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Automated prioritization of sick newborns for whole genome sequencing using clinical natural language processing and machine learning
Automated prioritization of sick newborns for whole genome sequencing using clinical natural language processing and machine learning
Rapidly and efficiently identifying critically ill infants for whole genome sequencing (WGS) is a costly and challenging t...
Combinatorial batching of DNA for ultralow-cost detection of pathogenic variants
Combinatorial batching of DNA for ultralow-cost detection of pathogenic variants
Next-generation sequencing (NGS) based population screening holds great promise for disease prevention and earlier diagnos...
spSeudoMap: cell type mapping of spatial transcriptomics using unmatched single-cell RNA-seq data
spSeudoMap: cell type mapping of spatial transcriptomics using unmatched single-cell RNA-seq data
Since many single-cell RNA-seq (scRNA-seq) data are obtained after cell sorting, such as when investigating immune cells, ...
Pharmacogenomic profiling reveals molecular features of chemotherapy resistance in IDH wild-type primary glioblastoma
Pharmacogenomic profiling reveals molecular features of chemotherapy resistance in IDH wild-type primary glioblastoma
Although temozolomide (TMZ) has been used as a standard adjuvant chemotherapeutic agent for primary glioblastoma (GBM), tr...
Influence network model uncovers relations between biological processes and mutational signatures
Influence network model uncovers relations between biological processes and mutational signatures
There has been a growing appreciation recently that mutagenic processes can be studied through the lenses of mutational si...
Tumor microenvironment remodeling after neoadjuvant immunotherapy in non-small cell lung cancer revealed by single-cell RNA sequencing
Tumor microenvironment remodeling after neoadjuvant immunotherapy in non-small cell lung cancer revealed by single-cell RNA sequencing
Immunotherapy has revolutionized cancer treatment, but most patients are refractory to immunotherapy or acquire resistance...
Identification of specific susceptibility loci for the early-onset colorectal cancer
Identification of specific susceptibility loci for the early-onset colorectal cancer
The incidence of early-onset colorectal cancer (EOCRC; patients < 50 years old) has been rising rapidly, whereas th...
Refining epigenetic prediction of chronological and biological age
Refining epigenetic prediction of chronological and biological age
Epigenetic clocks can track both chronological age (cAge) and biological age (bAge). The latter is typically defined by ph...
TREM2 splice isoforms generate soluble TREM2 species that disrupt long-term potentiation
TREM2 splice isoforms generate soluble TREM2 species that disrupt long-term potentiation
TREM2 is a transmembrane receptor expressed by myeloid cells and acts to regulate their immune response. TREM2 governs the...
Pervasiveness of HLA allele-specific expression loss across tumor types
Pervasiveness of HLA allele-specific expression loss across tumor types
Efficient presentation of mutant peptide fragments by the human leukocyte antigen class I (HLA-I) genes is necessary for i...
Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395
Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395
Klebsiella pneumoniae, which is frequently associated with hospital- and community-acquired infections, contains multidrug...
Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
Low-frequency variants play an important role in breast cancer (BC) susceptibility. Gene-based methods can increase power ...
The neuroimmune axis of Alzheimer’s disease
The neuroimmune axis of Alzheimer’s disease
Alzheimer’s disease (AD) is a genetically complex and heterogeneous disorder with multifaceted neuropathological fea...
Risk assessment for colorectal cancer via polygenic risk score and lifestyle exposure: a large-scale association study of East Asian and European populations
Risk assessment for colorectal cancer via polygenic risk score and lifestyle exposure: a large-scale association study of East Asian and European populations
The genetic architectures of colorectal cancer are distinct across different populations. To date, the majority of polygen...
Large-scale genomic analysis of global Klebsiella pneumoniae plasmids reveals multiple simultaneous clusters of carbapenem-resistant hypervirulent strains
Large-scale genomic analysis of global Klebsiella pneumoniae plasmids reveals multiple simultaneous clusters of carbapenem-resistant hypervirulent strains
Klebsiella pneumoniae (Kp) Gram-negative bacteria cause nosocomial infections and rapidly acquire antimicrobial resistance...
Single-cell transcriptomics reveals a mechanosensitive injury signaling pathway in early diabetic nephropathy
Single-cell transcriptomics reveals a mechanosensitive injury signaling pathway in early diabetic nephropathy
Diabetic nephropathy (DN) is the leading cause of end-stage renal disease, and histopathologic glomerular lesions are amon...
The gut microbiota in multiple sclerosis varies with disease activity
The gut microbiota in multiple sclerosis varies with disease activity
Multiple sclerosis is a chronic immune-mediated disease of the brain and spinal cord resulting in physical and cognitive i...
Neutralization sensitivity, fusogenicity, and infectivity of Omicron subvariants
Neutralization sensitivity, fusogenicity, and infectivity of Omicron subvariants
The emergence of SARS-CoV-2 Omicron subvariants has raised questions regarding resistance to immunity by natural infection...
A one-year genomic investigation of Escherichia coli epidemiology and nosocomial spread at a large US healthcare network
A one-year genomic investigation of Escherichia coli epidemiology and nosocomial spread at a large US healthcare network
Extra-intestinal pathogenic Escherichia coli (ExPEC) are a leading cause of bloodstream and urinary tract infections world...
Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA
Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA
The respiratory pathogen Streptococcus pneumoniae (the pneumococcus) is a genetically diverse bacterium associated with ov...
Spatiotemporal evolution of the clear cell renal cell carcinoma microenvironment links intra-tumoral heterogeneity to immune escape
Spatiotemporal evolution of the clear cell renal cell carcinoma microenvironment links intra-tumoral heterogeneity to immune escape
Intratumoral heterogeneity (ITH) is a hallmark of clear cell renal cell carcinoma (ccRCC) that reflects the trajectory of ...
Multi-region sequencing with spatial information enables accurate heterogeneity estimation and risk stratification in liver cancer
Multi-region sequencing with spatial information enables accurate heterogeneity estimation and risk stratification in liver cancer
Numerous studies have used multi-region sampling approaches to characterize intra-tumor heterogeneity (ITH) in hepatocellu...
Calculating variant penetrance from family history of disease and average family size in population-scale data
Calculating variant penetrance from family history of disease and average family size in population-scale data
Genetic penetrance is the probability of a phenotype when harbouring a particular pathogenic variant. Accurate penetrance ...
Mendelian randomization and genetic colocalization infer the effects of the multi-tissue proteome on 211 complex disease-related phenotypes
Mendelian randomization and genetic colocalization infer the effects of the multi-tissue proteome on 211 complex disease-related phenotypes
Human proteins are widely used as drug targets. Integration of large-scale protein-level genome-wide association studies (...
Therapy sculpts the complex interplay between cancer and the immune system during tumour evolution
Therapy sculpts the complex interplay between cancer and the immune system during tumour evolution
Cancer development is an evolutionary process. A key selection pressure is exerted by therapy, one of the few players in c...
CRAG: de novo characterization of cell-free DNA fragmentation hotspots in plasma whole-genome sequencing
CRAG: de novo characterization of cell-free DNA fragmentation hotspots in plasma whole-genome sequencing
The fine-scale cell-free DNA fragmentation patterns in early-stage cancers are poorly understood. We developed a de novo a...
Cell type-specific changes identified by single-cell transcriptomics in Alzheimer’s disease
Cell type-specific changes identified by single-cell transcriptomics in Alzheimer’s disease
The rapid advancement of single-cell transcriptomics in neurology has allowed for profiling of post-mortem human brain tis...
Neutrophil extracellular traps have auto-catabolic activity and produce mononucleosome-associated circulating DNA
Neutrophil extracellular traps have auto-catabolic activity and produce mononucleosome-associated circulating DNA
As circulating DNA (cirDNA) is mainly detected as mononucleosome-associated circulating DNA (mono-N cirDNA) in blood, apop...
Whole-exome sequencing identifies novel protein-altering variants associated with serum apolipoprotein and lipid concentrations
Whole-exome sequencing identifies novel protein-altering variants associated with serum apolipoprotein and lipid concentrations
Dyslipidemia is a major risk factor for cardiovascular disease, and diabetes impacts the lipid metabolism through multiple...
Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex
Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex
Neuropsychiatric disorders afflict a large portion of the global population and constitute a significant source of disabil...
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