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Article
Open AccessComparison of gene set scoring methods for reproducible evaluation of tuberculosis gene signatures
Blood-based transcriptional gene signatures for tuberculosis (TB) have been developed with potential use to diagnose disease. However, an unresolved issue is whether gene set enrichment analysis of the signatu...
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Article
Psychosocial stressors and breast cancer gene expression in the Black Women’s Health Study
Prior studies indicate that the physiologic response to stress can affect gene expression. We evaluated differential gene expression in breast cancers collected from Black women with high versus low exposure t...
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Article
Open AccessMetagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data
Most experiments studying bacterial microbiomes rely on the PCR amplification of all or part of the gene for the 16S rRNA subunit, which serves as a biomarker for identifying and quantifying the various taxa p...
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Article
Open AccessAuthor Correction: A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome
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Open AccessA comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome
H37Rv is the most widely used Mycobacterium tuberculosis strain, and its genome is globally used as the M. tuberculosis reference sequence. Here, we present Bact-Builder, a pipeline that uses consensus building t...
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Article
Open AccessComprehensive generation, visualization, and reporting of quality control metrics for single-cell RNA sequencing data
Single-cell RNA sequencing (scRNA-seq) can be used to gain insights into cellular heterogeneity within complex tissues. However, various technical artifacts can be present in scRNA-seq data and should be asses...
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The oral microbiome in relation to pancreatic cancer risk in African Americans
African Americans have the highest pancreatic cancer incidence of any racial/ethnic group in the United States. The oral microbiome was associated with pancreatic cancer risk in a recent study, but no such stu...
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Open AccessNovel temporal and spatial patterns of metastatic colonization from breast cancer rapid-autopsy tumor biopsies
Metastatic breast cancer is a deadly disease with a low 5-year survival rate. Tracking metastatic spread in living patients is difficult and thus poorly understood.
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Open AccessTuberculosis—Learning the Impact of Nutrition (TB LION): protocol for an interventional study to decrease TB risk in household contacts
Comorbidities such as undernutrition and parasitic infections are widespread in India and other tuberculosis (TB)-endemic countries. This study examines how these conditions as well as food supplementation and...
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Open AccessInhibition of colony stimulating factor 1 receptor corrects maternal inflammation-induced microglial and synaptic dysfunction and behavioral abnormalities
Maternal immune activation (MIA) disrupts the central innate immune system during a critical neurodevelopmental period. Microglia are primary innate immune cells in the brain although their direct influence on...
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Article
Open Accessanimalcules: interactive microbiome analytics and visualization in R
Microbial communities that live in and on the human body play a vital role in health and disease. Recent advances in sequencing technologies have enabled the study of microbial communities at unprecedented res...
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Open AccessComparing tuberculosis gene signatures in malnourished individuals using the TBSignatureProfiler
Gene expression signatures have been used as biomarkers of tuberculosis (TB) risk and outcomes. Platforms are needed to simplify access to these signatures and determine their validity in the setting of comorb...
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Article
Open AccessDecontamination of ambient RNA in single-cell RNA-seq with DecontX
Droplet-based microfluidic devices have become widely used to perform single-cell RNA sequencing (scRNA-seq). However, ambient RNA present in the cell suspension can be aberrantly counted along with a cell’s n...
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Open AccessPathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes
Gene expression profiling of rare cancers has proven challenging due to limited access to patient materials and requirement of intact, non-degraded RNA for next-generation sequencing. We customized a gene expr...
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Open Accessscruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data
Single-cell RNA sequencing (scRNA-seq) enables the high-throughput quantification of transcriptional profiles in single cells. In contrast to bulk RNA-seq, additional preprocessing steps such as cell barcode i...
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Open AccessAlternative empirical Bayes models for adjusting for batch effects in genomic studies
Combining genomic data sets from multiple studies is advantageous to increase statistical power in studies where logistical considerations restrict sample size or require the sequential generation of data. How...
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Open AccessPublisher Correction: Combating subclonal evolution of resistant cancer phenotypes
The originally published version of this Article contained an error in Figure 4. In panel a, grey boxes surrounding the subclones associated with patients #2 and #4 obscured adjacent portions of the heatmap. T...
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Article
Open AccessCombating subclonal evolution of resistant cancer phenotypes
Metastatic breast cancer remains challenging to treat, and most patients ultimately progress on therapy. This acquired drug resistance is largely due to drug-refractory sub-populations (subclones) within heter...
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Article
Open AccessActivity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes
The growth factor receptor network (GFRN) plays a significant role in driving key oncogenic processes. However, assessment of global GFRN activity is challenging due to complex crosstalk among GFRN components,...
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Open AccessGene-expression patterns in peripheral blood classify familial breast cancer susceptibility
Women with a family history of breast cancer face considerable uncertainty about whether to pursue standard screening, intensive screening, or prophylactic surgery. Accurate and individualized risk-estimation ...
