AIMC Topic: Mice
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Modeling transcriptional regulation of model species with deep learning.
Genome research
Apr 22, 2021
To enable large-scale analyses of transcription regulation in model species, we developed DeepArk, a set of deep learning models of the -regulatory activities for four widely studied species: , , , and DeepArk accurately predicts the presence of tho...
Machine learning-assisted high-content analysis of pluripotent stem cell-derived embryos in vitro.
Stem cell reports
Apr 22, 2021
Stem cell-based embryo models by cultured pluripotent and extra-embryonic lineage stem cells are novel platforms to model early postimplantation development. We showed that induced pluripotent stem cells (iPSCs) could form ITS (iPSCs and trophectoder...
Iterative single-cell multi-omic integration using online learning.
Nature biotechnology
Apr 19, 2021
Integrating large single-cell gene expression, chromatin accessibility and DNA methylation datasets requires general and scalable computational approaches. Here we describe online integrative non-negative matrix factorization (iNMF), an algorithm for...
Exploring photoacoustic spectroscopy-based machine learning together with metabolomics to assess breast tumor progression in a xenograft model ex vivo.
Laboratory investigation; a journal of technical methods and pathology
Apr 19, 2021
In the current study, a breast tumor xenograft was established in athymic nude mice by subcutaneous injection of the MCF-7 cell line and assessed the tumor progression by photoacoustic spectroscopy combined with machine learning tools. The advancemen...
Real-Time Closed-Loop Feedback in Behavioral Time Scales Using DeepLabCut.
eNeuro
Apr 16, 2021
Computer vision approaches have made significant inroads into offline tracking of behavior and estimating animal poses. In particular, because of their versatility, deep-learning approaches have been gaining attention in behavioral tracking without a...
Uncertainty measurement of radiomics features against inherent quantum noise in computed tomography imaging.
European radiology
Apr 14, 2021
OBJECTIVES: Quantum noise is a random process in X-ray-based imaging systems. We addressed and measured the uncertainty of radiomics features against this quantum noise in computed tomography (CT) images.
A deep learning approach to identifying immunogold particles in electron microscopy images.
Scientific reports
Apr 8, 2021
Electron microscopy (EM) enables high-resolution visualization of protein distributions in biological tissues. For detection, gold nanoparticles are typically used as an electron-dense marker for immunohistochemically labeled proteins. Manual annotat...
Deep Convolutional and Recurrent Neural Networks for Cell Motility Discrimination and Prediction.
IEEE/ACM transactions on computational biology and bioinformatics
Apr 8, 2021
Cells in culture display diverse motility behaviors that may reflect differences in cell state and function, providing motivation to discriminate between different motility behaviors. Current methods to do so rely upon manual feature engineering. How...
Neurovascular multiparametric MRI defines epileptogenic and seizure propagation regions in experimental mesiotemporal lobe epilepsy.
Epilepsia
Apr 5, 2021
OBJECTIVE: Improving the identification of the epileptogenic zone and associated seizure-spreading regions represents a significant challenge. Innovative brain-imaging modalities tracking neurovascular dynamics during seizures may provide new disease...
Analysis of ultrasonic vocalizations from mice using computer vision and machine learning.
eLife
Mar 31, 2021
Mice emit ultrasonic vocalizations (USVs) that communicate socially relevant information. To detect and classify these USVs, here we describe VocalMat. VocalMat is a software that uses image-processing and differential geometry approaches to detect U...
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