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Interactions between all pairs of neighboring trees in 16 forests worldwide reveal details of unique ecological processes in each forest, and provide windows into their evolutionary histories

期刊: PLOS COMPUTATIONAL BIOLOGY, 2021; 17 (4)

Author summary Worldwide, ecosystems are collapsing or in danger of collapse, but the precise causes of these collapses are often unknown. Observation......

Pseudocell Tracer-A method for inferring dynamic trajectories using scRNAseq and its application to B cells undergoing immunoglobulin class switch recombination

期刊: PLOS COMPUTATIONAL BIOLOGY, 2021; 17 (5)

Author summary In the past decade advances in computing and single cell sequencing technologies have ushered in a new era of discovery in biology and ......

Systematic comparison and prediction of the effects of missense mutations on protein-DNA and protein-RNA interactions

期刊: PLOS COMPUTATIONAL BIOLOGY, 2021; 17 (4)

The binding affinities of protein-nucleic acid interactions could be altered due to missense mutations occurring in DNA- or RNA-binding proteins, ther......

Evaluation of residue-residue contact prediction methods: From retrospective to prospective

期刊: PLOS COMPUTATIONAL BIOLOGY, 2021; 17 (5)

Sequence-based residue contact prediction plays a crucial role in protein structure reconstruction. In recent years, the combination of evolutionary c......

SCMFMDA: Predicting microRNA-disease associations based on similarity constrained matrix factorization

期刊: PLOS COMPUTATIONAL BIOLOGY, 2021; 17 (7)

miRNAs belong to small non-coding RNAs that are related to a number of complicated biological processes. Considerable studies have suggested that miRN......

Modeling the role of gap junctions between excitatory neurons in the developing visual cortex

期刊: PLOS COMPUTATIONAL BIOLOGY, 2021; 17 (7)

Author summary Gap junctions, or sites of direct electrical connections between neurons, have a significant presence in the cortex, both during develo......

A prediction tool for plaque progression based on patient-specific multi-physical modeling

期刊: PLOS COMPUTATIONAL BIOLOGY, 2021; 17 (3)

Atherosclerotic plaque rupture is responsible for a majority of acute vascular syndromes and this study aims to develop a prediction tool for plaque p......

A hybrid of light-field and light-sheet imaging to study myocardial function and intracardiac blood flow during zebrafish development

期刊: PLOS COMPUTATIONAL BIOLOGY, 2021; 17 (7)

Biomechanical forces intimately contribute to cardiac morphogenesis. However, volumetric imaging to investigate the cardiac mechanics with high tempor......

IUSMMT: Survival mediation analysis of gene expression with multiple DNA methylation exposures and its application to cancers of TCGA

期刊: PLOS COMPUTATIONAL BIOLOGY, 2021; 17 (8)

Effective and powerful survival mediation models are currently lacking. To partly fill such knowledge gap, we particularly focus on the mediation anal......

Tuned inhibition in perceptual decision-making circuits can explain seemingly suboptimal confidence behavior

期刊: PLOS COMPUTATIONAL BIOLOGY, 2021; 17 (3)

Author summary The dominant view of perceptual confidence proposes that confidence optimally reflects the probability that a decision is correct. But ......

Deep template-based protein structure prediction

期刊: PLOS COMPUTATIONAL BIOLOGY, 2021; 17 (5)

Author summary TBM (template-based modeling) is a popular method for protein structure prediction. However, existing methods cannot generate good mode......

Topology-preserving smoothing of retinotopic maps

期刊: PLOS COMPUTATIONAL BIOLOGY, 2021; 17 (8)

Retinotopic mapping, i.e., the mapping between visual inputs on the retina and neuronal activations in cortical visual areas, is one of the central to......

Evaluation and comparison of multi-omics data integration methods for cancer subtyping

期刊: PLOS COMPUTATIONAL BIOLOGY, 2021; 17 (8)

Author summary Cancer is one of the most heterogeneous diseases, characterized by diverse morphological, phenotypic, and genomic profiles between tumo......

Active head rolls enhance sonar-based auditory localization performance

期刊: PLOS COMPUTATIONAL BIOLOGY, 2021; 17 (5)

Animals utilize a variety of active sensing mechanisms to perceive the world around them. Echolocating bats are an excellent model for the study of ac......

Regulating synchronous oscillations of cerebellar granule cells by different types of inhibition

期刊: PLOS COMPUTATIONAL BIOLOGY, 2021; 17 (6)

Synchronous oscillations in neural populations are considered being controlled by inhibitory neurons. In the granular layer of the cerebellum, two maj......

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