Insight into the Evolution of Mitochondrial Genetic Basis of Amphibious Adaptation in the Goby (Teleostei: Gobiidae) [0.03%]
泥鳅科鱼类肉质棒海刺鱼适应两栖生活的线粒体遗传基础的进化研究
Chengyao Yang,Chaoyang Luo,Qiuping Wang et al.
Chengyao Yang et al.
The adaptation to terrestrial environments from aquatic environments has always been regarded as a major evolutionary transition in fishes, during which it has been accompanied with diverse phenotypic innovations. Mitochondrial energy metab...
First Report on Presence of Mitochondrial Introns in Freshwater Sponges, and Pseudogenic Evidence of Their Loss [0.03%]
淡水海绵中线粒体内含子的存在及其丢失的假基因证据
Zhen Zhao,Junye Ma,Qun Yang et al.
Zhen Zhao et al.
Mitochondrial introns have a patchy distribution in sponge lineages. Here, we report on the finding of a group-II-intron in Eunapius rarus (Demospongiae, Spongillidae), which constitutes the first report of a mitochondrial intron in freshwa...
Correlated Evolution Drives Structural Convergence of Interacting Proteins [0.03%]
协同进化驱动互作蛋白结构收敛性演化
Ksenia Macias Calix,Antara Anika Piya,Raquel Assis
Ksenia Macias Calix
Understanding the relationship between protein structures and their interactions is a fundamental biological problem. Here we broadly tackle this problem by examining associations between protein structural features and interaction patterns...
OrthoGrafter: Rapid Identification of Orthologs from Precomputed Placement in Phylogenetic Trees [0.03%]
OrthoGrafter：通过在系统发育树中预先计算的定位快速识别直系同源物
Christopher M Williams,Paul D Thomas
Christopher M Williams
The identification of orthologs plays an important role in comparative genomics and function inference. Here, we present OrthoGrafter, a bioinformatics tool for taking one or more query sequences and inferring a set of orthologs drawn from ...
Evaluating Pretrained Protein Language Model Embeddings as Proxies for Functional Similarity [0.03%]
评估预训练蛋白质语言模型嵌入作为功能相似性的代理指标
Robert Shaw,Samuel D Love,Claire D McWhite
Robert Shaw
Protein Language Models (PLMs) have emerged as powerful tools for representing protein sequences. We explore how embeddings (numeric vector representations) from pretrained PLMs can serve as direct numeric proxies for protein structure and ...
Garance Sarton-Lohéac,Nikolai Romashchenko,Clément Marie Train et al.
Garance Sarton-Lohéac et al.
With the rapid advancement of large-scale sequencing initiatives, the need for efficient and accurate methods for inferring orthologous and paralogous relationships has never been more critical. Hierarchical orthologous groups (HOGs) provid...
Natasha Glover,David A Liberles
Natasha Glover
This special issue from the Quest for Orthologs community highlights ongoing challenges in detecting and characterizing orthologous genes in the annotation of protein functions. Eleven articles are presented describing ongoing research in t...
Molecular Evolution of the Green-Sensitive Opsins (RH2) in Sulawesi Oryzias Species with a Single Origin [0.03%]
绿敏感视蛋白(RH2)在苏拉威西泥鳅属鱼类单一祖先种的分子进化分析
Nobuyuki Inomata,Yohey Terai,Junko Kusumi et al.
Nobuyuki Inomata et al.
The green-sensitive opsin (RH2) family has experienced considerably more gene duplication and loss events than other opsin families during evolution of teleost fishes. Although evolutionary patterns of RH2 genes in Oryzias species, which be...
MEGA 12.1: Cross-Platform Release for macOS and Linux Operating Systems [0.03%]
MEGA 12.1：适用于macOS和Linux操作系统的跨平台版本
Glen Stecher,Michael Suleski,Qiqing Tao et al.
Glen Stecher et al.
The Molecular Evolutionary Genetics Analysis (MEGA) software is widely used for molecular evolutionary and phylogenetic analyses. We present MEGA version 12.1, a cross-platform release that operates natively on macOS (Intel and Apple M-seri...
Transposable Elements Seed Transcription Factor Binding Sites to Sequence-Specific Double-Stranded DNA Binding TF Networks Contributing to Governance of Primate Brain Evolution [0.03%]
转座元件播种 transcription factor 结合位点以特异性双链DNA结合TF网络促进类脑进化
Gennadi V Glinsky
Gennadi V Glinsky
Transposable elements (TEs) have played a pivotal role in shaping the regulatory architecture of mammalian genomes. This contribution reports multiple lines of evidence suggesting that TE have made a significant impact on brain development ...