Pan-cancer surveys indicate cell cycle-related roles of primate-specific genes in tumors and embryonic cerebrum [0.03%]
泛癌症调查表明与细胞周期相关的灵长类特异性基因在肿瘤和胚胎脑中的作用
Chenyu Ma,Chunyan Li,Huijing Ma et al.
Chenyu Ma et al.
Background: Despite having been extensively studied, it remains largely unclear why humans bear a particularly high risk of cancer. The antagonistic pleiotropy hypothesis predicts that primate-specific genes (PSGs) tend t...
METTL4-mediated nuclear N6-deoxyadenosine methylation promotes metastasis through activating multiple metastasis-inducing targets [0.03%]
METTL4介导的核N6-脱氧腺苷甲基化通过激活多个转移诱导靶点来促进转移
Kai-Wen Hsu,Joseph Chieh-Yu Lai,Jeng-Shou Chang et al.
Kai-Wen Hsu et al.
Background: DNA N6-methyldeoxyadenosine (6mA) is rarely present in mammalian cells and its nuclear role remains elusive. Results: Here ...
SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data [0.03%]
SIEVE：从单细胞DNA测序数据中推断单核苷酸变异和细胞系统发育树
Senbai Kang,Nico Borgsmüller,Monica Valecha et al.
Senbai Kang et al.
We present SIEVE, a statistical method for the joint inference of somatic variants and cell phylogeny under the finite-sites assumption from single-cell DNA sequencing. SIEVE leverages raw read counts for all nucleotides and corrects the ac...
MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions [0.03%]
MoDLE：高保真随机建模DNA环挤出相互作用
Roberto Rossini,Vipin Kumar,Anthony Mathelier et al.
Roberto Rossini et al.
DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, a computational tool for fast, stochastic modeling of molecular contacts from DNA loop extrusion capable of simulating realistic con...
Cross-regulome profiling of RNA polymerases highlights the regulatory role of polymerase III on mRNA transcription by maintaining local chromatin architecture [0.03%]
RNA聚合酶的交叉调控谱分析强调了聚合酶III通过维持局部染色质结构对mRNA转录的调控作用
Yongpeng Jiang,Jie Huang,Kai Tian et al.
Yongpeng Jiang et al.
Background: Mammalian cells have three types of RNA polymerases (Pols), Pol I, II, and III. However, the extent to which these polymerases are cross-regulated and the underlying mechanisms remain unclear. ...
m6A RNA methylation impairs gene expression variability and reproductive thermotolerance in Arabidopsis [0.03%]
m6A RNA 甲基化影响拟南芥的基因表达变异性及生殖热耐受性
Ling Wang,Haiyan Zhuang,Wenwen Fan et al.
Ling Wang et al.
Heat-imposed crop failure is often attributed to reduced thermotolerance of floral tissues; however, the underlying mechanism remains unknown. Here, we demonstrate that m6A RNA methylation increases in Arabidopsis flowers and negatively reg...
The genetic and biochemical determinants of mRNA degradation rates in mammals [0.03%]
哺乳动物mRNA降解率的遗传和生化决定因素
Vikram Agarwal,David R Kelley
Vikram Agarwal
Background: Degradation rate is a fundamental aspect of mRNA metabolism, and the factors governing it remain poorly characterized. Understanding the genetic and biochemical determinants of mRNA half-life would enable more...
Meta-Analysis
Genome biology. 2022 Nov 23;23(1):245. DOI:10.1186/s13059-022-02811-x 2022
Parallel evolution of amphioxus and vertebrate small-scale gene duplications [0.03%]
amphioxus和脊椎动物小型基因复制的平行进化
Marina Brasó-Vives,Ferdinand Marlétaz,Amina Echchiki et al.
Marina Brasó-Vives et al.
Background: Amphioxus are non-vertebrate chordates characterized by a slow morphological and molecular evolution. They share the basic chordate body-plan and genome organization with vertebrates but lack their 2R whole-ge...
metaMIC: reference-free misassembly identification and correction of de novo metagenomic assemblies [0.03%]
metaMIC：从头宏基因组组装的无参考误装配识别和校正
Senying Lai,Shaojun Pan,Chuqing Sun et al.
Senying Lai et al.
Evaluating the quality of metagenomic assemblies is important for constructing reliable metagenome-assembled genomes and downstream analyses. Here, we present metaMIC ( https://github.com/ZhaoXM-Lab/metaMIC ), a machine learning-based tool ...
MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution [0.03%]
MEDICC2：考虑全基因组加倍的拷贝数系统发生树用于癌症进化的研究
Tom L Kaufmann,Marina Petkovic,Thomas B K Watkins et al.
Tom L Kaufmann et al.
Aneuploidy, chromosomal instability, somatic copy-number alterations, and whole-genome doubling (WGD) play key roles in cancer evolution and provide information for the complex task of phylogenetic inference. We present MEDICC2, a method fo...