Differential gene regulatory network analysis reveals transcriptional disruption in opioid [0.03%]
差异基因调控网络分析揭示阿片类药物的转录紊乱
Jianlan Ren,Xu Wang,Feiyang Luan et al.
Jianlan Ren et al.
Gene regulatory networks (GRNs) inferred from single-cell data offer a powerful lens for dissecting transcriptional regulation across biological conditions. Yet, statistical methods for comparing TF-level binary regulatory matrices-where ed...
Long-read nanopore shotgun metagenomic DNA sequencing for river biodiversity, wildlife, pollution, and environmental health monitoring [0.03%]
河流生物多样性、野生动物、污染和环境健康监测的长读纳米孔无标签宏基因组DNA测序技术
Orestis Nousias,Fiona G Duffy,Isabelle J Duffy et al.
Orestis Nousias et al.
As the human population expands and global temperatures rise, species, populations, and biodiversity decline at unprecedented rates, while the frequency of infectious disease emergence increases. Therefore, it is more vital than ever to acc...
CNV-Hub: an integrated web-based platform for CNV classification and interpretation using multi-algorithm consensus [0.03%]
CNV-Hub：一个使用多算法共识的集成网络平台用于CNV分类和解析
Vignesh Guru Victor Pillay,Anne-Laure Mosca,Davide Callegarin et al.
Vignesh Guru Victor Pillay et al.
Copy number variations (CNVs) are genomic alterations that can cause rare genetic diseases. Their interpretation requires consulting multiple databases and following classification guidelines, such as those from the American College of Medi...
Diploid dual assemblies reveal the telocentric structure and extensive allelic heterogeneity of canine genomes [0.03%]
二倍体基因组组装揭示犬类基因组的末端着丝粒结构及广泛的等位基因异质性
Jeffrey M Kidd,Yassine Souilmi,Benjamin D Rosen et al.
Jeffrey M Kidd et al.
Although an increasing number of long-read genome assemblies have been created from a diverse collection of dogs and wolves, most published assemblies represent the diploid genome as a single primary sequence. Here, we generate and analyze ...
Analysis and visualization of expression patterns with fuzzy sets as FlowSets [0.03%]
基于模糊集的流式细胞仪数据分析与可视化方法研究及实现
Felix Offensperger,Markus Joppich,Evi Sinn et al.
Felix Offensperger et al.
The growing availability of high-dimensional, complex datasets demands analysis methods that are both interpretable and flexible. We introduce FlowSets, a novel framework for identifying and analysing flows-fuzzy, interpretable patterns-acr...
Alexander Zee,Dori Z Q Deng,Luciano DiTacchio et al.
Alexander Zee et al.
The mammalian circadian clock is an autoregulatory feedback process that is responsible for homeostasis in mouse livers. These circadian processes are well understood at the gene level; however, they are not well understood at the isoform l...
T-ChroNet: Time-aware chromatin network reconstruction to detect dynamic regulatory programs in longitudinal epigenetic dataset [0.03%]
基于时间感知染色质网络重建的纵向表观遗传数据集中动态调控程序检测方法:T-CHRONET
Stefano Di Giovenale,Ottavio Lischio,Clelia Cortile et al.
Stefano Di Giovenale et al.
Networks are widely applied to investigate relationships among individual components of complex biological systems. Recent application of biological networks, such as gene co-expression networks and gene regulatory networks, has been instru...
Lancet2: Improved and accelerated somatic variant calling with joint multi-sample local assembly graphs [0.03%]
Lancet 2：基于联合多样本局部组装图的改善和加速体细胞变异调用
Rajeeva Lochan Musunuri,Bryan Zhu,Wayne E Clarke et al.
Rajeeva Lochan Musunuri et al.
Here, we present Lancet2, an open-source somatic variant caller designed to improve detection of small variants in short-read sequencing data. Lancet2 introduces significant enhancements, including: (i) Improved variant discovery and genoty...
SpNeigh: spatial neighborhood and differential expression analysis for high-resolution spatial transcriptomics [0.03%]
基于高分辨率空间转录组学的空间邻域和差异表达分析
Jinming Cheng,Pierce Kah Hoe Chow,Nan Liu
Jinming Cheng
Spatial transcriptomics technologies such as Xenium, MERFISH, and Visium HD enable high-resolution profiling of gene expression while preserving tissue architecture. However, most computational methods for spatial analysis do not explicitly...
A birth certificate for data to improve findability, accountability, and traceability [0.03%]
数据的出生证：提升查找性、问责性和可追溯性
Rongbin Li,Avisha Das,Yuntao Yang et al.
Rongbin Li et al.
Data quality is the foundational to scientific research and the rapid advancement of artificial intelligence. Ensuring data quality, provenance, and reproducibility requires robust mechanisms for traceability and accountability from the mom...