Analysis of new functional profiles of protein isoforms yielded by ds exonization in rice [0.03%]
对水稻ds外显子化产生蛋白质异构体的新功能谱系的分析
Ting-Ying Chien,Li-Yu Daisy Liu,Yuh-Chyang Charng
Ting-Ying Chien
Insertion of transposable elements (TEs) into introns can lead to their activation as alternatively spliced cassette exons, an event called exonization. Exonization can enrich the complexity of transcriptomes and proteomes. Previously, we p...
Identification, nomenclature, and evolutionary relationships of mitogen-activated protein kinase (MAPK) genes in soybean [0.03%]
大豆有丝分裂原活化蛋白激酶(MAPK)基因的鉴定、命名及其进化关系
Achal Neupane,Madhav P Nepal,Sarbottam Piya et al.
Achal Neupane et al.
Mitogen-activated protein kinase (MAPK) genes in eukaryotes regulate various developmental and physiological processes including those associated with biotic and abiotic stresses. Although MAPKs in some plant species including Arabidopsis h...
SBEToolbox: A Matlab Toolbox for Biological Network Analysis [0.03%]
SBEToolbox：一种用于生物学网络分析的Matlab工具箱
Kranti Konganti,Gang Wang,Ence Yang et al.
Kranti Konganti et al.
We present SBEToolbox (Systems Biology and Evolution Toolbox), an open-source Matlab toolbox for biological network analysis. It takes a network file as input, calculates a variety of centralities and topological metrics, clusters nodes int...
Daniel Garrigan
Daniel Garrigan
Background: While many bioinformatics tools currently exist for assembling and discovering variants from next-generation sequence data, there are very few tools available for performing evolutionary analyses from these da...
Analysis of protein thermostability enhancing factors in industrially important thermus bacteria species [0.03%]
分析工业重要热菌属物种中增强蛋白质耐热性的因素
Benjamin Kumwenda,Derek Litthauer,Ozlem Tastan Bishop et al.
Benjamin Kumwenda et al.
Elucidation of evolutionary factors that enhance protein thermostability is a critical problem and was the focus of this work on Thermus species. Pairs of orthologous sequences of T. scotoductus SA-01 and T. thermophilus HB27, with the larg...
Conventional simulation of biological sequences leads to a biased assessment of multi-Loci phylogenetic analysis [0.03%]
常规模拟生物序列会导致对多位点系统发育分析的评估产生偏差
Barbara O Aguiar,Carlos G Schrago
Barbara O Aguiar
Phylogenetic analysis based on multi-loci data sets is performed by means of supermatrix (SM) or supertree (ST) approaches. Recently, methods that rely on species tree (SppT) inference by the multi-species coalescence have also been impleme...
Evolutionary Modeling of Genotype-Phenotype Associations, and Application to Primate Coding and Non-coding mtDNA Rate Variation [0.03%]
基因型表型关联的谱系模型及其在灵长类线粒体编码和非编码DNA速率演化中的应用
Timothy D O&#x;Connor,Nicholas I Mundy
Timothy D O&#x;Connor
Variation in substitution rates across a phylogeny can be indicative of shifts in the evolutionary dynamics of a protein or non-protein coding regions. One way to understand these signals is to seek the phenotypic correlates of rate variati...
Identification of differentially evolved genes: an alternative approach to detection of accelerated molecular evolution from genome-wide comparative data [0.03%]
识别不同进化的基因：一种从全基因组比较数据中检测加速分子进化的方法
Kyu-Won Kim,David W Burt,Heebal Kim et al.
Kyu-Won Kim et al.
One of the most important measures for detecting molecular adaptations between species/lineages at the gene level is the comparison of relative fixation rates of synonymous (dS) and non-synonymous (dN) mutations. This study shows that the b...
SARP: A Novel Algorithm to Assess Compositional Biases in Protein Sequences [0.03%]
评估蛋白质序列组成偏差的新型算法SARP的研究
Kirill S Antonets,Anton A Nizhnikov
Kirill S Antonets
The composition of a defined set of subunits (nucleotides, amino acids) is one of the key features of biological sequences. Compositional biases are local shifts in amino acid or nucleotide frequencies that can occur as an adaptation of an ...
Conserved nonsense-prone CpG sites in apoptosis-regulatory genes: conditional stop signs on the road to cell death [0.03%]
凋亡调节基因中易突变的CpG位点：通向细胞死亡之路的条件性停止标志
Yongzhong Zhao,Richard J Epstein
Yongzhong Zhao
Methylation-prone CpG dinucleotides are strongly conserved in the germline, yet are also predisposed to somatic mutation. Here we quantify the relationship between germline codon mutability and somatic carcinogenesis by comparing usage of t...