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Mammals

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Automated identification of protein expression intensity and classification of protein cellular locations in mouse brain regions from immunofluorescence images.

Medical & biological engineering & computing
Knowledge of protein expression in mammalian brains at regional and cellular levels can facilitate understanding of protein functions and associated diseases. As the mouse brain is a typical mammalian brain considering cell type and structure, severa...

Single-Cell Radiation Response Scoring with the Deep Learning Algorithm CeCILE 2.0.

Cells
External stressors, such as ionizing radiation, have massive effects on life, survival, and the ability of mammalian cells to divide. Different types of radiation have different effects. In order to understand these in detail and the underlying mecha...

Mechanistic Model-Driven Biodesign in Mammalian Synthetic Biology.

Methods in molecular biology (Clifton, N.J.)
Mathematical modeling plays a vital role in mammalian synthetic biology by providing a framework to design and optimize design circuits and engineered bioprocesses, predict their behavior, and guide experimental design. Here, we review recent models ...

An integrated passive acoustic monitoring and deep learning pipeline for black-and-white ruffed lemurs (Varecia variegata) in Ranomafana National Park, Madagascar.

American journal of primatology
The urgent need for effective wildlife monitoring solutions in the face of global biodiversity loss has resulted in the emergence of conservation technologies such as passive acoustic monitoring (PAM). While PAM has been extensively used for marine m...

DL-SPhos: Prediction of serine phosphorylation sites using transformer language model.

Computers in biology and medicine
Serine phosphorylation plays a pivotal role in the pathogenesis of various cellular processes and diseases. Roughly 81% of human diseases have links to phosphorylation, and an overwhelming 86.4% of protein phosphorylation takes place at serine residu...

Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation.

Nature cell biology
In the mammalian liver, hepatocytes exhibit diverse metabolic and functional profiles based on their location within the liver lobule. However, it is unclear whether this spatial variation, called zonation, is governed by a well-defined gene regulato...

filoVision - using deep learning and tip markers to automate filopodia analysis.

Journal of cell science
Filopodia are slender, actin-filled membrane projections used by various cell types for environment exploration. Analyzing filopodia often involves visualizing them using actin, filopodia tip or membrane markers. Due to the diversity of cell types th...

Machine-learning based detection of marine mammal vocalizations in snapping-shrimp dominated ambient noise.

Marine environmental research
Passive acoustics is an effective method for monitoring marine mammals, facilitating both detection and population estimation. In warm tropical waters, this technique encounters challenges due to the high persistent level of ambient impulsive noise o...

A combined deep learning framework for mammalian m6A site prediction.

Cell genomics
N-methyladenosine (m6A) is the most prevalent chemical modification in eukaryotic mRNAs and plays key roles in diverse cellular processes. Precise localization of m6A sites is thus critical for characterizing the functional roles of m6A in various co...

Mammalian piRNA target prediction using a hierarchical attention model.

BMC bioinformatics
BACKGROUND: Piwi-interacting RNAs (piRNAs) are well established for monitoring and protecting the genome from transposons in germline cells. Recently, numerous studies provided evidence that piRNAs also play important roles in regulating mRNA transcr...