AIMC Topic: Software

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Simulation of adaptive immune receptors and repertoires with complex immune information to guide the development and benchmarking of AIRR machine learning.

Nucleic acids research
Machine learning (ML) has shown great potential in the adaptive immune receptor repertoire (AIRR) field. However, there is a lack of large-scale ground-truth experimental AIRR data suitable for AIRR-ML-based disease diagnostics and therapeutics disco...

SCREEN: A Graph-based Contrastive Learning Tool to Infer Catalytic Residues and Assess Enzyme Mutations.

Genomics, proteomics & bioinformatics
The accurate identification of catalytic residues contributes to our understanding of enzyme functions in biological processes and pathways. The increasing number of protein sequences necessitates computational tools for the automated prediction of c...

EnrichDO: a global weighted model for Disease Ontology enrichment analysis.

GigaScience
BACKGROUND: Disease Ontology (DO) has been widely studied in biomedical research and clinical practice to describe the roles of genes. DO enrichment analysis is an effective means to discover associations between genes and diseases. Compared to hundr...

miRStart 2.0: enhancing miRNA regulatory insights through deep learning-based TSS identification.

Nucleic acids research
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by binding to the 3'-untranslated regions of target mRNAs, influencing various biological processes at the post-transcriptional level. Identifying miRNA transcription start si...

UniProt: the Universal Protein Knowledgebase in 2025.

Nucleic acids research
The aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/) is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication, we describe o...

canSAR 2024-an update to the public drug discovery knowledgebase.

Nucleic acids research
canSAR (https://cansar.ai) continues to serve as the largest publicly available platform for cancer-focused drug discovery and translational research. It integrates multidisciplinary data from disparate and otherwise siloed public data sources as wel...

scTWAS Atlas: an integrative knowledgebase of single-cell transcriptome-wide association studies.

Nucleic acids research
Single-cell transcriptome-wide association studies (scTWAS) is a new method for conducting TWAS analysis at the cellular level to identify gene-trait associations with higher precision. This approach helps overcome the challenge of interpreting cell-...

CircaKB: a comprehensive knowledgebase of circadian genes across multiple species.

Nucleic acids research
Circadian rhythms, which are the natural cycles that dictate various physiological processes over a 24-h period, have been increasingly recognized as important in the management and treatment of various human diseases. However, the lack of sufficient...

DDoS attack detection method based on improved convolutional long short-term memory and three-way decision in SDN.

PloS one
Software Defined Networking (SDN) is an emerging network architecture and management method, whose core idea is to separate the network control plane from the data transmission plane. It is precisely because of this characteristic that SDN controller...