SSBlazer: a genome-wide nucleotide-resolution model for predicting single-strand break sites [0.03%]
SSBlazer：一个全基因组核苷酸分辨率模型，用于预测单链断裂位点
Sheng Xu,Junkang Wei,Siqi Sun et al.
Sheng Xu et al.
Single-strand breaks are the major DNA damage in the genome and serve a crucial role in various biological processes. To reveal the significance of single-strand breaks, multiple sequencing-based single-strand break detection methods have b...
IDHwt glioblastomas can be stratified by their transcriptional response to standard treatment, with implications for targeted therapy [0.03%]
具有IDHwt的多形性胶质母细胞瘤可以根据其对标准治疗的转录反应进行分层，这对靶向治疗有影响。
Georgette Tanner,Rhiannon Barrow,Shoaib Ajaib et al.
Georgette Tanner et al.
Background: Glioblastoma (GBM) brain tumors lacking IDH1 mutations (IDHwt) have the worst prognosis of all brain neoplasms. Patients receive surgery and chemoradiotherapy but tumors almost always fatally recur. ...
The androgen receptor interacts with GATA3 to transcriptionally regulate a luminal epithelial cell phenotype in breast cancer [0.03%]
雄激素受体与GATA3相互作用以转录调控乳腺癌的腔上皮细胞表型
Leila Hosseinzadeh,Zoya Kikhtyak,Geraldine Laven-Law et al.
Leila Hosseinzadeh et al.
Background: The androgen receptor (AR) is a tumor suppressor in estrogen receptor (ER) positive breast cancer, a role sustained in some ER negative breast cancers. Key factors dictating AR genomic activity in a breast con...
Simple but powerful interactive data analysis in R with R/LinekdCharts [0.03%]
使用R/R-LinekdCharts进行简单而强大的交互式数据统计分析
Svetlana Ovchinnikova,Simon Anders
Svetlana Ovchinnikova
In research involving data-rich assays, exploratory data analysis is a crucial step. Typically, this involves jumping back and forth between visualizations that provide overview of the whole data and others that dive into details. For examp...
Mapping the functional impact of non-coding regulatory elements in primary T cells through single-cell CRISPR screens [0.03%]
通过单细胞CRISPR筛选映射初始T细胞中非编码调控元件的功能影响
Celia Alda-Catalinas,Ximena Ibarra-Soria,Christina Flouri et al.
Celia Alda-Catalinas et al.
Background: Drug targets with genetic evidence are expected to increase clinical success by at least twofold. Yet, translating disease-associated genetic variants into functional knowledge remains a fundamental challenge ...
AnnoPRO: a strategy for protein function annotation based on multi-scale protein representation and a hybrid deep learning of dual-path encoding [0.03%]
AnnoPRO：一种基于多尺度蛋白质表示和双路径编码混合深度学习的蛋白质功能注释策略
Lingyan Zheng,Shuiyang Shi,Mingkun Lu et al.
Lingyan Zheng et al.
Protein function annotation has been one of the longstanding issues in biological sciences, and various computational methods have been developed. However, the existing methods suffer from a serious long-tail problem, with a large number of...
Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc [0.03%]
使用CNAqc从批量肿瘤测序中对克隆和亚克隆拷贝数改变进行计算验证
Alice Antonello,Riccardo Bergamin,Nicola Calonaci et al.
Alice Antonello et al.
Copy number alterations (CNAs) are among the most important genetic events in cancer, but their detection from sequencing data is challenging because of unknown sample purity, tumor ploidy, and general intra-tumor heterogeneity. Here, we pr...
RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci [0.03%]
RExPRT：一种预测串联重复序列致病性的机器学习工具
Sarah Fazal,Matt C Danzi,Isaac Xu et al.
Sarah Fazal et al.
Expansions of tandem repeats (TRs) cause approximately 60 monogenic diseases. We expect that the discovery of additional pathogenic repeat expansions will narrow the diagnostic gap in many diseases. A growing number of TR expansions are bei...
BORIS/CTCFL epigenetically reprograms clustered CTCF binding sites into alternative transcriptional start sites [0.03%]
BORIS/CTCFL表观遗传地将聚集的CTCF结合位点重新编程为替代转录起始位点
Elena M Pugacheva,Dharmendra Nath Bhatt,Samuel Rivero-Hinojosa et al.
Elena M Pugacheva et al.
Background: Pervasive usage of alternative promoters leads to the deregulation of gene expression in carcinogenesis and may drive the emergence of new genes in spermatogenesis. However, little is known regarding the mecha...
Qin Zhu,Daniel N Conrad,Zev J Gartner
Qin Zhu
Sample multiplexing enables pooled analysis during single-cell RNA sequencing workflows, thereby increasing throughput and reducing batch effects. A challenge for all multiplexing techniques is to link sample-specific barcodes with cell-spe...