Whole-genome sequencing with AVITI and NovaSeq X Plus reveals comparable performance with contextual biases [0.03%]
基于AVITI和NovaSeq X Plus的全基因组测序具有相当的性能和上下文偏倚
Pontus Höjer,Johannes Alneberg,Pär Lundin et al.
Pontus Höjer et al.
Element Biosciences' avidity sequencing has emerged as a competing technology to Illumina's short-read sequencing platform. Prior benchmarks of avidity sequencing have not included the latest Illumina NovaSeq X/X Plus instruments with XLEAP...
From gene correlations to cell clusters: COTAN improved scRNA-seq analysis [0.03%]
从基因相关性到细胞聚类：COTAN 改进 scRNA-seq 分析
Silvia Giulia Galfrè,Marco Fantozzi,Alina Sîrbu et al.
Silvia Giulia Galfrè et al.
Single-cell RNA-sequencing (scRNA-seq) now routinely profiles thousands of individual transcriptomes, yet no consensus pipeline exists for either laboratory protocol or downstream analysis. Droplet-based datasets are especially challenging:...
Novel examples of NMD escape through alternative intronic polyadenylation [0.03%]
通过替代内含子多聚腺苷酸化逃逸NMD的新例证
Maria Vlasenok,Antonina Kuznetsova,Dmitry A Skvortsov et al.
Maria Vlasenok et al.
The nonsense-mediated messenger RNA decay (NMD) surveillance system detects and selectively eliminates transcripts with premature stop codons. A stop codon is considered premature if it is followed by an exon-exon junction >50 nucleotides d...
Polina Bombina,Reginald L McGee Ii,Jake Reed et al.
Polina Bombina et al.
Understanding biological pathways requires more than static diagrams. We present WayFindR, an R package that converts pathway data from WikiPathways and KEGG into graph structures using igraph, enabling computational analysis of regulatory ...
The use of Benzonase to produce ribosome footprints simplifies translational levels quantification by Ribo-seq [0.03%]
Benzonase在Ribo-seq中生成核糖体 footprint图谱从而简化翻译水平的定量
Guillermo Eastman,George S Bloom,José R Sotelo-Silveira
Guillermo Eastman
Gene expression quantification through genomics methods is crucial for understanding diverse biological contexts. Among these methods, ribosome profiling (Ribo-seq) stands out as a valuable tool for uncovering post-transcriptional gene expr...
Beyond chromatin accessibility: bulk ATAC-seq as an integrative assay to portray genomes and epigenomes [0.03%]
超越染色质开放性：bulk ATAC-seq作为综合分析基因组和表观基因组的手段
Islem Toumi,Chaimae Kham,Lucille Stuani et al.
Islem Toumi et al.
Assay for transposase-accessible chromatin using sequencing (ATAC-seq) is a cornerstone for epigenomic profiling, yet its potential for genomic characterization remains poorly explored. Here, we systematically benchmarked bulk ATAC-seq agai...
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...