Pauline Trinh,David S Clausen,Amy D Willis
Pauline Trinh
Recovering metagenome-assembled genomes (MAGs) from shotgun sequencing data is an increasingly common task in microbiome studies, as MAGs provide deeper insight into the functional potential of both culturable and non-culturable microorgani...
Ruslan Deviatiiarov,Hiroki Nagai,Galym Ismagulov et al.
Ruslan Deviatiiarov et al.
In birds, sex is genetically determined; however, the molecular mechanism is not well-understood. The avian Z sex chromosome (chrZ) lacks whole chromosome inactivation, in contrast to the mammalian chrX. To investigate chrZ dosage compensat...
DISCERN: deep single-cell expression reconstruction for improved cell clustering and cell subtype and state detection [0.03%]
DISCERN：改进细胞聚类及细胞亚型和状态检测的深度单细胞转录组表达重构技术
Fabian Hausmann,Can Ergen,Robin Khatri et al.
Fabian Hausmann et al.
Background: Single-cell sequencing provides detailed insights into biological processes including cell differentiation and identity. While providing deep cell-specific information, the method suffers from technical constr...
Author Correction: Single-cell resolution analysis reveals the preparation for reprogramming the fate of stem cell niche in cotton lateral meristem [0.03%]
作者更正：单细胞分辨率分析揭示了棉花侧分生组织干细胞巢重塑的命运准备
Xiangqian Zhu,Zhongping Xu,Guanying Wang et al.
Xiangqian Zhu et al.
Published Erratum
Genome biology. 2023 Sep 18;24(1):210. DOI:10.1186/s13059-023-03051-3 2023
Disparities in spatially variable gene calling highlight the need for benchmarking spatial transcriptomics methods [0.03%]
空间可变基因呼叫的差异突显了对空间转录组学方法进行基准测试的需求
Natalie Charitakis,Agus Salim,Adam T Piers et al.
Natalie Charitakis et al.
Identifying spatially variable genes (SVGs) is a key step in the analysis of spatially resolved transcriptomics data. SVGs provide biological insights by defining transcriptomic differences within tissues, which was previously unachievable ...
Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment [0.03%]
东亚家牛基因组中的结构变异和来自野生群体的基因渗入使其适应当地环境
Xiaoting Xia,Fengwei Zhang,Shuang Li et al.
Xiaoting Xia et al.
Background: Structural variations (SVs) in individual genomes are major determinants of complex traits, including adaptability to environmental variables. The Mongolian and Hainan cattle breeds in East Asia are of taurine...
COLLAGENE enables privacy-aware federated and collaborative genomic data analysis [0.03%]
COLLAGENE实现隐私保护的联邦和协作基因组数据分析
Wentao Li,Miran Kim,Kai Zhang et al.
Wentao Li et al.
Growing regulatory requirements set barriers around genetic data sharing and collaborations. Moreover, existing privacy-aware paradigms are challenging to deploy in collaborative settings. We present COLLAGENE, a tool base for building secu...
Coupling of co-transcriptional splicing and 3' end Pol II pausing during termination in Arabidopsis [0.03%]
拟南芥中转录终止期间的协同转录剪接和Pol II在3'端的暂停耦合现象
Sixian Zhou,Fengli Zhao,Danling Zhu et al.
Sixian Zhou et al.
Background: In Arabidopsis, RNA Polymerase II (Pol II) often pauses within a few hundred base pairs downstream of the polyadenylation site, reflecting efficient transcriptional termination, but how such pausing is regulat...
PhaseDancer: a novel targeted assembler of segmental duplications unravels the complexity of the human chromosome 2 fusion going from 48 to 46 chromosomes in hominin evolution [0.03%]
相位舞者：一种新颖的靶向重复序列组装程序揭示了从四十八到四十六染色体的人类二号染色体融合复杂性
Barbara Poszewiecka,Krzysztof Gogolewski,Justyna A Karolak et al.
Barbara Poszewiecka et al.
Resolving complex genomic regions rich in segmental duplications (SDs) is challenging due to the high error rate of long-read sequencing. Here, we describe a targeted approach with a novel genome assembler PhaseDancer that extends SD-rich r...
The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees [0.03%]
人类和黑猩猩顺式和反式调控变化与基因表达进化的关系研究
Kenneth A Barr,Katherine L Rhodes,Yoav Gilad
Kenneth A Barr
Background: Comparative gene expression studies in apes are fundamentally limited by the challenges associated with sampling across different tissues. Here, we used single-cell RNA sequencing of embryoid bodies to collect...