Published in Nat Methods on March 07, 2010
DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics (2012) 9.31
Systems biology of vaccination for seasonal influenza in humans. Nat Immunol (2011) 6.09
Analysing and interpreting DNA methylation data. Nat Rev Genet (2012) 3.77
Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun (2013) 2.94
Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individuals. PLoS Genet (2011) 2.53
The kSORT assay to detect renal transplant patients at high risk for acute rejection: results of the multicenter AART study. PLoS Med (2014) 2.38
Systems vaccinology. Immunity (2010) 2.36
Robust enumeration of cell subsets from tissue expression profiles. Nat Methods (2015) 2.30
Global analyses of human immune variation reveal baseline predictors of postvaccination responses. Cell (2014) 2.23
Defining cell-type specificity at the transcriptional level in human disease. Genome Res (2013) 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
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
Integrating genome-wide genetic variations and monocyte expression data reveals trans-regulated gene modules in humans. PLoS Genet (2011) 1.40
Transcriptional Perturbations in Graft Rejection. Transplantation (2015) 1.40
Computational deconvolution: extracting cell type-specific information from heterogeneous samples. Curr Opin Immunol (2013) 1.40
Development of a blood-based gene expression algorithm for assessment of obstructive coronary artery disease in non-diabetic patients. BMC Med Genomics (2011) 1.37
Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy. Genome Biol (2015) 1.35
Systematic pan-cancer analysis of tumour purity. Nat Commun (2015) 1.35
Lessons from miR-143/145: the importance of cell-type localization of miRNAs. Nucleic Acids Res (2014) 1.34
Human asthma phenotypes: from the clinic, to cytokines, and back again. Immunol Rev (2011) 1.29
High resolution methylome map of rat indicates role of intragenic DNA methylation in identification of coding region. PLoS One (2012) 1.29
Democratizing systems immunology with modular transcriptional repertoire analyses. Nat Rev Immunol (2014) 1.29
MRI-localized biopsies reveal subtype-specific differences in molecular and cellular composition at the margins of glioblastoma. Proc Natl Acad Sci U S A (2014) 1.25
Epigenetic control of gene expression in the lung. Am J Respir Crit Care Med (2011) 1.24
TrAp: a tree approach for fingerprinting subclonal tumor composition. Nucleic Acids Res (2013) 1.23
Novel technologies and emerging biomarkers for personalized cancer immunotherapy. J Immunother Cancer (2016) 1.22
A diagnostic algorithm combining clinical and molecular data distinguishes Kawasaki disease from other febrile illnesses. BMC Med (2011) 1.21
Systems vaccinology: learning to compute the behavior of vaccine induced immunity. Wiley Interdiscip Rev Syst Biol Med (2011) 1.19
Managing drug resistance in cancer: lessons from HIV therapy. Nat Rev Cancer (2012) 1.19
Measuring cell-type specific differential methylation in human brain tissue. Genome Biol (2013) 1.19
Digital sorting of complex tissues for cell type-specific gene expression profiles. BMC Bioinformatics (2013) 1.18
Gene signatures related to B-cell proliferation predict influenza vaccine-induced antibody response. Eur J Immunol (2013) 1.15
Unifying immunology with informatics and multiscale biology. Nat Immunol (2014) 1.15
New tools for classification and monitoring of autoimmune diseases. Nat Rev Rheumatol (2012) 1.13
Gene expression deconvolution in linear space. Nat Methods (2011) 1.13
Early Pregnancy Maternal Blood DNA Methylation in Repeat Pregnancies and Change in Gestational Diabetes Mellitus Status—A Pilot Study. Reprod Sci (2015) 1.12
Combined image and genomic analysis of high-grade serous ovarian cancer reveals PTEN loss as a common driver event and prognostic classifier. Genome Biol (2014) 1.11
Evidence for additive and interaction effects of host genotype and infection in malaria. Proc Natl Acad Sci U S A (2012) 1.11
CTen: a web-based platform for identifying enriched cell types from heterogeneous microarray data. BMC Genomics (2012) 1.10
Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing. Genome Res (2014) 1.08
DeMix: deconvolution for mixed cancer transcriptomes using raw measured data. Bioinformatics (2013) 1.08
Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction. Genome Med (2013) 1.05
Cell subset prediction for blood genomic studies. BMC Bioinformatics (2011) 1.04
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
The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways. Bioinformatics (2011) 1.02
Systems vaccinology: its promise and challenge for HIV vaccine development. Curr Opin HIV AIDS (2012) 1.01
Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles. Proc Natl Acad Sci U S A (2014) 1.01
Molecular diagnostics in transplantation. Nat Rev Nephrol (2010) 1.01
Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution. PLoS Comput Biol (2013) 1.00
Cell type-specific expression analysis to identify putative cellular mechanisms for neurogenetic disorders. J Neurosci (2014) 0.99
Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets. J Biomed Inform (2011) 0.99
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
Systems immunology reveals markers of susceptibility to West Nile virus infection. Clin Vaccine Immunol (2014) 0.97
A robust hybrid approach based on estimation of distribution algorithm and support vector machine for hunting candidate disease genes. ScientificWorldJournal (2013) 0.96
Cell population-specific expression analysis of human cerebellum. BMC Genomics (2012) 0.95
Identification of common blood gene signatures for the diagnosis of renal and cardiac acute allograft rejection. PLoS One (2013) 0.95
Investigation of variation in gene expression profiling of human blood by extended principle component analysis. PLoS One (2011) 0.93
Genomic analysis reveals pre- and postchallenge differences in a rhesus macaque AIDS vaccine trial: insights into mechanisms of vaccine efficacy. J Virol (2010) 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
Identifying gnostic predictors of the vaccine response. Curr Opin Immunol (2012) 0.89
Epigenomics of idiopathic pulmonary fibrosis. Epigenomics (2012) 0.88
Identification of molecular pathways facilitating glioma cell invasion in situ. PLoS One (2014) 0.88
Systems-level analysis of innate immunity. Annu Rev Immunol (2014) 0.88
B-Cell and Monocyte Contribution to Systemic Lupus Erythematosus Identified by Cell-Type-Specific Differential Expression Analysis in RNA-Seq Data. Bioinform Biol Insights (2015) 0.88
Utilizing population variation, vaccination, and systems biology to study human immunology. Trends Immunol (2015) 0.88
Profiling immunity to HIV vaccines with systems biology. Curr Opin HIV AIDS (2012) 0.88
Decreased miR-192 expression in peripheral blood of asthmatic individuals undergoing an allergen inhalation challenge. BMC Genomics (2012) 0.87
Measuring cell identity in noisy biological systems. Nucleic Acids Res (2011) 0.87
Deconvoluting complex tissues for expression quantitative trait locus-based analyses. Philos Trans R Soc Lond B Biol Sci (2013) 0.87
Cell Specific eQTL Analysis without Sorting Cells. PLoS Genet (2015) 0.87
A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure. Cell Syst (2016) 0.86
Systems immunology of human malaria. Trends Parasitol (2012) 0.86
Lessons learned in the analysis of high-dimensional data in vaccinomics. Vaccine (2015) 0.86
Immune cell subsets and their gene expression profiles from human PBMC isolated by Vacutainer Cell Preparation Tube (CPT™) and standard density gradient. BMC Immunol (2015) 0.85
White blood cell differentials enrich whole blood expression data in the context of acute cardiac allograft rejection. Bioinform Biol Insights (2012) 0.85
Perspectives on systems biology applications in diabetic kidney disease. J Cardiovasc Transl Res (2012) 0.84
Whole blood gene expression and interleukin-6 levels. Genomics (2014) 0.84
Predicting novel histopathological microlesions in human epileptic brain through transcriptional clustering. Brain (2014) 0.83
Epigenetics of idiopathic pulmonary fibrosis. Transl Res (2014) 0.83
Transplantomics and biomarkers in organ transplantation: a report from the first international conference. Transplantation (2011) 0.82
Biomarkers of safety and immune protection for genetically modified live attenuated leishmania vaccines against visceral leishmaniasis - discovery and implications. Front Immunol (2014) 0.82
CellCODE: a robust latent variable approach to differential expression analysis for heterogeneous cell populations. Bioinformatics (2015) 0.82
Inflammatory and myeloid-associated gene expression before and one day after infant vaccination with MVA85A correlates with induction of a T cell response. BMC Infect Dis (2014) 0.81
DNA methylation changes in response to active smoking exposure are associated with leukocyte telomere length among older adults. Eur J Epidemiol (2016) 0.81
Identification of germ cell-specific genes in mammalian meiotic prophase. BMC Bioinformatics (2013) 0.80
Differentially expressed gene transcripts using RNA sequencing from the blood of immunosuppressed kidney allograft recipients. PLoS One (2015) 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
Blood transcriptomics and metabolomics for personalized medicine. Comput Struct Biotechnol J (2015) 0.79
Genetic analysis of the cardiac methylome at single nucleotide resolution in a model of human cardiovascular disease. PLoS Genet (2014) 0.79
Analysis of the transcriptome in molecular epidemiology studies. Environ Mol Mutagen (2013) 0.79
A Mixed Flavonoid-Fish Oil Supplement Induces Immune-Enhancing and Anti-Inflammatory Transcriptomic Changes in Adult Obese and Overweight Women-A Randomized Controlled Trial. Nutrients (2016) 0.79
Inter-Individual Differences in RNA Levels in Human Peripheral Blood. PLoS One (2016) 0.78
Mathematical modelling of transcriptional heterogeneity identifies novel markers and subpopulations in complex tissues. Sci Rep (2016) 0.78
Cell Type Specific Analysis of Human Brain Transcriptome Data to Predict Alterations in Cellular Composition. Syst Biomed (Austin) (2013) 0.78
Transcriptional Changes of Blood Eosinophils After Methacholine Inhalation Challenge in Asthmatics. Genomics Insights (2012) 0.78
Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A (2001) 132.88
Individuality and variation in gene expression patterns in human blood. Proc Natl Acad Sci U S A (2003) 6.49
In silico dissection of cell-type-associated patterns of gene expression in prostate cancer. Proc Natl Acad Sci U S A (2004) 3.65
Application of genome-wide expression analysis to human health and disease. Proc Natl Acad Sci U S A (2005) 3.49
Cell-type specific gene expression profiles of leukocytes in human peripheral blood. BMC Genomics (2006) 3.27
Whole blood and leukocyte RNA isolation for gene expression analyses. Physiol Genomics (2004) 3.22
Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations. Proc Natl Acad Sci U S A (2003) 3.19
Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus. PLoS One (2009) 2.98
Comparison of different isolation techniques prior gene expression profiling of blood derived cells: impact on physiological responses, on overall expression and the role of different cell types. Pharmacogenomics J (2004) 2.60
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
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
Regularization Paths for Generalized Linear Models via Coordinate Descent. J Stat Softw (2010) 38.65
Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A (2003) 34.68
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol (2006) 30.90
Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci U S A (2002) 30.32
Sparse inverse covariance estimation with the graphical lasso. Biostatistics (2007) 24.38
Coordinated reduction of genes of oxidative metabolism in humans with insulin resistance and diabetes: Potential role of PGC1 and NRF1. Proc Natl Acad Sci U S A (2003) 17.10
Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci U S A (2002) 12.68
Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32
Genome-wide association analysis by lasso penalized logistic regression. Bioinformatics (2009) 12.21
Global functional profiling of gene expression. Genomics (2003) 12.05
Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci U S A (2004) 10.99
Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival. Proc Natl Acad Sci U S A (2005) 10.85
Empirical bayes methods and false discovery rates for microarrays. Genet Epidemiol (2002) 10.56
Clinical assessment incorporating a personal genome. Lancet (2010) 10.18
Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia. N Engl J Med (2004) 9.81
A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis. Biostatistics (2009) 9.40
Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Nucleic Acids Res (2003) 9.30
miR-181a is an intrinsic modulator of T cell sensitivity and selection. Cell (2007) 9.08
Semi-supervised methods to predict patient survival from gene expression data. PLoS Biol (2004) 7.68
Performance comparison of exome DNA sequencing technologies. Nat Biotechnol (2011) 7.11
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol (2010) 7.08
Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics (2002) 7.07
A systems biology approach for pathway level analysis. Genome Res (2007) 6.95
Classification and prediction of clinical Alzheimer's diagnosis based on plasma signaling proteins. Nat Med (2007) 6.80
Reliability and reproducibility issues in DNA microarray measurements. Trends Genet (2005) 6.79
Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol (2012) 6.38
Circulating urokinase receptor as a cause of focal segmental glomerulosclerosis. Nat Med (2011) 6.35
Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinformatics (2009) 6.31
Classification of gene microarrays by penalized logistic regression. Biostatistics (2004) 6.20
Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers. PLoS Med (2006) 6.04
Comment on "The consensus coding sequences of human breast and colorectal cancers". Science (2007) 5.88
Performance comparison of whole-genome sequencing platforms. Nat Biotechnol (2011) 5.79
Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Transl Med (2011) 5.77
Penalized logistic regression for detecting gene interactions. Biostatistics (2007) 5.53
Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer. Genes Chromosomes Cancer (2006) 5.39
Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Sci Transl Med (2011) 5.30
Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes. Immunity (2012) 5.26
Direct observation of ligand recognition by T cells. Nature (2002) 5.21
A novel signaling pathway impact analysis. Bioinformatics (2008) 5.06
An Environment-Wide Association Study (EWAS) on type 2 diabetes mellitus. PLoS One (2010) 4.42
Statistical methods for identifying differentially expressed genes in DNA microarrays. Methods Mol Biol (2003) 4.28
TCR and Lat are expressed on separate protein islands on T cell membranes and concatenate during activation. Nat Immunol (2009) 4.22
Thymic selection determines gammadelta T cell effector fate: antigen-naive cells make interleukin-17 and antigen-experienced cells make interferon gamma. Immunity (2008) 4.21
Continuous T cell receptor signaling required for synapse maintenance and full effector potential. Nat Immunol (2003) 3.88
T cell killing does not require the formation of a stable mature immunological synapse. Nat Immunol (2004) 3.85
Human circulating PD-1+CXCR3-CXCR5+ memory Tfh cells are highly functional and correlate with broadly neutralizing HIV antibody responses. Immunity (2013) 3.72
Regularized linear discriminant analysis and its application in microarrays. Biostatistics (2006) 3.66
Plasma membrane-associated proteins are clustered into islands attached to the cytoskeleton. Proc Natl Acad Sci U S A (2006) 3.60
Agonist/endogenous peptide-MHC heterodimers drive T cell activation and sensitivity. Nature (2005) 3.55
FoxO3 regulates neural stem cell homeostasis. Cell Stem Cell (2009) 3.54
A framework for feature selection in clustering. J Am Stat Assoc (2010) 3.46
Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data. Stat Methods Med Res (2011) 3.44
Genetic and environmental determinants of human NK cell diversity revealed by mass cytometry. Sci Transl Med (2013) 3.41
TCR-peptide-MHC interactions in situ show accelerated kinetics and increased affinity. Nature (2010) 3.40
T-cell-antigen recognition and the immunological synapse. Nat Rev Immunol (2003) 3.38
Virus-specific CD4(+) memory-phenotype T cells are abundant in unexposed adults. Immunity (2013) 3.38
Covariance-regularized regression and classification for high-dimensional problems. J R Stat Soc Series B Stat Methodol (2009) 3.31
Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes. Proc Natl Acad Sci U S A (2012) 3.27
Costimulation and endogenous MHC ligands contribute to T cell recognition. Nat Immunol (2001) 3.24
Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets. PLoS Comput Biol (2010) 3.23
CD4 enhances T cell sensitivity to antigen by coordinating Lck accumulation at the immunological synapse. Nat Immunol (2004) 3.21
Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genet (2011) 3.20
Isolating highly enriched populations of circulating epithelial cells and other rare cells from blood using a magnetic sweeper device. Proc Natl Acad Sci U S A (2009) 3.19
T cells use two directionally distinct pathways for cytokine secretion. Nat Immunol (2006) 3.01
Challenges in the clinical application of whole-genome sequencing. Lancet (2010) 2.92
"MIATA"-minimal information about T cell assays. Immunity (2009) 2.90
Transcriptional programs activated by exposure of human prostate cancer cells to androgen. Genome Biol (2002) 2.87
How T cells 'see' antigen. Nat Immunol (2005) 2.87
A network model of a cooperative genetic landscape in brain tumors. JAMA (2009) 2.86
A method for calling gains and losses in array CGH data. Biostatistics (2005) 2.86
Genome-wide measurement of RNA folding energies. Mol Cell (2012) 2.85
Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. BMC Bioinformatics (2005) 2.83
Babel's tower revisited: a universal resource for cross-referencing across annotation databases. Bioinformatics (2006) 2.78
Presence-only data and the em algorithm. Biometrics (2009) 2.76
Outlier sums for differential gene expression analysis. Biostatistics (2006) 2.75
Lineage structure of the human antibody repertoire in response to influenza vaccination. Sci Transl Med (2013) 2.71
Prediction of preadipocyte differentiation by gene expression reveals role of insulin receptor substrates and necdin. Nat Cell Biol (2005) 2.68
Hematopoietic stem cell quiescence is maintained by compound contributions of the retinoblastoma gene family. Cell Stem Cell (2008) 2.67
NetPath: a public resource of curated signal transduction pathways. Genome Biol (2010) 2.62
Evidence that structural rearrangements and/or flexibility during TCR binding can contribute to T cell activation. Mol Cell (2003) 2.61
Computerized recruiting for clinical trials in real time. Ann Emerg Med (2003) 2.59
Gene expression profiling predicts survival in conventional renal cell carcinoma. PLoS Med (2005) 2.56
Gene expression patterns in ovarian carcinomas. Mol Biol Cell (2003) 2.55
Exploiting drug-disease relationships for computational drug repositioning. Brief Bioinform (2011) 2.52
Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinformatics (2004) 2.51
Retracted CD4+ T cell autoimmunity to hypocretin/orexin and cross-reactivity to a 2009 H1N1 influenza A epitope in narcolepsy. Sci Transl Med (2013) 2.51
Progressive histological damage in renal allografts is associated with expression of innate and adaptive immunity genes. Kidney Int (2011) 2.50
AILUN: reannotating gene expression data automatically. Nat Methods (2007) 2.47
Spermatozoal RNA profiles of normal fertile men. Lancet (2002) 2.46
A drug repositioning approach identifies tricyclic antidepressants as inhibitors of small cell lung cancer and other neuroendocrine tumors. Cancer Discov (2013) 2.46