Anna Nordin,Gianluca Zambanini,Pierfrancesco Pagella et al.
Anna Nordin et al.
Background: Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is an increasingly popular technique to map genome-wide binding profiles of histone modifications, transcription factors, and co-factors. The ENCODE ...
Zhou Jason Shi,Stephen Nayfach,Katherine S Pollard
Zhou Jason Shi
Existing single nucleotide polymorphism (SNP) genotyping algorithms do not scale for species with thousands of sequenced strains, nor do they account for conspecific redundancy. Here we present a bioinformatics tool, Maast, which empowers p...
Meta-Analysis
Genome biology. 2023 Aug 10;24(1):186. DOI:10.1186/s13059-023-03030-8 2023
LAST-seq: single-cell RNA sequencing by direct amplification of single-stranded RNA without prior reverse transcription and second-strand synthesis [0.03%]
利用单链RNA直接扩增进行无需逆转录和合成第二链的单细胞RNA测序(LAST-seq)
Jun Lyu,Chongyi Chen
Jun Lyu
Existing single-cell RNA sequencing (scRNA-seq) methods rely on reverse transcription (RT) and second-strand synthesis (SSS) to convert single-stranded RNA into double-stranded DNA prior to amplification, with the limited RT/SSS efficiency ...
Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome [0.03%]
基于183个基因组拼接的最后细菌共同祖先揭示了其多功能古核核心基因组
Jason C Hyun,Bernhard O Palsson
Jason C Hyun
Background: Cumulative sequencing efforts have yielded enough genomes to construct pangenomes for dozens of bacterial species and elucidate intraspecies gene conservation. Given the diversity of organisms for which this i...
Cross-protein transfer learning substantially improves disease variant prediction [0.03%]
跨蛋白质转移学习明显改善疾病变异预测能力
Milind Jagota,Chengzhong Ye,Carlos Albors et al.
Milind Jagota et al.
Background: Genetic variation in the human genome is a major determinant of individual disease risk, but the vast majority of missense variants have unknown etiological effects. Here, we present a robust learning framewor...
3D organization of regulatory elements for transcriptional regulation in Arabidopsis [0.03%]
拟南芥转录调控的染色体三维结构 организации регуляторных элементов для транскрипционного регулирования у арабидOPSIS
Li Deng,Qiangwei Zhou,Jie Zhou et al.
Li Deng et al.
Background: Although spatial organization of compartments and topologically associating domains at large scale is relatively well studied, the spatial organization of regulatory elements at fine scale is poorly understood...
Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning [0.03%]
基于序列预测蛋白质-RNA相互作用的计算方法研究
Marc Horlacher,Nils Wagner,Lambert Moyon et al.
Marc Horlacher et al.
We present RBPNet, a novel deep learning method, which predicts CLIP-seq crosslink count distribution from RNA sequence at single-nucleotide resolution. By training on up to a million regions, RBPNet achieves high generalization on eCLIP, i...
A syntelog-based pan-genome provides insights into rice domestication and de-domestication [0.03%]
基于同源基因的水稻泛基因组揭示了栽培稻驯化和逆向驯化的遗传机制
Dongya Wu,Lingjuan Xie,Yanqing Sun et al.
Dongya Wu et al.
Background: Asian rice is one of the world's most widely cultivated crops. Large-scale resequencing analyses have been undertaken to explore the domestication and de-domestication genomic history of Asian rice, but the ev...
BEDwARS: a robust Bayesian approach to bulk gene expression deconvolution with noisy reference signatures [0.03%]
具有噪声参考信号的批量基因表达去卷积的稳健贝叶斯方法BEDwARS
Saba Ghaffari,Kelly J Bouchonville,Ehsan Saleh et al.
Saba Ghaffari et al.
Differential gene expression in bulk transcriptomics data can reflect change of transcript abundance within a cell type and/or change in the proportions of cell types. Expression deconvolution methods can help differentiate these scenarios....
Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes [0.03%]
利用scnRNA-seq转录组进行批量RNA-seq去卷积的有效方法
Francisco Avila Cobos,Mohammad Javad Najaf Panah,Jessica Epps et al.
Francisco Avila Cobos et al.
Background: RNA profiling technologies at single-cell resolutions, including single-cell and single-nuclei RNA sequencing (scRNA-seq and snRNA-seq, scnRNA-seq for short), can help characterize the composition of tissues a...