799 Result(s)
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Lu**g Li
Evolutionary Biology
Human Genetics
Plant Genetics and Genomics
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Article
Open AccessSETDB1 regulates short interspersed nuclear elements and chromatin loop organization in mouse neural precursor cells
Transposable elements play a critical role in maintaining genome architecture during neurodevelopment. Short Interspersed Nuclear Elements (SINEs), a major subtype of transposable elements, are known to harbor...
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Dual-trait genomic analysis in highly stratified Arabidopsis thaliana populations using genome-wide association summary statistics
Genome-wide association study (GWAS) is a powerful tool to identify genomic loci underlying complex traits. However, the application in natural populations comes with challenges, especially power loss due to p...
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Open AccessBenchmarking computational variant effect predictors by their ability to infer human traits
Computational variant effect predictors offer a scalable and increasingly reliable means of interpreting human genetic variation, but concerns of circularity and bias have limited previous methods for evaluati...
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Open AccessA feedback loop driven by H3K9 lactylation and HDAC2 in endothelial cells regulates VEGF-induced angiogenesis
Vascular endothelial growth factor (VEGF) is one of the most powerful proangiogenic factors and plays an important role in multiple diseases. Increased glycolytic rates and lactate accumulation are associated ...
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Open AccessEvaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome
Copy number variation (CNV) is a key genetic characteristic for cancer diagnostics and can be used as a biomarker for the selection of therapeutic treatments. Using data sets established in our previous study,...
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Open AccessDNA methylation variations underlie lettuce domestication and divergence
Lettuce (Lactuca sativa L.) is an economically important vegetable crop worldwide. Lettuce is believed to be domesticated from a single wild ancestor Lactuca serriola and subsequently diverged into two major morp...
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Open AccessLABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA
Methylation-based liquid biopsies show promises in detecting cancer using circulating cell-free DNA; however, current limitations impede clinical application. Most assays necessitate substantial DNA inputs, po...
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Open AccessTMO-Net: an explainable pretrained multi-omics model for multi-task learning in oncology
Cancer is a complex disease composing systemic alterations in multiple scales. In this study, we develop the Tumor Multi-Omics pre-trained Network (TMO-Net) that integrates multi-omics pan-cancer datasets for ...
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Open AccessiIMPACT: integrating image and molecular profiles for spatial transcriptomics analysis
Current clustering analysis of spatial transcriptomics data primarily relies on molecular information and fails to fully exploit the morphological features present in histology images, leading to compromised a...
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Open AccessStructural variant landscapes reveal convergent signatures of evolution in sheep and goats
Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level refere...
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Open AccessSystematic evaluation with practical guidelines for single-cell and spatially resolved transcriptomics data simulation under multiple scenarios
Single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) have led to groundbreaking advancements in life sciences. To develop bioinformatics tools for scRNA-seq and SRT data and perf...
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Open AccessscCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data
In droplet-based single-cell and single-nucleus RNA-seq assays, systematic contamination of ambient RNA molecules biases the quantification of gene expression levels. Existing methods correct the contamination...
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Open AccessIn vivo rescue of genetic dilated cardiomyopathy by systemic delivery of nexilin
Dilated cardiomyopathy (DCM) is one of the most common causes of heart failure. Multiple identified mutations in nexilin (NEXN) have been suggested to be linked with severe DCM. However, the exact association ...
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Open AccessConditional knockdown of OsMLH1 to improve plant prime editing systems without disturbing fertility in rice
High-efficiency prime editing (PE) is desirable for precise genome manipulation. The activity of mammalian PE systems can be largely improved by inhibiting DNA mismatch repair by coexpressing a dominant-negati...
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Open AccessSCIPAC: quantitative estimation of cell-phenotype associations
Numerous algorithms have been proposed to identify cell types in single-cell RNA sequencing data, yet a fundamental problem remains: determining associations between cells and phenotypes such as cancer. We dev...
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Open AccessSingle-cell 3D genome structure reveals distinct human pluripotent states
Pluripotent states of embryonic stem cells (ESCs) with distinct transcriptional profiles affect ESC differentiative capacity and therapeutic potential. Although single-cell RNA sequencing has revealed addition...
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Open AccessMap** and functional characterization of structural variation in 1060 pig genomes
Structural variations (SVs) have significant impacts on complex phenotypes by rearranging large amounts of DNA sequence.
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Open AccessDisruption of maternal vascular remodeling by a fetal endoretrovirus-derived gene in preeclampsia
Preeclampsia, one of the most lethal pregnancy-related diseases, is associated with the disruption of uterine spiral artery remodeling during placentation. However, the early molecular events leading to preecl...
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Hybrids of two destructive subterranean termites established in the field, revealing a potential for gene flow between species
Hybridization between invasive pest species may lead to significant genetic and economic impacts that require close monitoring. The two most invasive and destructive termite species worldwide, Coptotermes formosa...
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Open AccessNextDenovo: an efficient error correction and accurate assembly tool for noisy long reads
Long-read sequencing data, particularly those derived from the Oxford Nanopore sequencing platform, tend to exhibit high error rates. Here, we present NextDenovo, an efficient error correction and assembly too...
