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Phylogenetic Analysis That Models Compositional Heterogeneity over the Tree
Molecular sequences in a phylogenetic analysis can differ in composition, and that shows that the process of evolution can change over time. However,...
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A framework for integrating inferred movement behavior into disease risk models
Movement behavior is an important contributor to habitat selection and its incorporation in disease risk models has been somewhat neglected. The...
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Identifying common transcriptome signatures of cancer by interpreting deep learning models
BackgroundCancer is a set of diseases characterized by unchecked cell proliferation and invasion of surrounding tissues. The many genes that have...
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Unraveling the Drivers of Tumorigenesis in the Context of Evolution: Theoretical Models and Bioinformatics Tools
Cancer originates from somatic cells that have accumulated mutations. These mutations alter the phenotype of the cells, allowing them to escape...
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Molecular, Brownian, kinetic and stochastic models of the processes in photosynthetic membrane of green plants and microalgae
The paper presents the results of recent work at the Department of Biophysics of the Biological Faculty, Lomonosov Moscow State University on the...
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AcousticIA, a deep neural network for multi-species fish detection using multiple models of acoustic cameras
Acoustic cameras, or imaging sonars, are high-potential devices for many applications in aquatic ecology, notably for fisheries management and...
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Rhizosphere models: their concepts and application to plant-soil ecosystems
BackgroundThe rhizosphere is the influence-sphere of the root. It is a local ecosystem with complex functions that determine nutrient uptake, cycling...
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The interplay of cells, polymers, and vascularization in three-dimensional lung models and their applications in COVID-19 research and therapy
Millions of people have been affected ever since the emergence of the corona virus disease of 2019 (COVID-19) outbreak, leading to an urgent need for...
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Analysis of asymptomatic Drosophila models for ALS and SMA reveals convergent impact on functional protein complexes linked to neuro-muscular degeneration
BackgroundSpinal Muscular Atrophy (SMA) and Amyotrophic Lateral Sclerosis (ALS) share phenotypic and molecular commonalities, including the fact that...
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Defining landscape-level forest types: application of latent Dirichlet allocation to species distribution models
ContextForest type (FT) classification provides useful information to ecologists and forest managers by representing similar sites based on species...
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Analyzing Photoactivation with Diffusion Models to Study Transport in the Endoplasmic Reticulum Network
Photoactivation is a paradigm consisting in local molecular fluorescent activation by laser illumination in a chosen region (source) while measuring...
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Representing Insect Movement in Agricultural Areas using Spatially Explicit Models
Understanding the movement of organisms is fundamental for comprehending how life thrives and the changes in population dynamics of a species. It is...
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Animal behaviour on the move: the use of auxiliary information and semi-supervision to improve behavioural inferences from Hidden Markov Models applied to GPS tracking datasets
BackgroundState-space models, such as Hidden Markov Models (HMMs), are increasingly used to classify animal tracks into behavioural states....
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Movement models and simulation reveal highway impacts and mitigation opportunities for a metapopulation-distributed species
ContextWhen human-made barriers impact wildlife by limiting habitat connectivity, simulation can reveal movements lost to fragmentation, strategies...
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Multifaceted assessment of stream fish alpha and beta diversity using spatial models
Our understanding of the factors determining stream community assembly has mainly been built upon taxonomic diversity. Additionally, most...
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The Use of Net Energy Intake Models to Predict Microhabitat Selection by Drift-Feeding Fishes: Are Common Assumptions Warranted?
Net energy intake (NEI) models are useful for quantifying mechanisms driving habitat selection in drift-feeding stream fishes; nonetheless, their...
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Generation of multicellular spatiotemporal models of population dynamics from ordinary differential equations, with applications in viral infection
BackgroundThe biophysics of an organism span multiple scales from subcellular to organismal and include processes characterized by spatial...
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Learning protein fitness models from evolutionary and assay-labeled data
Machine learning-based models of protein fitness typically learn from either unlabeled, evolutionarily related sequences or variant sequences with...
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Identification of potential PIM-2 inhibitors via ligand-based generative models, molecular docking and molecular dynamics simulations
Proviral Integrations of Moloney-2 (PIM-2) kinase is a promising target for various cancers and other diseases, and its inhibitors hold potential for...
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Determination of optimal tree height models and calibration designs for Araucaria araucana and Nothofagus pumilio in mixed stands affected to different levels by anthropogenic disturbance in South-Central Chile
Key messageHere, we present a workflow for determining the optimal tree height model and calibration design for forests affected to varying degrees...
