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Article
Open AccessMap** human tissues with highly multiplexed RNA in situ hybridization
In situ transcriptomic techniques promise a holistic view of tissue organization and cell-cell interactions. There has been a surge of multiplexed RNA in situ map** techniques but their application to human ...
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Article
Open AccessAccurate detection of early-stage lung cancer using a panel of circulating cell-free DNA methylation biomarkers
Lung cancer remains the leading cause of cancer mortality worldwide. Early detection of lung cancer helps improve treatment and survival. Numerous aberrant DNA methylations have been reported in early-stage lu...
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Article
Open AccessPredicting disease-free survival in colorectal cancer by circulating tumor DNA methylation markers
Recurrence represents a well-known poor prognostic factor for colorectal cancer (CRC) patients. This study aimed to establish an effective prognostic prediction model based on noninvasive circulating tumor DNA...
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Article
Open AccessA novel DNA methylation signature associated with lymph node metastasis status in early gastric cancer
Lymph node metastasis (LNM) is an important factor for both treatment and prognosis of early gastric cancer (EGC). Current methods are insufficient to evaluate LNM in EGC due to suboptimal accuracy. Herein, we...
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Article
Open AccessDiagnosis of pulmonary nodules by DNA methylation analysis in bronchoalveolar lavage fluids
Lung cancer is the leading cause of cancer-related mortality. The alteration of DNA methylation plays a major role in the development of lung cancer. Methylation biomarkers become a possible method for lung ca...
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Open AccessCirculating cell-free DNA-based methylation patterns for breast cancer diagnosis
Mammography is used to detect breast cancer (BC), but its sensitivity is limited, especially for dense breasts. Circulating cell-free DNA (cfDNA) methylation tests is expected to compensate for the deficiency ...
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Article
Open AccessA urine-based DNA methylation assay to facilitate early detection and risk stratification of bladder cancer
Current non-invasive tests have limited sensitivities and lack capabilities of pre-operative risk stratification for bladder cancer (BC) diagnosis. We aimed to develop and validate a urine-based DNA methylatio...
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Article
Open AccessSensitive detection of colorectal cancer in peripheral blood by a novel methylation assay
Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide. Early detection of CRC can significantly reduce its mortality rate. Current method of CRC diagnosis relies on the invasive endosco...
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Article
Open AccessAssessing characteristics of RNA amplification methods for single cell RNA sequencing
Recently, measurement of RNA at single cell resolution has yielded surprising insights. Methods for single-cell RNA sequencing (scRNA-seq) have received considerable attention, but the broad reliability of sin...
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Article
Open AccessEpigenetic signature of Gleason score and prostate cancer recurrence after radical prostatectomy
Identifying the subset of patients with clinically localized prostate cancer (PCa) at the highest risk of recurrence remains challenging, and better prognostic markers are needed. Gleason score is the best pre...
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Article
Open AccessGenetic suppression reveals DNA repair-independent antagonism between BRCA1 and COBRA1 in mammary gland development
The breast cancer susceptibility gene BRCA1 is well known for its function in double-strand break (DSB) DNA repair. While BRCA1 is also implicated in transcriptional regulation, the physiological significance rem...
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Article
Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis
By testing potential sources of biological signal that drive population-level variation in single-cell gene expression, the PAGODA software enables cells to be characterized on the basis of multiple functional...
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Article
Open AccessEpigenomic profiling of prostate cancer identifies differentially methylated genes in TMPRSS2:ERG fusion-positive versus fusion-negative tumors
About half of all prostate cancers harbor the TMPRSS2:ERG (T2E) gene fusion. While T2E-positive and T2E-negative tumors represent specific molecular subtypes of prostate cancer (PCa), previous studies have not ye...
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Open AccessTargeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells
CRISPR/Cas9 has demonstrated a high-efficiency in site-specific gene targeting. However, potential off-target effects of the Cas9 nuclease represent a major safety concern for any therapeutic application. Here...
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Open AccessMutation in ST6GALNAC5 identified in family with coronary artery disease
We aimed to identify the genetic cause of coronary artery disease (CAD) in an Iranian pedigree. Genetic linkage analysis identified three loci with an LOD score of 2.2. Twelve sequence variations identified by...
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Article
The transcriptional architecture of early human hematopoiesis identifies multilevel control of lymphoid commitment
Dick and colleagues map the transcriptional dynamics of human hematopoietic stem cells and early progenitor populations. The authors show that transcriptional programs are extensively shared, extend across lin...
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Article
Regulation of adipose oestrogen output by mechanical stress
Adipose stromal cells are the primary source of local oestrogens in adipose tissue, aberrant production of which promotes oestrogen receptor-positive breast cancer. Here we show that extracellular matrix compl...
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Article
Open AccessMicroRNA paraffin-based studies in osteosarcoma reveal reproducible independent prognostic profiles at 14q32
Although microRNAs (miRNAs) are implicated in osteosarcoma biology and chemoresponse, miRNA prognostic models are still needed, particularly because prognosis is imperfectly correlated with chemoresponse. Form...
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Article
Identification of Disease-Associated DNA Methylation in B Cells from Crohn’s Disease and Ulcerative Colitis Patients
Changes in the methylation status of inflammatory bowel disease (IBD)-associated genes could significantly alter levels of gene expression, thereby contributing to disease onset and progression. We previously ...
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Open AccessSalinomycin induces cell death and differentiation in head and neck squamous cell carcinoma stem cells despite activation of epithelial-mesenchymal transition and Akt
Cancer stem cells (CSC) are believed to play a crucial role in cancer recurrence due to their resistance to conventional chemotherapy and capacity for self-renewal. Recent studies have reported that salinomyci...
