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Computational Biology

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Generative AI extracts ecological meaning from the complex three dimensional shapes of bird bills.

PLoS computational biology
Data on the three dimensional shape of organismal morphology is becoming increasingly available, and forms part of a new revolution in high-throughput phenomics that promises to help understand ecological and evolutionary processes that influence phe...

Predictive reward-prediction errors of climbing fiber inputs integrate modular reinforcement learning with supervised learning.

PLoS computational biology
Although the cerebellum is typically associated with supervised learning algorithms, it also exhibits extensive involvement in reward processing. In this study, we investigated the cerebellum's role in executing reinforcement learning algorithms, wit...

Machine learning-based prediction reveals kinase MAP4K4 regulates neutrophil differentiation through phosphorylating apoptosis-related proteins.

PLoS computational biology
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
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...

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...

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...

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...

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...