Rapid divergence of a gamete recognition gene promoted macroevolution of Eutheria [0.03%]
受精相关基因的快速演化促进真兽类的宏进化事件发生
Emma K Roberts,Steve Tardif,Emily A Wright et al.
Emma K Roberts et al.
Background: Speciation genes contribute disproportionately to species divergence, but few examples exist, especially in vertebrates. Here we test whether Zan, which encodes the sperm acrosomal protein zonadhesin that medi...
An ORFeome of rice E3 ubiquitin ligases for global analysis of the ubiquitination interactome [0.03%]
水稻E3泛素连接酶ORFeome的构建及其在泛素化互作组全局分析中的应用
Ruyi Wang,Xiaoman You,Chongyang Zhang et al.
Ruyi Wang et al.
Background: Ubiquitination is essential for many cellular processes in eukaryotes, including 26S proteasome-dependent protein degradation, cell cycle progression, transcriptional regulation, and signal transduction. Altho...
DeCAF: a novel method to identify cell-type specific regulatory variants and their role in cancer risk [0.03%]
一种识别特定细胞类型调控变异及其在癌症风险中的作用的新型方法
Cynthia A Kalita,Alexander Gusev
Cynthia A Kalita
Here, we propose DeCAF (DEconvoluted cell type Allele specific Function), a new method to identify cell-fraction (cf) QTLs in tumors by leveraging both allelic and total expression information. Applying DeCAF to RNA-seq data from TCGA, we i...
RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing [0.03%]
基于纳米孔测序的转录组无参重建和定量软件Rattle
Ivan de la Rubia,Akanksha Srivastava,Wenjing Xue et al.
Ivan de la Rubia et al.
Nanopore sequencing enables the efficient and unbiased measurement of transcriptomes. Current methods for transcript identification and quantification rely on mapping reads to a reference genome, which precludes the study of species with a ...
Qi Song,Jingtao Wang,Ziv Bar-Joseph
Qi Song
We develop scSTEM, single-cell STEM, a method for clustering dynamic profiles of genes in trajectories inferred from pseudotime ordering of single-cell RNA-seq (scRNA-seq) data. scSTEM uses one of several metrics to summarize the expression...
A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis [0.03%]
基于Iso-seq分析的新方法的高分辨率单分子测序拟南芥转录组
Runxuan Zhang,Richard Kuo,Max Coulter et al.
Runxuan Zhang et al.
Background: Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technolog...
Toward a base-resolution panorama of the in vivo impact of cytosine methylation on transcription factor binding [0.03%]
朝向胞嘧啶甲基化对转录因子结合的活体影响的碱基分辨率全景图
Aldo Hernandez-Corchado,Hamed S Najafabadi
Aldo Hernandez-Corchado
Background: While methylation of CpG dinucleotides is traditionally considered antagonistic to the DNA-binding activity of most transcription factors (TFs), recent in vitro studies have revealed a more complex picture, su...
PtoNF-YC9-SRMT-PtoRD26 module regulates the high saline tolerance of a triploid poplar [0.03%]
无性系三倍体杨树中PtoNF-YC9-SRMT-PtoRD26模块调控其耐盐性的机制研究
Shaofei Tong,Yubo Wang,Ningning Chen et al.
Shaofei Tong et al.
Background: Sensing and responding to stresses determine the tolerance of plants to adverse environments. The triploid Chinese white poplar is widely cultivated in North China because of its adaptation to a wide range of ...
Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes [0.03%]
Minos：细菌基因组队列的变体判定及联合基因分型
Martin Hunt,Brice Letcher,Kerri M Malone et al.
Martin Hunt et al.
There are many short-read variant-calling tools, with different strengths and weaknesses. We present a tool, Minos, which combines outputs from arbitrary variant callers, increasing recall without loss of precision. We benchmark on 62 sampl...
William M Yashar,Garth Kong,Jake VanCampen et al.
William M Yashar et al.
Genome-wide mapping of histone modifications is critical to understanding transcriptional regulation. CUT&Tag is a new method for profiling histone modifications, offering improved sensitivity and decreased cost compared with ChIP-seq. Here...