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%]
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%]
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%]
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. ...
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%]
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...
The genetic heist: how transposable elements capture and repurpose genes in plants [0.03%]
植物中的基因盗窃案：转座元件捕获和重新利用基因的方式
Navei Cerda-Hernandez,Thomas Bureau
Navei Cerda-Hernandez
Transposable elements are pervasive components of plant genomes, and their role as dynamic architects of genome evolution is increasingly recognized. Beyond their ability to mobilize within genomes, transposable elements facilitate the capt...
CRAK-Velo: chromatin accessibility kinetics integration improves RNA velocity estimation [0.03%]
基于染色质可及性动力学整合的RNA速度估算方法CRAK-Velo
Nour El Kazwini,Mingze Gao,Idris Kouadri Boudjelthia et al.
Nour El Kazwini et al.
RNA velocity has recently emerged as a key tool in the analysis of single-cell transcriptomic data, yet connecting RNA velocity analyses to underlying regulatory processes has proved challenging. Here, we propose CRAK-Velo, a semi-mechanist...
A LINE-1 insertion upstream of FOXP2 promotes neuronal differentiation during primate evolution [0.03%]
类人猿进化中FOXP2上游的LINE-1插入促进神经元分化
Jinhao Liu,Zihang Yin,Yonglin Peng et al.
Jinhao Liu et al.
Background: The evolutionary trajectory of FOXP2, a key regulator of language acquisition and higher-order cognitive function, remains incompletely understood. Retrotransposons such as long interspersed element-1 (LINE-1)...