AIMC Topic: Computational Biology

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Predicting transcriptional changes induced by molecules with MiTCP.

Briefings in bioinformatics
Studying the changes in cellular transcriptional profiles induced by small molecules can significantly advance our understanding of cellular state alterations and response mechanisms under chemical perturbations, which plays a crucial role in drug di...

Spatially aligned graph transfer learning for characterizing spatial regulatory heterogeneity.

Briefings in bioinformatics
Spatially resolved transcriptomics (SRT) technologies facilitate the exploration of cell fates or states within tissue microenvironments. Despite these advances, the field has not adequately addressed the regulatory heterogeneity influenced by microe...

Therapeutic gene target prediction using novel deep hypergraph representation learning.

Briefings in bioinformatics
Identifying therapeutic genes is crucial for developing treatments targeting genetic causes of diseases, but experimental trials are costly and time-consuming. Although many deep learning approaches aim to identify biomarker genes, predicting therape...

scHiClassifier: a deep learning framework for cell type prediction by fusing multiple feature sets from single-cell Hi-C data.

Briefings in bioinformatics
Single-cell high-throughput chromosome conformation capture (Hi-C) technology enables capturing chromosomal spatial structure information at the cellular level. However, to effectively investigate changes in chromosomal structure across different cel...

scGO: interpretable deep neural network for cell status annotation and disease diagnosis.

Briefings in bioinformatics
Machine learning has emerged as a transformative tool for elucidating cellular heterogeneity in single-cell RNA sequencing. However, a significant challenge lies in the "black box" nature of deep learning models, which obscures the decision-making pr...

Techniques for learning and transferring knowledge for microbiome-based classification and prediction: review and assessment.

Briefings in bioinformatics
The volume of microbiome data is growing at an exponential rate, and the current methodologies for big data mining are encountering substantial obstacles. Effectively managing and extracting valuable insights from these vast microbiome datasets has e...

A deep learning feature importance test framework for integrating informative high-dimensional biomarkers to improve disease outcome prediction.

Briefings in bioinformatics
Many human diseases result from a complex interplay of behavioral, clinical, and molecular factors. Integrating low-dimensional behavioral and clinical features with high-dimensional molecular profiles can significantly improve disease outcome predic...

VirDetect-AI: a residual and convolutional neural network-based metagenomic tool for eukaryotic viral protein identification.

Briefings in bioinformatics
This study addresses the challenging task of identifying viruses within metagenomic data, which encompasses a broad array of biological samples, including animal reservoirs, environmental sources, and the human body. Traditional methods for virus ide...

Deep learning in integrating spatial transcriptomics with other modalities.

Briefings in bioinformatics
Spatial transcriptomics technologies have been extensively applied in biological research, enabling the study of transcriptome while preserving the spatial context of tissues. Paired with spatial transcriptomics data, platforms often provide histolog...

Integrating scRNA-seq and scATAC-seq with inter-type attention heterogeneous graph neural networks.

Briefings in bioinformatics
Single-cell multi-omics techniques, which enable the simultaneous measurement of multiple modalities such as RNA gene expression and Assay for Transposase-Accessible Chromatin (ATAC) within individual cells, have become a powerful tool for decipherin...