) 0.75
Development of a high-speed, multiplexed sample-delivery instrument for LC-MS/MS bioanalysis. Bioanalysis (2012) 0.75
Using noisy gene expression mediated by engineered adenovirus to probe signaling dynamics in mammalian cells. Methods Enzymol (2011) 0.75
A different life? Curr Opin Chem Biol (2012) 0.75
Promoting collaborative interdisciplinary research at the Duke Center for Systems Biology. ACS Synth Biol (2012) 0.75