AIMC Topic: Computational Biology
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Machine learning-based prediction reveals kinase MAP4K4 regulates neutrophil differentiation through phosphorylating apoptosis-related proteins.
PLoS computational biology
Mar 17, 2025
Neutrophils, an essential innate immune cell type with a short lifespan, rely on continuous replenishment from bone marrow (BM) precursors. Although it is established that neutrophils are derived from the granulocyte-macrophage progenitor (GMP), the ...
Pre-training artificial neural networks with spontaneous retinal activity improves motion prediction in natural scenes.
PLoS computational biology
Mar 17, 2025
The ability to process visual stimuli rich with motion represents an essential skill for animal survival and is largely already present at the onset of vision. Although the exact mechanisms underlying its maturation remain elusive, spontaneous activi...
A critical address to advancements and challenges in computational strategies for structural prediction of protein in recent past.
Computational biology and chemistry
Mar 16, 2025
Protein structure prediction has undergone significant advancements, driven by the limitations of experimental techniques like X-ray crystallography, NMR, and cryo-EM, which are costly and time-consuming. To bridge the gap between protein sequences a...
MuCST: restoring and integrating heterogeneous morphology images and spatial transcriptomics data with contrastive learning.
Genome medicine
Mar 13, 2025
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
Mar 12, 2025
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
Mar 12, 2025
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
Mar 11, 2025
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
Mar 11, 2025
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
Mar 11, 2025
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
Mar 11, 2025
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...
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