ICCTax: a hierarchical taxonomic classifier for metagenomic sequences on a large language model [0.03%]
ICCTax：一种基于大型语言模型的元基因组序列分层分类方法
Yichun Gao,Jiaxing Bai,Feng Zhou et al.
Yichun Gao et al.
Motivation: Metagenomic data increasingly reflect the coexistence of species from Archaea, Bacteria, Eukaryotes, and Viruses in complex environments. Taxonomic classification across the four superkingdoms is essential for...
Genomic optimum contribution selection and mate allocation using JuMP [0.03%]
基于JuMP的基因组最优贡献选择和配对分配算法
Patrik Waldmann
Patrik Waldmann
Motivation: Artificial selection improves desired traits, but reduces genetic diversity within populations. Modern breeding programs aim to balance genetic gain with the maintenance of genetic variation to ensure long-ter...
ProCaliper: functional and structural analysis, visualization, and annotation of proteins [0.03%]
ProCaliper：蛋白质的功能和结构分析、可视化及注释
Jordan C Rozum,Hunter Ufford,Alexandria K Im et al.
Jordan C Rozum et al.
Summary: Understanding protein function at the molecular level requires connecting residue-level annotations with physical and structural properties. This can be cumbersome and error-prone when functional annotation, comp...
DSA-DeepFM: a dual-stage attention-enhanced DeepFM model for predicting anticancer synergistic drug combinations [0.03%]
一种双重注意机制增强的DeepFM模型用于预测抗癌药物协同组合
Yuexi Gu,Yongheng Sun,Louxin Zhang et al.
Yuexi Gu et al.
Motivation: Drug combinations are crucial in combating drug resistance, reducing toxicity, and improving therapeutic outcomes in disease management. Because a large number of drugs are available, the potential combination...
ProkBERT PhaStyle: accurate phage lifestyle prediction with pretrained genomic language models [0.03%]
基于预训练基因组语言模型的准确噬菌体生活方式预测
Judit Juhász,Noémi Ligeti-Nagy,Babett Bodnár et al.
Judit Juhász et al.
Motivation: Phage lifestyle prediction, i.e. classifying phage sequences as virulent or temperate, is crucial in biomedical and ecological applications. Phage sequences from metagenome or virome assemblies are often fragm...
Long short-term memory-based deep learning model for the discovery of antimicrobial peptides targeting Mycobacterium tuberculosis [0.03%]
基于长短期记忆的深层学习模型用于发现抗结核分枝杆菌抗菌肽
Linfeng Wang,Susana Campino,Taane G Clark et al.
Linfeng Wang et al.
Motivation: Tuberculosis, caused by Mycobacterium tuberculosis, remains a global health challenge driven by rising antibiotic resistance. Antimicrobial peptides offer a promising alternative due to membrane-disruptive act...
zAMP and zAMPExplorer: reproducible scalable amplicon-based metagenomics analysis and visualization [0.03%]
zAMP和zAMPExplorer：可重复的宏基因组学分析和可视化平台
Valentin Scherz,Sedreh Nassirnia,Farid Chaabane et al.
Valentin Scherz et al.
Summary: To enable flexible, scalable, and reproducible microbiota profiling, we have developed zAMP, an open-source bioinformatics pipeline for the analysis of amplicon sequence data, such as 16S rRNA gene for bacteria a...
Atlantool: a command line tool to retrieve DNA and RNA sequencing reads from BAM files by the read identifier [0.03%]
Atlantool：一种通过读取识别符从BAM文件中获取DNA和RNA测序读的命令行工具
Emma M Rath,Huy Le,Yukhym Pyshnohraiev et al.
Emma M Rath et al.
Motivation: DNA or RNA sequencing produce a large volume of data that is usually stored in a Binary Alignment Map (BAM) file format. Processing and analysis of this large genomic data require specialized software tools. T...
FinaleToolkit: accelerating cell-free DNA fragmentation analysis with a high-speed computational toolkit [0.03%]
Finale Toolkit：一种加速细胞无DNA片段分析的高速计算工具包
James Wenhan Li,Ravi Bandaru,Kundan Baliga et al.
James Wenhan Li et al.
Motivation: Cell-free DNA (cfDNA) fragmentation pattern represents a promising non-invasive biomarker for disease diagnosis and prognosis. Numerous fragmentation features, such as end motif and window protection score (WP...
TidyGWAS: a scalable approach for standardized cleaning of genome-wide association study summary statistics [0.03%]
tidygwas：一种用于全基因组关联研究汇总统计数据标准化处理的可扩展方法
Arvid Harder,Jerry Guintivano,Joëlle A Pasman et al.
Arvid Harder et al.
Motivation: Genome-wide association studies (GWAS) have transformed human genetics by identifying tens of thousands of trait-associated variants, enabling applications from drug discovery to polygenic risk prediction. The...