AIMC Topic: Computational Biology

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MuCST: restoring and integrating heterogeneous morphology images and spatial transcriptomics data with contrastive learning.

Genome medicine
Spatially resolved transcriptomics (SRT) simultaneously measure spatial location, histology images, and transcriptional profiles of cells or regions in undissociated tissues. Integrative analysis of multi-modal SRT data holds immense potential for un...

Machine learning methods to study sequence-ensemble-function relationships in disordered proteins.

Current opinion in structural biology
Recent years have seen tremendous developments in the use of machine learning models to link amino-acid sequence, structure, and function of folded proteins. These methods are, however, rarely applicable to the wide range of proteins and sequences th...

Molecular structure and mechanism of protein MSMB, TPPP3, SPI1: Construction of novel 4 pancreatic cancer-related protein signatures model based on machine learning.

International journal of biological macromolecules
The high mortality rate of pancreatic cancer is closely related to its inconspicuous early symptoms and difficult diagnosis. In recent years, with the rapid development of proteomics and bioinformatics, the use of machine learning technology to analy...

Advancing the Accuracy of Anti-MRSA Peptide Prediction Through Integrating Multi-Source Protein Language Models.

Interdisciplinary sciences, computational life sciences
The emergence of methicillin-resistant Staphylococcus aureus (MRSA) as a recognized cause of community-acquired and hospital infections has brought about a need for the efficient and accurate identification of peptides with anti-MRSA properties in dr...

scMDCL: A Deep Collaborative Contrastive Learning Framework for Matched Single-Cell Multiomics Data Clustering.

Journal of chemical information and modeling
Single-cell multiomics clustering integrates multiple omics data to analyze cellular heterogeneity and is crucial for uncovering complex biological processes and disease mechanisms. However, existing matched single-cell multiomics clustering methods ...

RBPsuite 2.0: an updated RNA-protein binding site prediction suite with high coverage on species and proteins based on deep learning.

BMC biology
BACKGROUND: RNA-binding proteins (RBPs) play crucial roles in many biological processes, and computationally identifying RNA-RBP interactions provides insights into the biological mechanism of diseases associated with RBPs.

Predicting the diversity of photosynthetic light-harvesting using thermodynamics and machine learning.

PLoS computational biology
Oxygenic photosynthesis is responsible for nearly all biomass production on Earth, and may have been a prerequisite for establishing a complex biosphere rich in multicellular life. Life on Earth has evolved to perform photosynthesis in a wide range o...

Harnessing Computational Strategies to Overcome Challenges in mRNA Vaccines.

Physiology (Bethesda, Md.)
In recent years, the introduction of mRNA vaccines for SARS-CoV2 and respiratory syncytial virus (RSV) has highlighted the success of the mRNA technology platform. Designing mRNA sequences involves multiple components and requires balancing several p...

Biochemical Characterization of Disease-Associated Variants of Human Ornithine Transcarbamylase.

ACS chemical biology
Human ornithine transcarbamylase deficiency (OTCD) is the most common ureagenesis disorder in the world. OTCD is an X-linked genetic deficiency in which patients experience hyperammonemia to varying degrees depending on the severity of the genetic mu...

Cancer Drug Sensitivity Prediction Based on Deep Transfer Learning.

International journal of molecular sciences
In recent years, many approved drugs have been discovered using phenotypic screening, which elaborates the exact mechanisms of action or molecular targets of drugs. Drug susceptibility prediction is an important type of phenotypic screening. Large-sc...