Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data [0.03%]
基于单细胞RNA测序伪批量数据的群体异质性建模
Yue You,Xueyi Dong,Yong Kiat Wee et al.
Yue You et al.
Group heteroscedasticity is commonly observed in pseudo-bulk single-cell RNA-seq datasets and its presence can hamper the detection of differentially expressed genes. Since most bulk RNA-seq methods assume equal group variances, we introduc...
EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations [0.03%]
EvoAug：利用受进化启发的数据增强改进基因组深度神经网络的泛化能力和可解释性
Nicholas Keone Lee,Ziqi Tang,Shushan Toneyan et al.
Nicholas Keone Lee et al.
Deep neural networks (DNNs) hold promise for functional genomics prediction, but their generalization capability may be limited by the amount of available data. To address this, we propose EvoAug, a suite of evolution-inspired augmentations...
Caloric restriction remodels the hepatic chromatin landscape and bile acid metabolism by modulating the gut microbiota [0.03%]
热量限制通过调节肠道微生物组重塑肝脏染色质景观和胆汁酸代谢
Yun Fan,Hong Qian,Meijia Zhang et al.
Yun Fan et al.
Background: Caloric restriction (CR) has been known to promote health by reprogramming metabolism, yet little is known about how the epigenome and microbiome respond during metabolic adaptation to CR. ...
Author Correction: DNA methylation entropy as a measure of stem cell replication and aging [0.03%]
作者更正：将DNA甲基化熵用作测量干细胞复制和衰老的指标
Himani Vaidya,Hye Seon Jeong,Kelsey Keith et al.
Himani Vaidya et al.
Published Erratum
Genome biology. 2023 Apr 30;24(1):104. DOI:10.1186/s13059-023-02943-8 2023
m6A readers ECT2/ECT3/ECT4 enhance mRNA stability through direct recruitment of the poly(A) binding proteins in Arabidopsis [0.03%]
拟南芥中m6A阅读蛋白ECT2/3/4通过直接招募多聚腺苷酸结合蛋白来增强mRNA稳定性
Peizhe Song,Lianhuan Wei,Zixin Chen et al.
Peizhe Song et al.
Background: RNA N6-methyladenosine (m6A) modification is critical for plant growth and crop yield. m6A reader proteins can recognize m6A modifications to facilitate the functions of m6A in gene regulation. ECT2, ECT3, and...
Boosting genome editing efficiency in human cells and plants with novel LbCas12a variants [0.03%]
新型Lbcas12a变异株可提升人类细胞和植物的基因组编辑效率
Liyang Zhang,Gen Li,Yingxiao Zhang et al.
Liyang Zhang et al.
Background: Cas12a (formerly known as Cpf1), the class II type V CRISPR nuclease, has been widely used for genome editing in mammalian cells and plants due to its distinct characteristics from Cas9. Despite being one of t...
David Porubsky,William T Harvey,Allison N Rozanski et al.
David Porubsky et al.
The telomere-to-telomere (T2T) complete human reference has significantly improved our ability to characterize genome structural variation. To understand its impact on inversion polymorphisms, we remapped data from 41 genomes against the T2...
DREAMS: deep read-level error model for sequencing data applied to low-frequency variant calling and circulating tumor DNA detection [0.03%]
针对低频变异检测和循环肿瘤DNA检测的深度测序数据读水平错误模型研究
Mikkel H Christensen,Simon O Drue,Mads H Rasmussen et al.
Mikkel H Christensen et al.
Circulating tumor DNA detection using next-generation sequencing (NGS) data of plasma DNA is promising for cancer identification and characterization. However, the tumor signal in the blood is often low and difficult to distinguish from err...
SNV-FEAST: microbial source tracking with single nucleotide variants [0.03%]
基于单核苷酸变异的微生物源解析工具SNV-FEAST
Leah Briscoe,Eran Halperin,Nandita R Garud
Leah Briscoe
Elucidating the sources of a microbiome can provide insight into the ecological dynamics responsible for the formation of these communities. Source tracking approaches to date leverage species abundance information; however, single nucleoti...
A metabolic perspective of selection for fruit quality related to apple domestication and improvement [0.03%]
从代谢角度探讨苹果育种改良中与果实品质相关的选择作用
Qiong Lin,Jing Chen,Xuan Liu et al.
Qiong Lin et al.
Background: Apple is an economically important fruit crop. Changes in metabolism accompanying human-guided evolution can be revealed using a multiomics approach. We perform genome-wide metabolic analysis of apple fruits c...