Correcting gradient-based interpretations of deep neural networks for genomics [0.03%]
用于基因组学的深度神经网络的梯度解释的纠正方法
Antonio Majdandzic,Chandana Rajesh,Peter K Koo
Antonio Majdandzic
Post hoc attribution methods can provide insights into the learned patterns from deep neural networks (DNNs) trained on high-throughput functional genomics data. However, in practice, their resultant attribution maps can be challenging to i...
Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize [0.03%]
杂交特异性染色质免疫沉淀测序分析鉴定出与玉米性状相关的 brassinosteroid 响应型转录因子结合位点变异
Thomas Hartwig,Michael Banf,Gisele Passaia Prietsch et al.
Thomas Hartwig et al.
Background: Genetic variation in regulatory sequences that alter transcription factor (TF) binding is a major cause of phenotypic diversity. Brassinosteroid is a growth hormone that has major effects on plant phenotypes. ...
DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis [0.03%]
拟南芥中DDM1介导的基因体DNA甲基化与防卫相关诱导基因激活有关
Seungchul Lee,Jaemyung Choi,Jihwan Park et al.
Seungchul Lee et al.
Background: Plants memorize previous pathogen attacks and are "primed" to produce a faster and stronger defense response, which is critical for defense against pathogens. In plants, cytosines in transposons and gene bodie...
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...