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Predicting lncRNA-disease associations based on heterogeneous graph convolutional generative adversarial network. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-29 Zhonghao Lu,Hua Zhong,Lin Tang,Jing Luo,Wei Zhou,Lin Liu
There is a growing body of evidence indicating the crucial roles that long non-coding RNAs (lncRNAs) play in the development and progression of various diseases, including cancers, cardiovascular diseases, and neurological disorders. However, accurately predicting potential lncRNA-disease associations remains a challenge, as existing methods have limitations in extracting heterogeneous association
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The SKMT Algorithm: A method for assessing and comparing underlying protein entanglement. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-27 Arron Bale,Robert Rambo,Christopher Prior
We present fast and simple-to-implement measures of the entanglement of protein tertiary structures which are appropriate for highly flexible structure comparison. These are performed using the SKMT algorithm, a novel method of smoothing the Cα backbone to achieve a minimal complexity curve representation of the manner in which the protein's secondary structure elements fold to form its tertiary structure
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Facilitating bioinformatics reproducibility with QIIME 2 provenance Replay. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-27 Christopher R Keefe,Matthew R Dillon,Elizabeth Gehret,Chloe Herman,Mary Jewell,Colin V Wood,Evan Bolyen,J Gregory Caporaso
Study reproducibility is essential to corroborate, build on, and learn from the results of scientific research but is notoriously challenging in bioinformatics, which often involves large data sets and complex analytic workflows involving many different tools. Additionally, many biologists are not trained in how to effectively record their bioinformatics analysis steps to ensure reproducibility, so
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On convolutional neural networks for selection inference: Revealing the effect of preprocessing on model learning and the capacity to discover novel patterns. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-27 Ryan M Cecil,Lauren A Sugden
A central challenge in population genetics is the detection of genomic footprints of selection. As machine learning tools including convolutional neural networks (CNNs) have become more sophisticated and applied more broadly, these provide a logical next step for increasing our power to learn and detect such patterns; indeed, CNNs trained on simulated genome sequences have recently been shown to be
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GENERALIST: A latent space based generative model for protein sequence families. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-27 Hoda Akl,Brooke Emison,Xiaochuan Zhao,Arup Mondal,Alberto Perez,Purushottam D Dixit
Generative models of protein sequence families are an important tool in the repertoire of protein scientists and engineers alike. However, state-of-the-art generative approaches face inference, accuracy, and overfitting- related obstacles when modeling moderately sized to large proteins and/or protein families with low sequence coverage. Here, we present a simple to learn, tunable, and accurate generative
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Adaptive oscillators support Bayesian prediction in temporal processing. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-27 Keith B Doelling,Luc H Arnal,M Florencia Assaneo
Humans excel at predictively synchronizing their behavior with external rhythms, as in dance or music performance. The neural processes underlying rhythmic inferences are debated: whether predictive perception relies on high-level generative models or whether it can readily be implemented locally by hard-coded intrinsic oscillators synchronizing to rhythmic input remains unclear and different underlying
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Biased placement of Mitochondria fission facilitates asymmetric inheritance of protein aggregates during yeast cell division. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-27 Gordon Sun,Christine Hwang,Tony Jung,Jian Liu,Rong Li
Mitochondria are essential and dynamic eukaryotic organelles that must be inherited during cell division. In yeast, mitochondria are inherited asymmetrically based on quality, which is thought to be vital for maintaining a rejuvenated cell population; however, the mechanisms underlying mitochondrial remodeling and segregation during this process are not understood. We used high spatiotemporal imaging
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Network analysis of patterns and relevance of enteric pathogen co-infections among infants in a diarrhea-endemic setting. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-22 E Ross Colgate,Connor Klopfer,Dorothy M Dickson,Benjamin Lee,Matthew J Wargo,Ashraful Alam,Beth D Kirkpatrick,Laurent Hébert-Dufresne
Despite significant progress in recent decades toward ameliorating the excess burden of diarrheal disease globally, childhood diarrhea remains a leading cause of morbidity and mortality in low-and-middle-income countries (LMICs). Recent large-scale studies of diarrhea etiology in these populations have revealed widespread co-infection with multiple enteric pathogens, in both acute and asymptomatic
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A multiscale model of the role of microenvironmental factors in cell segregation and heterogeneity in breast cancer development. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-22 J Roberto Romero-Arias,Carlos A González-Castro,Guillermo Ramírez-Santiago
We analyzed a quantitative multiscale model that describes the epigenetic dynamics during the growth and evolution of an avascular tumor. A gene regulatory network (GRN) formed by a set of ten genes that are believed to play an important role in breast cancer development was kinetically coupled to the microenvironmental agents: glucose, estrogens, and oxygen. The dynamics of spontaneous mutations was
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IDP-LM: Prediction of protein intrinsic disorder and disorder functions based on language models. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-22 Yihe Pang,Bin Liu
Intrinsically disordered proteins (IDPs) and regions (IDRs) are a class of functionally important proteins and regions that lack stable three-dimensional structures under the native physiologic conditions. They participate in critical biological processes and thus are associated with the pathogenesis of many severe human diseases. Identifying the IDPs/IDRs and their functions will be helpful for a
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Only a topological method can identify all possible network structures capable of Robust Perfect Adaptation. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-22 Robyn P Araujo,Lance A Liotta
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Overcoming chemotherapy resistance in low-grade gliomas: A computational approach. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-20 Thibault Delobel,Luis E Ayala-Hernández,Jesús J Bosque,Julián Pérez-Beteta,Salvador Chulián,Manuel García-Ferrer,Pilar Piñero,Philippe Schucht,Michael Murek,Víctor M Pérez-García
Low-grade gliomas are primary brain tumors that arise from glial cells and are usually treated with temozolomide (TMZ) as a chemotherapeutic option. They are often incurable, but patients have a prolonged survival. One of the shortcomings of the treatment is that patients eventually develop drug resistance. Recent findings show that persisters, cells that enter a dormancy state to resist treatment
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Exploring strategy differences between humans and monkeys with recurrent neural networks. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-20 Ben Tsuda,Barry J Richmond,Terrence J Sejnowski
Animal models are used to understand principles of human biology. Within cognitive neuroscience, non-human primates are considered the premier model for studying decision-making behaviors in which direct manipulation experiments are still possible. Some prominent studies have brought to light major discrepancies between monkey and human cognition, highlighting problems with unverified extrapolation
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Omnidirectional propulsion in a metachronal swimmer. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-17 Adrian Herrera-Amaya,Margaret L Byron
Aquatic organisms often employ maneuverable and agile swimming behavior to escape from predators, find prey, or navigate through complex environments. Many of these organisms use metachronally coordinated appendages to execute complex maneuvers. However, though metachrony is used across body sizes ranging from microns to tens of centimeters, it is understudied compared to the swimming of fish, cetaceans
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Understanding heterogeneous mechanisms of heart failure with preserved ejection fraction through cardiorenal mathematical modeling. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-13 Sanchita Basu,Hongtao Yu,Jonathan R Murrow,K Melissa Hallow
In contrast to heart failure (HF) with reduced ejection fraction (HFrEF), effective interventions for HF with preserved ejection fraction (HFpEF) have proven elusive, in part because it is a heterogeneous syndrome with incompletely understood pathophysiology. This study utilized mathematical modeling to evaluate mechanisms distinguishing HFpEF and HFrEF. HF was defined as a state of chronically elevated
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A general hypergraph learning algorithm for drug multi-task predictions in micro-to-macro biomedical networks. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-13 Shuting Jin,Yue Hong,Li Zeng,Yinghui Jiang,Yuan Lin,Leyi Wei,Zhuohang Yu,Xiangxiang Zeng,Xiangrong Liu
The powerful combination of large-scale drug-related interaction networks and deep learning provides new opportunities for accelerating the process of drug discovery. However, chemical structures that play an important role in drug properties and high-order relations that involve a greater number of nodes are not tackled in current biomedical networks. In this study, we present a general hypergraph
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External mechanical loading overrules cell-cell mechanical communication in sprouting angiogenesis during early bone regeneration. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-13 Chiara Dazzi,Julia Mehl,Mounir Benamar,Holger Gerhardt,Petra Knaus,Georg N Duda,Sara Checa
Sprouting angiogenesis plays a key role during bone regeneration. For example, insufficient early revascularization of the injured site can lead to delayed or non-healing. During sprouting, endothelial cells are known to be mechano-sensitive and respond to local mechanical stimuli. Endothelial cells interact and communicate mechanically with their surroundings, such as outer-vascular stromal cells
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Bayesian spatial modelling of localised SARS-CoV-2 transmission through mobility networks across England. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-13 Thomas Ward,Mitzi Morris,Andrew Gelman,Bob Carpenter,William Ferguson,Christopher Overton,Martyn Fyles
In the early phases of growth, resurgent epidemic waves of SARS-CoV-2 incidence have been characterised by localised outbreaks. Therefore, understanding the geographic dispersion of emerging variants at the start of an outbreak is key for situational public health awareness. Using telecoms data, we derived mobility networks describing the movement patterns between local authorities in England, which
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Attention-based deep clustering method for scRNA-seq cell type identification. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-10 Shenghao Li,Hui Guo,Simai Zhang,Yizhou Li,Menglong Li
Single-cell sequencing (scRNA-seq) technology provides higher resolution of cellular differences than bulk RNA sequencing and reveals the heterogeneity in biological research. The analysis of scRNA-seq datasets is premised on the subpopulation assignment. When an appropriate reference is not available, such as specific marker genes and single-cell reference atlas, unsupervised clustering approaches
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Architecture of the brain's visual system enhances network stability and performance through layers, delays, and feedback. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-10 Osvaldo Matias Velarde,Hernán A Makse,Lucas C Parra
In the visual system of primates, image information propagates across successive cortical areas, and there is also local feedback within an area and long-range feedback across areas. Recent findings suggest that the resulting temporal dynamics of neural activity are crucial in several vision tasks. In contrast, artificial neural network models of vision are typically feedforward and do not capitalize
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Using normative modeling and machine learning for detecting mild traumatic brain injury from magnetoencephalography data. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-09 Veera Itälinna,Hanna Kaltiainen,Nina Forss,Mia Liljeström,Lauri Parkkonen
New biomarkers are urgently needed for many brain disorders; for example, the diagnosis of mild traumatic brain injury (mTBI) is challenging as the clinical symptoms are diverse and nonspecific. EEG and MEG studies have demonstrated several population-level indicators of mTBI that could serve as objective markers of brain injury. However, deriving clinically useful biomarkers for mTBI and other brain
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Geometric and topological characterization of the cytoarchitecture of islets of Langerhans. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-09 Manu Aggarwal,Deborah A Striegel,Manami Hara,Vipul Periwal
The islets of Langerhans are critical endocrine micro-organs that secrete hormones regulating energy metabolism in animals. Insulin and glucagon, secreted by beta and alpha cells, respectively, are responsible for metabolic switching between fat and glucose utilization. Dysfunction in their secretion and/or counter-regulatory influence leads to diabetes. Debate in the field centers on the cytoarchitecture
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Ten simple rules for students navigating summer research experiences for undergraduates (REU) programs: From application to program completion. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-09 Maria Manzanares,Courtney Peña,Kayla C Kobak,Miranda B Stratton
For many emerging scientists, research experiences for undergraduates (REU) programs are an important gateway to graduate school and a career in science, technology, engineering, and mathematics (STEM). REUs provide guided mentorship and learning experiences in a summer-long program where students develop research skills, build scientific knowledge, and strengthen their scientific identity. While the
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MIGGRI: A multi-instance graph neural network model for inferring gene regulatory networks for Drosophila from spatial expression images. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-08 Yuyang Huang,Gufeng Yu,Yang Yang
Recent breakthrough in spatial transcriptomics has brought great opportunities for exploring gene regulatory networks (GRNs) from a brand-new perspective. Especially, the local expression patterns and spatio-temporal regulation mechanisms captured by spatial expression images allow more delicate delineation of the interplay between transcript factors and their target genes. However, the complexity
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A data-driven semi-parametric model of SARS-CoV-2 transmission in the United States. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-08 John M Drake,Andreas Handel,Éric Marty,Eamon B O'Dea,Tierney O'Sullivan,Giovanni Righi,Andrew T Tredennick
To support decision-making and policy for managing epidemics of emerging pathogens, we present a model for inference and scenario analysis of SARS-CoV-2 transmission in the USA. The stochastic SEIR-type model includes compartments for latent, asymptomatic, detected and undetected symptomatic individuals, and hospitalized cases, and features realistic interval distributions for presymptomatic and symptomatic
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Modeling cell populations metabolism and competition under maximum power constraints. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-08 Luigi Conte,Francesco Gonella,Andrea Giansanti,Axel Kleidon,Alessandra Romano
Ecological interactions are fundamental at the cellular scale, addressing the possibility of a description of cellular systems that uses language and principles of ecology. In this work, we use a minimal ecological approach that encompasses growth, adaptation and survival of cell populations to model cell metabolisms and competition under energetic constraints. As a proof-of-concept, we apply this
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CGG toolkit: Software components for computational genomics. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-07 Dimitrios Vasileiou,Christos Karapiperis,Ismini Baltsavia,Anastasia Chasapi,Dag Ahrén,Paul J Janssen,Ioannis Iliopoulos,Vasilis J Promponas,Anton J Enright,Christos A Ouzounis
Public-domain availability for bioinformatics software resources is a key requirement that ensures long-term permanence and methodological reproducibility for research and development across the life sciences. These issues are particularly critical for widely used, efficient, and well-proven methods, especially those developed in research settings that often face funding discontinuities. We re-launch
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Interaction between decision-making and motor learning when selecting reach targets in the presence of bias and noise. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-11-02 Tianyao Zhu,Jason P Gallivan,Daniel M Wolpert,J Randall Flanagan
Motor errors can have both bias and noise components. Bias can be compensated for by adaptation and, in tasks in which the magnitude of noise varies across the environment, noise can be reduced by identifying and then acting in less noisy regions of the environment. Here we examine how these two processes interact when participants reach under a combination of an externally imposed visuomotor bias
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Genome-scale metabolic modeling of the human gut bacterium Bacteroides fragilis strain 638R. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-10-30 Maxwell Neal,Deepan Thiruppathy,Karsten Zengler
Bacteroides fragilis is a universal member of the dominant commensal gut phylum Bacteroidetes. Its fermentation products and abundance have been linked to obesity, inflammatory bowel disease, and other disorders through its effects on host metabolic regulation and the immune system. As of yet, there has been no curated systems-level characterization of B. fragilis' metabolism that provides a comprehensive
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Inference of transmission dynamics and retrospective forecast of invasive meningococcal disease. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-10-27 Jaime Cascante-Vega,Marta Galanti,Katharina Schley,Sen Pei,Jeffrey Shaman
The pathogenic bacteria Neisseria meningitidis, which causes invasive meningococcal disease (IMD), predominantly colonizes humans asymptomatically; however, invasive disease occurs in a small proportion of the population. Here, we explore the seasonality of IMD and develop and validate a suite of models for simulating and forecasting disease outcomes in the United States. We combine the models into
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Correction: Hybrid predictive coding: Inferring, fast and slow. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-10-27
[This corrects the article DOI: 10.1371/journal.pcbi.1011280.].
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Correction: A quantitative modelling approach for DNA repair on a population scale. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-10-27
[This corrects the article DOI: 10.1371/journal.pcbi.1010488.].
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Genes for highly abundant proteins in Escherichia coli avoid 5' codons that promote ribosomal initiation. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-10-25 Loveday E Lewin,Kate G Daniels,Laurence D Hurst
In many species highly expressed genes (HEGs) over-employ the synonymous codons that match the more abundant iso-acceptor tRNAs. Bacterial transgene codon randomization experiments report, however, that enrichment with such "translationally optimal" codons has little to no effect on the resultant protein level. By contrast, consistent with the view that ribosomal initiation is rate limiting, synonymous
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Spatial Configurations of 3D Extracellular Matrix Collagen Density and Anisotropy Simultaneously Guide Angiogenesis. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-10-23 Steven A LaBelle,A Marsh Poulson,Steve A Maas,Adam Rauff,Gerard A Ateshian,Jeffrey A Weiss
Extracellular matrix (ECM) collagen density and fibril anisotropy are thought to affect the development of new vasculatures during pathologic and homeostatic angiogenesis. Computational simulation is emerging as a tool to investigate the role of matrix structural configurations on cell guidance. However, prior computational models have only considered the orientation of collagen as a model input. Recent
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The role of leptomeningeal collaterals in redistributing blood flow during stroke. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-10-23 Robert Epp,Chaim Glück,Nadine Felizitas Binder,Mohamad El Amki,Bruno Weber,Susanne Wegener,Patrick Jenny,Franca Schmid
Leptomeningeal collaterals (LMCs) connect the main cerebral arteries and provide alternative pathways for blood flow during ischaemic stroke. This is beneficial for reducing infarct size and reperfusion success after treatment. However, a better understanding of how LMCs affect blood flow distribution is indispensable to improve therapeutic strategies. Here, we present a novel in silico approach that
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Modelling how plant cell-cycle progression leads to cell size regulation. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-10-20 Daniel Williamson,William Tasker-Brown,James A H Murray,Angharad R Jones,Leah R Band
Populations of cells typically maintain a consistent size, despite cell division rarely being precisely symmetrical. Therefore, cells must possess a mechanism of "size control", whereby the cell volume at birth affects cell-cycle progression. While size control mechanisms have been elucidated in a number of other organisms, it is not yet clear how this mechanism functions in plants. Here, we present
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Phi fluctuates with surprisal: An empirical pre-study for the synthesis of the free energy principle and integrated information theory. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-10-20 Christoffer Lundbak Olesen,Peter Thestrup Waade,Larissa Albantakis,Christoph Mathys
The Free Energy Principle (FEP) and Integrated Information Theory (IIT) are two ambitious theoretical approaches. The first aims to make a formal framework for describing self-organizing and life-like systems in general, and the second attempts a mathematical theory of conscious experience based on the intrinsic properties of a system. They are each concerned with complementary aspects of the properties
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Analyzing histone ChIP-seq data with a bin-based probability of being signal. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-10-20 Vivian Hecht,Kevin Dong,Sreshtaa Rajesh,Polina Shpilker,Siddarth Wekhande,Noam Shoresh
Histone ChIP-seq is one of the primary methods for charting the cellular epigenomic landscape, the components of which play a critical regulatory role in gene expression. Analyzing the activity of regulatory elements across datasets and cell types can be challenging due to shifting peak positions and normalization artifacts resulting from, for example, differing read depths, ChIP efficiencies, and
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PARROT: Prediction of enzyme abundances using protein-constrained metabolic models. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-10-19 Mauricio Alexander de Moura Ferreira,Wendel Batista da Silveira,Zoran Nikoloski
Protein allocation determines the activity of cellular pathways and affects growth across all organisms. Therefore, different experimental and machine learning approaches have been developed to quantify and predict protein abundance and how they are allocated to different cellular functions, respectively. Yet, despite advances in protein quantification, it remains challenging to predict condition-specific
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Combining the dynamic model and deep neural networks to identify the intensity of interventions during COVID-19 pandemic. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-10-18 Mengqi He,Sanyi Tang,Yanni Xiao
During the COVID-19 pandemic, control measures, especially massive contact tracing following prompt quarantine and isolation, play an important role in mitigating the disease spread, and quantifying the dynamic contact rate and quarantine rate and estimate their impacts remain challenging. To precisely quantify the intensity of interventions, we develop the mechanism of physics-informed neural network
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A 2D model to study how secondary growth affects the self-supporting behaviour of climbing plants. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-10-16 Giacomo Vecchiato,Tom Hattermann,Michele Palladino,Fabio Tedone,Patrick Heuret,Nick P Rowe,Pierangelo Marcati
Climbing plants exhibit specialized shoots, called "searchers", to cross spaces and alternate between spatially discontinuous supports in their natural habitats. To achieve this task, searcher shoots combine both primary and secondary growth processes of their stems in order to support, orientate and explore their extensional growth into the environment. Currently, there is an increasing interest in
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Establishing brain states in neuroimaging data. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-10-16 Zalina Dezhina,Jonathan Smallwood,Ting Xu,Federico E Turkheimer,Rosalyn J Moran,Karl J Friston,Robert Leech,Erik D Fagerholm
The definition of a brain state remains elusive, with varying interpretations across different sub-fields of neuroscience-from the level of wakefulness in anaesthesia, to activity of individual neurons, voltage in EEG, and blood flow in fMRI. This lack of consensus presents a significant challenge to the development of accurate models of neural dynamics. However, at the foundation of dynamical systems
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Short-term neuronal and synaptic plasticity act in synergy for deviance detection in spiking networks. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-10-13 Felix Benjamin Kern,Zenas C Chao
Sensory areas of cortex respond more strongly to infrequent stimuli when these violate previously established regularities, a phenomenon known as deviance detection (DD). Previous modeling work has mainly attempted to explain DD on the basis of synaptic plasticity. However, a large fraction of cortical neurons also exhibit firing rate adaptation, an underexplored potential mechanism. Here, we investigate
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Mechanistic modelling of within-mosquito viral dynamics: Insights into infection and dissemination patterns. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-10-09 Jennifer S Lord,Michael B Bonsall
Vector or host competence can be defined as the ability of an individual to become infected and subsequently transmit a pathogen. Assays to measure competence play a key part in the assessment of the factors affecting mosquito-borne virus transmission and of potential pathogen-blocking control tools for these viruses. For mosquitoes, competence for arboviruses can be measured experimentally and results
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Force-dependent focal adhesion assembly and disassembly: A computational study. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-10-06 Kailas Shankar Honasoge,Zeynep Karagöz,Benjamin T Goult,Haguy Wolfenson,Vanessa L S LaPointe,Aurélie Carlier
Cells interact with the extracellular matrix (ECM) via cell-ECM adhesions. These physical interactions are transduced into biochemical signals inside the cell which influence cell behaviour. Although cell-ECM interactions have been studied extensively, it is not completely understood how immature (nascent) adhesions develop into mature (focal) adhesions and how mechanical forces influence this process
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Rapid runtime learning by curating small datasets of high-quality items obtained from memory. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-10-04 Joseph Scott German,Guofeng Cui,Chenliang Xu,Robert A Jacobs
We propose the "runtime learning" hypothesis which states that people quickly learn to perform unfamiliar tasks as the tasks arise by using task-relevant instances of concepts stored in memory during mental training. To make learning rapid, the hypothesis claims that only a few class instances are used, but these instances are especially valuable for training. The paper motivates the hypothesis by
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Metacommunity structure preserves genome diversity in the presence of gene-specific selective sweeps under moderate rates of horizontal gene transfer. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-10-04 Simone Pompei,Edoardo Bella,Joshua S Weitz,Jacopo Grilli,Marco Cosentino Lagomarsino
The horizontal transfer of genes is fundamental for the eco-evolutionary dynamics of microbial communities, such as oceanic plankton, soil, and the human microbiome. In the case of an acquired beneficial gene, classic population genetics would predict a genome-wide selective sweep, whereby the genome spreads clonally within the community and together with the beneficial gene, removing genome diversity
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Mechanistic characterization of oscillatory patterns in unperturbed tumor growth dynamics: The interplay between cancer cells and components of tumor microenvironment. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-10-04 Aymara Sancho-Araiz,Zinnia P Parra-Guillen,Jean Bragard,Sergio Ardanza,Victor Mangas-Sanjuan,Iñaki F Trocóniz
Mathematical modeling of unperturbed and perturbed tumor growth dynamics (TGD) in preclinical experiments provides an opportunity to establish translational frameworks. The most commonly used unperturbed tumor growth models (i.e. linear, exponential, Gompertz and Simeoni) describe a monotonic increase and although they capture the mean trend of the data reasonably well, systematic model misspecifications
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Perfusion estimation using synthetic MRI-based measurements and a porous media flow model. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-10-02 Rolf Johan Lorentzen,Geir Nævdal,Ove Sævareid,Erlend Hodneland,Erik Andreas Hanson,Antonella Munthe-Kaas
The measurement of perfusion and filtration of blood in biological tissue give rise to important clinical parameters used in diagnosis, follow-up, and therapy. In this paper, we address techniques for perfusion analysis using processed contrast agent concentration data from dynamic MRI acquisitions. A new methodology for analysis is evaluated and verified using synthetic data generated on a tissue
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Evaluating a large language model's ability to solve programming exercises from an introductory bioinformatics course. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-09-28 Stephen R Piccolo,Paul Denny,Andrew Luxton-Reilly,Samuel H Payne,Perry G Ridge
Computer programming is a fundamental tool for life scientists, allowing them to carry out essential research tasks. However, despite various educational efforts, learning to write code can be a challenging endeavor for students and researchers in life-sciences disciplines. Recent advances in artificial intelligence have made it possible to translate human-language prompts to functional code, raising
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A role for cortical interneurons as adversarial discriminators. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-09-28 Ari S Benjamin,Konrad P Kording
The brain learns representations of sensory information from experience, but the algorithms by which it does so remain unknown. One popular theory formalizes representations as inferred factors in a generative model of sensory stimuli, meaning that learning must improve this generative model and inference procedure. This framework underlies many classic computational theories of sensory learning, such
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Ten quick tips for building FAIR workflows. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-09-28 Casper de Visser,Lennart F Johansson,Purva Kulkarni,Hailiang Mei,Pieter Neerincx,K Joeri van der Velde,Péter Horvatovich,Alain J van Gool,Morris A Swertz,Peter A C 't Hoen,Anna Niehues
Research data is accumulating rapidly and with it the challenge of fully reproducible science. As a consequence, implementation of high-quality management of scientific data has become a global priority. The FAIR (Findable, Accesible, Interoperable and Reusable) principles provide practical guidelines for maximizing the value of research data; however, processing data using workflows-systematic executions
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Ten simple rules for interpreting and evaluating a meta-analysis. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-09-28 Rebecca B Carlson,Jennifer R Martin,Robert D Beckett
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Personalized prediction for multiple chronic diseases by developing the multi-task Cox learning model. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-09-21 Shuaijie Zhang,Fan Yang,Lijie Wang,Shucheng Si,Jianmei Zhang,Fuzhong Xue
Personalized prediction of chronic diseases is crucial for reducing the disease burden. However, previous studies on chronic diseases have not adequately considered the relationship between chronic diseases. To explore the patient-wise risk of multiple chronic diseases, we developed a multitask learning Cox (MTL-Cox) model for personalized prediction of nine typical chronic diseases on the UK Biobank
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Fourteen quick tips for crowdsourcing geographically linked data for public health advocacy. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-09-21 Joshua Atienza,Anjalee Benedict,Lincoln D Stein,Kashif Pirzada,Cheryl White,Shraddha Pai
This article presents 14 quick tips to build a team to crowdsource data for public health advocacy. It includes tips around team building and logistics, infrastructure setup, media and industry outreach, and project wrap-up and archival for posterity.
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Mechanistic multiscale modelling of energy metabolism in human astrocytes reveals the impact of morphology changes in Alzheimer's Disease. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-09-20 Sofia Farina,Valérie Voorsluijs,Sonja Fixemer,David S Bouvier,Susanne Claus,Mark H Ellisman,Stéphane P A Bordas,Alexander Skupin
Astrocytes with their specialised morphology are essential for brain homeostasis as metabolic mediators between blood vessels and neurons. In neurodegenerative diseases such as Alzheimer's disease (AD), astrocytes adopt reactive profiles with molecular and morphological changes that could lead to the impairment of their metabolic support and impact disease progression. However, the underlying mechanisms
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Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the principle of parsimony. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-09-18 Seirana Hashemi,Zahra Razaghi-Moghadam,Zoran Nikoloski
Intracellular fluxes represent a joint outcome of cellular transcription and translation and reflect the availability and usage of nutrients from the environment. While approaches from the constraint-based metabolic framework can accurately predict cellular phenotypes, such as growth and exchange rates with the environment, accurate prediction of intracellular fluxes remains a pressing problem. Parsimonious
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Marginal effects of public health measures and COVID-19 disease burden in China: A large-scale modelling study. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-09-18 Zengmiao Wang,Peiyi Wu,Lin Wang,Bingying Li,Yonghong Liu,Yuxi Ge,Ruixue Wang,Ligui Wang,Hua Tan,Chieh-Hsi Wu,Marko Laine,Henrik Salje,Hongbin Song
China had conducted some of the most stringent public health measures to control the spread of successive SARS-CoV-2 variants. However, the effectiveness of these measures and their impacts on the associated disease burden have rarely been quantitatively assessed at the national level. To address this gap, we developed a stochastic age-stratified metapopulation model that incorporates testing, contact
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Excalibur: A new ensemble method based on an optimal combination of aggregation tests for rare-variant association testing for sequencing data. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-09-14 Simon Boutry,Raphaël Helaers,Tom Lenaerts,Miikka Vikkula
The development of high-throughput next-generation sequencing technologies and large-scale genetic association studies produced numerous advances in the biostatistics field. Various aggregation tests, i.e. statistical methods that analyze associations of a trait with multiple markers within a genomic region, have produced a variety of novel discoveries. Notwithstanding their usefulness, there is no
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Mixtures of strategies underlie rodent behavior during reversal learning. PLoS Comput. Biol. (IF 4.3) Pub Date : 2023-09-14 Nhat Minh Le,Murat Yildirim,Yizhi Wang,Hiroki Sugihara,Mehrdad Jazayeri,Mriganka Sur
In reversal learning tasks, the behavior of humans and animals is often assumed to be uniform within single experimental sessions to facilitate data analysis and model fitting. However, behavior of agents can display substantial variability in single experimental sessions, as they execute different blocks of trials with different transition dynamics. Here, we observed that in a deterministic reversal