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PLoS Computational Biology
Scopus
ISSN 1553-734X · Public Library of Science (PLoS) · 25,956 articles in the index
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Journal Article
Overcoming the widespread flaws in the annotation of vertebrate selenoprotein genes in public databases.
Genome annotations provide the essential framework for genomic analyses, capturing our current knowledge of gene structure and function as inferred from computational predictions and experimental evidence. Even as automated annotation pipelines become more sophisticated, their accuracy in…
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Journal Article
TCR2HLA: Calibrated inference of HLA genotypes from TCR repertoires enables identification of immunologically relevant metaclonotypes.
T cell receptors (TCRs) recognize peptides presented by polymorphic human leukocyte antigen (HLA) molecules, but HLA genotype data are often missing from TCR repertoire sequencing studies. To address this, we developed TCR2HLA, an open-source tool that infers HLA genotypes from TCRβ repertoires…
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Journal Article
Learning genetic perturbation effects with variational causal inference.
Advances in sequencing technologies have enhanced the understanding of gene regulation in cells. In particular, Perturb-seq has enabled high-resolution profiling of the transcriptomic response to genetic perturbations at the single-cell level. This understanding has implications in functional…
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Journal Article
DSCA-HLAII: A dual-stream cross-attention model for predicting peptide-HLA class II interaction and presentation.
MotivationThe interaction between peptides and human leukocyte antigen class II (HLA-II) molecules plays a pivotal role in adaptive immune responses, as HLA-II mediates the recognition of exogenous antigens and initiates T cell activation through peptide presentation. Accurate prediction of…
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Journal Article
CellPredX, a computational framework for cross-data type, cross-sample, and cross-protocol cell type annotation through domain adaptation and deep metric learning.
Accurate cell type annotation is fundamental to single-cell analysis, yet remains challenging across heterogeneous datasets and modalities. In particular, transferring labels between scRNA-seq and scATAC-seq data poses unique difficulties due to discrepancies in sequencing protocols and feature…
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Journal Article
TEPEAK: A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations.
Transposable elements (TEs) replicate within genomes and are an active source of genetic variability in many species. Their role in immunity and domestication underscores their biological significance. However, analyzing TEs, especially within lesser-studied and wild populations, poses considerable…
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Journal Article
GAN-enhanced machine learning and metabolic modeling identify reprogramming in pancreatic cancer.
Pancreatic ductal adenocarcinoma is one of the deadliest forms of cancer, presenting significant clinical challenges due to poor prognosis and limited treatment options. Understanding the metabolic reprogramming that drives this disease is crucial for identifying new therapeutic targets and…
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Journal Article
Beyond the first glance: How human presence enhances visual entropy and promotes spatial learning.
Spatial learning emerges not only from static environmental cues but also from the social and semantic context embedded in our surroundings. This study investigates how human agents influence visual exploration and spatial knowledge acquisition in a controlled Virtual Reality (VR) environment…
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Journal Article
ShapeSpaceExplorer: Analysis of morphological transitions in migrating cells using similarity-based shape space mapping.
Here we describe the development of ShapeSpaceExplorer, an interactive software for the extraction, visualisation and analysis of complex 2D shape series. We also demonstrate its application to the analysis of cell morphology changes during cell migration. Cell migration is essential for many…
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Journal Article
Dynamics of the formation of flat clathrin lattices in response to growth factor stimulus.
Clathrin assemblies on the cell membrane are critical for endocytosis and signal transduction in cells. Specifically, the Ω-shaped clathrin assembly functions as the coat of endocytic vesicles, while the flat clathrin assembly, also known as the flat clathrin lattice (FCL), serves as a signaling…
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Journal Article
Learning, sleep replay and consolidation of contextual fear memories: A neural network model.
Contextual fear conditioning is an experimental framework widely used to investigate how aversive experiences affect the valence an animal associates with an environment. While the initial formation of associative context-fear memories is well studied - dependent on plasticity in hippocampus and…
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Journal Article
iSTTC: A robust method for accurate estimation of intrinsic neural timescales from single-unit recordings.
Intrinsic neural timescales (ITs) are an emerging measure of how neural circuits integrate information over time. ITs are dynamically regulated by behavioral context and cognitive demands, making them suitable for mapping high-level cognitive phenomena onto the underlying neural computations. In…
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Journal Article
Dynamic cholinergic signaling differentially desynchronizes cortical microcircuits dependent on modulation rate and network connectivity.
Acetylcholine (ACh) affects both the intrinsic properties of individual neurons and the oscillatory tendencies of cortical microcircuits by modulating the muscarinic-receptor gated m-current. ACh concentrations have historically been assumed to vary exclusively over long (supra-second)…
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Journal Article
Nonlinear effects of noise on outbreaks of mosquito-borne diseases.
Mosquito-borne diseases are a significant and growing public health burden globally. Predictions about the spread and impact of mosquito-borne disease outbreaks can help inform direct control and prevention measures. However, climate change is expected to increase weather variability, potentially…
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Journal Article
Topological metrics as evolutionary and dynamical descriptors of conformational landscapes within protein families.
Identifying the key order parameters that connect a protein's native structure to its dynamical and evolutionary behavior remains a central challenge. We introduce topological and geometrical metrics-specifically, writhe and Local Topological Energy (LTE)-to investigate these connections. Applying…
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Journal Article
A framework for evaluating predicted sperm trajectories in crowded microscopy videos.
Since the 1980s, semi-automated sperm motility analysis of phase contrast microscopy videos has been used to measure and categorize sperm motility patterns. Motility categories are determined from various kinematic parameters such as Curvilinear Velocity (VCL) and Beat Cross Frequency (BCF). These…
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Journal Article
Integrated multi-modal data analysis for computational modeling of healthy and location-dependent myocardial infarction conditions in porcine hearts.
Porcine hearts are widely used for preclinical cardiac evaluation. Computational models, by effectively integrating comprehensive experimental data, often reinforce this preclinical assessment. Using extensive multi-modal data, we developed swine ventricular digital twins for healthy and chronic…
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Journal Article
A novel transformer-based platform for the prediction and design of biosynthetic gene clusters for (un)natural products.
Biosynthetic gene clusters (BGCs), comprising sets of functionally related genes responsible for synthesizing complex natural products, are a rich source of bioactive compounds with pharmaceutical potential. Here, we present a transformer-based framework that models functional domains as linguistic…
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Journal Article
Ten common misconceptions about Galaxy (and why they are wrong!).
Galaxy is a widely used open-source platform for accessible, reproducible, transparent and scalable data analysis in the life sciences and beyond. Despite its growing adoption across domains, several misconceptions persist about its scope, usability, scalability and relevance to academia and…
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