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SETDB1 regulates short interspersed nuclear elements and chromatin loop organization in mouse neural precursor cells
BackgroundTransposable elements play a critical role in maintaining genome architecture during neurodevelopment. Short Interspersed Nuclear Elements...
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Gut microbiota DPP4-like enzymes are increased in type-2 diabetes and contribute to incretin inactivation
BackgroundThe gut microbiota controls broad aspects of human metabolism and feeding behavior, but the basis for this control remains largely unclear....
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Filter bank temporally local multivariate synchronization index for SSVEP-based BCI
BackgroundMultivariate synchronization index (MSI) has been successfully applied for frequency detection in steady state visual evoked potential...
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Identification of common genetic factors and immune-related pathways associating more than two autoimmune disorders: implications on risk, diagnosis, and treatment
Autoimmune disorders (ADs) are chronic conditions resulting from failure or breakdown of immunological tolerance, resulting in the host immune system...
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SGCP: a spectral self-learning method for clustering genes in co-expression networks
BackgroundA widely used approach for extracting information from gene expression data employs the construction of a gene co-expression network and...
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Detecting haplotype-specific transcript variation in long reads with FLAIR2
BackgroundRNA-seq has brought forth significant discoveries regarding aberrations in RNA processing, implicating these RNA variants in a variety of...
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Tracking-seq reveals the heterogeneity of off-target effects in CRISPR–Cas9-mediated genome editing
The continued development of novel genome editors calls for a universal method to analyze their off-target effects. Here we describe a versatile...
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Unsupervised modeling of mutational landscapes of adeno-associated viruses viability
Adeno-associated viruses 2 (AAV2) are minute viruses renowned for their capacity to infect human cells and akin organisms. They have recently emerged...
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Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2
BackgroundFungi play a key role in several important ecological functions, ranging from organic matter decomposition to symbiotic associations with...
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Patient-derived mini-colons enable long-term modeling of tumor–microenvironment complexity
Existing organoid models fall short of fully capturing the complexity of cancer because they lack sufficient multicellular diversity, tissue-level...
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High-throughput discovery of MHC class I- and II-restricted T cell epitopes using synthetic cellular circuits
Antigen discovery technologies have largely focused on major histocompatibility complex (MHC) class I-restricted human T cell receptors (TCRs),...
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Heterogeneous pseudobulk simulation enables realistic benchmarking of cell-type deconvolution methods
BackgroundComputational cell type deconvolution enables the estimation of cell type abundance from bulk tissues and is important for understanding...
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Tagging large CNV blocks in wheat boosts digitalization of germplasm resources by ultra-low-coverage sequencing
BackgroundThe massive structural variations and frequent introgression highly contribute to the genetic diversity of wheat, while the huge and...
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Benchmarking computational variant effect predictors by their ability to infer human traits
BackgroundComputational variant effect predictors offer a scalable and increasingly reliable means of interpreting human genetic variation, but...
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RIBAP: a comprehensive bacterial core genome annotation pipeline for pangenome calculation beyond the species level
Microbial pangenome analysis identifies present or absent genes in prokaryotic genomes. However, current tools are limited when analyzing species...
