A dual approach to evaluate the performance of RNA-Seq data analysis pipelines with weak signals [0.03%]
一种评估RNA测序数据分析流程中弱信号性能的双管齐下方法
Malek Baroudi,Fadoum Ousmane Ly,Elen Goujon et al.
Malek Baroudi et al.
Purpose: In this study, we evaluated 90 bioinformatics pipelines using RNA-Seq datasets from Rats, Zebrafish and Mice. The analysis was conducted in the context of weak signals, including exposure to metallic particles (t...
LiraSearch-ultrafast ligand shape and electrostatic matching server [0.03%]
LiraSearch-超快配体形状和静电匹配服务器
Rinaldo W Montalvão,Simon Bray,Marcos Veríssimo-Alves et al.
Rinaldo W Montalvão et al.
Summary: Spherical harmonics have emerged as a powerful framework for molecular shape and electrostatic comparison in ligand-based virtual screening. Here, we present LiraSearch, a high-performance implementation and web ...
Haplo2D6: a web-based tool for automated CYP2D6 haplotype and phenotype inference [0.03%]
Haplo2D6：一个用于自动推断CYP2D6基因型和表型的网络工具
Maria Carolina Silva de Barros Puça,Diego Mariano,Yanka Evellyn Alves Rodrigues Salazar et al.
Maria Carolina Silva de Barros Puça et al.
Motivation: Haplo2D6 is a free, browser-based tool that automates the translation of CYP2D6 genotype data into metabolizer phenotypes. Using haplotype reconstruction with the PHASE algorithm, integration of copy number va...
Transformer-based operon prediction using textual representations of gene pairs [0.03%]
基于变压器的 operon 预测利用基因对的文本表示
Rida Assaf,Basel Fakhri
Rida Assaf
Motivation: Operons are fundamental units of gene regulation in bacteria and can provide valuable insights into genome organization, co-expression, and functional relationships between genes. Computational prediction of o...
InterProScan 6: a modern large-scale protein function annotation pipeline [0.03%]
InterProScan 6：一个现代的蛋白质功能注释流程
Matthias Blum,Emma Hobbs,Laise Florentino et al.
Matthias Blum et al.
Motivation: InterProScan is a widely used software package for large-scale protein function classification and an essential component of UniProt, Ensembl and MGnify Genomes large-scale annotation pipelines. For the past 1...
Development and comparison of evaluation metrics for batch correction reveals performance differences [0.03%]
开发和比较批量校正的评估指标并揭示其性能差异
Aleksi Laiho,Marjaana Laitinen,Liisa Holm et al.
Aleksi Laiho et al.
Motivation: Batch effects are a common challenge in the analysis of biological datasets, particularly RNA-seq data. Although numerous methods exist to correct batch effects, their comparative evaluation has received limit...
CardioVar: a machine learning framework for pathogenicity prediction of cardiomyopathy genetic variants [0.03%]
CardioVar：一种用于预测心肌病基因变异致病性的机器学习框架
Nabras Al-Mahrami,Aaisha Albalushi,Fahad Al Hattali et al.
Nabras Al-Mahrami et al.
Motivation: CardioVar is a machine learning framework developed to predict the pathogenicity of cardiomyopathy-associated genetic variants, providing a rapid and disease-focused classification score to support variant int...
Jason Liang,Chloe Wang,Lei Zhou
Jason Liang
Motivation: Serine protease inhibitors (serpins) are a large family of proteins conserved in all animals. A prominent enigma about serpins is that, while members of this family share an archetypal folding scheme, individu...
Vijini Mallawaarachchi,George Bouras,Ryan R Wick et al.
Vijini Mallawaarachchi et al.
Motivation: Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap information, facilitating the assembler in constructing longer genomic fragmen...
The impact of biologically relevant negative samples on machine learning-based B-cell epitope prediction for Influenza A [0.03%]
生物相关阴性样本对机器学习基于的流感病毒A型B细胞表位预测的影响研究
Claudia Pareja-Barrueto,Jose Reyes-Suarez,Felipe Del Canto et al.
Claudia Pareja-Barrueto et al.
Motivation: Predicting linear B-cell epitopes remains a major challenge in immunoinformatics, particularly for rapidly evolving viruses such as Influenza A. Many existing predictors rely on heterogeneous training datasets...