MxlPy-Python package for mechanistic learning and hybrid modelling in life science [0.03%]
MxlPy-用于生命科学机制学习和混合建模的Python包
Marvin van Aalst,Tim Nies,Tobias Pfennig et al.
Marvin van Aalst et al.
Summary: Recent advances in artificial intelligence have accelerated the adoption of machine learning (ML) in biology, enabling powerful predictive models across diverse applications. However, in scientific research, the ...
NifFinder: improved Nif protein prediction using SWeeP vectors and neural networks [0.03%]
改进的Nif蛋白质预测：使用SWeeP向量和神经网络
Bruno Thiago de Lima Nichio,Roxana Beatriz Ribeiro Chaves,Jeroniza Nunes Marchaukoski et al.
Bruno Thiago de Lima Nichio et al.
Motivation: Biological nitrogen fixation is a vital process for global ecosystems and agriculture; however, the diversity and complexity of nif genes present significant challenges for the accurate identification of Nif p...
pyALRA: python implementation of low-rank zero-preserving approximation of single cell RNA-seq [0.03%]
pyALRA：单细胞RNA测序的低阶零保持近似 python实现
Alexandre Lanau,Joshua J Waterfall
Alexandre Lanau
Motivation: Some recently published methods for single-cell RNA-seq preprocessing and correction are not necessarily available in both Python and R, which limits the accessibility of these tools to the wider community. ...
KSMoFinder-knowledge graph embedding of proteins and motifs for predicting kinases of human phosphosites [0.03%]
基于蛋白质和基序的知识图谱嵌入预测磷酸化位点激酶
Manju Anandakrishnan,Karen E Ross,Chuming Chen et al.
Manju Anandakrishnan et al.
Motivation: Protein kinases regulate cellular signaling pathways through a cascade of phosphorylation activity, selectively targeting specific residues on substrate proteins (phosphosites). Determining the characteristics...
MutSeqR: an open source R package for standardized analysis of error-corrected next-generation sequencing data in genetic toxicology [0.03%]
MutSeqR：一种用于遗传毒理学中错误修正的下一代测序数据的标准分析的开源R包
Annette E Dodge,Andrew Williams,Danielle P M LeBlanc et al.
Annette E Dodge et al.
Motivation: Error-corrected next-generation sequencing (ECS) methods are increasingly used to assess mutagenicity and other genetic toxicology endpoints. The lack of open and standardized bioinformatic workflows and tools...
Orthonormal pairwise logratio selection (OPALS) algorithm for compositional data analysis in high dimensions [0.03%]
高维组成数据分析的正交对数比选择（OPALS）算法
Paulína Jašková,Javier Palarea-Albaladejo,Karel Hron et al.
Paulína Jašková et al.
Summary: In the analysis of compositional data, the most fundamental information is conveyed by the pairwise logratios between components. While logratio coordinate representations, such as balances and pivot coordinates,...
SiaScoreNet: a siamese neural network-based model integrating prediction scores for HLA-peptide interaction prediction [0.03%]
基于孪生神经网络的HLA-肽相互作用预测积分打分模型Siascorenet
Mahsa Saadat,Fatemeh Zare-Mirakabad,Milad Besharatifard
Mahsa Saadat
Motivation: Cancer immunotherapy uses the immune system to recognize and eliminate tumor cells by presenting tumor antigens through Human Leukocyte Antigen (HLA) molecules. Accurate prediction of HLA-peptide interactions ...
Retention order prediction of peptides containing non-proteinogenic amino acids [0.03%]
非蛋白氨基酸修饰肽的滞留顺序预测
Shohei Nakamukai,Eisuke Hayakawa,Tetsuya Mori et al.
Shohei Nakamukai et al.
Motivation: Peptides containing non-proteinogenic amino acids (PNPAs) are promising targets in drug development for their unique pharmacological properties. The lack of their mass spectra or retention data has been hinder...
BacExplorer: an integrated platform for de novo bacterial genome annotation [0.03%]
BacExplorer：一个从头开始的细菌基因组注释集成平台
Grete Francesca Privitera,Adriana Antonella Cannata,Floriana Campanile et al.
Grete Francesca Privitera et al.
Motivation: High-throughput sequencing (HTS) has become an integral part of routine analysis for microbiologists. The process of sequencing dozens of samples generates vast amounts of data that cannot be annotated manuall...
CoRTE: a web-service for constructing temporal networks from genotype-tissue expression data [0.03%]
基于基因型-组织表达数据的时变网络构建的网络服务系统CoRTE
Pietro Cinaglia,Mario Cannataro
Pietro Cinaglia
Motivation: A comprehensive and in-depth deciphering of the dynamics concerning gene expressions is essential for understanding intricate biological mechanisms; for instance, the latter can be effectively addressed via ne...