Reconstruction of Cell Diversity and Cell Lineages from Somatic Mutations in Single-Cell Transcriptomic Data [0.03%]
从单细胞 transcriptome 数据中的体细胞性变重构细胞多样性和细胞谱系
Satoshi Oota,Kuniya Abe,Cheng-Tsung Pan et al.
Satoshi Oota et al.
Single-cell RNA sequencing (scRNA-seq) enables high-resolution profiling of individual cells. However, inferring temporal relationships among cells remains a challenge. Here, we present Real-Time Course Analysis (RTCA), a simple direct phyl...
Chromosomal evolution and speciation inferred from chromosome-scale genome assemblies in three Cupressaceae species [0.03%]
基于柏科三个物种染色体水平基因组组装的染色体进化和物种形成推断
Kenta Shirasawa,Yuta B Aoyagi,Kentaro Mishima et al.
Kenta Shirasawa et al.
Chromosome-scale genome assemblies in gymnosperms have lagged behind those of angiosperms, likely due to their large genomes. Coniferous tree species, which belong to the gymnosperms, are important resources for wood production in the fores...
SIEVEseq: Unified differential expression, variability, and skewness analyses using RNA-Seq data [0.03%]
基于RNA-Seq数据的统一路线偏好、差异表达和方差分析方法(SIEVEseq)
Hongxiang Li,Tsung Fei Khang
Hongxiang Li
RNA-Seq data analysis is commonly biased towards detecting differentially expressed genes and insufficiently conveys the complexity of gene expression changes between biological conditions. This bias arises because discrete count models can...
Enrichment-Free Deep Proteomics Enables Proteome-Scale Analysis of Methionine Oxidation [0.03%]
无富集的深度蛋白质组学可实现甲硫氨酸氧化的蛋白质组规模分析
Hiromasa Mitsui,Yusei Okuda,Ryo Konno et al.
Hiromasa Mitsui et al.
Advances in mass spectrometry (MS)-based proteomics have enabled the large-scale characterization of posttranslational modifications (PTMs) through affinity-based enrichment. However, this technique introduces a bias towards selectively enr...
Chromosome-scale genome of European anchovy (Engraulis encrasicolus L., 1758) and comparative genomics uncover clupeid-specific immune gene expansions [0.03%]
欧洲anchovy（Engraulis encrasicolus L., 1758）染色体水平基因组及刺骨鱼目的比较基因组揭示了特异的免疫基因扩张现象
Tuana Öğretici,Selahattin Barış Çay,Onur Obut et al.
Tuana Öğretici et al.
The European anchovy is a keystone forage species in the Mediterranean and Northeast Atlantic, yet a chromosome-scale reference genome has been lacking. Here, we present a 1.4 Gb assembly anchored to 24 chromosomes (scaffold N50 = 56.4 Mb; ...
The genome of a keystone predator: Adaptive innovations in Charonia tritonis drive specialized predation and coral reef resilience [0.03%]
贝类顶盖石种基因组：Charonia tritonis适应性创新推动了特化捕食和珊瑚礁的恢复力
Yu Shi,Zhaoyan Zhong,Wenguang Liu et al.
Yu Shi et al.
The giant triton snail (Charonia tritonis) is an ecologically critical predator that controls coral reef ecosystems by preying on crown-of-thorns starfish (COTS). However, overharvesting has driven severe population declines, threatening re...
Increased abundance of Limosilactobacillus reuteri in the gut of selectively bred high-tameness mice and its association with behavioural changes [0.03%]
肠道内罗伊特氏乳酸菌丰度增加与行为变化相关性研究及其在高温顺鼠中的选择育种效应
Bhim B Biswa,Hiroshi Mori,Atsushi Toyoda et al.
Bhim B Biswa et al.
Domestication alters animal behaviour, particularly tameness. We previously established 2 tamed mouse groups by selective breeding for active tameness-defined as the motivation to approach a human hand-from genetically heterogeneous wild-de...
PFGPred: A stack ensemble classifier for the identification of fusion genes in plants [0.03%]
基于堆叠集成分类器的植物融合基因识别方法(PFGPred)
Fiza Hamid,Kanka Mukherjee,Sakshi Chaudhary et al.
Fiza Hamid et al.
Fusion genes play crucial roles in plant biological processes but remain far less explored than their human counterparts, largely due to limited validated datasets and the absence of plant-specific prediction tools. Existing approaches ofte...
AlleleMiner: A long-read pipeline for gene-wise de novo allele phasing and variant detection in diploid citrus cultivars [0.03%]
基于长读段的二倍体柑橘品种基因型新 alleles 相位及变异检测Pipeline：AlleleMiner
Yukinari Kiryu,Yoshihiro Kawahara,Tomoko Endo et al.
Yukinari Kiryu et al.
Allelic variation is a critical determinant of agronomic traits in heterozygous crops. Most existing approaches define variation as reference-anchored differences, such as SNPs or structural variants, confining allelic diversity to variant ...
Silver chimaera genome highlights lineage-specific sex chromosome and opsin gene evolution in holocephalans [0.03%]
银皱唇鲨基因组揭示了全头类动物谱系特异性性染色体和视蛋白基因的进化
Akinori Teramura,Mitsutaka Kadota,Shotaro Hirase et al.
Akinori Teramura et al.
Cartilaginous fishes are divided into holocephalans and elasmobranchs, and they offer valuable systems for analyzing the genetic basis of adaptation to diverse habitats and the evolution of chromosomal organization. Genomic studies on carti...