Pablo Millan Arias,Niousha Sadjadi,Monireh Safari et al.
Pablo Millan Arias et al.
Motivation: In the global effort to characterize biodiversity, short species-specific genomic sequences known as DNA barcodes enable fine-grained comparisons among organisms within the same kingdom of life. Although machi...
parsomics: a data-driven framework for metagenomics data integration powered by a local relational database [0.03%]
Pedro Sader de Azevedo,Meiski Mariá Vedovatto,Pedro Coelho Gimenes de Freitas et al.
Pedro Sader de Azevedo et al.
Motivation: Metagenomics enables the analysis of complex microbial communities directly from environmental samples, resulting in massive datasets that are processed using multiple tools and workflows. Data integration is ...
Desiderata for a biomedical knowledge network: opportunities, challenges and future directions [0.03%]
Chunlei Wu,Hongfang Liu,Jason Flannick et al.
Chunlei Wu et al.
Motivation: Knowledge graphs (KGs), collectively as a knowledge network, have become critical tools for knowledge discovery in computable and explainable knowledge systems. Due to the semantic and structural complexities ...
Chandana Tennakoon,Thibaut Freville,Tim Downing
Chandana Tennakoon
Motivation: Constructing and studying pangenome variation graphs (PVGs) supports new insights into viral genomic diversity. This is because such pangenomes are less prone to reference bias, which affects mutation detectio...
Pavel Beran,Michael Rost,Kristina Beranová et al.
Pavel Beran et al.
Motivation: Efficient and collision-free hashing of DNA sequences is essential for accuracy and performance in bioinformatics applications such as genome assembly, sequence alignment, and metagenomic classification. Tradi...
Classification of driver and passenger mutations in different cancer types using deep neural networks [0.03%]
基于深度神经网络的不同癌症类型司机突变及乘客突变的分类
Medha Pandey,Anoosha Paruchuri,M Michael Gromiha
Medha Pandey
Motivation: Cancer is driven by genetic changes, known as mutations, that lead to the uncontrolled division of cells. The functional significance of a vast number of these cancer somatic mutations is unknown, and it is on...
SLE-diseaseome: a comprehensive meta-collection of systemic lupus erythematosus relevant functional pathways [0.03%]
SLE疾病组学：系统性红斑狼疮相关功能途径的全面元集合
Daniel Toro-Domínguez,Chang Wang,Iván Ellson-Lancho et al.
Daniel Toro-Domínguez et al.
Motivation: Systemic lupus erythematosus patients exhibit a broad clinical spectrum of manifestations and suffer from high rates of treatment failure. These can be attributed to disease heterogeneity due to differentially...
gLeiden: accelerated community detection algorithms using directed and undirected graphs on GPUs [0.03%]
基于GPU的有向和无向图的加速社区检测算法
Beenish Gul,Maria Murach,Stefan Bekarinov et al.
Beenish Gul et al.
Motivation: Community detection methods are applied to single cell RNA sequencing (i.e. scRNA-seq) and mass cytometry data to efficiently identify major cell types and their subtypes, but their computational demands incre...
A kernel density estimation-based approach for quantifying O-GlcNAcylation dysregulation in cancer from gene expression data [0.03%]
基于核密度估计的癌症O-连接N-乙酰氨基葡萄糖基化失调定量方法研究基因表达数据
Rastko Stojšin,Jinlian Wang,Hongfang Liu
Rastko Stojšin
Motivation: O-GlcNAcylation, a dynamic post-translational modification regulated by O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), influences critical biological processes and is dysregulated in cancers. Direct measure...
optTMT: optimizing any experimental design to minimize false positives caused by TMT reporter ion interference [0.03%]
OptTMT：优化任何实验设计以最小化TMT报告子离子干扰引起的假阳性
Marc-Antoine Gerault
Marc-Antoine Gerault
Summary: To enable multiplexing in large-scale proteomics experiment, TMT-plex isobaric tag has been the gold standard. However, tandem mass tag (TMT) reporter ion interference, also named cross-label isotopic impurity, c...