SyMetrics: an integrated machine learning model for evaluating the pathogenicity of synonymous variants in the human genome [0.03%]
SyMetrics：一种用于评估人类基因组同义变异致病性的集成机器学习模型
Linnaeus Bundalian,Martina Schmidt Strnadová,Felix Garten et al.
Linnaeus Bundalian et al.
Synonymous single nucleotide variants (sSNVs), traditionally seen as neutral, are now recognized for their biological impact. To assess their relevance, we developed SyMetrics, a framework that integrates predictors of splicing, RNA stabili...
RNA-KG v2.0: an RNA-centered Knowledge Graph with Properties [0.03%]
RNA-KG v2.0：一种具有属性的以RNA为中心的知识图谱
Emanuele Cavalleri,Paolo Perlasca,Marco Mesiti
Emanuele Cavalleri
RNA-KG is a recently developed biomedical knowledge graph that integrates the interactions involving coding and non-coding RNA molecules extracted from public data sources. It can be used to support the classification of new molecules, iden...
OmNI: a modular open-source framework for interactive multi-omics data integration and visualization [0.03%]
OmNI：一个模块化的开源框架，用于交互式的多组学数据整合和可视化
Grace Potter,Jacob A Beierle,Camron Bryant et al.
Grace Potter et al.
Omics Notebook Interactive (OmNI) is an R-based, open-source, and modular framework engineered for streamlined multi-omics data integration and analysis across diverse data types, incorporating interactive visualizations at each processing ...
Insights into the architecture of earthworm metallothionein genes, powered by long-read genomics and transcriptomics [0.03%]
基于长读长基因组学和转录组学的蚯蚓金属硫蛋白基因结构研究
Maxim A Karpov,Stephen Short,Peter Kille et al.
Maxim A Karpov et al.
The metal-handling metallothionein gene family is subjected to a strong selection pressure in earthworms inhabiting metalliferous soils. The resultant single nucleotide polymorphisms and structural variants within metallothionein's characte...
Wim L Cuypers,Halil Ceylan,Eline Turcksin et al.
Wim L Cuypers et al.
Nucleotide sequences in the FASTQ or BAM format are widely shared, yet derived from platform-specific raw data outputs that differ across sequencing platforms. In Oxford Nanopore Technologies (ONT) sequencing, raw signal data contain valuab...
DNA methylation profiles aid to identify putative genome activation histories along lymphomagenesis [0.03%]
DNA甲基化谱有助识别淋巴瘤发生过程中的潜在基因组激活历史
Leone Albinati,Irene D&#x;Onofrio,Rabia Gül Aydin et al.
Leone Albinati et al.
DNA methylation (DNAm) is widely used to leverage biological information in the context of cancer. Active regulatory elements marked by increased chromatin accessibility and specific transcription factor (TF) binding, such as enhancers, sho...
MUSICiAn: genome-wide identification of genes involved in DNA repair via control-free mutational spectra analysis [0.03%]
基于无参突变谱分析的全基因组DNA修复相关基因识别方法
Colm Seale,Marco Barazas,Robin van Schendel et al.
Colm Seale et al.
Understanding DNA double-strand break (DSB) repair is crucial for the development of targeted anticancer therapies, yet the roles of many genes remain unclear. Recent studies show that disruption of known DSB repair genes can alter the sequ...
Sebastian J Arteaga,Brent M Znosko
Sebastian J Arteaga
Naturally occurring uridine modifications in RNA play critical roles in modulating RNA stability, translation, and immune responses. While detection methods have advanced, a comprehensive structural analysis across experimentally determined...
Very high CO2 concentrations inhibit photosynthesis and trigger transcriptomic stress responses in cyanobacteria [0.03%]
高浓度二氧化碳抑制蓝藻光合作用并引发转录组应激响应
Adrian Sven Geissler,Elena Carrasquer-Alvarez,Jan Gorodkin et al.
Adrian Sven Geissler et al.
CO[Formula: see text] concentrations above air level (0.04%) are beneficial for the growth of cyanobacteria. However, very high CO[Formula: see text] levels inhibit growth, limiting the usability of cyanobacteria for carbon capture and biot...
Simon Cabello-Aguilar,Charles Van Goethem,Jean-Charles Delmas et al.
Simon Cabello-Aguilar et al.
MobiCT is a bioinformatics pipeline designed to detect ultra-low-frequency variants present in cell-free DNA samples using unique molecular identifier (UMI). The pipeline is composed of three main stages: (i) UMI deduplication, (ii) alignme...