Published in PLoS Genet on January 13, 2006
An extracellular interactome of immunoglobulin and LRR proteins reveals receptor-ligand networks. Cell (2013) 2.36
Post-transcriptional gene regulation: from genome-wide studies to principles. Cell Mol Life Sci (2008) 2.18
Delivering proteins for export from the cytosol. Nat Rev Mol Cell Biol (2009) 2.00
The rough endoplasmatic reticulum is a central nucleation site of siRNA-mediated RNA silencing. EMBO J (2013) 1.68
Gene expression patterns in pancreatic tumors, cells and tissues. PLoS One (2007) 1.61
Primary role for endoplasmic reticulum-bound ribosomes in cellular translation identified by ribosome profiling. J Biol Chem (2011) 1.56
Signal sequence- and translation-independent mRNA localization to the endoplasmic reticulum. RNA (2008) 1.49
Bioinformatics construction of the human cell surfaceome. Proc Natl Acad Sci U S A (2009) 1.45
Signal initiation in biological systems: the properties and detection of transient extracellular protein interactions. Mol Biosyst (2009) 1.36
Divergent regulation of protein synthesis in the cytosol and endoplasmic reticulum compartments of mammalian cells. Mol Biol Cell (2007) 1.25
Tom20 mediates localization of mRNAs to mitochondria in a translation-dependent manner. Mol Cell Biol (2010) 1.23
p180 promotes the ribosome-independent localization of a subset of mRNA to the endoplasmic reticulum. PLoS Biol (2012) 1.11
Translating DRiPs: progress in understanding viral and cellular sources of MHC class I peptide ligands. Cell Mol Life Sci (2011) 1.11
Hierarchical regulation of mRNA partitioning between the cytoplasm and the endoplasmic reticulum of mammalian cells. Mol Biol Cell (2011) 1.10
Homozygosity mapping and targeted genomic sequencing reveal the gene responsible for cerebellar hypoplasia and quadrupedal locomotion in a consanguineous kindred. Genome Res (2011) 1.08
Diversity and selectivity in mRNA translation on the endoplasmic reticulum. Nat Rev Mol Cell Biol (2015) 1.04
Analyzing mRNA localization to the endoplasmic reticulum via cell fractionation. Methods Mol Biol (2011) 1.04
The 3'-UTR mediates the cellular localization of an mRNA encoding a short plasma membrane protein. RNA (2008) 1.01
Analogue encoding of physicochemical properties of proteins in their cognate messenger RNAs. Nat Commun (2013) 0.91
The Role of the Transmembrane RING Finger Proteins in Cellular and Organelle Function. Membranes (Basel) (2011) 0.87
Regulation of polysome assembly on the endoplasmic reticulum by a coiled-coil protein, p180. Nucleic Acids Res (2011) 0.86
Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells. Genome Res (2011) 0.86
Obstacles and opportunities in the functional analysis of extracellular vesicle RNA - an ISEV position paper. J Extracell Vesicles (2017) 0.80
GFP-based evaluation system of recombinant expression through the secretory pathway in insect cells and its application to the extracellular domains of class C GPCRs. Protein Sci (2011) 0.79
Control of cell migration through mRNA localization and local translation. Wiley Interdiscip Rev RNA (2014) 0.79
ER stress and distinct outputs of the IRE1α RNase control proliferation and senescence in response to oncogenic Ras. Proc Natl Acad Sci U S A (2017) 0.76
Hydrophobicity of protein determinants influences the recognition of substrates by EDEM1 and EDEM2 in human cells. BMC Cell Biol (2015) 0.76
Hypoxia-induced gene expression results from selective mRNA partitioning to the endoplasmic reticulum. Nucleic Acids Res (2015) 0.76
Control of tissue size and development by a regulatory element in the yorkie 3'UTR. Am J Cancer Res (2017) 0.75
Progesterone inhibition of oxytocin signaling in endometrium. Front Neurosci (2013) 0.75
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A (1998) 192.97
Molecular portraits of human breast tumours. Nature (2000) 94.14
Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A (2001) 71.82
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol (2001) 66.87
Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A (2003) 34.68
Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet (2000) 24.22
GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics (2004) 20.23
Database resources of the National Center for Biotechnology Information: 2002 update. Nucleic Acids Res (2002) 19.40
Diversity of gene expression in adenocarcinoma of the lung. Proc Natl Acad Sci U S A (2001) 17.36
Immunohistochemical and clinical characterization of the basal-like subtype of invasive breast carcinoma. Clin Cancer Res (2004) 16.51
A randomized trial of bevacizumab, an anti-vascular endothelial growth factor antibody, for metastatic renal cancer. N Engl J Med (2003) 14.59
SWISS-PROT: connecting biomolecular knowledge via a protein database. Curr Issues Mol Biol (2001) 13.14
DNA arrays for analysis of gene expression. Methods Enzymol (1999) 12.50
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res (2003) 10.28
Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome. Cell (2001) 8.04
Molecular characterisation of soft tissue tumours: a gene expression study. Lancet (2002) 7.05
High-fidelity mRNA amplification for gene profiling. Nat Biotechnol (2000) 6.97
Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme. Proc Natl Acad Sci U S A (2005) 6.54
Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics (2001) 6.53
Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol (2004) 6.38
The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res (2003) 6.31
Prediction of signal peptides and signal anchors by a hidden Markov model. Proc Int Conf Intell Syst Mol Biol (1998) 5.89
Plasma membrane compartmentalization in yeast by messenger RNA transport and a septin diffusion barrier. Science (2000) 4.95
Gene expression patterns in human embryonic stem cells and human pluripotent germ cell tumors. Proc Natl Acad Sci U S A (2003) 4.67
Signal sequence trap: a cloning strategy for secreted proteins and type I membrane proteins. Science (1993) 4.64
Cell membrane and nuclear estrogen receptors (ERs) originate from a single transcript: studies of ERalpha and ERbeta expressed in Chinese hamster ovary cells. Mol Endocrinol (1999) 3.74
Exploration of global gene expression patterns in pancreatic adenocarcinoma using cDNA microarrays. Am J Pathol (2003) 3.40
Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery. Nat Genet (2003) 3.25
Widespread cytoplasmic mRNA transport in yeast: identification of 22 bud-localized transcripts using DNA microarray analysis. Proc Natl Acad Sci U S A (2003) 3.16
The mystery of nonclassical protein secretion. A current view on cargo proteins and potential export routes. Eur J Biochem (2003) 2.95
A DNA microarray survey of gene expression in normal human tissues. Genome Biol (2005) 2.90
Large-scale identification of secreted and membrane-associated gene products using DNA microarrays. Nat Genet (2000) 2.79
Gene expression patterns in renal cell carcinoma assessed by complementary DNA microarray. Am J Pathol (2003) 2.59
Gene expression patterns in ovarian carcinomas. Mol Biol Cell (2003) 2.55
Peroxisome biogenesis. Annu Rev Cell Dev Biol (2001) 2.53
Variation in gene expression patterns in human gastric cancers. Mol Biol Cell (2003) 2.39
A comparison of signal sequence prediction methods using a test set of signal peptides. Bioinformatics (2000) 2.25
Plasma membrane localization and function of the estrogen receptor alpha variant (ER46) in human endothelial cells. Proc Natl Acad Sci U S A (2003) 2.22
Comparing function and structure between entire proteomes. Protein Sci (2001) 2.18
Do more complex organisms have a greater proportion of membrane proteins in their genomes? Proteins (2000) 2.16
Therapeutic antibodies for human diseases at the dawn of the twenty-first century. Nat Rev Drug Discov (2003) 2.13
A high throughput screen to identify secreted and transmembrane proteins involved in Drosophila embryogenesis. Proc Natl Acad Sci U S A (1998) 1.79
Non-Hodgkin lymphoma: an update. Lancet Oncol (2004) 1.78
Variation in gene expression patterns in follicular lymphoma and the response to rituximab. Proc Natl Acad Sci U S A (2003) 1.58
Patched1 interacts with cyclin B1 to regulate cell cycle progression. EMBO J (2001) 1.52
Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans. Am J Pathol (2003) 1.49
The tyrosine kinase ACK1 associates with clathrin-coated vesicles through a binding motif shared by arrestin and other adaptors. J Biol Chem (2001) 1.35
A cofactor of tRNA synthetase, p43, is secreted to up-regulate proinflammatory genes. J Biol Chem (2001) 1.32
Cloning and expression of secretagogin, a novel neuroendocrine- and pancreatic islet of Langerhans-specific Ca2+-binding protein. J Biol Chem (2000) 1.22
Distinct spatial expression patterns of AP-2alpha and AP-2gamma in non-neoplastic human breast and breast cancer. Mod Pathol (2005) 1.10
Immunohistochemical identification of tumor markers in metastatic adenocarcinoma. A diagnostic adjunct in the determination of primary site. Am J Clin Pathol (1997) 1.08
An immunohistochemical study of the breast using antibodies to basal and luminal keratins, alpha-smooth muscle actin, vimentin, collagen IV and laminin. Part I: Normal breast and benign proliferative lesions. Virchows Arch A Pathol Anat Histopathol (1992) 0.99
Molecular approach to breast cancer treatment. Semin Oncol (2004) 0.95
Practice guidelines for tumor marker use in the clinic. Clin Chem (2002) 0.95
A new signal sequence trap using alkaline phosphatase as a reporter. Nucleic Acids Res (1999) 0.90
Requirements for activation and RAFT localization of the T-lymphocyte kinase Rlk/Txk. BMC Immunol (2001) 0.89
Isolation of messenger RNA from membrane-bound polysomes. Methods Enzymol (1987) 0.88
Molecular genetic tumor markers in non-small cell lung cancer. Anticancer Res (2005) 0.87
Circulating tumour markers in breast cancer. Eur J Nucl Med Mol Imaging (2004) 0.86
Protein translocation into the endoplasmic reticulum (ER)--two similar routes with different modes. Eur J Biochem (1998) 0.83
Characterization of Cdk2-cyclin E complexes in plasma membrane and endosomes of liver parenchyma. Insulin-dependent regulation. J Biol Chem (2000) 0.82
The role of the epidermal growth factor receptor in human gliomas: I. The control of cell growth. J Neurosurg (1995) 0.82
Signal-exon trap: a novel method for the identification of signal sequences from genomic DNA. Nucleic Acids Res (2000) 0.82
cDNA structure, tissue-specific expression, and chromosomal localization of the murine band 7.2b gene. Blood (1995) 0.82
Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A (2003) 34.68
GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics (2004) 20.23
Development of the human infant intestinal microbiota. PLoS Biol (2007) 18.91
Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell (2002) 17.32
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet (2003) 14.56
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
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
Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res (2002) 10.65
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res (2003) 10.28
Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res (2004) 10.18
Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS Biol (2004) 9.38
Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res (2007) 9.03
Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A (2002) 8.20
Introductory science and mathematics education for 21st-Century biologists. Science (2004) 7.69
Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2003) 7.45
Molecular characterisation of soft tissue tumours: a gene expression study. Lancet (2002) 7.05
Diversity, topographic differentiation, and positional memory in human fibroblasts. Proc Natl Acad Sci U S A (2002) 6.98
Gene expression patterns in human liver cancers. Mol Biol Cell (2002) 6.93
Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes. N Engl J Med (2004) 6.91
Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme. Proc Natl Acad Sci U S A (2005) 6.54
Individuality and variation in gene expression patterns in human blood. Proc Natl Acad Sci U S A (2003) 6.49
Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol (2004) 6.38
The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res (2003) 6.31
A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci U S A (2003) 6.19
Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers. PLoS Med (2006) 6.04
Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res (2003) 5.69
Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One (2012) 5.28
Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome. Am J Pathol (2002) 5.20
Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2002) 4.97
Anatomic demarcation by positional variation in fibroblast gene expression programs. PLoS Genet (2006) 4.75
Gene expression patterns in human embryonic stem cells and human pluripotent germ cell tumors. Proc Natl Acad Sci U S A (2003) 4.67
Autoantigen microarrays for multiplex characterization of autoantibody responses. Nat Med (2002) 4.54
Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol (2008) 4.34
Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS Biol (2009) 4.32
Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Mol Biol Cell (2007) 4.27
The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res (2005) 4.17
Endothelial cell diversity revealed by global expression profiling. Proc Natl Acad Sci U S A (2003) 3.98
Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc Natl Acad Sci U S A (2002) 3.85
The novel marker, DOG1, is expressed ubiquitously in gastrointestinal stromal tumors irrespective of KIT or PDGFRA mutation status. Am J Pathol (2004) 3.84
Different gene expression patterns in invasive lobular and ductal carcinomas of the breast. Mol Biol Cell (2004) 3.73
The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res (2006) 3.66
Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics (2002) 3.65
Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res (2006) 3.59
The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genet (2008) 3.58
Saccharomyces genome database: underlying principles and organisation. Brief Bioinform (2004) 3.46
Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res (2005) 3.43
Exploration of global gene expression patterns in pancreatic adenocarcinoma using cDNA microarrays. Am J Pathol (2003) 3.40
Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res (2009) 3.38
Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. PLoS One (2008) 3.38
Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science (2006) 3.32
Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res (2006) 3.31
Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation. Proc Natl Acad Sci U S A (2002) 3.28
Cell-type specific gene expression profiles of leukocytes in human peripheral blood. BMC Genomics (2006) 3.27
Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster. Proc Natl Acad Sci U S A (2006) 3.27
Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae. J Biol Chem (2002) 3.26
Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms. Proc Natl Acad Sci U S A (2003) 3.14
Why PLoS became a publisher. PLoS Biol (2003) 3.09
A transcriptional response to Wnt protein in human embryonic carcinoma cells. BMC Dev Biol (2002) 3.09
Diverse and specific gene expression responses to stresses in cultured human cells. Mol Biol Cell (2004) 3.02
Cell-type specific features of circular RNA expression. PLoS Genet (2013) 2.98
A DNA microarray survey of gene expression in normal human tissues. Genome Biol (2005) 2.90
Transcriptional programs activated by exposure of human prostate cancer cells to androgen. Genome Biol (2002) 2.87
Systemic and cell type-specific gene expression patterns in scleroderma skin. Proc Natl Acad Sci U S A (2003) 2.87
Determination of stromal signatures in breast carcinoma. PLoS Biol (2005) 2.84
Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res (2006) 2.75
Bone morphogenetic protein antagonist gremlin 1 is widely expressed by cancer-associated stromal cells and can promote tumor cell proliferation. Proc Natl Acad Sci U S A (2006) 2.72
Conservation of the metabolomic response to starvation across two divergent microbes. Proc Natl Acad Sci U S A (2006) 2.68
Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biol (2004) 2.60
Genomewide view of gene silencing by small interfering RNAs. Proc Natl Acad Sci U S A (2003) 2.56
The role of heat shock transcription factor 1 in the genome-wide regulation of the mammalian heat shock response. Mol Biol Cell (2003) 2.56
Gene expression patterns in ovarian carcinomas. Mol Biol Cell (2003) 2.55
Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature (2013) 2.53
Dissecting eukaryotic translation and its control by ribosome density mapping. Nucleic Acids Res (2005) 2.52
Saccharomyces Genome Database. Methods Enzymol (2002) 2.47
Ammonium toxicity and potassium limitation in yeast. PLoS Biol (2006) 2.39
Variation in gene expression patterns in human gastric cancers. Mol Biol Cell (2003) 2.39