Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data [0.03%]
全面的增强子-目标基因匹配可提高基因集水平解读基因组范围调控数据的能力
Tingting Qin,Christopher Lee,Shiting Li et al.
Tingting Qin et al.
Background: Revealing the gene targets of distal regulatory elements is challenging yet critical for interpreting regulome data. Experiment-derived enhancer-gene links are restricted to a small set of enhancers and/or cel...
Author Correction: scINSIGHT for interpreting single-cell gene expression from biologically heterogeneous data [0.03%]
作者更正：scINSIGHT可对来自生物学异质性数据的单细胞基因表达进行解释
Kun Qian,Shiwei Fu,Hongwei Li et al.
Kun Qian et al.
Published Erratum
Genome biology. 2022 Apr 21;23(1):104. DOI:10.1186/s13059-022-02672-4 2022
Tony Zeng,Yang I Li
Tony Zeng
Recent progress in deep learning has greatly improved the prediction of RNA splicing from DNA sequence. Here, we present Pangolin, a deep learning model to predict splice site strength in multiple tissues. Pangolin outperforms state-of-the-...
One Cell At a Time (OCAT): a unified framework to integrate and analyze single-cell RNA-seq data [0.03%]
一次一个细胞（OCAT）：整合和分析单细胞RNA测序数据的统一框架
Chloe X Wang,Lin Zhang,Bo Wang
Chloe X Wang
Integrative analysis of large-scale single-cell RNA sequencing (scRNA-seq) datasets can aggregate complementary biological information from different datasets. However, most existing methods fail to efficiently integrate multiple large-scal...
Metacell-2: a divide-and-conquer metacell algorithm for scalable scRNA-seq analysis [0.03%]
Meta细胞-2：一种用于可扩展scRNA-seq分析的分治型Meta细胞算法
Oren Ben-Kiki,Akhiad Bercovich,Aviezer Lifshitz et al.
Oren Ben-Kiki et al.
Scaling scRNA-seq to profile millions of cells is crucial for constructing high-resolution maps of transcriptional manifolds. Current analysis strategies, in particular dimensionality reduction and two-phase clustering, offer only limited s...
Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis [0.03%]
拟南芥中气候相关核糖体SNitches的实验演示和泛结构组预测
Ángel Ferrero-Serrano,Megan M Sylvia,Peter C Forstmeier et al.
Ángel Ferrero-Serrano et al.
Background: Genome-wide association studies (GWAS) aim to correlate phenotypic changes with genotypic variation. Upon transcription, single nucleotide variants (SNVs) may alter mRNA structure, with potential impacts on tr...
PEGR: a flexible management platform for reproducible epigenomic and genomic research [0.03%]
基于PEGR的灵活易用的表观基因组和基因组研究重现性管理平台
Danying Shao,Gretta D Kellogg,Ali Nematbakhsh et al.
Danying Shao et al.
Reproducibility is a significant challenge in (epi)genomic research due to the complexity of experiments composed of traditional biochemistry and informatics. Recent advances have exacerbated this as high-throughput sequencing data is gener...
MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect [0.03%]
基于多联体变异效应测定的基因型表型图谱学习方法MAVE-NN
Ammar Tareen,Mahdi Kooshkbaghi,Anna Posfai et al.
Ammar Tareen et al.
Multiplex assays of variant effect (MAVEs) are a family of methods that includes deep mutational scanning experiments on proteins and massively parallel reporter assays on gene regulatory sequences. Despite their increasing popularity, a ge...
Explainable multiview framework for dissecting spatial relationships from highly multiplexed data [0.03%]
一种解释性的多视图框架，用于从高度多重化的数据中解析空间关系
Jovan Tanevski,Ricardo Omar Ramirez Flores,Attila Gabor et al.
Jovan Tanevski et al.
The advancement of highly multiplexed spatial technologies requires scalable methods that can leverage spatial information. We present MISTy, a flexible, scalable, and explainable machine learning framework for extracting relationships from...
mbDenoise: microbiome data denoising using zero-inflated probabilistic principal components analysis [0.03%]
基于零膨胀概率主成分分析的微生物组数据去噪方法
Yanyan Zeng,Jing Li,Chaochun Wei et al.
Yanyan Zeng et al.
The analysis of microbiome data has several technical challenges. In particular, count matrices contain a large proportion of zeros, some of which are biological, whereas others are technical. Furthermore, the measurements suffer from unequ...