Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction [0.03%]
整合蛋白质和DNA嵌入式表示以改善全基因组转录因子结合位点预测
Shreya Basnet,Jianlin Cheng
Shreya Basnet
Transcription factors (TFs) regulate gene expression by binding to specific DNA sites on genome, making accurate TF binding site prediction critical for understanding gene regulation and downstream phenotypes. Almost all current deep learni...
Nuclear genome profiling of two species of Epidendrum (Orchidaceae): genome size, repeatome, and ploidy [0.03%]
石斛属两个物种的核基因组分析：基因组大小、转座子和倍性水平
Miguel A Alcalá-Gaxiola,Gerardo A Salazar,Eric Hágsater et al.
Miguel A Alcalá-Gaxiola et al.
Characterizing genomic properties such as genome size, ploidy level, heterozygosity, and repetitive DNA proportion and composition without relying on genome assembly is crucial for profiling the genomes of non-model species. This study comp...
A multimodal human protein embeddings database: DeepDrug Protein Embeddings Bank (DPEB) [0.03%]
一种用于药物发现的多模态人类蛋白质嵌入数据库：DeepDrug 蛋白质嵌入银行（DPEB）
Md Saiful Islam Sajol,Magesh Rajasekaran,Hayden Gemeinhardt et al.
Md Saiful Islam Sajol et al.
Computationally predicting protein-protein interactions (PPIs) is challenging due to the lack of integrated, multimodal protein representations. DeepDrug Protein Embeddings Bank (DPEB) is a curated collection of 22 043 human proteins that i...
RNAStructuromeDB: a transcriptome-wide database of predicted RNA secondary structures with integrated APIs for functional annotation and RNA-targeted drug discovery [0.03%]
RNA结构组学数据库：具有综合注释和面向RNA靶向药物发现API的预测性转录本二级结构数据库
Abdelraouf O Dapour,Jacopo Manigrasso,Warren B Rouse et al.
Abdelraouf O Dapour et al.
RNA structure critically governs biological function in both physiological and pathological contexts, making high-resolution structural maps essential for RNA-targeted therapeutics. Yet, despite recent advances, well-validated structural ta...
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...