AIMC Topic: Computational Biology

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MLGCN-Driver: a cancer driver gene identification method based on multi-layer graph convolutional neural network.

BMC bioinformatics
BACKGROUND: The progression of cancer is driven by the accumulation of mutations in driver genes. Many researches promote to identify cancer driver genes. However, most of them ignore the high-order features in the network.

Boosting K-nearest neighbor regression performance for longitudinal data through a novel learning approach.

BMC bioinformatics
BACKGROUND: Longitudinal studies often require flexible methodologies for predicting response trajectories based on time-dependent and time-independent covariates. To address the complexities of longitudinal data, this study proposes a novel extensio...

SpaCross deciphers spatial structures and corrects batch effects in multi-slice spatially resolved transcriptomics.

Communications biology
Spatially Resolved Transcriptomics (SRT) has revolutionized tissue architecture analysis by integrating gene expression with spatial coordinates. However, existing spatial domain identification methods struggle with unsupervised learning constraints,...

SARST2 high-throughput and resource-efficient protein structure alignment against massive databases.

Nature communications
The flood of protein structural Big Data is coming. With the belief that biotech researchers deserve powerful analysis engines to overcome the challenge of rapidly increasing computational demands, we are devoted to developing efficient protein struc...

MEMO-Stab2: Multi-View Sequence-Based Deep Learning Framework for Predicting Mutation-Induced Stability Changes in Transmembrane Proteins.

Journal of chemical information and modeling
Accurately predicting the impact of point mutations on protein thermodynamic stability is essential for understanding structure-function relationships and guiding protein design. This challenge is particularly acute for transmembrane proteins (TMPs),...

A deep learning model for epidermal growth factor receptor prediction using ensemble residual convolutional neural network.

Scientific reports
Epidermal growth factor receptor (EGFR) overexpression is a key oncogenic driver in breast cancer, making it an important therapeutic target. Conventional approaches for EGFR identification, including motif- and homology-based methods, often lack acc...

A comprehensive application of FiveFold for conformation ensemble-based protein structure prediction.

Scientific reports
The emergence of artificial intelligence in protein structure prediction has significantly advanced our understanding of protein folding. Yet, challenges remain in accurately modeling intrinsically disordered proteins (IDPs) and capturing conformatio...

DeepMaT: Prediction of Target Peptide Classification and Cleavage Site by Combining Mamba2 and Multiple Attention Mechanisms.

Journal of chemical information and modeling
Signal peptides and transit peptides are essential for directing mature proteins to their proper cellular locations, particularly through cleavage following transport. Although various prediction tools achieve strong performance in identifying and cl...

AI cancer driver mutation predictions are valid in real-world data.

Nature communications
Characterizing and validating which mutations influence development of cancer is challenging. Artificial intelligence (AI) has delivered significant advances in protein structure prediction, but its utility for identifying cancer drivers is less expl...

Computational pathology in precision oncology: Evolution from task-specific models to foundation models.

Chinese medical journal
With the rapid development of artificial intelligence, computational pathology has been seamlessly integrated into the entire clinical workflow, which encompasses diagnosis, treatment, prognosis, and biomarker discovery. This integration has signific...