Inferring context-specific site variation with evotuned protein language models [0.03%]
使用进化调优的蛋白质语言模型推理特定情境下的位点变异
Spyros Lytras,Adam Strange,Jumpei Ito et al.
Spyros Lytras et al.
Multiple sequence alignments (MSAs) have been traditionally used for making inferences about site-specific diversity in proteins. Recent advancements in the field of artificial intelligence have highlighted the potential of protein language...
ANOMALY: a Snakemake pipeline for identifying NuMTs from long-read sequencing data [0.03%]
ANOMALY：一种从长读测序数据中识别NuMTs的Snakemake管道
Nirmal S Mahar,Rachit Singh,Ishaan Gupta et al.
Nirmal S Mahar et al.
Nuclear mitochondrial DNA segments (NuMTs) can contribute to cancer development and disease progression by disrupting protein-coding genes. Furthermore, their presence confounds mitochondrial variant detection, underscoring the critical nee...
Andrew Chen,Lina Kroehling,Christina S Ennis et al.
Andrew Chen et al.
In this study, we developed an integrated single-cell transcriptomic (scRNAseq) atlas of human breast cancer (BC), the largest resource of its kind, totaling >600 000 cells across 138 patients. Rigorous integration and annotation of publicl...
Federated learning frameworks: quality and interoperability for biomedical research [0.03%]
联合学习框架：生物医学研究中的质量和互操作性
María Chavero-Diez,Carles Hernandez-Ferrer,Laia Codó et al.
María Chavero-Diez et al.
This review examines the current landscape of federated learning frameworks to evaluate their long-term sustainability, flexibility, and usability in biomedical research, where strict data regulations limit data sharing across institutions....
Evolutionary and methodological considerations when interpreting gene presence-absence variation in pangenomes [0.03%]
泛基因组研究中解释基因增缺变异时的进化和方法学考量
Tomáš Brůna,Avinash Sreedasyam,Avril M Harder et al.
Tomáš Brůna et al.
While graph-based pangenomes have become a standard and interoperable foundation for comparisons across multiple reference genomes, integrating protein-coding gene annotations across pangenomes in a single 'pangene set' remains challenging,...
Robin: an advanced tool for comparative loop caller result analysis leveraging large language models [0.03%]
Robin：一种利用大型语言模型进行比较循环调用结果分析的先进工具
H M A Mohit Chowdhury,Mattie Fuller,Oluwatosin Oluwadare
H M A Mohit Chowdhury
There has been significant interest in genomics research, leading to the development of numerous new methods. One notable area of progress is in chromosome loop detection algorithms (also known as loop callers). However, despite these advan...
A novel explainable deep-learning approach for network analysis of epistatic interactions [0.03%]
一种新颖的可解释深度学习方法用于分析上位性相互作用的网络
Andrea Mastropietro,Georgios Markopoulos,Evangelos Evangelou et al.
Andrea Mastropietro et al.
Epistatic interactions of gene loci often determine complex trait phenotypes and may indicate the underlying molecular mechanisms of traits and diseases. Yet, the inference of epistatic interactions and gene-gene networks remains challengin...
RAZOR: a database of PCR primers targeting human respiratory viruses [0.03%]
针对人类呼吸道病毒的PCR引物数据库(RAZOR)
Hunter M Gill,Quoseena Mir,Rajneesh Srivastava et al.
Hunter M Gill et al.
Respiratory viruses like SARS-CoV-2, Influenza A, and others represent a considerable threat to public health, infecting millions of people annually. Previous respiratory virus outbreaks have demonstrated the value of polymerase chain react...
NGSTroubleFinder: a tool for detection and quantification of contamination and kinship across human NGS data [0.03%]
NGSTroubleFinder：一种检测和量化人类NGS数据中的污染和亲缘关系的工具
Samuel Valentini,Tecla Venturelli,Xavier Gallego et al.
Samuel Valentini et al.
Quality control constitutes a critical component of any next-generation sequencing (NGS) pipeline; however, most existing pipelines emphasize technical quality assessment (e.g. read quality, alignment metrics, duplication rates) while overl...
SM3DD with segmented PCA: a comprehensive method for interpreting 3D spatial transcriptomics [0.03%]
用于解释3D空间转录组学的SM3DD与分段PCA：一种全面的方法
Tony Blick,Aaron Kilgallon,James Monkman et al.
Tony Blick et al.
We developed Standardised Minimum 3D Distance (SM3DD), an entirely cell segmentation/annotation-free approach to the analysis of spatial RNA datasets, using it to compare lung tissue from 16 clinically normal individuals to that of 18 SARS-...