Genome assemblies of the liverwort Blasia pusilla uncover a well-defined pseudoautosomal region on homomorphic UV sex chromosomes [0.03%]
拟斑叶苔基因组拼装揭示了同型UV性别染色体上有明确界定的假常染色体区
Yuling Yue,Gaurav Sablok,Xiaolan He et al.
Yuling Yue et al.
Background: Sex chromosomes evolve from autosomes and are expected to be initially homomorphic, though they may become heteromorphic over time. In diploid systems, one sex chromosome often degenerates, whereas homomorphy ...
Human SRD5A1 as a case of gene expression indel-resistance in triple-coding region [0.03%]
人类SRD5A1基因在三码区域的表达缺失-插入抵抗性变异的一个实例
Martina M Yordanova,Jack A S Tierney,Kyle A Meiklejohn et al.
Martina M Yordanova et al.
Background: Nucleotide sequence can be translated in three reading frames producing distinct protein products. Many examples of RNA translation in two reading frames (dual coding) have been identified so far. ...
scArchon: a scalable benchmarking framework for assessing single-cell perturbation models [0.03%]
scArchon：评估单细胞扰动模型的可扩展基准测试框架
Jean Radig,Robin Droit,Daria Doncevic et al.
Jean Radig et al.
Background: The accurate prediction of cellular responses to perturbations, such as drug treatments, remains a pivotal challenge in single-cell transcriptomics. While numerous deep learning tools have been developed for t...
Data-driven AI system for learning how to run transcript assemblers [0.03%]
一种基于数据驱动的人工智能系统用于学习如何运行转录组组装工具
Yihang Shen,Zhiwen Yan,Carl Kingsford
Yihang Shen
We introduce AutoTuneX, a data-driven, AI system designed to automatically predict optimal parameters for transcript assemblers - tools for reconstructing transcripts from the reads in a given RNA-seq sample. AutoTuneX is built by learning ...
Demetrios S Maxim,Juliet Sostena,Najani Shanee Johnson et al.
Demetrios S Maxim et al.
While many computational tools exist for designing CRISPR-Cas experiments, there is a need for a centralized resource that combines individual tools to predict the most efficient genome editing strategy for a given application. To fill this...
AVITI sequencing of a four-generation CEPH/Utah pedigree confirms low mutation rates at homopolymer loci despite their low sequence complexity [0.03%]
利用CEPH/犹他四代家系进行的AVITI测序表明，尽管同聚碱基序列的复杂度较低，但该序列突变率仍然很低
Hannah C Happ,Thomas A Sasani,Derek Warner et al.
Hannah C Happ et al.
Background: Short tandem repeats (STRs) and homopolymers are among the most mutable loci in the human genome. Despite their presumed mutability owing to replication slippage, homopolymer loci exhibit lower mutation rates ...
DeepSAP: improved RNA-seq alignment by integrating transcriptome guidance with transformer-based splice junction scoring [0.03%]
通过整合转录组指导与基于Transformer的剪接连接评分改进RNA测序比对(DEEPsap)
Fadel Berakdar,Thomas D Wu,Tong Zhu et al.
Fadel Berakdar et al.
Advancements in high-throughput sequencing have revolutionized transcriptomics, enabling insights into gene expression, splicing, and fusions. However, RNA-seq analysis remains challenging due to complex splice junctions, multi-mapped reads...
LINE1 RNA demethylation sensitizes cancer cells to PARPi through global chromatin remodeling [0.03%]
LINE1 RNA 去甲基化通过全局染色质重塑使癌细胞对 PARP 抑制剂敏感
Zihong Kang,Ruimeng Li,Lei Xu et al.
Zihong Kang et al.
Background: Repression of DNA damage repair by PARP inhibitors (PARPi) has shown great efficacy in cancer treatment. However, therapy resistance remains a significant clinical challenge. ...
Assessment of nanopore RNA modification calling in human cell lines and synthetic systems [0.03%]
评估纳米孔测序在人类细胞系和合成系统中检测RNA修饰的能力
Neda Ghohabi Esfahani,Andrew J Stein,Stuart Akeson et al.
Neda Ghohabi Esfahani et al.
Background: Nanopore technology enables the direct sequencing of intact RNA molecules allowing for the detection of native chemical modifications. In 2024, Oxford Nanopore Technologies updated direct RNA sequencing from R...
10 × Genomics Flex Gene Expression is a powerful tool for single-cell transcriptomics of xenografts models [0.03%]
灵活的基因表达分析是异种移植模型单细胞转录组学的有力工具
Oriol Llorà-Batlle,Anca Farcas,Doreth Fransen et al.
Oriol Llorà-Batlle et al.
The 10 × Genomics Flex Gene Expression protocol is a probe-based method that profiles fixed or frozen material, simplifying sample handling before scRNA-seq. Although probes exist only for human and mouse, we show that xenograft samples co...