Published in Genome Biol on January 01, 2006
Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res (2006) 13.32
Initial impact of the sequencing of the human genome. Nature (2011) 9.18
Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell (2011) 7.03
MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome Biol (2007) 6.41
Large-scale chemical dissection of mitochondrial function. Nat Biotechnol (2008) 2.91
Tight coordination of protein translation and HSF1 activation supports the anabolic malignant state. Science (2013) 2.79
Proteomic and genetic approaches identify Syk as an AML target. Cancer Cell (2009) 2.39
High-throughput Phenotyping of Lung Cancer Somatic Mutations. Cancer Cell (2016) 2.31
Humanized mice with ectopic artificial liver tissues. Proc Natl Acad Sci U S A (2011) 2.03
An erythroid differentiation signature predicts response to lenalidomide in myelodysplastic syndrome. PLoS Med (2008) 1.97
Multi-parameter phenotypic profiling: using cellular effects to characterize small-molecule compounds. Nat Rev Drug Discov (2009) 1.95
Chemical genomics identifies small-molecule MCL1 repressors and BCL-xL as a predictor of MCL1 dependency. Cancer Cell (2012) 1.93
Complementary genomic screens identify SERCA as a therapeutic target in NOTCH1 mutated cancer. Cancer Cell (2013) 1.86
Applications of high-throughput RNA interference screens to problems in cell and developmental biology. Genetics (2007) 1.82
Signature-based small molecule screening identifies cytosine arabinoside as an EWS/FLI modulator in Ewing sarcoma. PLoS Med (2007) 1.82
Chemical genetic strategy identifies histone deacetylase 1 (HDAC1) and HDAC2 as therapeutic targets in sickle cell disease. Proc Natl Acad Sci U S A (2010) 1.72
Pathway reporter genes define molecular phenotypes of human cells. BMC Genomics (2015) 1.43
Characterization of Notch1 antibodies that inhibit signaling of both normal and mutated Notch1 receptors. PLoS One (2010) 1.41
LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. Nucleic Acids Res (2014) 1.34
Proteogenomics connects somatic mutations to signalling in breast cancer. Nature (2016) 1.33
Expression-based screening identifies the combination of histone deacetylase inhibitors and retinoids for neuroblastoma differentiation. Proc Natl Acad Sci U S A (2008) 1.27
The intersection of genetic and chemical genomic screens identifies GSK-3α as a target in human acute myeloid leukemia. J Clin Invest (2012) 1.24
Strategies to discover regulatory circuits of the mammalian immune system. Nat Rev Immunol (2011) 1.10
FlyPrimerBank: an online database for Drosophila melanogaster gene expression analysis and knockdown evaluation of RNAi reagents. G3 (Bethesda) (2013) 1.09
Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling. Proc Natl Acad Sci U S A (2014) 1.09
Rapid microRNA profiling on encoded gel microparticles. Angew Chem Int Ed Engl (2011) 1.07
High-throughput gene expression profiling of memory differentiation in primary human T cells. BMC Immunol (2008) 0.99
Compound signature detection on LINCS L1000 big data. Mol Biosyst (2015) 0.97
Identification of AML1-ETO modulators by chemical genomics. Blood (2009) 0.97
Multiplexed protein quantification with barcoded hydrogel microparticles. Anal Chem (2010) 0.97
Translation: screening for novel therapeutics with disease-relevant cell types derived from human stem cell models. Biol Psychiatry (2013) 0.95
Conversion of a capture ELISA to a Luminex xMAP assay using a multiplex antibody screening method. J Vis Exp (2012) 0.94
High-throughput flow alignment of barcoded hydrogel microparticles. Lab Chip (2009) 0.93
Ultrasensitive multiplexed microRNA quantification on encoded gel microparticles using rolling circle amplification. Anal Chem (2011) 0.93
Gene expression-based screening for inhibitors of PDGFR signaling. Genome Biol (2008) 0.92
Selective HDAC1/HDAC2 inhibitors induce neuroblastoma differentiation. Chem Biol (2013) 0.92
Connecting synthetic chemistry decisions to cell and genome biology using small-molecule phenotypic profiling. Curr Opin Chem Biol (2009) 0.90
SYK regulates mTOR signaling in AML. Leukemia (2013) 0.90
Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data. PLoS One (2013) 0.88
Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes. Nat Protoc (2016) 0.88
A Quantitative Approach to Screen for Nephrotoxic Compounds In Vitro. J Am Soc Nephrol (2015) 0.87
Gene expression inference with deep learning. Bioinformatics (2016) 0.85
High-throughput identification of genotype-specific cancer vulnerabilities in mixtures of barcoded tumor cell lines. Nat Biotechnol (2016) 0.84
Aptamer-functionalized microgel particles for protein detection. Anal Chem (2011) 0.84
Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles. Cancer Discov (2016) 0.83
Modulators of hepatic lipoprotein metabolism identified in a search for small-molecule inducers of tribbles pseudokinase 1 expression. PLoS One (2015) 0.81
Public data and open source tools for multi-assay genomic investigation of disease. Brief Bioinform (2015) 0.80
Genetic and proteomic approaches to identify cancer drug targets. Br J Cancer (2011) 0.79
Current advances in systems and integrative biology. Comput Struct Biotechnol J (2014) 0.79
Applications of chemogenomic library screening in drug discovery. Nat Rev Drug Discov (2017) 0.79
High throughput toxicity screening and intracellular detection of nanomaterials. Wiley Interdiscip Rev Nanomed Nanobiotechnol (2016) 0.78
Transcriptional Characterization of Compounds: Lessons Learned from the Public LINCS Data. Assay Drug Dev Technol (2016) 0.78
FutureTox II: in vitro data and in silico models for predictive toxicology. Toxicol Sci (2015) 0.78
Stochastic particle barcoding for single-cell tracking and multiparametric analysis. Small (2014) 0.76
Drug Repositioning for Cancer Therapy Based on Large-Scale Drug-Induced Transcriptional Signatures. PLoS One (2016) 0.76
Systematic Identification and Assessment of Therapeutic Targets for Breast Cancer Based on Genome-Wide RNA Interference Transcriptomes. Genes (Basel) (2017) 0.75
Elucidating the modes of action for bioactive compounds in a cell-specific manner by large-scale chemically-induced transcriptomics. Sci Rep (2017) 0.75
Systematic discovery of drug action mechanisms by an integrated chemical genomics approach: identification of functional disparities between azacytidine and decitabine. Oncotarget (2016) 0.75
Systematic Quality Control Analysis of LINCS Data. CPT Pharmacometrics Syst Pharmacol (2016) 0.75
Representing high throughput expression profiles via perturbation barcodes reveals compound targets. PLoS Comput Biol (2017) 0.75
Studying Cellular Signal Transduction with OMIC Technologies. J Mol Biol (2015) 0.75
From molecular interaction to acute promyelocytic leukemia: Calculating leukemogenesis and remission from endogenous molecular-cellular network. Sci Rep (2016) 0.75
Integrative network and transcriptomics-based approach predicts genotype- specific drug combinations for melanoma. AMIA Jt Summits Transl Sci Proc (2017) 0.75
Altered peritumoral microRNA expression predicts head and neck cancer patients with a high risk of recurrence. Mod Pathol (2017) 0.75
Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States. Cell Syst (2017) 0.75
A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med (2002) 58.15
A mechanism of cyclin D1 action encoded in the patterns of gene expression in human cancer. Cell (2003) 9.81
A ligase-mediated gene detection technique. Science (1988) 7.61
A versatile assay for high-throughput gene expression profiling on universal array matrices. Genome Res (2004) 4.19
Profiling alternative splicing on fiber-optic arrays. Nat Biotechnol (2002) 3.94
Gene expression-based high-throughput screening(GE-HTS) and application to leukemia differentiation. Nat Genet (2004) 3.84
Novel, ligation-dependent PCR assay for detection of hepatitis C in serum. J Clin Microbiol (1996) 2.19
BADGE, Beads Array for the Detection of Gene Expression, a high-throughput diagnostic bioassay. Genome Res (2001) 2.05
Enhanced detection and distinction of RNA by enzymatic probe ligation. Nat Biotechnol (2000) 1.90
Molecular classification of Crohn's disease and ulcerative colitis patients using transcriptional profiles in peripheral blood mononuclear cells. J Mol Diagn (2006) 1.89
Gene expression profiling in follicular lymphoma to assess clinical aggressiveness and to guide the choice of treatment. Blood (2004) 1.56
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
MicroRNA expression profiles classify human cancers. Nature (2005) 69.12
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet (2003) 53.59
The landscape of somatic copy-number alteration across human cancers. Nature (2010) 31.88
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature (2012) 31.78
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature (2005) 31.60
The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science (2006) 25.99
A molecular signature of metastasis in primary solid tumors. Nat Genet (2002) 21.36
Activating mutation in the tyrosine kinase JAK2 in polycythemia vera, essential thrombocythemia, and myeloid metaplasia with myelofibrosis. Cancer Cell (2005) 17.41
Initial genome sequencing and analysis of multiple myeloma. Nature (2011) 17.28
BRAF mutation predicts sensitivity to MEK inhibition. Nature (2005) 17.14
The mutational landscape of head and neck squamous cell carcinoma. Science (2011) 16.88
Gene expression correlates of clinical prostate cancer behavior. Cancer Cell (2002) 16.27
Impaired microRNA processing enhances cellular transformation and tumorigenesis. Nat Genet (2007) 15.46
Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature (2002) 15.36
Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature (2005) 15.28
The genomic complexity of primary human prostate cancer. Nature (2011) 14.06
Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med (2002) 14.01
MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nat Genet (2001) 13.79
mTOR inhibition reverses Akt-dependent prostate intraepithelial neoplasia through regulation of apoptotic and HIF-1-dependent pathways. Nat Med (2004) 13.57
Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res (2006) 13.32
Transformation from committed progenitor to leukaemia stem cell initiated by MLL-AF9. Nature (2006) 11.90
Molecular profiling of diffuse large B-cell lymphoma identifies robust subtypes including one characterized by host inflammatory response. Blood (2004) 11.07
SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med (2011) 11.07
An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nat Genet (2004) 10.92
Metagenes and molecular pattern discovery using matrix factorization. Proc Natl Acad Sci U S A (2004) 10.47
Tumour micro-environment elicits innate resistance to RAF inhibitors through HGF secretion. Nature (2012) 10.39
Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet (2012) 9.93
Increased expression of genes converting adrenal androgens to testosterone in androgen-independent prostate cancer. Cancer Res (2006) 9.87
A mechanism of cyclin D1 action encoded in the patterns of gene expression in human cancer. Cell (2003) 9.81
Gene expression in fixed tissues and outcome in hepatocellular carcinoma. N Engl J Med (2008) 9.20
Identification of RPS14 as a 5q- syndrome gene by RNA interference screen. Nature (2008) 8.38
Gene expression-based classification of malignant gliomas correlates better with survival than histological classification. Cancer Res (2003) 8.06
MPLW515L is a novel somatic activating mutation in myelofibrosis with myeloid metaplasia. PLoS Med (2006) 7.95
Melanoma genome sequencing reveals frequent PREX2 mutations. Nature (2012) 7.77
Sequence analysis of mutations and translocations across breast cancer subtypes. Nature (2012) 7.76
Highly parallel identification of essential genes in cancer cells. Proc Natl Acad Sci U S A (2008) 7.45
The immunosuppressant rapamycin mimics a starvation-like signal distinct from amino acid and glucose deprivation. Mol Cell Biol (2002) 7.44
Punctuated evolution of prostate cancer genomes. Cell (2013) 7.23
Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing. Proc Natl Acad Sci U S A (2012) 7.14
Selective killing of cancer cells by a small molecule targeting the stress response to ROS. Nature (2011) 7.03
Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell (2011) 7.03
Gene expression signatures define novel oncogenic pathways in T cell acute lymphoblastic leukemia. Cancer Cell (2002) 6.64
Lin28 promotes transformation and is associated with advanced human malignancies. Nat Genet (2009) 6.35
Modeling genomic diversity and tumor dependency in malignant melanoma. Cancer Res (2008) 5.95
Comment on "The consensus coding sequences of human breast and colorectal cancers". Science (2007) 5.88
Altered microRNA expression in human heart disease. Physiol Genomics (2007) 5.64
Stem cell gene expression programs influence clinical outcome in human leukemia. Nat Med (2011) 5.24
Dicer1 functions as a haploinsufficient tumor suppressor. Genes Dev (2009) 5.21
SMAD4-dependent barrier constrains prostate cancer growth and metastatic progression. Nature (2011) 4.57
Gene expression signature-based chemical genomic prediction identifies a novel class of HSP90 pathway modulators. Cancer Cell (2006) 4.52
Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity. Nat Genet (2013) 4.48
Gene expression-based chemical genomics identifies rapamycin as a modulator of MCL1 and glucocorticoid resistance. Cancer Cell (2006) 3.93
MicroRNA-mediated control of cell fate in megakaryocyte-erythrocyte progenitors. Dev Cell (2008) 3.84
Gene expression-based high-throughput screening(GE-HTS) and application to leukemia differentiation. Nat Genet (2004) 3.84
Integrative transcriptome analysis reveals common molecular subclasses of human hepatocellular carcinoma. Cancer Res (2009) 3.77
Inhibition of FLT3 in MLL. Validation of a therapeutic target identified by gene expression based classification. Cancer Cell (2003) 3.75
Bcl2 regulation by the melanocyte master regulator Mitf modulates lineage survival and melanoma cell viability. Cell (2002) 3.72
Estrogen-dependent signaling in a molecularly distinct subclass of aggressive prostate cancer. J Natl Cancer Inst (2008) 3.55
Prostate intraepithelial neoplasia induced by prostate restricted Akt activation: the MPAKT model. Proc Natl Acad Sci U S A (2003) 3.34
Expression profiling of EWS/FLI identifies NKX2.2 as a critical target gene in Ewing's sarcoma. Cancer Cell (2006) 3.29
Identification of driver and passenger mutations of FLT3 by high-throughput DNA sequence analysis and functional assessment of candidate alleles. Cancer Cell (2007) 3.23
Distinct microRNA expression profiles in acute myeloid leukemia with common translocations. Proc Natl Acad Sci U S A (2008) 3.13
Targeting MYCN in neuroblastoma by BET bromodomain inhibition. Cancer Discov (2013) 3.11
MicroRNA expression signatures accurately discriminate acute lymphoblastic leukemia from acute myeloid leukemia. Proc Natl Acad Sci U S A (2007) 3.00
Identifying the proteins to which small-molecule probes and drugs bind in cells. Proc Natl Acad Sci U S A (2009) 2.94
Large-scale chemical dissection of mitochondrial function. Nat Biotechnol (2008) 2.91
Critical role of CDK2 for melanoma growth linked to its melanocyte-specific transcriptional regulation by MITF. Cancer Cell (2004) 2.80
Tight coordination of protein translation and HSF1 activation supports the anabolic malignant state. Science (2013) 2.79
Bead-based profiling of tyrosine kinase phosphorylation identifies SRC as a potential target for glioblastoma therapy. Nat Biotechnol (2008) 2.75
MicroRNA miR-125a controls hematopoietic stem cell number. Proc Natl Acad Sci U S A (2010) 2.53
Androgens induce prostate cancer cell proliferation through mammalian target of rapamycin activation and post-transcriptional increases in cyclin D proteins. Cancer Res (2006) 2.46
A remarkably simple genome underlies highly malignant pediatric rhabdoid cancers. J Clin Invest (2012) 2.42
MicroRNA dynamics in the stages of tumorigenesis correlate with hallmark capabilities of cancer. Genes Dev (2009) 2.41
DNA microarrays in clinical oncology. J Clin Oncol (2002) 2.40
Epidermal growth factor receptor inhibition attenuates liver fibrosis and development of hepatocellular carcinoma. Hepatology (2014) 2.40
Molecular sampling of prostate cancer: a dilemma for predicting disease progression. BMC Med Genomics (2010) 2.40
Proteomic and genetic approaches identify Syk as an AML target. Cancer Cell (2009) 2.39
Androgen-induced differentiation and tumorigenicity of human prostate epithelial cells. Cancer Res (2004) 2.32
Subclass mapping: identifying common subtypes in independent disease data sets. PLoS One (2007) 2.32
The Ewing's sarcoma oncoprotein EWS/FLI induces a p53-dependent growth arrest in primary human fibroblasts. Cancer Cell (2002) 2.28
Phase II study of intermediate-dose cytarabine in patients with relapsed or refractory Ewing sarcoma: a report from the Children's Oncology Group. Pediatr Blood Cancer (2009) 2.26
Estimating dataset size requirements for classifying DNA microarray data. J Comput Biol (2003) 2.23
A zebrafish bmyb mutation causes genome instability and increased cancer susceptibility. Proc Natl Acad Sci U S A (2005) 2.19
MicroRNA-1 negatively regulates expression of the hypertrophy-associated calmodulin and Mef2a genes. Mol Cell Biol (2009) 2.18
Small-molecule inhibitors of HIF-2a translation link its 5'UTR iron-responsive element to oxygen sensing. Mol Cell (2008) 2.15
Prognostic gene expression signature for patients with hepatitis C-related early-stage cirrhosis. Gastroenterology (2013) 2.13