MOREshiny: a user-friendly application for the inference of phenotype-specific multi-omic regulatory networks [0.03%]
MOREshiny：一种用于推断特定表型多组学调控网络的用户友好型应用程序
Maider Aguerralde-Martin,Roxana Andreea Moldovan,María Verdú et al.
Maider Aguerralde-Martin et al.
Motivation: Deciphering phenotype-specific regulatory mechanisms is key to understanding the molecular basis of complex diseases and traits. However, constructing multi-omic regulatory networks (MO-RNs) is challenging, as...
spammR: an R package designed for analysis and integration of spatial multi-omic measurements [0.03%]
spammR：一种用于空间多组学测量分析和整合的R语言包
Yannick Mahlich,Harkirat Sohi,Marija Veličković et al.
Yannick Mahlich et al.
Motivation: Spatial omics is a young and evolving field and as such shows rapid development of novel technologies and analysis methods to measure transcripts, proteins, metabolites, and post-translational modifications at...
Interpretable prediction and generation of ASC-speck aptamers using multiscale deep biological learning models [0.03%]
使用多尺度深度生物学习模型解释和生成ASC-speck核酸适配体的预测及合成能力
Mengting Niu,Quan Zou,Lei Xu
Mengting Niu
Motivation: Aptamers are functional nucleic acids that can bind to corresponding ligands and effectively replace monoclonal antibodies. However, some target proteins may lack binding candidate DNA sequence, necessitating ...
vClassifier: a toolkit for high-resolution phylogenetic classification of prokaryotic viruses [0.03%]
vClassifier：一个用于噬菌体的高分辨率系统发育分类工具包
Kun Zhou,James C Kosmopoulos,Karthik Anantharaman
Kun Zhou
Motivation: As the most abundant and diverse biological entities, prokaryotic viruses play pivotal roles in ecological systems. Their taxonomic classification has been instrumental in elucidating their diversity and ecolo...
GWAIS-Web: a free and secure web service for ultra-fast and large-scale genome-wide association interaction studies [0.03%]
GWAIS-Web：一个免费且安全的用于超快和大规模全基因组关联交互研究的网络服务平台
Lars Wienbrandt,Christoph Prieß,David Ellinghaus
Lars Wienbrandt
Summary: Genome-wide association interaction studies (GWAIS) are essential for identifying non-additive genetic effects underlying complex diseases, but exhaustive screening of SNP-SNP combinations across millions of vari...
Folding the unfoldable 2: using AlphaFold and ESMFold to explore spurious proteins [0.03%]
探索虚假蛋白质：使用AlphaFold和ESMFold折叠不可折叠的第2部分
Ailsa K Orr,Alex Bateman
Ailsa K Orr
Motivation: Spurious protein sequences, resulting from gene prediction errors, theoretically should not yield folded structures. AlphaFold2 was previously shown to predict short spurious sequences with high pLDDT scores a...
From randomness to recognition: modeling the evolution of DNA sequence information during enrichment for binding [0.03%]
从随机到识别：在结合过程中富集DNA序列信息的进化模型
Varun Maher,Daniel Martin,David Spetzler et al.
Varun Maher et al.
Motivation: Enrichment of random nucleic acid libraries for binding to a target can result in a specific aptamer sequence, but quantitative models describing the detailed evolution of molecular information during such pro...
pygenoscape: a Python package for spatial interpolation and visualization of genetic distance landscapes [0.03%]
PyGenoScapes：用于遗传距离景观空间插值和可视化的Python软件包
Andrew A Davinack,Rylie A Seaberg
Andrew A Davinack
Motivation: Spatial genetic structure is central to population genetics and phylogeography, but many approaches rely on discrete population models or summary statistics that can obscure continuous geographic patterns. ...
SMTrackR: an R/Bioconductor package for mapping protein binding at individual DNA molecules [0.03%]
SMTrackR：一个将蛋白质与单个DNA分子结合的映射图的R/Bioconductor包
Aashna Bansal,Himani Barmola,Shivam Yadav et al.
Aashna Bansal et al.
Motivation: Single-molecule assays like NOMe-seq, dSMF, and Nanopore are superior to DNase-seq and ATAC-seq as they do not destroy DNA. Thus, they enable quantification of all three, that is, protein-free, Transcription F...
Estelle Talouarn,Yoann Seeleuthner,Astrid Marchal et al.
Estelle Talouarn et al.
Motivation: The Gene Damage Index (GDI) quantifies the cumulative mutational damage of protein-coding genes in the general population and helps prioritize candidate disease genes in sequencing studies. However, the origin...