A message passing framework for precise cell state identification with scClassify2 [0.03%]
基于scClassify2的精确细胞状态识别消息传递框架
Wenze Ding,Yue Cao,Xiaohang Fu et al.
Wenze Ding et al.
Cell annotation is crucial for downstream exploration. Although many approaches, spanning from classic statistics to large language models, have been developed, most of their focus is on distinct cell types and overlook sequential cell popu...
KAT6A chimeras form a self-reinforcing epigenetic module with NURF and MLL/COMPASS to sustain AML [0.03%]
Kat6a融合蛋白通过与NURF和MLL/COMPASS形成自强化表观遗传模块来维持急性髓系白血病
Junhui Lv,Zhinang Yin,Conghui Li et al.
Junhui Lv et al.
Background: KAT6A-CBP (K/C) and KAT6A-P300 (K/P) fusions are recurrent genetic alterations in acute myeloid leukemia (AML) associated with poor prognosis. Despite their strong oncogenic potential, the mechanisms underlyin...
TRsv: simultaneous detection of tandem repeat variations, structural variations, and short indels using long read sequencing data [0.03%]
TRsv：利用长读测序数据同时检测串联重复序列变异、结构变异和短插入缺失
Shunichi Kosugi,Chikashi Terao
Shunichi Kosugi
Tandem repeat copy number variations (TR-CNVs), structural variations (SVs), and short indels have been responsible for many diseases and traits, but no tools exist to distinguish and detect these variants. In this study, we developed a com...
Uncovering the multi-layer cis-regulatory landscape of rice via integrative nascent RNA analysis [0.03%]
通过整合新转录本分析解码水稻多层次的顺式调控景观
Marina Goliasse,Aurore Johary,Adrian E Platts et al.
Marina Goliasse et al.
Background: Efforts to characterize regulatory elements in plant genomes traditionally rely on evolutionary conservation and chromatin accessibility. Recently, intergenic bi-directional nascent transcript has emerged as a...
Conservation of bilaterian genome structure is the exception, not the rule [0.03%]
两侧对称动物基因组结构的保守性是例外而非常态
Thomas D Lewin,Isabel Jiah-Yih Liao,Yi-Jyun Luo
Thomas D Lewin
Species from diverse animal lineages have conserved groups of orthologous genes together on the same chromosome for over half a billion years since the last common ancestor of bilaterians. Although notable exceptions exist, the stability of...
Xavier Roca-Rada,Roberta Davidson,Matthew P Williams et al.
Xavier Roca-Rada et al.
Background: Recent ancient DNA studies uncovering large-scale demographic events in Iberia have presented very limited data for Portugal, a country located at the westernmost edge of continental Eurasia. Here, we present ...
Melody: meta-analysis of microbiome association studies for discovering generalizable microbial signatures [0.03%]
旋律：元分析微生物关联研究以发现具普适性的微生物标志物
Zhoujingpeng Wei,Guanhua Chen,Zheng-Zheng Tang
Zhoujingpeng Wei
Standard protocols for meta-analysis of association studies are inadequate for microbiome data due to their complex compositional structure, leading to inaccurate and unstable microbial signature selection. To address this issue, we introdu...
Beware of counter-intuitive levels of false discoveries in datasets with strong intra-correlations [0.03%]
谨防强相关数据集中反直觉的假阳性水平
Chakravarthi Kanduri,Maria Mamica,Emilie Willoch Olstad et al.
Chakravarthi Kanduri et al.
The false discovery rate (FDR) controlling method by Benjamini and Hochberg (BH) is a popular choice in the omics fields. Here, we demonstrate that in datasets with a large degree of dependencies between features, FDR correction methods lik...
Direct and bisulfite-free 5-methylcytosine and 5-hydroxymethylcytosine sequencing at single-cell resolution with scTAPS and scCAPS + [0.03%]
基于scTAPS和scCAPS +的单细胞直接非硫酸盐测序分辨5-甲基胞嘧啶和5-羟甲基胞嘧啶
Xiufei Chen,Jingfei Cheng,Linzhen Kong et al.
Xiufei Chen et al.
We present direct sequencing methodologies, scTAPS for 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) and scCAPS + specifically for 5hmC, enabling quantitative detection of 5mC and 5hmC at single-base resolution and single-cell l...
The epigenetics effects of transposable elements are genomic context dependent and not restricted to gene silencing in Drosophila [0.03%]
果蝇转座子的表观遗传效应依赖于基因组背景且不局限于基因沉默作用
Marta Coronado-Zamora,Josefa González
Marta Coronado-Zamora
Background: Transposable elements (TEs) represent a threat to genome integrity due to their proliferative capacity. Eukaryotic cells silence TEs through different molecular mechanisms, including the deposition of repressi...