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Article
Open AccessBulk brain tissue cell-type deconvolution with bias correction for single-nuclei RNA sequencing data using DeTREM
Quantifying cell-type abundance in bulk tissue RNA-sequencing enables researchers to better understand complex systems. Newer deconvolution methodologies, such as MuSiC, use cell-type signatures derived from s...
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Article
Open AccessIntegrative genetic and genomic networks identify microRNA associated with COPD and ILD
Chronic obstructive pulmonary disease (COPD) and interstitial lung disease (ILD) are clinically and molecularly heterogeneous diseases. We utilized clustering and integrative network analyses to elucidate role...
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Article
Open AccessSmoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airways
SARS-CoV-2 infection and disease severity are influenced by viral entry (VE) gene expression patterns in the airway epithelium. The similarities and differences of VE gene expression (ACE2, TMPRSS2, and CTSL) ...
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Article
Open AccessInactivation of the Hippo tumor suppressor pathway promotes melanoma
Melanoma is commonly driven by activating mutations in the MAP kinase BRAF; however, oncogenic BRAF alone is insufficient to promote melanomagenesis. Instead, its expression induces a transient proliferative b...
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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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Article
Open AccessMulti-modal profiling of human fetal liver hematopoietic stem cells reveals the molecular signature of engraftment
The human hematopoietic stem cell harbors remarkable regenerative potential that can be harnessed therapeutically. During early development, hematopoietic stem cells in the fetal liver undergo active expansion...
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Article
Publisher Correction: Whole-genome doubling confers unique genetic vulnerabilities on tumour cells
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Article
Whole-genome doubling confers unique genetic vulnerabilities on tumour cells
Whole-genome doubling (WGD) is common in human cancers, occurring early in tumorigenesis and generating genetically unstable tetraploid cells that fuel tumour development1,2. Cells that undergo WGD (WGD+ cells) m...
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Article
Open AccessCross organelle stress response disruption promotes gentamicin-induced proteotoxicity
Gentamicin is a nephrotoxic antibiotic that causes acute kidney injury (AKI) primarily by targeting the proximal tubule epithelial cell. The development of an effective therapy for gentamicin-induced renal cel...
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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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Chapter
Genetics of Lung Cancer
Unlike other lung diseases that have a significant heritable genetic component (e.g., cystic fibrosis), lung cancer is primarily caused by somatic mutations induced by environmental toxins such as cigarette sm...
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Article
Open AccessGenomic and immune profiling of pre-invasive lung adenocarcinoma
Adenocarcinoma in situ and minimally invasive adenocarcinoma are the pre-invasive forms of lung adenocarcinoma. The genomic and immune profiles of these lesions are poorly understood. Here we report exome and ...
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Article
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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Article
Open AccessMolecular subty** reveals immune alterations associated with progression of bronchial premalignant lesions
Bronchial premalignant lesions (PMLs) are precursors of lung squamous cell carcinoma, but have variable outcome, and we lack tools to identify and treat PMLs at risk for progression to cancer. Here we report t...
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Article
NetSig: network-based discovery from cancer genomes
NetSig is a network-based statistic that identifies cancer driver genes with high accuracy and can be combined with gene-based statistical tests; results are validated with a large-scale in vivo tumorigenesis ass...
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Article
Open AccessThe cellular and molecular determinants of emphysematous destruction in COPD
The introduction of microCT has made it possible to show that the terminal bronchioles are narrowed and destroyed before the onset of emphysematous destruction in COPD. This report extends those observations t...
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Article
Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas
Matthew Meyerson, Ramaswamy Govindan and colleagues examine the exome sequences and copy number profiles of 660 lung adenocarcinoma and 484 lung squamous cell carcinoma tumors. They identify novel significantl...
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Article
Open AccessTranscription factor and microRNA interactions in lung cells: an inhibitory link between NK2 homeobox 1, miR-200c and the developmental and oncogenic factors Nfib and Myb
The transcription factor NK2 homeobox 1 (Nkx2-1) plays essential roles in epithelial cell proliferation and differentiation in mouse and human lung development and tumorigenesis. A better understanding of gene...
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Article
Open AccessmiR-638 regulates gene expression networks associated with emphysematous lung destruction
Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease characterized by varying degrees of emphysematous lung destruction and small airway disease, each with distinct effects on clinical outco...
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Article
Open AccessCharacterizing the small RNA transcriptome associated with COPD and ILD using next-generation sequencing
