NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data [0.03%]
NAP：一个使用纳米孔测序数据进行跨领域微生物组分析的开源工作流程
Luke B Jones,Stefan Bagby
Luke B Jones
Background: Nanopore sequencing offers a cost-effective and portable platform for microbiome analysis, but amplicon-based approaches remain limited by higher sequencing error rates and a lack of workflows tailored to mixe...
SurvGME: an R package for survival analysis with graphical and measurement error models [0.03%]
SurvGME：一个用于生存分析的R包，结合图形和测量误差模型
Li-Pang Chen,Grace Y Yi
Li-Pang Chen
Background: Analyzing time-to-event data, such as cancer patient survival time, is a central task in survival analysis. Numerous modeling methods and inference strategies have been developed for various application settin...
SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint [0.03%]
基于本体相似性的贝叶斯网络推断方法研究基因调控网络inferencing_gene_regulatory_network_using_gene_ontology_similarity-based_bayesian_network_method
Maryam Shahdoust,Rosa Aghdam,Mehdi Sadeghi
Maryam Shahdoust
Gene regulatory network (GRN) reconstruction is a fundamental challenge in computational biology, and is crucial for understanding gene interactions. In this study, we aim to incorporate Gene Ontology (GO) similarities into the construction...
Dual channel drug-drug interactions extraction based on cross attention [0.03%]
基于交叉注意力的双通道药物相互作用提取方法研究
Yaxun Jia,Zhu Yuan,Yunchao Gong et al.
Yaxun Jia et al.
Drug-drug interactions (DDIs) play a critical role in several biomedical applications, particularly in pharmacovigilance. While neural networks have shown promise in DDI extraction, existing methods often overlook salient information. To ad...
FeSseqdb: a curated sequence-level database and interpretable machine learning framework for identifying iron-sulfur proteins [0.03%]
FeSseqdb：用于识别铁硫蛋白的序列水平数据库和可解释机器学习框架
Jiyeon Min,Bernard R Brooks,Muhamed Amin
Jiyeon Min
Iron-sulfur (Fe-S) clusters are ubiquitous cofactors in metalloproteins, supporting essential biological functions such as electron transfer, enzymatic catalysis, and metabolic regulation. Despite their importance, large-scale identificatio...
Franco Poma-Soto,Hanne Van Droogenbroeck,Brecht Soulliaert et al.
Franco Poma-Soto et al.
Background: DNA barcoding enables multiplexed identification of biomolecules in pooled sequencing experiments, with broad applications including spatial transcriptomics. Photolithographic synthesis of high-density barcode...
pyVIPER: a fast and scalable Python package for protein activity estimation and master regulator analysis of single-cell RNA sequencing data [0.03%]
pyVIPER：一个快速且可扩展的Python包，用于单细胞RNA测序数据的蛋白质活性估算和主调节因子分析
Alexander L E Wang,Luca Zanella,Zizhao Lin et al.
Alexander L E Wang et al.
Single-cell sequencing has revolutionized biomedical research by offering insights into cellular heterogeneity at unprecedented resolution. Yet, the low signal-to-noise ratio characteristic of single-cell RNA sequencing (scRNA-seq) challeng...
PAVSAT: an automated blood vessel analysis tool using deep learning-based segmentation and image processing [0.03%]
基于深度学习的分割和图像处理的自动化血管分析工具(PAVSAT)
Ryozo Ishida,Naoi Hosoe,Anna Shimizu et al.
Ryozo Ishida et al.
Background: Accurate blood vessel morphology analysis is essential for understanding vascular system development and pathology. Although advanced imaging technologies. have enabled the rapid acquisition of complex vascula...
CAGNet: a structure-aware clustering-alternated graph network for cell-cell interaction inference in spatial transcriptomics [0.03%]
一种基于结构感知的聚类交替图网络，用于空间转录组学中细胞间相互作用推断(CAGNet)
Han Ma,Xin Zhang,Hang Chen et al.
Han Ma et al.
Motivation: Understanding cell-cell interactions (CCIs) in spatial transcriptomics is crucial for uncovering the spatial organization and functional heterogeneity of tissues. However, existing graph-based models typically...
Accelign: a GPU-based library for accelerating pairwise sequence alignment [0.03%]
基于GPU的加速成对序列比对库Accelerign
Felix Kallenborn,Fawaz Dabbaghie,Martin Steinegger et al.
Felix Kallenborn et al.
Background: The continually increasing volume of sequence data results in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments based on dynamic programming is an important part ...