RUBICON: a framework for designing efficient deep learning-based genomic basecallers [0.03%]
RUBICON：设计高效的基于深度学习的基因组碱基识别器的框架
Gagandeep Singh,Mohammed Alser,Kristof Denolf et al.
Gagandeep Singh et al.
Nanopore sequencing generates noisy electrical signals that need to be converted into a standard string of DNA nucleotide bases using a computational step called basecalling. The performance of basecalling has critical implications for all ...
Dissecting the sequence and structural determinants guiding m6A deposition and evolution via inter- and intra-species hybrids [0.03%]
通过种内和种间杂交剖析指导m6A沉积和演化的序列及结构因子
Ran Shachar,David Dierks,Miguel Angel Garcia-Campos et al.
Ran Shachar et al.
Background: N6-methyladenosine (m6A) is the most abundant mRNA modification, and controls mRNA stability. m6A distribution varies considerably between and within species. Yet, it is unclear to what extent this variability...
pyHiM: a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging [0.03%]
pyHiM：一个新的开源多平台软件包，基于多重DNA-FISH成像的空间基因组学技术
Xavier Devos,Jean-Bernard Fiche,Marion Bardou et al.
Xavier Devos et al.
Genome-wide ensemble sequencing methods improved our understanding of chromatin organization in eukaryotes but lack the ability to capture single-cell heterogeneity and spatial organization. To overcome these limitations, new imaging-based ...
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...