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LETSmix: a spatially informed and learning-based domain adaptation method for cell-type deconvolution in spatial transcriptomics
LETSmix: a spatially informed and learning-based domain adaptation method for cell-type deconvolution in spatial transcriptomics
Spatial transcriptomics (ST) enables the study of gene expression in spatial context, but many ST technologies face challe...
STModule: identifying tissue modules to uncover spatial components and characteristics of transcriptomic landscapes
STModule: identifying tissue modules to uncover spatial components and characteristics of transcriptomic landscapes
Here we present STModule, a Bayesian method developed to identify tissue modules from spatially resolved transcriptomics t...
Non-coding cis-regulatory variants in HK1 cause congenital hyperinsulinism with variable disease severity
Non-coding cis-regulatory variants in HK1 cause congenital hyperinsulinism with variable disease severity
We recently reported non-coding variants in a cis-regulatory element of the beta-cell disallowed gene hexokinase 1 (HK1) a...
Structural variants linked to Alzheimer’s disease and other common age-related clinical and neuropathologic traits
Structural variants linked to Alzheimer’s disease and other common age-related clinical and neuropathologic traits
Alzheimer’s disease (AD) is a complex neurodegenerative disorder with substantial genetic influence. While genome-wi...
Genomic insights into the plasmidome of non-tuberculous mycobacteria
Genomic insights into the plasmidome of non-tuberculous mycobacteria
Non-tuberculous mycobacteria (NTM) are a diverse group of environmental bacteria that are increasingly associated with hum...
Mendelian randomization analyses suggest a causal role for circulating GIP and IL-1RA levels in homeostatic model assessment-derived measures of β-cell function and insulin sensitivity in Africans without type 2 diabetes
Mendelian randomization analyses suggest a causal role for circulating GIP and IL-1RA levels in homeostatic model assessment-derived measures of β-cell function and insulin sensitivity in Africans without type 2 diabetes
In vitro and in vivo studies have shown that certain cytokines and hormones may play a role in the development and progres...
Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity
Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity
Biallelic variants in OGDHL, encoding part of the α-ketoglutarate dehydrogenase complex, have been associated with hi...
Genome-wide prediction of pathogenic gain- and loss-of-function variants from ensemble learning of a diverse feature set
Genome-wide prediction of pathogenic gain- and loss-of-function variants from ensemble learning of a diverse feature set
Gain-of-function (GOF) variants give rise to increased/novel protein functions whereas loss-of-function (LOF) variants lea...
Mobilizable plasmids drive the spread of antimicrobial resistance genes and virulence genes in Klebsiella pneumoniae
Mobilizable plasmids drive the spread of antimicrobial resistance genes and virulence genes in Klebsiella pneumoniae
Klebsiella pneumoniae is a notorious clinical pathogen and frequently carries various plasmids, which are the main carrier...
Personalized tumor combination therapy optimization using the single-cell transcriptome
Personalized tumor combination therapy optimization using the single-cell transcriptome
The precise characterization of individual tumors and immune microenvironments using transcriptome sequencing has provided...
A phenome-wide scan reveals convergence of common and rare variant associations
A phenome-wide scan reveals convergence of common and rare variant associations
Common and rare variants contribute to the etiology of complex traits. However, the extent to which the phenotypic effects...
GITR and TIGIT immunotherapy provokes divergent multicellular responses in the tumor microenvironment of gastrointestinal cancers
GITR and TIGIT immunotherapy provokes divergent multicellular responses in the tumor microenvironment of gastrointestinal cancers
Understanding the mechanistic effects of novel immunotherapy agents is critical to improving their successful clinical tra...
Massive underrepresentation of Arabs in genomic studies of common disease
Massive underrepresentation of Arabs in genomic studies of common disease
Arabs represent 5% of the world population and have a high prevalence of common disease, yet remain greatly underrepresent...
Loss of p53-DREAM-mediated repression of cell cycle genes as a driver of lymph node metastasis in head and neck cancer
Loss of p53-DREAM-mediated repression of cell cycle genes as a driver of lymph node metastasis in head and neck cancer
The prognosis for patients with head and neck cancer (HNC) is poor and has improved little in recent decades, partially du...
The role of admixture in the rare variant contribution to inflammatory bowel disease
The role of admixture in the rare variant contribution to inflammatory bowel disease
Identification of rare variants involved in complex, polygenic diseases like Crohn’s disease (CD) has accelerated wi...
Building blocks for better biorepositories in Africa
Building blocks for better biorepositories in Africa
Biorepositories archive and distribute well-characterized biospecimens for research to support the development of medical ...
Early detection of hepatocellular carcinoma via no end-repair enzymatic methylation sequencing of cell-free DNA and pre-trained neural network
Early detection of hepatocellular carcinoma via no end-repair enzymatic methylation sequencing of cell-free DNA and pre-trained neural network
Early detection of hepatocellular carcinoma (HCC) is important in order to improve patient prognosis and survival rate. Me...
Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases
Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases
Whole genome sequencing is increasingly being used for the diagnosis of patients with rare diseases. However, the diagnost...
Rapid profiling of Plasmodium parasites from genome sequences to assist malaria control
Rapid profiling of Plasmodium parasites from genome sequences to assist malaria control
Malaria continues to be a major threat to global public health. Whole genome sequencing (WGS) of the underlying Plasmodium...
Skeletal muscle regeneration failure in ischemic-damaged limbs is associated with pro-inflammatory macrophages and premature differentiation of satellite cells
Skeletal muscle regeneration failure in ischemic-damaged limbs is associated with pro-inflammatory macrophages and premature differentiation of satellite cells
Chronic limb-threatening ischemia (CLTI), a severe manifestation of peripheral arterial disease (PAD), is associated with ...
Analysis of transcriptomic features reveals molecular endotypes of SLE with clinical implications
Analysis of transcriptomic features reveals molecular endotypes of SLE with clinical implications
Systemic lupus erythematosus (SLE) is known to be clinically heterogeneous. Previous efforts to characterize subsets of SL...
Single-cell RNA sequencing distinctly characterizes the wide heterogeneity in pediatric mixed phenotype acute leukemia
Single-cell RNA sequencing distinctly characterizes the wide heterogeneity in pediatric mixed phenotype acute leukemia
Mixed phenotype acute leukemia (MPAL), a rare subgroup of leukemia characterized by blast cells with myeloid and lymphoid ...
Recommendations for the classification of germline variants in the exonuclease domain of POLE and POLD1
Recommendations for the classification of germline variants in the exonuclease domain of POLE and POLD1
Germline variants affecting the proofreading activity of polymerases epsilon and delta cause a hereditary cancer and adeno...
Cancer origin tracing and timing in two high-risk prostate cancers using multisample whole genome analysis: prospects for personalized medicine
Cancer origin tracing and timing in two high-risk prostate cancers using multisample whole genome analysis: prospects for personalized medicine
Prostate cancer (PrCa) genomic heterogeneity causes resistance to therapies such as androgen deprivation. Such heterogenei...
Small extrachromosomal circular DNA harboring targeted tumor suppressor gene mutations supports intratumor heterogeneity in mouse liver cancer induced by multiplexed CRISPR/Cas9
Small extrachromosomal circular DNA harboring targeted tumor suppressor gene mutations supports intratumor heterogeneity in mouse liver cancer induced by multiplexed CRISPR/Cas9
Primary liver cancer has significant intratumor genetic heterogeneity (IGH), which drives cancer evolution and prevents ef...
Global analysis of suppressor mutations that rescue human genetic defects
Global analysis of suppressor mutations that rescue human genetic defects
Genetic suppression occurs when the deleterious effects of a primary “query” mutation, such as a disease-causi...
Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar Study
Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar Study
Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by impaired social and communication skills...
Meiotic and mitotic aneuploidies drive arrest of in vitro fertilized human preimplantation embryos
Meiotic and mitotic aneuploidies drive arrest of in vitro fertilized human preimplantation embryos
The high incidence of aneuploidy in early human development, arising either from errors in meiosis or postzygotic mitosis,...
Integrated study of systemic and local airway transcriptomes in asthma reveals causal mediation of systemic effects by airway key drivers
Integrated study of systemic and local airway transcriptomes in asthma reveals causal mediation of systemic effects by airway key drivers
Systemic and local profiles have each been associated with asthma, but parsing causal relationships between system-wide an...
Identification of novel genetic risk factors of dilated cardiomyopathy: from canine to human
Identification of novel genetic risk factors of dilated cardiomyopathy: from canine to human
Dilated cardiomyopathy (DCM) is a life-threatening heart disease and a common cause of heart failure due to systolic dysfu...
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