Published in Proc Natl Acad Sci U S A on August 21, 2003
Cell type-specific gene expression differences in complex tissues. Nat Methods (2010) 4.75
In silico dissection of cell-type-associated patterns of gene expression in prostate cancer. Proc Natl Acad Sci U S A (2004) 3.65
Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus. PLoS One (2009) 2.98
Robust enumeration of cell subsets from tissue expression profiles. Nat Methods (2015) 2.30
In silico microdissection of microarray data from heterogeneous cell populations. BMC Bioinformatics (2005) 2.26
Computational expression deconvolution in a complex mammalian organ. BMC Bioinformatics (2006) 2.18
Strategies for aggregating gene expression data: the collapseRows R function. BMC Bioinformatics (2011) 1.96
Assessing the human immune system through blood transcriptomics. BMC Biol (2010) 1.86
Population-specific expression analysis (PSEA) reveals molecular changes in diseased brain. Nat Methods (2011) 1.70
Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis. Cell (2015) 1.67
Optimal deconvolution of transcriptional profiling data using quadratic programming with application to complex clinical blood samples. PLoS One (2011) 1.62
Computational solutions for omics data. Nat Rev Genet (2013) 1.58
Sample matching by inferred agonal stress in gene expression analyses of the brain. BMC Genomics (2007) 1.54
Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer. Genome Biol (2007) 1.54
Interactions with fibroblasts are distinct in Basal-like and luminal breast cancers. Mol Cancer Res (2010) 1.53
Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription. Proc Natl Acad Sci U S A (2004) 1.47
Statistical expression deconvolution from mixed tissue samples. Bioinformatics (2010) 1.34
Biomarker discovery in heterogeneous tissue samples -taking the in-silico deconfounding approach. BMC Bioinformatics (2010) 1.30
Digital sorting of complex tissues for cell type-specific gene expression profiles. BMC Bioinformatics (2013) 1.18
PERT: a method for expression deconvolution of human blood samples from varied microenvironmental and developmental conditions. PLoS Comput Biol (2012) 1.18
Systematic bias in genomic classification due to contaminating non-neoplastic tissue in breast tumor samples. BMC Med Genomics (2011) 1.17
DeMix: deconvolution for mixed cancer transcriptomes using raw measured data. Bioinformatics (2013) 1.08
MMAD: microarray microdissection with analysis of differences is a computational tool for deconvoluting cell type-specific contributions from tissue samples. Bioinformatics (2013) 1.04
An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples. Brief Bioinform (2014) 1.03
Digital cell quantification identifies global immune cell dynamics during influenza infection. Mol Syst Biol (2014) 1.02
Integrated transcriptome analysis of mouse spermatogenesis. BMC Genomics (2014) 0.98
Systems biological approaches to measure and understand vaccine immunity in humans. Semin Immunol (2013) 0.98
Cell cycle population effects in perturbation studies. Mol Syst Biol (2014) 0.95
RNA-Seq Differentiates Tumour and Host mRNA Expression Changes Induced by Treatment of Human Tumour Xenografts with the VEGFR Tyrosine Kinase Inhibitor Cediranib. PLoS One (2013) 0.95
Cell population-specific expression analysis of human cerebellum. BMC Genomics (2012) 0.95
Investigation of variation in gene expression profiling of human blood by extended principle component analysis. PLoS One (2011) 0.93
Gene expression deconvolution in clinical samples. Genome Med (2010) 0.93
A self-directed method for cell-type identification and separation of gene expression microarrays. PLoS Comput Biol (2013) 0.93
MicroRNA dysregulation in spinal cord injury: causes, consequences and therapeutics. Front Cell Neurosci (2014) 0.91
Model-based deconvolution of cell cycle time-series data reveals gene expression details at high resolution. PLoS Comput Biol (2009) 0.90
Robust computational reconstitution - a new method for the comparative analysis of gene expression in tissues and isolated cell fractions. BMC Bioinformatics (2006) 0.89
Deconvoluting complex tissues for expression quantitative trait locus-based analyses. Philos Trans R Soc Lond B Biol Sci (2013) 0.87
A signature-based method for indexing cell cycle phase distribution from microarray profiles. BMC Genomics (2009) 0.86
White blood cell differentials enrich whole blood expression data in the context of acute cardiac allograft rejection. Bioinform Biol Insights (2012) 0.85
Multivariate curve resolution of time course microarray data. BMC Bioinformatics (2006) 0.80
Two-stage, in silico deconvolution of the lymphocyte compartment of the peripheral whole blood transcriptome in the context of acute kidney allograft rejection. PLoS One (2014) 0.80
Estimation of Cell-Type Composition Including T and B Cell Subtypes for Whole Blood Methylation Microarray Data. Front Genet (2016) 0.80
Perturbation-expression analysis identifies RUNX1 as a regulator of human mammary stem cell differentiation. PLoS Comput Biol (2015) 0.79
PDE7B is a novel, prognostically significant mediator of glioblastoma growth whose expression is regulated by endothelial cells. PLoS One (2014) 0.79
ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles. BMC Bioinformatics (2015) 0.78
Mathematical modelling of transcriptional heterogeneity identifies novel markers and subpopulations in complex tissues. Sci Rep (2016) 0.78
A sample selection strategy to boost the statistical power of signature detection in cancer expression profile studies. Anticancer Agents Med Chem (2013) 0.77
Quantitative analysis of tumor mitochondrial RNA using microarray. World J Gastroenterol (2005) 0.77
Enumerateblood - an R package to estimate the cellular composition of whole blood from Affymetrix Gene ST gene expression profiles. BMC Genomics (2017) 0.76
Protein complex, gene, and regulatory modules in cancer heterogeneity. Mol Med (2008) 0.76
A method for cell type marker discovery by high-throughput gene expression analysis of mixed cell populations. BMC Biotechnol (2013) 0.75
Correspondence regarding Zhong et al., BMC Bioinformatics 2013 Mar 7;14:89. BMC Bioinformatics (2014) 0.75
Detect tissue heterogeneity in gene expression data with BioQC. BMC Genomics (2017) 0.75
Regulatory complexity revealed by integrated cytological and RNA-seq analyses of meiotic substages in mouse spermatocytes. BMC Genomics (2016) 0.75
Convex Analysis of Mixtures for Separating Non-negative Well-grounded Sources. Sci Rep (2016) 0.75
Deconvolution of isotope signals from bundles of multiple hairs. Oecologia (2014) 0.75
Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science (1999) 83.27
Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A (2001) 71.82
Optimization by simulated annealing. Science (1983) 71.02
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell (1998) 62.20
Exploring the metabolic and genetic control of gene expression on a genomic scale. Science (1997) 60.15
The transcriptional program of sporulation in budding yeast. Science (1998) 37.23
Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10
Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell (2000) 36.09
Functional discovery via a compendium of expression profiles. Cell (2000) 31.39
Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A (2002) 25.47
Checkpoints: controls that ensure the order of cell cycle events. Science (1989) 21.01
A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell (1998) 19.67
The RAD9 gene controls the cell cycle response to DNA damage in Saccharomyces cerevisiae. Science (1988) 11.90
Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Mol Biol Cell (2001) 6.39
A checkpoint regulates the rate of progression through S phase in S. cerevisiae in response to DNA damage. Cell (1995) 6.00
HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription. Proc Natl Acad Sci U S A (1996) 5.61
Extremely conserved histone H4 N terminus is dispensable for growth but essential for repressing the silent mating loci in yeast. Cell (1988) 5.09
DAF1, a mutant gene affecting size control, pheromone arrest, and cell cycle kinetics of Saccharomyces cerevisiae. Mol Cell Biol (1988) 5.08
Analysis of the Saccharomyces spindle pole by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. J Cell Biol (1998) 4.08
A novel Mcm1-dependent element in the SWI4, CLN3, CDC6, and CDC47 promoters activates M/G1-specific transcription. Genes Dev (1997) 3.28
RAD9, RAD17, and RAD24 are required for S phase regulation in Saccharomyces cerevisiae in response to DNA damage. Genetics (1997) 2.84
ZDS1 and ZDS2, genes whose products may regulate Cdc42p in Saccharomyces cerevisiae. Mol Cell Biol (1996) 2.84
Differential function and expression of Saccharomyces cerevisiae B-type cyclins in mitosis and meiosis. Mol Cell Biol (1993) 2.76
Control of mitotic spindle position by the Saccharomyces cerevisiae formin Bni1p. J Cell Biol (1999) 2.38
Distinct chromosome segregation roles for spindle checkpoint proteins. Mol Biol Cell (2002) 2.29
Heat shock response of Saccharomyces cerevisiae mutants altered in cyclic AMP-dependent protein phosphorylation. Mol Cell Biol (1987) 2.05
The yeast dynactin complex is involved in partitioning the mitotic spindle between mother and daughter cells during anaphase B. Mol Biol Cell (1998) 2.02
Genome-wide expression patterns in Saccharomyces cerevisiae: comparison of drug treatments and genetic alterations affecting biosynthesis of ergosterol. Antimicrob Agents Chemother (2000) 1.90
Casein kinase II is required for cell cycle progression during G1 and G2/M in Saccharomyces cerevisiae. J Biol Chem (1995) 1.81
Cloning of the late genes in the ergosterol biosynthetic pathway of Saccharomyces cerevisiae--a review. Lipids (1995) 1.69
Molecular genetic analysis of Rts1p, a B' regulatory subunit of Saccharomyces cerevisiae protein phosphatase 2A. Mol Cell Biol (1997) 1.66
Tracing the lineage of tracing cell lineages. Nat Cell Biol (2001) 1.63
Identification of mouse histone deacetylase 1 as a growth factor-inducible gene. Mol Cell Biol (1997) 1.62
Loss of the plasma membrane-bound protein Gas1p in Saccharomyces cerevisiae results in the release of beta1,3-glucan into the medium and induces a compensation mechanism to ensure cell wall integrity. J Bacteriol (1998) 1.61
Diverse essential functions revealed by complementing yeast calmodulin mutants. Science (1994) 1.60
Review: an overview of the Saccharomyces cerevisiae microtubule and microfilament cytoskeleton. Yeast (1997) 1.46
On the physiological role of casein kinase II in Saccharomyces cerevisiae. Prog Nucleic Acid Res Mol Biol (1998) 1.44
Biochemical and physiological effects of sterol alterations in yeast--a review. Lipids (1995) 1.40
Transcriptional regulation of flocculation genes in Saccharomyces cerevisiae. Yeast (1995) 1.25
The regulation of gene activity by histones and the histone deacetylase RPD3. Cold Spring Harb Symp Quant Biol (1998) 1.12
Monoclonal antibodies and the FACS: complementary tools for immunobiology and medicine. Immunol Today (2000) 1.11
A galactose-dependent cmd1 mutant of Saccharomyces cerevisiae: involvement of calmodulin in nuclear division. Curr Genet (1989) 0.96
Signaling to chromatin through histone modifications: how clear is the signal? Cold Spring Harb Symp Quant Biol (1998) 0.96
Saccharomyces cerevisiae MATa mutant cells defective in pointed projection formation in response to alpha-factor at high concentrations. Yeast (1994) 0.91
Yeast calmodulin: structural and functional elements essential for the cell cycle. Cell Calcium (1992) 0.89
New plasmid system to select for Saccharomyces cerevisiae purine-cytosine permease affinity mutants. J Bacteriol (2001) 0.87
Cell size specific binding of the fluorescent dye calcofluor to budding yeast. Biochim Biophys Acta (1990) 0.81
Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol (2006) 9.95
Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat Rev Genet (2012) 8.55
A probabilistic functional network of yeast genes. Science (2004) 8.35
Comparative experiments on learning information extractors for proteins and their interactions. Artif Intell Med (2005) 5.44
Characterising and predicting haploinsufficiency in the human genome. PLoS Genet (2010) 4.85
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
The need for a public proteomics repository. Nat Biotechnol (2004) 4.60
Synthetic biology: engineering Escherichia coli to see light. Nature (2005) 4.58
Global signatures of protein and mRNA expression levels. Mol Biosyst (2009) 4.43
Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome Res (2011) 4.39
A census of human soluble protein complexes. Cell (2012) 3.90
Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biol (2005) 3.79
A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nat Genet (2008) 3.62
Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Mol Syst Biol (2010) 3.56
How complete are current yeast and human protein-interaction networks? Genome Biol (2006) 3.50
A synthetic genetic edge detection program. Cell (2009) 3.20
Protein interaction networks from yeast to human. Curr Opin Struct Biol (2004) 3.15
Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat Biotechnol (2010) 2.90
An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae. PLoS One (2007) 2.84
Systematic discovery of nonobvious human disease models through orthologous phenotypes. Proc Natl Acad Sci U S A (2010) 2.61
Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat Biotechnol (2003) 2.40
Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation. Proc Natl Acad Sci U S A (2009) 2.39
Exploiting the co-evolution of interacting proteins to discover interaction specificity. J Mol Biol (2003) 2.24
A probabilistic view of gene function. Nat Genet (2004) 1.99
The planar cell polarity effector Fuz is essential for targeted membrane trafficking, ciliogenesis and mouse embryonic development. Nat Cell Biol (2009) 1.90
Chromatographic alignment of ESI-LC-MS proteomics data sets by ordered bijective interpolated warping. Anal Chem (2006) 1.85
Rational extension of the ribosome biogenesis pathway using network-guided genetics. PLoS Biol (2009) 1.81
Defining the pathway of cytoplasmic maturation of the 60S ribosomal subunit. Mol Cell (2010) 1.79
Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes. Genome Biol (2007) 1.73
Protein abundances are more conserved than mRNA abundances across diverse taxa. Proteomics (2010) 1.71
LGL: creating a map of protein function with an algorithm for visualizing very large biological networks. J Mol Biol (2004) 1.65
Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data. Nat Protoc (2008) 1.62
Predicting genetic modifier loci using functional gene networks. Genome Res (2010) 1.59
Evolutionarily repurposed networks reveal the well-known antifungal drug thiabendazole to be a novel vascular disrupting agent. PLoS Biol (2012) 1.58
It's the machine that matters: Predicting gene function and phenotype from protein networks. J Proteomics (2010) 1.57
The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results. BMC Bioinformatics (2008) 1.54
Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy. Genome Biol (2008) 1.54
A map of human protein interactions derived from co-expression of human mRNAs and their orthologs. Mol Syst Biol (2008) 1.53
Parallel evolution in Pseudomonas aeruginosa over 39,000 generations in vivo. MBio (2010) 1.50
Identification and characterization of the constituent human serum antibodies elicited by vaccination. Proc Natl Acad Sci U S A (2014) 1.50
Predicting functional linkages from gene fusions with confidence. Appl Bioinformatics (2002) 1.46
Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias. Genome Res (2005) 1.43
Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits. Mol Cell Biol (2008) 1.38
Integrating shotgun proteomics and mRNA expression data to improve protein identification. Bioinformatics (2009) 1.36
Protein expression regulation under oxidative stress. Mol Cell Proteomics (2011) 1.34
Genetic dissection of the biotic stress response using a genome-scale gene network for rice. Proc Natl Acad Sci U S A (2011) 1.27
Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response. Proc Natl Acad Sci U S A (2013) 1.26
Mechanisms of cell cycle control revealed by a systematic and quantitative overexpression screen in S. cerevisiae. PLoS Genet (2008) 1.23
Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence. PLoS Comput Biol (2008) 1.23
Coordinated genomic control of ciliogenesis and cell movement by RFX2. Elife (2014) 1.20
MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines. J Proteome Res (2011) 1.19
Ribosome stalk assembly requires the dual-specificity phosphatase Yvh1 for the exchange of Mrt4 with P0. J Cell Biol (2009) 1.17
A Bacteriophage tailspike domain promotes self-cleavage of a human membrane-bound transcription factor, the myelin regulatory factor MYRF. PLoS Biol (2013) 1.16
Systematic profiling of cellular phenotypes with spotted cell microarrays reveals mating-pheromone response genes. Genome Biol (2006) 1.16
Dynamic reorganization of metabolic enzymes into intracellular bodies. Annu Rev Cell Dev Biol (2012) 1.15
Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network. Nat Protoc (2011) 1.14
Two-tiered approach identifies a network of cancer and liver disease-related genes regulated by miR-122. J Biol Chem (2011) 1.11
A fast coarse filtering method for peptide identification by mass spectrometry. Bioinformatics (2006) 1.08
mspire: mass spectrometry proteomics in Ruby. Bioinformatics (2008) 1.07
Flaws in evaluation schemes for pair-input computational predictions. Nat Methods (2012) 1.06
RFX2 is broadly required for ciliogenesis during vertebrate development. Dev Biol (2011) 1.06
Prediction and validation of gene-disease associations using methods inspired by social network analyses. PLoS One (2013) 1.05
ComplexQuant: high-throughput computational pipeline for the global quantitative analysis of endogenous soluble protein complexes using high resolution protein HPLC and precision label-free LC/MS/MS. J Proteomics (2012) 1.05
Diametrical clustering for identifying anti-correlated gene clusters. Bioinformatics (2003) 1.01
Role of Pseudomonas aeruginosa peptidoglycan-associated outer membrane proteins in vesicle formation. J Bacteriol (2012) 0.99
Prediction of gene-phenotype associations in humans, mice, and plants using phenologs. BMC Bioinformatics (2013) 0.99
Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways. BMC Genomics (2007) 0.97
Mining gene functional networks to improve mass-spectrometry-based protein identification. Bioinformatics (2009) 0.96
Group II intron protein localization and insertion sites are affected by polyphosphate. PLoS Biol (2008) 0.96
Systematic definition of protein constituents along the major polarization axis reveals an adaptive reuse of the polarization machinery in pheromone-treated budding yeast. J Proteome Res (2009) 0.96
Revisiting the negative example sampling problem for predicting protein-protein interactions. Bioinformatics (2011) 0.96
RIDDLE: reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network. Genome Biol (2012) 0.95
Protein function prediction using the Protein Link EXplorer (PLEX). Bioinformatics (2005) 0.95
Pseudomonas aeruginosa enhances production of a non-alginate exopolysaccharide during long-term colonization of the cystic fibrosis lung. PLoS One (2013) 0.94
Development through the eyes of functional genomics. Curr Opin Genet Dev (2004) 0.93
Global metabolic changes following loss of a feedback loop reveal dynamic steady states of the yeast metabolome. Metab Eng (2006) 0.91
A role for central spindle proteins in cilia structure and function. Cytoskeleton (Hoboken) (2011) 0.90
Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation. BMC Genomics (2008) 0.89
The proteomic response of Mycobacterium smegmatis to anti-tuberculosis drugs suggests targeted pathways. J Proteome Res (2008) 0.88
Human cell chips: adapting DNA microarray spotting technology to cell-based imaging assays. PLoS One (2009) 0.87
Label-free protein quantitation using weighted spectral counting. Methods Mol Biol (2012) 0.86
Statistical approach to protein quantification. Mol Cell Proteomics (2013) 0.86
Id2a functions to limit Notch pathway activity and thereby influence the transition from proliferation to differentiation of retinoblasts during zebrafish retinogenesis. Dev Biol (2012) 0.84
Integrating functional genomics data. Methods Mol Biol (2008) 0.84
Proteomic identification of monoclonal antibodies from serum. Anal Chem (2014) 0.84
Yeast cells expressing the human mitochondrial DNA polymerase reveal correlations between polymerase fidelity and human disease progression. J Biol Chem (2014) 0.83
Proteomic and protein interaction network analysis of human T lymphocytes during cell-cycle entry. Mol Syst Biol (2012) 0.82
Transiently transfected purine biosynthetic enzymes form stress bodies. PLoS One (2013) 0.81
Protein-to-mRNA ratios are conserved between Pseudomonas aeruginosa strains. J Proteome Res (2014) 0.81
The proteomic response to mutants of the Escherichia coli RNA degradosome. Mol Biosyst (2013) 0.80
Effects of functional bias on supervised learning of a gene network model. Methods Mol Biol (2009) 0.80
Revisiting and revising the purinosome. Mol Biosyst (2014) 0.78
A self-assembling lanthanide molecular nanoparticle for optical imaging. Dalton Trans (2015) 0.77
Efforts to make and apply humanized yeast. Brief Funct Genomics (2015) 0.77
Corrigendum: The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery. Nat Genet (2016) 0.76
Absolute abundance for the masses. Nat Biotechnol (2009) 0.76
Lanthanide nano-drums: a new class of molecular nanoparticles for potential biomedical applications. Faraday Discuss (2014) 0.75
High-throughput immunofluorescence microscopy using yeast spheroplast cell-based microarrays. Methods Mol Biol (2011) 0.75