Predicting isocitrate dehydrogenase mutation status in acute myeloid leukemia from gene expression profiles by machine learning [0.03%]
基于基因表达谱用机器学习预测急性髓系白血病的异柠檬酸脱氢酶突变状态
Ina Jung,Anne-Laure Vitte,Florent Chuffart et al.
Ina Jung et al.
We developed machine-learning models to predict isocitrate dehydrogenase (IDH) mutation status in acute myeloid leukemia (AML) from gene expression profiles and to reconstruct missing IDH annotations across public datasets. Transcriptomic d...
TSProm: deep learning framework to predict tissue-specific regulatory logic [0.03%]
基于深度学习的预测组织特异性调控逻辑框架
Pallavi Surana,Pratik Dutta,Nimisha Papineni et al.
Pallavi Surana et al.
Characterizing tissue-specific (TSp) gene expression is crucial for understanding development and disease; however, traditional expression-based methods often overlook the latent "regulatory grammar" embedded in non-coding DNA, particularly...
Mitsu Raval,Yancheng Zhou,Miki Lynch et al.
Mitsu Raval et al.
Protein translation is a highly regulated process influenced by multiple factors at the initiation, elongation, and termination stages. One notable regulatory element of the ribosome is the CAR interaction surface, a three-residue motif in ...
TF-DWGNet: a directed weighted graph neural network with tensor fusion for multi-omics cancer subtype classification [0.03%]
基于张量融合的有向加权图神经网络的癌症亚型分类方法
Tiantian Yang,Zhiqian Chen
Tiantian Yang
Integration and analysis of multi-omics data provide valuable insights for improving cancer subtype classification. However, such data are inherently heterogeneous, high-dimensional, and exhibit complex intra- and inter-modality dependencie...
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...