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View article: Detecting latent interaction effects when analyzing binary traits
Detecting latent interaction effects when analyzing binary traits Open
In genome-wide association studies (GWAS), it is often desirable to test for interactions, such as gene–environment ( G x E ) or gene–gene ( G x G ) interactions, between single-nucleotide polymorphisms (SNPs, G ’s) and environmental varia…
View article: Qige San regulates paclitaxel resistance in esophageal cancer by targeting ferroptosis
Qige San regulates paclitaxel resistance in esophageal cancer by targeting ferroptosis Open
BACKGROUND Abnormal iron metabolism plays a critical role in paclitaxel (PTX) resistance in esophageal cancer cells. Qige San (QG) is a traditional Chinese herbal formula that is reported to improve short-term therapeutic effects of esopha…
View article: Winner’s curse in rare variant analysis: effect size estimation bias depends on effect direction and the association method used
Winner’s curse in rare variant analysis: effect size estimation bias depends on effect direction and the association method used Open
For complex human traits, a large portion of genetic heritability remains unaccounted for beyond common genetic variants; therefore, estimating the contribution of rare variants (RVs) to the etiology of complex traits is of interest. Resea…
View article: Clinicopathological Features of Hepatobiliary Cells in Primary Biliary Cholangitis Patients with Ursodeoxycholic acid respond incompletely
Clinicopathological Features of Hepatobiliary Cells in Primary Biliary Cholangitis Patients with Ursodeoxycholic acid respond incompletely Open
Background: The mechanisms underlying the incomplete response to ursodeoxycholic acid (UDCA) in primary biliary cholangitis (PBC) patients are not clear. This study investigated the Clinicopathological characteristics and mechanism of hepa…
View article: The demic expansion of Yangshao culture inferred from ancient human genomes
The demic expansion of Yangshao culture inferred from ancient human genomes Open
Our findings support a demic diffusion model for Yangshao culture expansion, where human migration, rather than mere cultural diffusion, played a dominant role in spreading Yangshao-related ancestry across northern China.
View article: TFSNet: A Time–Frequency Synergy Network Based on EEG Signals for Autism Spectrum Disorder Classification
TFSNet: A Time–Frequency Synergy Network Based on EEG Signals for Autism Spectrum Disorder Classification Open
Autism Spectrum Disorder (ASD) seriously affects social, communication, and behavioral functions, and early accurate diagnosis is crucial to improve the prognosis of patients. Traditional diagnosis methods rely on professional doctors to m…
View article: Patients with uHCC and Child-Pugh B8/9 also benefit from a combination of antiangiogenic agents and PD-1 inhibitors: a multicenter real-world study
Patients with uHCC and Child-Pugh B8/9 also benefit from a combination of antiangiogenic agents and PD-1 inhibitors: a multicenter real-world study Open
Background and purpose: Patients with unresectable hepatocellular carcinoma (uHCC) and Child-Pugh grade B face limited treatment options and poor outcomes. This study aims to evaluate whether the effect and safety of combining tyrosine kin…
View article: Correction: Canadian COVID-19 host genetics cohort replicates known severity associations
Correction: Canadian COVID-19 host genetics cohort replicates known severity associations Open
[This corrects the article DOI: 10.1371/journal.pgen.1011192.].
View article: An Atomic Skill Library Construction Method for Data-Efficient Embodied Manipulation
An Atomic Skill Library Construction Method for Data-Efficient Embodied Manipulation Open
Embodied manipulation is a fundamental ability in the realm of embodied artificial intelligence. Although current embodied manipulation models show certain generalizations in specific settings, they struggle in new environments and tasks d…
View article: The X chromosome’s influences on the human brain
The X chromosome’s influences on the human brain Open
Genes on the X chromosome are extensively expressed in the human brain. However, little is known for the X chromosome’s impact on the brain anatomy, microstructure, and functional networks. We examined 1045 complex brain imaging traits fro…
View article: Chromosome X-wide common variant association study in autism spectrum disorder
Chromosome X-wide common variant association study in autism spectrum disorder Open
View article: Plasma exosomes carrying mmu-miR-146a-5p and Notch signalling pathway–mediated synaptic activity in schizophrenia
Plasma exosomes carrying mmu-miR-146a-5p and Notch signalling pathway–mediated synaptic activity in schizophrenia Open
Background: Schizophrenia is characterized by a complex interplay of genetic and environmental factors, leading to alterations in various molecular pathways that may contribute to its pathogenesis. Recent studies have shown that exosomal m…
View article: Detecting latent gene-environment interaction when analyzing binary traits
Detecting latent gene-environment interaction when analyzing binary traits Open
In genome-wide association studies (GWAS), it is desirable to test for interactions (GxE) between single-nucleotide polymorphisms (SNPs,G's) and environmental variables (E's). However, directly accounting for interaction is often infeasibl…
View article: Esrra regulates Rplp1-mediated translation of lysosome proteins suppressed in metabolic dysfunction-associated steatohepatitis and reversed by alternate day fasting
Esrra regulates Rplp1-mediated translation of lysosome proteins suppressed in metabolic dysfunction-associated steatohepatitis and reversed by alternate day fasting Open
Esrra regulation of Rplp1-mediated translation of lysosome/autolysosome proteins was downregulated during MASH. Alternate day fasting activated this novel pathway and improved MASH, suggesting that Esrra and Rplp1 may serve as therapeutic …
View article: Multigram-scale Synthesis of Volasertib, an Inhibitor of Polo-like Kinases in Clinical Evaluation
Multigram-scale Synthesis of Volasertib, an Inhibitor of Polo-like Kinases in Clinical Evaluation Open
This paper described the development of a practical, improved and efficient method for the multigram-scale synthesis of Volasertib, an injectable bioavailable potent and selective inhibitor of PLK1. The key to this optimization was the des…
View article: Patients with uHCC and Child-Pugh B8/9 also benefit from a combination of antiangiogenic agents and PD-1 inhibitors: a multicenter real-world study
Patients with uHCC and Child-Pugh B8/9 also benefit from a combination of antiangiogenic agents and PD-1 inhibitors: a multicenter real-world study Open
Background: Unresectable hepatocellular carcinoma (uHCC) patients with Child-Pugh grade B have limited treatment options and poor outcomes. Methods: Patients with uHCC and Child-pugh B who received lenvatinib plus PD-1 inhibitors or sorafe…
View article: Association of whole-person eigen-polygenic risk scores with Alzheimer’s disease
Association of whole-person eigen-polygenic risk scores with Alzheimer’s disease Open
Late-Onset Alzheimer’s Disease (LOAD) is a heterogeneous neurodegenerative disorder with complex etiology and high heritability. Its multifactorial risk profile and large portions of unexplained heritability suggest the involvement of yet …
View article: Better together against genetic heterogeneity: A sex-combined joint main and interaction analysis of 290 quantitative traits in the UK Biobank
Better together against genetic heterogeneity: A sex-combined joint main and interaction analysis of 290 quantitative traits in the UK Biobank Open
Genetic effects can be sex-specific, particularly for traits such as testosterone, a sex hormone. While sex-stratified analysis provides easily interpretable sex-specific effect size estimates, the presence of sex-differences in SNP effect…
View article: Canadian COVID-19 host genetics cohort replicates known severity associations
Canadian COVID-19 host genetics cohort replicates known severity associations Open
The HostSeq initiative recruited 10,059 Canadians infected with SARS-CoV-2 between March 2020 and March 2023, obtained clinical information on their disease experience and whole genome sequenced (WGS) their DNA. We analyzed the WGS data fo…
View article: Tumor associated neutrophils governs tumor progression through an IL-10/STAT3/PD-L1 feedback signaling loop in lung cancer
Tumor associated neutrophils governs tumor progression through an IL-10/STAT3/PD-L1 feedback signaling loop in lung cancer Open
View article: Comprehensive whole-genome analyses of the UK Biobank reveal significant sex differences in both genotype missingness and allele frequency on the X chromosome
Comprehensive whole-genome analyses of the UK Biobank reveal significant sex differences in both genotype missingness and allele frequency on the X chromosome Open
The UK Biobank is the most used dataset for genome-wide association studies (GWAS). GWAS of sex, essentially sex differences in minor allele frequencies (sdMAF), has identified autosomal SNPs with significant sdMAF, including in the UK Bio…
View article: The pivotal role of the X-chromosome in the genetic architecture of the human brain
The pivotal role of the X-chromosome in the genetic architecture of the human brain Open
Genes on the X-chromosome are extensively expressed in the human brain. However, little is known for the X-chromosome’s impact on the brain anatomy, microstructure, and functional network. We examined 1,045 complex brain imaging traits fro…
View article: Table of Contents
Table of Contents Open
View article: Statistical Learning of Large-Scale Genetic Data: How to Run a Genome-Wide Association Study of Gene-Expression Data Using the 1000 Genomes Project Data
Statistical Learning of Large-Scale Genetic Data: How to Run a Genome-Wide Association Study of Gene-Expression Data Using the 1000 Genomes Project Data Open
View article: eXclusionarY: 10 years later, where are the sex chromosomes in GWASs?
eXclusionarY: 10 years later, where are the sex chromosomes in GWASs? Open
View article: HostSeq: a Canadian whole genome sequencing and clinical data resource
HostSeq: a Canadian whole genome sequencing and clinical data resource Open
View article: The hidden factor: accounting for covariate effects in power and sample size computation for a binary trait
The hidden factor: accounting for covariate effects in power and sample size computation for a binary trait Open
Motivation Accurate power and sample size estimation is crucial to the design and analysis of genetic association studies. When analyzing a binary trait via logistic regression, important covariates such as age and sex are typically includ…
View article: eXclusionarY: Ten years later, where are the sex chromosomes in GWAS?
eXclusionarY: Ten years later, where are the sex chromosomes in GWAS? Open
Summary Ten years ago, a detailed analysis of genome-wide association studies showed that only 33% of the studies included the X chromosome. Multiple recommendations were made to combat eXclusion. Here we re-surveyed the research landscape…
View article: High-quality read-based phasing of cystic fibrosis cohort informs genetic understanding of disease modification
High-quality read-based phasing of cystic fibrosis cohort informs genetic understanding of disease modification Open
View article: Unifying genetic association tests via regression: Prospective and retrospective, parametric and nonparametric, and genotype‐ and allele‐based tests
Unifying genetic association tests via regression: Prospective and retrospective, parametric and nonparametric, and genotype‐ and allele‐based tests Open
Genetic association analysis, which evaluates relationships between genetic markers and complex, heritable traits, is the basis of genome‐wide association studies. The many association tests that have been developed can generally be classi…