MIDAA: deep archetypal analysis for interpretable multi-omic data integration based on biological principles [0.03%]
基于生物原理的可解释多组学数据集成的深度原型分析（MIDAA）
Salvatore Milite,Giulio Caravagna,Andrea Sottoriva
Salvatore Milite
High-throughput multi-omic molecular profiling allows the probing of biological systems at unprecedented resolution. However, integrating and interpreting high-dimensional, sparse, and noisy multimodal datasets remains challenging. Deriving...
CNRein: an evolution-aware deep reinforcement learning algorithm for single-cell DNA copy number calling [0.03%]
基于进化且适用于单细胞DNA拷贝数呼叫的深度强化学习算法CNRein
Stefan Ivanovic,Mohammed El-Kebir
Stefan Ivanovic
Low-pass single-cell DNA sequencing technologies and algorithmic advancements have enabled haplotype-specific copy number calling on thousands of cells within tumors. However, measurement uncertainty may result in spurious CNAs inconsistent...
Missing cell types in single-cell references impact deconvolution of bulk data but are detectable [0.03%]
单细胞参考中缺失的细胞类型会影响批量数据的去卷积但可以检测到
Adriana Ivich,Natalie R Davidson,Laurie Grieshober et al.
Adriana Ivich et al.
Background: Advancements in RNA sequencing have expanded our ability to study gene expression profiles of biological samples in bulk tissue and single cells. Deconvolution of bulk data with single-cell references provides...
Benchmark of cellular deconvolution methods using a multi-assay dataset from postmortem human prefrontal cortex [0.03%]
基于死后人大脑额叶皮层多模态数据的细胞去卷积方法评估研究
Louise A Huuki-Myers,Kelsey D Montgomery,Sang Ho Kwon et al.
Louise A Huuki-Myers et al.
Cellular deconvolution of bulk RNA-sequencing data using single cell/nuclei RNA-seq reference data is an important strategy for estimating cell type composition in heterogeneous tissues, such as the human brain. Here, we generate a multi-as...
Systematic optimization and prediction of cre recombinase for precise genome editing in mice [0.03%]
系统优化和预测Cre重组酶以实现小鼠的精准基因组编辑
Valerie Erhardt,Elli Hartig,Kristian Lorenzo et al.
Valerie Erhardt et al.
Background: The Cre-Lox system is a powerful tool in mouse genetics, enabling precise spatiotemporal control of gene expression and conditional knockout models. Since its development, it has transformed genome editing by ...
Genomic prediction with kinship-based multiple kernel learning produces hypothesis on the underlying inheritance mechanisms of phenotypic traits [0.03%]
基于亲缘关系的多核学习基因组预测产生表型性状潜在遗传机制的假设
Daniele Raimondi,Nora Verplaetse,Antoine Passemiers et al.
Daniele Raimondi et al.
Background: Genomic prediction encompasses the techniques used in agricultural technology to predict the genetic merit of individuals towards valuable phenotypic traits. It is related to Genome Interpretation in humans, w...
Integrative omics analysis reveals the genetic basis of fatty acid composition in Brassica napus seeds [0.03%]
整合组学分析揭示了油菜籽中脂肪酸组成变化的遗传基础
Yuting Zhang,Yunhao Liu,Zhanxiang Zong et al.
Yuting Zhang et al.
Background: The fatty acid content represents a crucial quality trait in Brassica napus or rapeseed. Improvements in fatty acid composition markedly enhance the quality of rapeseed oil. ...
Chromosome-level genome assembly and single-cell analysis unveil molecular mechanisms of arm regeneration in the ophiuroid Ophiura sarsii vadicola [0.03%]
染色体水平基因组组装和单细胞分析揭示了Ophiura sarsii vadicola海星臂再生的分子机制
Qin-Zeng Xu,Yi-Xuan Li,Wen-Ge Shi et al.
Qin-Zeng Xu et al.
Background: Ophiuroids, belonging to Ophiuroidea in Echinodermata, possess remarkable regenerative capacities in their arms, relying on cellular recruitment and de-differentiation. However, limited high-quality genomic re...
Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms [0.03%]
从聚合染色质可及性数据中推断基因型揭示了遗传调控机制
Brandon M Wenz,Yuan He,Nae-Chyun Chen et al.
Brandon M Wenz et al.
Background: Understanding the genetic causes underlying variability in chromatin accessibility can shed light on the molecular mechanisms through which genetic variants may affect complex traits. Thousands of ATAC-seq sam...
SOAPy: a Python package to dissect spatial architecture, dynamics, and communication [0.03%]
SOAPy：用于解析空间架构、动力学和通信的Python包
Heqi Wang,Jiarong Li,Siyu Jing et al.
Heqi Wang et al.
Advances in spatial omics enable deeper insights into tissue microenvironments while posing computational challenges. Therefore, we developed SOAPy, a comprehensive tool for analyzing spatial omics data, which offers methods for spatial dom...