GTM-decon: guided-topic modeling of single-cell transcriptomes enables sub-cell-type and disease-subtype deconvolution of bulk transcriptomes [0.03%]
基于主题模型的单细胞转录组分析实现批量测序数据中亚类及疾病亚型解析
Lakshmipuram Seshadri Swapna,Michael Huang,Yue Li
Lakshmipuram Seshadri Swapna
Cell-type composition is an important indicator of health. We present Guided Topic Model for deconvolution (GTM-decon) to automatically infer cell-type-specific gene topic distributions from single-cell RNA-seq data for deconvolving bulk tr...
Predicting the impact of sequence motifs on gene regulation using single-cell data [0.03%]
利用单细胞数据预测序列基序对基因调控的影响
Jacob Hepkema,Nicholas Keone Lee,Benjamin J Stewart et al.
Jacob Hepkema et al.
The binding of transcription factors at proximal promoters and distal enhancers is central to gene regulation. Identifying regulatory motifs and quantifying their impact on expression remains challenging. Using a convolutional neural networ...
Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture [0.03%]
十万狗联盟的两千犬科动物基因组测序计划推动犬科动物种群遗传学、基因组功能及结构研究
Jennifer R S Meadows,Jeffrey M Kidd,Guo-Dong Wang et al.
Jennifer R S Meadows et al.
Background: The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and...
BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens [0.03%]
BamQuery：一种用于探索免疫肽组并优先处理可操作肿瘤抗原的蛋白质基因组工具
Maria Virginia Ruiz Cuevas,Marie-Pierre Hardy,Jean-David Larouche et al.
Maria Virginia Ruiz Cuevas et al.
MHC-I-associated peptides deriving from non-coding genomic regions and mutations can generate tumor-specific antigens, including neoantigens. Quantifying tumor-specific antigens' RNA expression in malignant and benign tissues is critical fo...
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...