Microarrays: retracing steps.

PubWeight™: 2.39‹?› | Rank: Top 2%

🔗 View Article (PMID 17987014)

Published in Nat Med on November 01, 2007

Authors

Kevin R Coombes, Jing Wang, Keith A Baggerly

Articles citing this

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

Increasing value and reducing waste: addressing inaccessible research. Lancet (2014) 4.83

Challenges translating breast cancer gene signatures into the clinic. Nat Rev Clin Oncol (2011) 1.86

Robust gene expression signature from formalin-fixed paraffin-embedded samples predicts prognosis of non-small-cell lung cancer patients. Clin Cancer Res (2011) 1.59

Validation of biomarker-based risk prediction models. Clin Cancer Res (2008) 1.57

Prospective comparison of clinical and genomic multivariate predictors of response to neoadjuvant chemotherapy in breast cancer. Clin Cancer Res (2010) 1.44

Concordant gene expression signatures predict clinical outcomes of cancer patients undergoing systemic therapy. Cancer Res (2009) 1.44

Functional proteomic analysis of advanced serous ovarian cancer using reverse phase protein array: TGF-beta pathway signaling indicates response to primary chemotherapy. Clin Cancer Res (2010) 1.38

Microarrays in the 2010s: the contribution of microarray-based gene expression profiling to breast cancer classification, prognostication and prediction. Breast Cancer Res (2011) 1.30

Nuclear receptor expression defines a set of prognostic biomarkers for lung cancer. PLoS Med (2010) 1.19

Exploratory analysis of the copy number alterations in glioblastoma multiforme. PLoS One (2008) 1.17

Gene expression profiling predicts the development of oral cancer. Cancer Prev Res (Phila) (2011) 1.13

Lost in translation: problems and pitfalls in translating laboratory observations to clinical utility. Eur J Cancer (2008) 1.02

Cancer trial errors revealed. Nature (2011) 0.98

Preclinical strategies to define predictive biomarkers for therapeutically relevant cancer subtypes. Hum Genet (2011) 0.96

Predicting response to multidrug regimens in cancer patients using cell line experiments and regularised regression models. BMC Cancer (2015) 0.95

Impact of intertumoral heterogeneity on predicting chemotherapy response of BRCA1-deficient mammary tumors. Cancer Res (2012) 0.95

Data handling errors spur debate over clinical trial. Nat Med (2010) 0.92

Independent validation of a model using cell line chemosensitivity to predict response to therapy. J Natl Cancer Inst (2013) 0.92

Generation of a predictive melphalan resistance index by drug screen of B-cell cancer cell lines. PLoS One (2011) 0.90

Using drug response data to identify molecular effectors, and molecular "omic" data to identify candidate drugs in cancer. Hum Genet (2014) 0.89

A lung cancer molecular prognostic test ready for prime time. Lancet (2012) 0.89

Implementation of the CDC translational informatics platform--from genetic variants to the national Swedish Rheumatology Quality Register. J Transl Med (2013) 0.86

Specific kinesin expression profiles associated with taxane resistance in basal-like breast cancer. Breast Cancer Res Treat (2011) 0.85

Evaluation of gene expression classification studies: factors associated with classification performance. PLoS One (2014) 0.84

Perspectives on systems biology applications in diabetic kidney disease. J Cardiovasc Transl Res (2012) 0.84

Identification of a gene signature in cell cycle pathway for breast cancer prognosis using gene expression profiling data. BMC Med Genomics (2008) 0.83

Functional genomic analysis of drug sensitivity pathways to guide adjuvant strategies in breast cancer. Breast Cancer Res (2008) 0.83

Exploiting the noise: improving biomarkers with ensembles of data analysis methodologies. Genome Med (2012) 0.82

Precision medicine for cancer patients: lessons learned and the path forward. J Natl Cancer Inst (2013) 0.80

Reproducible probe-level analysis of the Affymetrix Exon 1.0 ST array with R/Bioconductor. Brief Bioinform (2014) 0.80

ASTM international workshop on standards and measurements for tissue engineering scaffolds. J Biomed Mater Res B Appl Biomater (2014) 0.79

The reproducibility of biomedical research: Sleepers awake! Biomol Detect Quantif (2015) 0.79

Genomancy: predicting tumour response to cancer therapy based on the oracle of genetics. Curr Oncol (2009) 0.78

Information systems for cancer research. Cancer Invest (2008) 0.76

Analytic model for academic research productivity having factors, interactions and implications. Cancer Biol Ther (2011) 0.76

Extracting patterns of morphometry distinguishing HIV associated neurodegeneration from mild cognitive impairment via group cardinality constrained classification. Hum Brain Mapp (2016) 0.75

How to Tell the Truth with Statistics: The Case for Accountable Data Analyses in Team-based Science. J Transl Med Epidemiol (2015) 0.75

Discovering novel pharmacogenomic biomarkers by imputing drug response in cancer patients from large genomics studies. Genome Res (2017) 0.75

Articles cited by this

Retracted Genomic signatures to guide the use of chemotherapeutics. Nat Med (2006) 7.45

Articles by these authors

A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78

WEGO: a web tool for plotting GO annotations. Nucleic Acids Res (2006) 13.06

Using FlyAtlas to identify better Drosophila melanogaster models of human disease. Nat Genet (2007) 12.62

Transformation from committed progenitor to leukaemia stem cell initiated by MLL-AF9. Nature (2006) 11.90

Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1. Science (2011) 11.12

Lymphoproliferative disease and autoimmunity in mice with increased miR-17-92 expression in lymphocytes. Nat Immunol (2008) 10.42

MiR-150 controls B cell differentiation by targeting the transcription factor c-Myb. Cell (2007) 9.33

Effect of aciclovir on HIV-1 acquisition in herpes simplex virus 2 seropositive women and men who have sex with men: a randomised, double-blind, placebo-controlled trial. Lancet (2008) 9.17

Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol (2010) 9.01

Changes in diabetes-related complications in the United States, 1990-2010. N Engl J Med (2014) 8.73

The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67

A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science (2004) 6.62

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature (2004) 5.24

Self-monitoring in weight loss: a systematic review of the literature. J Am Diet Assoc (2011) 5.12

AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol (2011) 4.71

The E3 ligase TRAF6 regulates Akt ubiquitination and activation. Science (2009) 4.63

Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. Bioinformatics (2004) 4.58

Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum. Bioinformatics (2005) 4.26

Priming of naive T cells inside tumors leads to eradication of established tumors. Nat Immunol (2004) 3.95

Steps toward mapping the human vasculature by phage display. Nat Med (2002) 3.82

Glycolytic enzymes can modulate cellular life span. Cancer Res (2005) 3.78

Phosphatidylinositol 4 phosphate regulates targeting of clathrin adaptor AP-1 complexes to the Golgi. Cell (2003) 3.75

Large-gap quantum spin Hall insulators in tin films. Phys Rev Lett (2013) 3.60

Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet (2010) 3.56

Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res (2005) 3.56

An epithelial-mesenchymal transition gene signature predicts resistance to EGFR and PI3K inhibitors and identifies Axl as a therapeutic target for overcoming EGFR inhibitor resistance. Clin Cancer Res (2012) 3.48

Signal in noise: evaluating reported reproducibility of serum proteomic tests for ovarian cancer. J Natl Cancer Inst (2005) 3.31

Non-parametric quantification of protein lysate arrays. Bioinformatics (2007) 3.18

Sofosbuvir and Velpatasvir for HCV Genotype 2 and 3 Infection. N Engl J Med (2015) 3.13

Skp2 targeting suppresses tumorigenesis by Arf-p53-independent cellular senescence. Nature (2010) 3.09

HIV/STD risk behaviors and perceptions among rural-to-urban migrants in China. AIDS Educ Prev (2004) 3.04

Patterns of gene expression in different histotypes of epithelial ovarian cancer correlate with those in normal fallopian tube, endometrium, and colon. Clin Cancer Res (2005) 2.98

Selection of potential markers for epithelial ovarian cancer with gene expression arrays and recursive descent partition analysis. Clin Cancer Res (2004) 2.96

Evolution of the immunoglobulin heavy chain class switch recombination mechanism. Adv Immunol (2007) 2.94

Functional proteomic profiling of AML predicts response and survival. Blood (2008) 2.90

The cholesterol absorption inhibitor ezetimibe acts by blocking the sterol-induced internalization of NPC1L1. Cell Metab (2008) 2.84

Variants in the fat mass- and obesity-associated (FTO) gene are not associated with obesity in a Chinese Han population. Diabetes (2007) 2.83

Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform. Proteomics (2005) 2.81

Effect of KRAS oncogene substitutions on protein behavior: implications for signaling and clinical outcome. J Natl Cancer Inst (2012) 2.79

Rapid cardiotonic effects of lipid emulsion infusion*. Crit Care Med (2013) 2.76

Plasma protein profiling for diagnosis of pancreatic cancer reveals the presence of host response proteins. Clin Cancer Res (2005) 2.76

BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. Nucleic Acids Res (2004) 2.69

Proteomic profiling identifies dysregulated pathways in small cell lung cancer and novel therapeutic targets including PARP1. Cancer Discov (2012) 2.68

Trends in physical activity, sedentary behavior, diet, and BMI among US adolescents, 2001-2009. Pediatrics (2013) 2.66

Nuclear receptor Rev-erbalpha is a critical lithium-sensitive component of the circadian clock. Science (2006) 2.62

A developmental approach to complex PTSD: childhood and adult cumulative trauma as predictors of symptom complexity. J Trauma Stress (2009) 2.59

PDGF signalling controls age-dependent proliferation in pancreatic β-cells. Nature (2011) 2.53

The effect of passengers and risk-taking friends on risky driving and crashes/near crashes among novice teenagers. J Adolesc Health (2011) 2.53

Involvement of the ubiquitin-proteasome system in the early stages of wallerian degeneration. Neuron (2003) 2.51

Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers. Cancer Discov (2013) 2.49

Physics. Learning and scientific reasoning. Science (2009) 2.49

PILRalpha is a herpes simplex virus-1 entry coreceptor that associates with glycoprotein B. Cell (2008) 2.49

A glimpse of streptococcal toxic shock syndrome from comparative genomics of S. suis 2 Chinese isolates. PLoS One (2007) 2.47

Differential response to neoadjuvant chemotherapy among 7 triple-negative breast cancer molecular subtypes. Clin Cancer Res (2013) 2.30

The spectrum of SCN1A-related infantile epileptic encephalopathies. Brain (2007) 2.30

Crystal structure of the clathrin adaptor protein 1 core. Proc Natl Acad Sci U S A (2004) 2.28

BMP4 supports self-renewal of embryonic stem cells by inhibiting mitogen-activated protein kinase pathways. Proc Natl Acad Sci U S A (2004) 2.25

Crash and risky driving involvement among novice adolescent drivers and their parents. Am J Public Health (2011) 2.25

microRNA fingerprinting of CLL patients with chromosome 17p deletion identify a miR-21 score that stratifies early survival. Blood (2010) 2.25

Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. Proc Natl Acad Sci U S A (2012) 2.22

The completion of the Mammalian Gene Collection (MGC). Genome Res (2009) 2.21

Enhanced striatal dopamine transmission and motor performance with LRRK2 overexpression in mice is eliminated by familial Parkinson's disease mutation G2019S. J Neurosci (2010) 2.20

Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research. Nucleic Acids Res (2006) 2.14

Proteomic markers of DNA repair and PI3K pathway activation predict response to the PARP inhibitor BMN 673 in small cell lung cancer. Clin Cancer Res (2013) 2.09

The importance of experimental design in proteomic mass spectrometry experiments: some cautionary tales. Brief Funct Genomic Proteomic (2005) 2.08

Increased expression of CYP17 and CYP11B1 in subclinical Cushing's syndrome due to adrenal adenomas. Int J Urol (2011) 2.07

Disrupted autophagy leads to dopaminergic axon and dendrite degeneration and promotes presynaptic accumulation of α-synuclein and LRRK2 in the brain. J Neurosci (2012) 2.06

Applications of beta-mixture models in bioinformatics. Bioinformatics (2005) 2.04

Concordance of sustained virological response 4, 12, and 24 weeks post-treatment with sofosbuvir-containing regimens for hepatitis C virus. Hepatology (2014) 2.04

A TNF receptor family member, TROY, is a coreceptor with Nogo receptor in mediating the inhibitory activity of myelin inhibitors. Neuron (2005) 2.03

Identification of cell cycle regulatory genes as principal targets of p53-mediated transcriptional repression. J Biol Chem (2006) 2.01

Bayesian analysis of mass spectrometry proteomic data using wavelet-based functional mixed models. Biometrics (2007) 2.01

Pregnancy, contraceptive use, and HIV acquisition in HPTN 039: relevance for HIV prevention trials among African women. J Acquir Immune Defic Syndr (2010) 2.01

A comprehensive approach to the analysis of matrix-assisted laser desorption/ionization-time of flight proteomics spectra from serum samples. Proteomics (2003) 2.01

The bimodality index: a criterion for discovering and ranking bimodal signatures from cancer gene expression profiling data. Cancer Inform (2009) 1.98

Serum proteomics profiling--a young technology begins to mature. Nat Biotechnol (2005) 1.98

Wld S requires Nmnat1 enzymatic activity and N16-VCP interactions to suppress Wallerian degeneration. J Cell Biol (2009) 1.98

A novel CCCH-zinc finger protein family regulates proinflammatory activation of macrophages. J Biol Chem (2008) 1.98

How many human genes can be defined as housekeeping with current expression data? BMC Genomics (2008) 1.97

Run batch effects potentially compromise the usefulness of genomic signatures for ovarian cancer. J Clin Oncol (2008) 1.96

Curcumin (diferuloylmethane) alters the expression profiles of microRNAs in human pancreatic cancer cells. Mol Cancer Ther (2008) 1.92

SNARE proteins: one to fuse and three to keep the nascent fusion pore open. Science (2012) 1.89

Structure acquisition of the T1 domain of Kv1.3 during biogenesis. Neuron (2004) 1.89

Quality control and peak finding for proteomics data collected from nipple aspirate fluid by surface-enhanced laser desorption and ionization. Clin Chem (2003) 1.88

Androgen receptor-negative human prostate cancer cells induce osteogenesis in mice through FGF9-mediated mechanisms. J Clin Invest (2008) 1.87

Regulation of endothelial nitric oxide synthase by small RNA. Proc Natl Acad Sci U S A (2005) 1.85

MCP-induced protein 1 deubiquitinates TRAF proteins and negatively regulates JNK and NF-kappaB signaling. J Exp Med (2010) 1.84

i-GSEA4GWAS: a web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study. Nucleic Acids Res (2010) 1.83

Design, synthesis and cytotoxicity of novel podophyllotoxin derivatives. Chem Pharm Bull (Tokyo) (2008) 1.83

The role of herpesvirus entry mediator as a negative regulator of T cell-mediated responses. J Clin Invest (2005) 1.82