Published in Proc Natl Acad Sci U S A on January 21, 2014
An analysis of critical factors for quantitative immunoblotting. Sci Signal (2015) 0.91
Cell-to-cell variability in cell death: can systems biology help us make sense of it all? Cell Death Dis (2014) 0.87
Integrating single-molecule experiments and discrete stochastic models to understand heterogeneous gene transcription dynamics. Methods (2015) 0.83
Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development. PLoS Genet (2015) 0.82
MCA: Multiresolution Correlation Analysis, a graphical tool for subpopulation identification in single-cell gene expression data. BMC Bioinformatics (2014) 0.82
Variation is function: Are single cell differences functionally important?: Testing the hypothesis that single cell variation is required for aggregate function. Bioessays (2015) 0.80
Single cell transcriptional analysis reveals novel innate immune cell types. PeerJ (2014) 0.79
Profiling Subcellular Protein Phosphatase Responses to Coxsackievirus B3 Infection of Cardiomyocytes. Mol Cell Proteomics (2017) 0.79
End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data. Genome Res (2016) 0.76
TNF-insulin crosstalk at the transcription factor GATA6 is revealed by a model that links signaling and transcriptomic data tensors. Sci Signal (2016) 0.76
MEMO: multi-experiment mixture model analysis of censored data. Bioinformatics (2016) 0.75
Non-genetic heterogeneity caused by differential single-cell adhesion. Cell Cycle (2014) 0.75
Single-cell states versus single-cell atlases - two classes of heterogeneity that differ in meaning and method. Curr Opin Biotechnol (2016) 0.75
Robust Inference of Cell-to-Cell Expression Variations from Single- and K-Cell Profiling. PLoS Comput Biol (2016) 0.75
Tumour evolution inferred by single-cell sequencing. Nature (2011) 19.13
A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell (2006) 18.81
Morphogenesis and oncogenesis of MCF-10A mammary epithelial acini grown in three-dimensional basement membrane cultures. Methods (2003) 18.51
Stromal fibroblasts present in invasive human breast carcinomas promote tumor growth and angiogenesis through elevated SDF-1/CXCL12 secretion. Cell (2005) 18.20
Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science (2011) 15.45
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature (2006) 12.92
Stochastic mRNA synthesis in mammalian cells. PLoS Biol (2006) 12.58
The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature (2012) 11.91
mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods (2009) 11.71
Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods (2008) 10.40
A pharmacological map of the PI3-K family defines a role for p110alpha in insulin signaling. Cell (2006) 10.06
Modelling glandular epithelial cancers in three-dimensional cultures. Nat Rev Cancer (2005) 8.70
Noise in protein expression scales with natural protein abundance. Nat Genet (2006) 8.03
Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nat Biotechnol (2011) 7.84
Truncating mutations in the Fanconi anemia J gene BRIP1 are low-penetrance breast cancer susceptibility alleles. Nat Genet (2006) 7.72
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol (2012) 7.37
Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells. Cell (2011) 7.30
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature (2013) 6.50
Variability in gene expression underlies incomplete penetrance. Nature (2010) 5.85
Multilineage transcriptional priming and determination of alternate hematopoietic cell fates. Cell (2006) 5.39
Transcription factor profiling in individual hematopoietic progenitors by digital RT-PCR. Proc Natl Acad Sci U S A (2006) 5.21
CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Rep (2012) 5.17
Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels. Genome Res (2005) 4.98
Cell type-specific gene expression differences in complex tissues. Nat Methods (2010) 4.75
An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis. Nucleic Acids Res (2006) 4.26
Gene expression and the myth of the average cell. Trends Cell Biol (2003) 3.78
Using gene expression noise to understand gene regulation. Science (2012) 3.49
Single-cell transcriptional analysis of neuronal progenitors. Neuron (2003) 3.38
Sequencing technology does not eliminate biological variability. Nat Biotechnol (2011) 3.20
Stochastic spineless expression creates the retinal mosaic for colour vision. Nature (2006) 3.09
Single-cell systems biology by super-resolution imaging and combinatorial labeling. Nat Methods (2012) 2.98
MAPKAP kinases - MKs - two's company, three's a crowd. Nat Rev Mol Cell Biol (2006) 2.80
Cellular noise regulons underlie fluctuations in Saccharomyces cerevisiae. Mol Cell (2012) 2.16
Quantitative analysis of gene expression in a single cell by qPCR. Nat Methods (2009) 2.15
Identifying single-cell molecular programs by stochastic profiling. Nat Methods (2010) 2.11
Characterizing heterogeneous cellular responses to perturbations. Proc Natl Acad Sci U S A (2008) 2.03
Patterns of basal signaling heterogeneity can distinguish cellular populations with different drug sensitivities. Mol Syst Biol (2010) 1.77
Optimal deconvolution of transcriptional profiling data using quadratic programming with application to complex clinical blood samples. PLoS One (2011) 1.62
Heterogeneity in the physiological states and pharmacological responses of differentiating 3T3-L1 preadipocytes. J Cell Biol (2009) 1.51
Activity of any class IA PI3K isoform can sustain cell proliferation and survival. Proc Natl Acad Sci U S A (2010) 1.40
Probabilistic analysis of gene expression measurements from heterogeneous tissues. Bioinformatics (2010) 1.31
Biomarker discovery in heterogeneous tissue samples -taking the in-silico deconfounding approach. BMC Bioinformatics (2010) 1.30
Intersection of FOXO- and RUNX1-mediated gene expression programs in single breast epithelial cells during morphogenesis and tumor progression. Proc Natl Acad Sci U S A (2011) 1.26
An approach for extensibly profiling the molecular states of cellular subpopulations. Nat Methods (2009) 1.18
Fractional proliferation: a method to deconvolve cell population dynamics from single-cell data. Nat Methods (2012) 1.16
Normal morphogenesis of epithelial tissues and progression of epithelial tumors. Wiley Interdiscip Rev Syst Biol Med (2011) 1.10
Quantification noise in single cell experiments. Nucleic Acids Res (2011) 0.98
Interferon regulatory factor expression in human breast cancer. Ann Surg (2001) 0.98
Robust unmixing of tumor states in array comparative genomic hybridization data. Bioinformatics (2010) 0.95
Stochastic profiling of transcriptional regulatory heterogeneities in tissues, tumors and cultured cells. Nat Protoc (2013) 0.88
Frequent down-regulation of HIVEP2 in human breast cancer. Breast Cancer Res Treat (2005) 0.82
Statistical mechanics approach to the sample deconvolution problem. Phys Rev E Stat Nonlin Soft Matter Phys (2013) 0.77
Discovery of sexual dimorphisms in metabolic and genetic biomarkers. PLoS Genet (2011) 2.68
Unraveling the complexity of tyrosine kinase inhibitor-resistant populations by ultra-deep sequencing of the BCR-ABL kinase domain. Blood (2013) 2.53
Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis. Nat Cell Biol (2013) 2.40
A multiplexed homogeneous fluorescence-based assay for protein kinase activity in cell lysates. Nat Methods (2005) 2.39
A compendium of signals and responses triggered by prodeath and prosurvival cytokines. Mol Cell Proteomics (2005) 2.20
Common effector processing mediates cell-specific responses to stimuli. Nature (2007) 2.20
Intronic microRNAs support their host genes by mediating synergistic and antagonistic regulatory effects. BMC Genomics (2010) 1.99
SRSF2 mutations in 275 cases with chronic myelomonocytic leukemia (CMML). Blood (2012) 1.85
MicroRNA loss enhances learning and memory in mice. J Neurosci (2010) 1.82
PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes. Genome Biol (2010) 1.79
Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. BMC Syst Biol (2009) 1.78
A novel hierarchical prognostic model of AML solely based on molecular mutations. Blood (2012) 1.64
Live imaging of astrocyte responses to acute injury reveals selective juxtavascular proliferation. Nat Neurosci (2013) 1.62
The dynamic range of the human metabolome revealed by challenges. FASEB J (2012) 1.61
Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data. BMC Syst Biol (2011) 1.52
Vertex centralities in input-output networks reveal the structure of modern economies. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 1.43
Mining the unknown: a systems approach to metabolite identification combining genetic and metabolic information. PLoS Genet (2012) 1.41
The molecular profile of adult T-cell acute lymphoblastic leukemia: mutations in RUNX1 and DNMT3A are associated with poor prognosis in T-ALL. Genes Chromosomes Cancer (2013) 1.39
Odefy--from discrete to continuous models. BMC Bioinformatics (2010) 1.38
The mTOR pathway and its role in human genetic diseases. Mutat Res (2008) 1.33
The nature and perception of fluctuations in human musical rhythms. PLoS One (2011) 1.30
Social transfer of pathogenic fungus promotes active immunisation in ant colonies. PLoS Biol (2012) 1.28
Lessons learned from quantitative dynamical modeling in systems biology. PLoS One (2013) 1.28
Intersection of FOXO- and RUNX1-mediated gene expression programs in single breast epithelial cells during morphogenesis and tumor progression. Proc Natl Acad Sci U S A (2011) 1.26
MicroRNAs coordinately regulate protein complexes. BMC Syst Biol (2011) 1.17
Blind source separation techniques for the decomposition of multiply labeled fluorescence images. Biophys J (2009) 1.14
Robustness of amplicon deep sequencing underlines its utility in clinical applications. J Mol Diagn (2013) 1.13
Contribution of human amniotic fluid stem cells to renal tissue formation depends on mTOR. Hum Mol Genet (2010) 1.11
Functional interaction of mammalian target of rapamycin complexes in regulating mammalian cell size and cell cycle. Hum Mol Genet (2009) 1.11
A unilateral negative feedback loop between miR-200 microRNAs and Sox2/E2F3 controls neural progenitor cell-cycle exit and differentiation. J Neurosci (2012) 1.10
Normal morphogenesis of epithelial tissues and progression of epithelial tumors. Wiley Interdiscip Rev Syst Biol Med (2011) 1.10
Hierarchical differentiation of myeloid progenitors is encoded in the transcription factor network. PLoS One (2011) 1.09
Applying computational modeling to drug discovery and development. Drug Discov Today (2006) 1.08
miTALOS: analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs. RNA (2011) 1.05
Body fat free mass is associated with the serum metabolite profile in a population-based study. PLoS One (2012) 1.04
Adenoviral vector saturates Akt pro-survival signaling and blocks insulin-mediated rescue of tumor necrosis-factor-induced apoptosis. J Cell Sci (2006) 1.04
Spatial analysis of expression patterns predicts genetic interactions at the mid-hindbrain boundary. PLoS Comput Biol (2009) 1.03
An evolutionary and structural characterization of mammalian protein complex organization. BMC Genomics (2008) 1.03
Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine. Genome Biol (2009) 1.03
An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy. BMC Bioinformatics (2013) 1.01
Efficient siRNA-mediated prolonged gene silencing in human amniotic fluid stem cells. Nat Protoc (2010) 1.00
On the hypothesis-free testing of metabolite ratios in genome-wide and metabolome-wide association studies. BMC Bioinformatics (2012) 0.99
Reconsidering pluripotency tests: do we still need teratoma assays? Stem Cell Res (2013) 0.98
Pairwise network mechanisms in the host signaling response to coxsackievirus B3 infection. Proc Natl Acad Sci U S A (2010) 0.97
A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst. Bioinformatics (2012) 0.96
Bayesian model selection validates a biokinetic model for zirconium processing in humans. BMC Syst Biol (2012) 0.92
Stability and multiattractor dynamics of a toggle switch based on a two-stage model of stochastic gene expression. Biophys J (2012) 0.92
An ERK-p38 subnetwork coordinates host cell apoptosis and necrosis during coxsackievirus B3 infection. Cell Host Microbe (2013) 0.92
Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation. BMC Bioinformatics (2010) 0.91
Wound-healing growth factor, basic FGF, induces Erk1/2-dependent mechanical hyperalgesia. Pain (2013) 0.91
Frequency and prognostic impact of CEBPA proximal, distal and core promoter methylation in normal karyotype AML: a study on 623 cases. PLoS One (2013) 0.90
CEBPA double-mutated acute myeloid leukaemia harbours concomitant molecular mutations in 76·8% of cases with TET2 and GATA2 alterations impacting prognosis. Br J Haematol (2013) 0.90
Dissection of cell cycle-dependent dynamics of Dnmt1 by FRAP and diffusion-coupled modeling. Nucleic Acids Res (2013) 0.90
A modular framework for gene set analysis integrating multilevel omics data. Nucleic Acids Res (2013) 0.90
The Sox17-mCherry fusion mouse line allows visualization of endoderm and vascular endothelial development. Genesis (2011) 0.90
Simultaneous profiling of 194 distinct receptor transcripts in human cells. Sci Signal (2013) 0.90
Multi-omic signature of body weight change: results from a population-based cohort study. BMC Med (2015) 0.89
Tissue-specific target analysis of disease-associated microRNAs in human signaling pathways. PLoS One (2010) 0.89
Induction of mesenchymal/epithelial marker expression in human amniotic fluid stem cells. Reprod Biomed Online (2009) 0.88
Stochastic profiling of transcriptional regulatory heterogeneities in tissues, tumors and cultured cells. Nat Protoc (2013) 0.88
Feature ranking of type 1 diabetes susceptibility genes improves prediction of type 1 diabetes. Diabetologia (2014) 0.87
Sharpening of expression domains induced by transcription and microRNA regulation within a spatio-temporal model of mid-hindbrain boundary formation. BMC Syst Biol (2013) 0.87
The a(d) coefficient as a descriptive measure of the within-group agreement of ratings. Br J Math Stat Psychol (2010) 0.87
Specific temperature-induced perturbations of secondary mRNA structures are associated with the cold-adapted temperature-sensitive phenotype of influenza A virus. RNA Biol (2012) 0.87
Bayesian independent component analysis recovers pathway signatures from blood metabolomics data. J Proteome Res (2012) 0.86
The human transcriptome is enriched for miRNA-binding sites located in cooperativity-permitting distance. RNA Biol (2013) 0.85
miR-335 promotes mesendodermal lineage segregation and shapes a transcription factor gradient in the endoderm. Development (2014) 0.85
A strategy to find gene combinations that identify children who progress rapidly to type 1 diabetes after islet autoantibody seroconversion. Acta Diabetol (2013) 0.84
From binary to multivalued to continuous models: the lac operon as a case study. J Integr Bioinform (2010) 0.84
Structuring heterogeneous biological information using fuzzy clustering of k-partite graphs. BMC Bioinformatics (2010) 0.83
Investigation of 305 patients with myelodysplastic syndromes and 20q deletion for associated cytogenetic and molecular genetic lesions and their prognostic impact. Br J Haematol (2013) 0.82
Modeling the latent dimensions of multivariate signaling datasets. Phys Biol (2012) 0.82
Effective parameters determining the information flow in hierarchical biological systems. Bull Math Biol (2010) 0.82
MCA: Multiresolution Correlation Analysis, a graphical tool for subpopulation identification in single-cell gene expression data. BMC Bioinformatics (2014) 0.82
Expression of mTOR pathway proteins in human amniotic fluid stem cells. Int J Mol Med (2009) 0.81
Network-based approach for analyzing intra- and interfluid metabolite associations in human blood, urine, and saliva. J Proteome Res (2014) 0.81
New insights into the role of the tuberous sclerosis genes in leukemia. Leuk Res (2009) 0.81
Identification and quantification of 1-hydroxybutene-2-yl mercapturic acid in human urine by UPLC- HILIC-MS/MS as a novel biomarker for 1,3-butadiene exposure. Chem Res Toxicol (2012) 0.81
Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli. PLoS Comput Biol (2010) 0.81
Posttranscriptional regulatory networks: from expression profiling to integrative analysis of mRNA and microRNA data. Methods Mol Biol (2014) 0.80
Multiscale models of cell signaling. Ann Biomed Eng (2012) 0.80
Huge splicing frequency in human Y chromosomal UTY gene. OMICS (2011) 0.80
Renal differentiation of amniotic fluid stem cells: perspectives for clinical application and for studies on specific human genetic diseases. Eur J Clin Invest (2011) 0.80
Multi-scale modeling of GMP differentiation based on single-cell genealogies. FEBS J (2012) 0.79
Paring down signaling complexity. Nat Biotechnol (2010) 0.78
Modeling of 2D diffusion processes based on microscopy data: parameter estimation and practical identifiability analysis. BMC Bioinformatics (2013) 0.78
An ensemble approach for inferring semi-quantitative regulatory dynamics for the differentiation of mouse embryonic stem cells using prior knowledge. Adv Exp Med Biol (2012) 0.77
A high-throughput assay for phosphoprotein-specific phosphatase activity in cellular extracts. Mol Cell Proteomics (2012) 0.77
Bringing systems biology to cancer, immunology and infectious disease. Genome Biol (2014) 0.76
Bayesian blind source separation for data with network structure. J Comput Biol (2014) 0.75
iVUN: interactive Visualization of Uncertain biochemical reaction Networks. BMC Bioinformatics (2013) 0.75
Biologically meaningful update rules increase the critical connectivity of generalized Kauffman networks. J Theor Biol (2010) 0.75
Erratum to: Feature ranking of type 1 diabetes susceptibility genes improves prediction of type 1 diabetes. Diabetologia (2015) 0.75