Deep tissue profiling of Populus stem at single nucleus level reveals uncharacterized cell types and cell-specific gene regulatory networks [0.03%]
单细胞核水平深入鉴定杨树茎的细胞类型及特异基因表达网络
Henry W Schmidt,Daniel Conde,Wendell J Pereira et al.
Henry W Schmidt et al.
Background: Single-cell genomics is revolutionizing plant developmental biology, enabling the transcriptome profiling of individual cells and their lineage relationships. However, plant cell walls polymers hamper the diss...
Enhancing transcriptome expression quantification through accurate assignment of long RNA sequencing reads with TranSigner [0.03%]
通过TranSigner准确分配长RNA测序读段以增强转录组表达定量
Hyun Joo Ji,Mihaela Pertea
Hyun Joo Ji
Long-read RNA sequencing captures transcripts at full lengths, but existing methods for transcriptome profiling using long-read data often produce inconsistent transcript identification and quantification results. Here, we introduce TranSig...
DelSIEVE: cell phylogeny modeling of single nucleotide variants and deletions from single-cell DNA sequencing data [0.03%]
利用单细胞DNA测序数据对单核苷酸变异和缺失进行细胞谱系建模：DelSieve方法
Senbai Kang,Nico Borgsmüller,Monica Valecha et al.
Senbai Kang et al.
With rapid advancements in single-cell DNA sequencing (scDNA-seq), various computational methods have been developed to study evolution and call variants on single-cell level. However, modeling deletions remains challenging because they aff...
Hongyan Gao,Bowen Li,Zihan Guo et al.
Hongyan Gao et al.
As important mobile elements in prokaryotes, prophages shape the genomic context of their hosts and regulate the structure of bacterial populations. However, it is challenging to precisely identify prophages through computational methods. H...
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 ...