AIMC Topic: Computational Biology

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Integrative transcriptomic analysis identifies shared EndMT-related gene signatures in endometriosis and recurrent miscarriage.

Scientific reports
Endometriosis (EMs) and recurrent miscarriage (RM) represent major reproductive health challenges. This study investigates the involvement of endothelial-mesenchymal transition (EndMT) in these conditions through integrative bioinformatics analysis, ...

Engineering enhanced signal peptides: A high-throughput computational pipeline for optimizing therapeutic protein production in CHO cells.

New biotechnology
Rational design of signal peptides (SPs), crucial for efficient therapeutic protein secretion in Chinese hamster ovary (CHO) cells, remains challenging due to their context-dependency activity. To overcome this limitation and enable the discovery of ...

Unveiling manganese metabolism-related biomarkers in Alzheimer's disease: Insights into diagnosis and therapeutic targets.

Clinica chimica acta; international journal of clinical chemistry
BACKGROUND: Alzheimer's disease (AD), a neurodegenerative disorder with multifactorial etiologies, has been closely associated with disturbances in manganese metabolism. However, its specific biomarkers remain insufficiently characterized. This study...

Germline-aware deep learning models and benchmarks for predicting antibody VH-VL pairing.

mAbs
Variable heavy (VH) and variable light (VL) chain pairing is a critical determinant of antibody diversity, stability, and antigen-binding specificity. Identifying productive VH - VL combinations experimentally is labor-intensive and costly, motivatin...

AIPred: comprehensive prediction and analysis of non-histone acetylation via protein language model and interpretable machine learning.

BMC biology
BACKGROUND: Non-histone lysine acetylation is a widespread protein post-translational modification that regulates almost all key cellular processes, and its dysregulation is closely associated with various human diseases. Precise identification of no...

Spatial domain identification method based on multi-view graph convolutional network and contrastive learning.

PLoS computational biology
Spatial transcriptomics is a rapidly developing field of single-cell genomics that quantitatively measures gene expression while providing spatial information within tissues. A key challenge in spatial transcriptomics is identifying spatially structu...

NoAC: an automatic builder for knowledge bases and query interfaces on genomes of non-model organisms.

Journal of molecular biology
The cost of sequencing a genome has become affordable for many research groups. However, with the growing number of sequenced genomes from non-model organisms, manually building functional genome annotation knowledge databases for each species is no ...

Identification and validation of aryl hydrocarbon receptor-associated hub genes in ulcerative colitis via integrated bioinformatics analysis.

Human genomics
OBJECTIVE: Ulcerative colitis (UC), a chronic inflammatory bowel disease, continues to pose substantial challenges in both diagnosis and treatment. The aryl hydrocarbon receptor (AhR) plays a pivotal role in intestinal immune regulation; however, its...

BiMA-DTI: a bidirectional Mamba-Attention hybrid framework for enhanced drug-target interaction prediction.

BMC biology
BACKGROUND: Predicting drug-target interactions (DTIs) is essential for accelerating drug discovery, yet traditional experimental methods are time-consuming and costly. Computational approaches, especially those using machine learning and deep learni...

DCMF-PPI: a protein-protein interaction predictor based on dynamic condition and multi-feature fusion.

BMC bioinformatics
BACKGROUND: The identification of protein-protein interaction (PPI) plays a crucial role in understanding the mechanisms of complex biological processes. Current research in predicting PPI has shown remarkable progress by integrating protein informat...