DEprot: a comprehensive R-package for the analysis of label-free quantitation mass spectrometry data [0.03%]
DEprot：一个用于分析无标签定量质谱数据的全面R包
Nils Eickhoff,Liesbeth Hoekman,Onno Bleijerveld et al.
Nils Eickhoff et al.
In recent years, studies investigating protein-protein interactions on a proteome-wide scale have increased exponentially. These developments were achieved through implementation of new techniques, as well as improvements in mass spectromet...
An ELIXIR scoping review on domain-specific evaluation metrics for synthetic data in life sciences [0.03%]
ELIXIR范围审查：生命科学合成数据领域特定评估指标
Styliani-Christina Fragkouli,Somya Iqbal,Lisa Crossman et al.
Styliani-Christina Fragkouli et al.
Synthetic data (SD) has become an increasingly important asset in the life sciences, helping address data scarcity, privacy concerns, and barriers to data access. Creating artificial datasets that mirror the characteristics of real data all...
Accelerating rare disease diagnostics by linking DNA and RNA through an explainable and interactive RNA-guided workflow [0.03%]
通过可解释的和交互式的RNA引导的工作流程连接DNA和RNA加速罕见病诊断
Willem T K Maassen,Charlotte C E T Pape,Carlos G Urzua-Traslavina et al.
Willem T K Maassen et al.
Challenges preventing mainstream use of RNA-sequencing (RNA-seq) in genome diagnostics are sources of biological and technical variation, typically caused by intrinsic differences in gene expression between tissue types, cellular conditions...
A comprehensive annotation of conserved protein domains in human endogenous retroviruses [0.03%]
人类内源性逆转录病毒保守蛋白质域的全面注释
Tomàs Montserrat-Ayuso,Aurora Pujol,Anna Esteve-Codina
Tomàs Montserrat-Ayuso
Human endogenous retroviruses (HERVs) occupy nearly 8% of the human genome, yet their protein-coding potential remains largely unexplored. Originating from ancestral retroviruses that infected germline cells, HERVs typically follow the cano...
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...