Bojian Zhong,Linhua Sun,David Penny
Bojian Zhong
Land plants are a natural group, and Charophyte algae are the closest lineages of land plants and have six morphologically diverged groups. The conjugating green algae (Zygnematales) are now suggested to be the extant sister group to land p...
RNA-seq Reveals Complicated Transcriptomic Responses to Drought Stress in a Nonmodel Tropic Plant, Bombax ceiba L [0.03%]
基于RNA-seq的热带非模式植物木棉干旱响应转录组学研究
Zhili Zhou,Huancheng Ma,Kevin Lin et al.
Zhili Zhou et al.
High-throughput transcriptome provides an unbiased approach for understanding the genetic basis and gene functions in response to different conditions. Here we sequenced RNA-seq libraries derived from a Bombax ceiba L. system under a contro...
MSL: A Measure to Evaluate Three-dimensional Patterns in Gene Expression Data [0.03%]
MSL：一种用于评估基因表达数据中三维模式的度量标准
David Gutiérrez-Avilés,Cristina Rubio-Escudero
David Gutiérrez-Avilés
Microarray technology is highly used in biological research environments due to its ability to monitor the RNA concentration levels. The analysis of the data generated represents a computational challenge due to the characteristics of these...
MITOSCISSOR: A Useful Tool for Auto-Assembly of Mitogenomic Datasets in the Evolutionary Analysis of Fishes [0.03%]
MITOSCISSOR：一种鱼类进化分析的线粒体基因组数据自动组装有用工具
Zheng Sun,Yuanzhi Cheng,Junbin Zhang
Zheng Sun
As a result of the development of rapid and efficient sequencing technologies, complete sequences of numerous mitochondrial genomes are now available. Mitochondrial genomes have been widely used to evaluate relationships between species in ...
Jianbo Tu,Diyan Li,Qingqing Li et al.
Jianbo Tu et al.
Vertebrate β-defensins comprise an important family of antimicrobial peptides that protect organisms from a diverse spectrum of bacteria, viruses, fungi, and protozoan parasites. Previous studies have shown a marked variation in the number...
TRUFA: A User-Friendly Web Server for de novo RNA-seq Analysis Using Cluster Computing [0.03%]
TRUFA：使用集群计算进行从头RNA序列分析的用户友好型web服务器
Etienne Kornobis,Luis Cabellos,Fernando Aguilar et al.
Etienne Kornobis et al.
Application of next-generation sequencing (NGS) methods for transcriptome analysis (RNA-seq) has become increasingly accessible in recent years and are of great interest to many biological disciplines including, eg, evolutionary biology, ec...
Roles of solvent accessibility and gene expression in modeling protein sequence evolution [0.03%]
可溶性访问量和基因表达在蛋白质序列进化建模中的作用分析
Kuangyu Wang,Shuhui Yu,Xiang Ji et al.
Kuangyu Wang et al.
Models of protein evolution tend to ignore functional constraints, although structural constraints are sometimes incorporated. Here we propose a probabilistic framework for codon substitution that evaluates joint effects of relative solvent...
Surendra Kumar,Anders K Krabberød,Ralf S Neumann et al.
Surendra Kumar et al.
Summary: We present a pipeline named BIR (Blast, Identify and Realign) developed for phylogenomic analyses. BIR is intended for the identification of gene sequences applicable for phylogenomic inference. The pipeline allo...
Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity [0.03%]
叶绿体基因组的同义密码子使用偏好与基因结构无关且在进化上具有异质性
Yueying Qi,Wenjing Xu,Tian Xing et al.
Yueying Qi et al.
Synonymous codon usage bias (SCUB) is the nonuniform usage of codons, occurring often in nearly all organisms. Our previous study found that SCUB is correlated with intron number, is unequal among exons in the plant nuclear genome, and mirr...
CNL Disease Resistance Genes in Soybean and Their Evolutionary Divergence [0.03%]
大豆冠群芳病抗性基因及其演化分化分析
Madhav P Nepal,Benjamin V Benson
Madhav P Nepal
Disease resistance genes (R-genes) encode proteins involved in detecting pathogen attack and activating downstream defense molecules. Recent availability of soybean genome sequences makes it possible to examine the diversity of gene familie...