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PLoS Computational Biology, Volume 20
Volume 20, Number 1, January 2024
- Marcus Kaiser
:
Ten simple rules for establishing an experimental lab. - Gabriel Reuben Smith
Ten simple rules for using large language models in science, version 1.0.
- Alice Bruel
The spinal cord facilitates cerebellar upper limb motor learning and control; inputs from neuromusculoskeletal simulation. - Enrique R. Sebastian, Julio Esparza
Quantifying the distribution of feature values over data represented in arbitrary dimensional spaces. - Aakash Pandey
Wildlife vaccination strategies for eliminating bovine tuberculosis in white-tailed deer populations. - Yoav Ger
Harnessing the flexibility of neural networks to predict dynamic theoretical parameters underlying human choice behavior. - Jinchao Lv, Jin Wang
Landscape quantifies the intermediate state and transition dynamics in ecological networks. - Yong-Jin Huang
Detecting shifts in nonlinear dynamics using Empirical Dynamic Modeling with Nested-Library Analysis. - Jiarui Feng, S. Peter Goedegebuure, Amanda Zeng, Ye Bi, Ting Wang, Philip R. O. Payne, Li Ding, David DeNardo, William Hawkins, Ryan C. Fields, Fuhai Li
sc2MeNetDrug: A computational tool to uncover inter-cell signaling targets and identify relevant drugs based on single cell RNA-seq data. - Elizabeth Lawson-Keister, Tao Zhang, Fatemeh Nazari, François Fagotto
Differences in boundary behavior in the 3D vertex and Voronoi models. - Lucas Castillo
Explaining the flaws in human random generation as local sampling with momentum. - Haiqing Zhao
The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea. - Florian G. Pflug
Genome replication in asynchronously growing microbial populations. - Paul F. Lang
Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells. - Chin-Hsuan Sophie Lin
Are we really Bayesian? Probabilistic inference shows sub-optimal knowledge transfer. - Tijl Grootswagers
Mapping the dynamics of visual feature coding: Insights into perception and integration. - Michael J. Plank
Near-term forecasting of Covid-19 cases and hospitalisations in Aotearoa New Zealand. - Avik Mukherjee
Plasticity of growth laws tunes resource allocation strategies in bacteria. - Sjoerd Terpstra
Adaptive foraging of pollinators fosters gradual tipping under resource competition and rapid environmental change. - Christopher A. Mancuso
Joint representation of molecular networks from multiple species improves gene classification. - Eric Elmoznino
High-performing neural network models of visual cortex benefit from high latent dimensionality. - Jian Zou
Systems approach for congruence and selection of cancer models towards precision medicine. - Eduardo Jardón-Valadez
Tracking conformational transitions of the gonadotropin hormone receptors in a bilayer of (SDPC) poly-unsaturated lipids from all-atom molecular dynamics simulations. - H. Robert Frost
Tissue-adjusted pathway analysis of cancer (TPAC): A novel approach for quantifying tumor-specific gene set dysregulation relative to normal tissue. - Tyler S. Manning
Transformations of sensory information in the brain suggest changing criteria for optimality. - Karan Kabbur Hanumanthappa Manjunatha
Controlling target brain regions by optimal selection of input nodes. - Kaiser J. Loell, Ryan Z. Friedman
Transcription factor interactions explain the context-dependent activity of CRX binding sites. - Hong An
Gene expression bias between the subgenomes of allopolyploid hybrids is an emergent property of the kinetics of expression. - Janne J. Luppi
Virtual neural network-guided optimization of non-invasive brain stimulation in Alzheimer's disease. - Maki Sudo
Diffusive mediator feedbacks control the health-to-disease transition of skin inflammation. - Giovanni Lo Iacono, Alasdair J. C. Cook, Gianne Derks, Lora E. Fleming, Nigel French, Emma L. Gillingham, Laura C. Gonzalez Villeta, Clare Heaviside, Roberto La Ragione, Giovanni Leonardi, Christophe E. Sarran, Sotiris Vardoulakis, Francis Senyah, Arnoud H. M. van Vliet, Gordon Nichols:
A mathematical, classical stratification modeling approach to disentangling the impact of weather on infectious diseases: A case study using spatio-temporally disaggregated Campylobacter surveillance data for England and Wales. - Martin Grunnill
Modelling disease mitigation at mass gatherings: A case study of COVID-19 at the 2022 FIFA World Cup. - Shunsuke Koseki
Identifying essential factors for energy-efficient walking control across a wide range of velocities in reflex-based musculoskeletal systems. - Virginia Dominguez-Garcia
The structure and robustness of ecological networks with two interaction types. - Sebastian Idesis
Functional hierarchies in brain dynamics characterized by signal reversibility in ferret cortex. - Laura Schmid
Postinhibitory excitation in motoneurons can be facilitated by hyperpolarization-activated inward currents: A simulation study. - Anand Ramachandran
PandoGen: Generating complete instances of future SARS-CoV-2 sequences using Deep Learning. - Chen Beer
Revealing and reshaping attractor dynamics in large networks of cortical neurons. - Sizhe Qiu
Inferred regulons are consistent with regulator binding sequences in E. coli. - Pablo Alvarez
Predicting primate tongue morphology based on geometrical skull matching. A first step towards an application on fossil hominins. - Marine Louarn, Guillaume Collet, Ève Barré, Thierry Fest, Olivier Dameron
Regulus infers signed regulatory relations from few samples' information using discretization and likelihood constraints. - Javier Robles
Integrated meta-analysis of colorectal cancer public proteomic datasets for biomarker discovery and validation. - Bryan Shin
Examining B-cell dynamics and responsiveness in different inflammatory milieus using an agent-based model. - Leo Zeitler
A genome-wide comprehensive analysis of nucleosome positioning in yeast. - Pascal P. Klamser
Inferring country-specific import risk of diseases from the world air transportation network. - Andrea Papale
Chromatin phase separated nanoregions explored by polymer cross-linker models and reconstructed from single particle trajectories. - Kieran D. Lamb
Mutational signature dynamics indicate SARS-CoV-2's evolutionary capacity is driven by host antiviral molecules. - Ian T. Ellwood
Short-term Hebbian learning can implement transformer-like attention. - Raymond Copeland, Christopher Zhang
Spatial constraints and stochastic seeding subvert microbial arms race. - Michiel van Boven
Estimation of introduction and transmission rates of SARS-CoV-2 in a prospective household study. - David L. Krongauz
Vision-based collective motion: A locust-inspired reductionist model. - Mehran Fazli
Conversion of spikers to bursters in pituitary cell networks: Is it better to disperse for maximum exposure or circle the wagons? - Beatriz Ocaña-Tienda
Radiation necrosis after radiation therapy treatment of brain metastases: A computational approach. - Ata Kalirad
Spatial and temporal heterogeneity alter the cost of plasticity in Pristionchus pacificus. - Magdalena Kozielska
A neural network model for the evolution of learning in changing environments. - Yaojia Chen
AutoEdge-CCP: A novel approach for predicting cancer-associated circRNAs and drugs based on automated edge embedding. - Louis Yat Hin Chan
Modeling geographic vaccination strategies for COVID-19 in Norway.
- Paul J. N. Brodersen
Somnotate: A probabilistic sleep stage classifier for studying vigilance state transitions. - Rituparna Samanta
Implicit model to capture electrostatic features of membrane environment. - Said el Bouhaddani
Statistical integration of multi-omics and drug screening data from cell lines.
- Sebastian Himbert
MEDUSA: A cloud-based tool for the analysis of X-ray diffuse scattering to obtain the bending modulus from oriented membrane stacks. - Hua-Chang Chen, Jing Wang
FindAdapt: A python package for fast and accurate adapter detection in small RNA sequencing.
Volume 20, Number 2, February 2024
- Joachim Goedhart
Studentsourcing - Aggregating and reusing data from a practical cell biology course.
- Helena Klara Jambor
Ten simple rules for designing graphical abstracts.
- Martijn A. de Jong
The shapes of elongating gastruloids are consistent with convergent extension driven by a combination of active cell crawling and differential adhesion. - Kameel Khabaz
The geometric evolution of aortic dissections: Predicting surgical success using fluctuations in integrated Gaussian curvature. - Jacob B. Roberts
Foldy: An open-source web application for interactive protein structure analysis. - Sarah Percival, Joyce G. Onyenedum, Daniel H. Chitwood, Aman Y. Husbands
Topological data analysis reveals core heteroblastic and ontogenetic programs embedded in leaves of grapevine (Vitaceae) and maracuyá (Passifloraceae). - Matthijs Pals
Trained recurrent neural networks develop phase-locked limit cycles in a working memory task. - Jane Knöchel
Index analysis: An approach to understand signal transduction with application to the EGFR signalling pathway. - Etienne Thoret
Sleep deprivation detected by voice analysis. - Sarvenaz Sarabipour
Trafficking dynamics of VEGFR1, VEGFR2, and NRP1 in human endothelial cells. - Connor R. King
Stochastic model of vesicular stomatitis virus replication reveals mutational effects on virion production. - Te Liu
Reconciling ASPP-p53 binding mode discrepancies through an ensemble binding framework that bridges crystallography and NMR data. - Yu Feng
Attractor neural networks with double well synapses. - Keith E. Kennedy
Multiscale networks in multiple sclerosis. - Zhijie Feng, Robert Marsland III, Jason W. Rocks, Pankaj Mehta
Emergent competition shapes top-down versus bottom-up control in multi-trophic ecosystems. - Joe Hilton
A beta-Poisson model for infectious disease transmission. - Josepha Godivier
Compressive stress gradients direct mechanoregulation of anisotropic growth in the zebrafish jaw joint. - Linxing Preston Jiang
Dynamic predictive coding: A model of hierarchical sequence learning and prediction in the neocortex. - Xiang Liu
An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level. - Meenal Datta
Mathematical model of oxygen, nutrient, and drug transport in tuberculosis granulomas. - Samuel H. A. von der Dunk
Intracellular signaling in proto-eukaryotes evolves to alleviate regulatory conflicts of endosymbiosis. - Nathan LaPierre
Accounting for isoform expression increases power to identify genetic regulation of gene expression. - Kemin Zhu, Ling Yin
Generating synthetic population for simulating the spatiotemporal dynamics of epidemics. - Carlos S. N. Brito, Wulfram Gerstner
Learning what matters: Synaptic plasticity with invariance to second-order input correlations. - Zhenxing Guo, Daoyu Duan, Wen Tang
magpie: A power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing. - Lachlan Baer
Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis. - Jiao Zhao, Ke Chen, Bernhard O. Palsson
StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses. - Li-Dunn Chen
Enhancing predictive performance for spectroscopic studies in wildlife science through a multi-model approach: A case study for species classification of live amphibians. - Jakub Köry
Enhanced perfusion following exposure to radiotherapy: A theoretical investigation. - András Zeke, Toby J. Gibson, Laszlo Dobson
Linear motifs regulating protein secretion, sorting and autophagy in Leishmania parasites are diverged with respect to their host equivalents. - Martin L. L. R. Barry
Fast adaptation to rule switching using neuronal surprise. - Sven Wientjes
The successor representation subserves hierarchical abstraction for goal-directed behavior. - Alexander D. Bird
Robust and consistent measures of pattern separation based on information theory and demonstrated in the dentate gyrus. - Jose Gabriel Nino Barreat
Ecological and evolutionary dynamics of cell-virus-virophage systems. - Natalie Schieferstein
Intra-ripple frequency accommodation in an inhibitory network model for hippocampal ripple oscillations. - Francesco Pinotti
EPINEST, an agent-based model to simulate epidemic dynamics in large-scale poultry production and distribution networks. - Quintessa Hay
Age-dependent ventilator-induced lung injury: Mathematical modeling, experimental data, and statistical analysis. - Juliette Cooke
Genome scale metabolic network modelling for metabolic profile predictions. - Eshan S. King
Diverse mutant selection windows shape spatial heterogeneity in evolving populations. - Tom Van Wouwe
A simulation framework to determine optimal strength training and musculoskeletal geometry for sprinting and distance running. - Tomas Barta
Shared input and recurrency in neural networks for metabolically efficient information transmission. - Moritz Groden
A biologically inspired repair mechanism for neuronal reconstructions with a focus on human dendrites. - Nicholas Tolley
Methods and considerations for estimating parameters in biophysically detailed neural models with simulation based inference. - Paul Soulos, Leyla Isik
Disentangled deep generative models reveal coding principles of the human face processing network. - Pan Li, Jae Kyoung Kim
Circadian regulation of sinoatrial nodal cell pacemaking function: Dissecting the roles of autonomic control, body temperature, and local circadian rhythmicity. - Sangjeong Lee, Hyunwoo Kim
Bidirectional de novo peptide sequencing using a transformer model. - R. Dustin Schaeffer
ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2. - Chen Zhang
STGIC: A graph and image convolution-based method for spatial transcriptomic clustering. - Rui Wang, Zhilin Qu
Dissecting the roles of calcium cycling and its coupling with voltage in the genesis of early afterdepolarizations in cardiac myocyte models. - Takahiro Kohsokabe
Developmental hourglass: Verification by numerical evolution and elucidation by dynamical-systems theory. - Denise Vlachou, Maria Veretennikova, Laura Usselmann, Vadim Vasilyev, Sascha Ott, Georg A. Bjarnason, Robert Dallmann
TimeTeller: A tool to probe the circadian clock as a multigene dynamical system. - Bonnie V. Dougherty, Connor J. Moore, Kristopher D. Rawls
Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism. - Bastiaan J. R. Cockx
Is it selfish to be filamentous in biofilms? Individual-based modeling links microbial growth strategies with morphology using the new and modular iDynoMiCS 2.0. - Margaritis Voliotis
HormoneBayes: A novel Bayesian framework for the analysis of pulsatile hormone dynamics.
- Daniele Dall'Olio
Covering Hierarchical Dirichlet Mixture Models on binary data to enhance genomic stratifications in onco-hematology. - Yongtao Ye, Marcus H. Shum, Joseph L. Tsui, Guangchuang Yu
Robust expansion of phylogeny for fast-growing genome sequence data. - Aaron L. Phillips
CLAW: An automated Snakemake workflow for the assembly of chloroplast genomes from long-read data. - Luca Sesta
Inference of annealed protein fitness landscapes with AnnealDCA. - Alexander Borst
Connectivity Matrix Seriation via Relaxation. - Dennis Eschweiler
Denoising diffusion probabilistic models for generation of realistic fully-annotated microscopy image datasets. - Lily Monnier
A novel batch-effect correction method for scRNA-seq data based on Adversarial Information Factorization. - Martin H. P. Fernholz, Drago A. Guggiana Nilo, Tobias Bonhoeffer, Andreas M. Kist
DeepD3, an open framework for automated quantification of dendritic spines.
- Tyson L. Swetnam
CyVerse: Cyberinfrastructure for open science. - Hong Seo Lim
Quantifying the clusterness and trajectoriness of single-cell RNA-seq data.
Volume 20, Number 3, 2024
- Takehiro Ajioka, Nobuhiro Nakai
End-to-end deep learning approach to mouse behavior classification from cortex-wide calcium imaging. 1011074 - Kosaku Kitagawa, Kwang Su Kim, Masashi Iwamoto, Sanae Hayashi, Hyeongki Park, Takara Nishiyama, Naotoshi Nakamura
Multiscale modeling of HBV infection integrating intra- and intercellular viral propagation to analyze extracellular viral markers. 1011238 - Wencel Valega-Mackenzie
Dose optimization of an adjuvanted peptide-based personalized neoantigen melanoma vaccine. 1011247 - Emma L. Davis
An analytically tractable, age-structured model of the impact of vector control on mosquito-transmitted infections. 1011440 - Tyler Cassidy
Modeling resistance to the broadly neutralizing antibody PGT121 in people living with HIV-1. 1011518 - Matteo Martin, Morten Gram Pedersen
Modelling and analysis of cAMP-induced mixed-mode oscillations in cortical neurons: Critical roles of HCN and M-type potassium channels. 1011559 - Yucai Shao
Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models. 1011640 - Siobhan Mackenzie Hall
Ten simple rules for pushing boundaries of inclusion at academic events. 1011797 - Cecilia Wieder
PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration. 1011814 - Lauren A. Fromont
Twelve quick tips for deploying a Beacon. 1011817 - Edgar Peña, Nicole A. Pelot
Computational models of compound nerve action potentials: Efficient filter-based methods to quantify effects of tissue conductivities, conduction distance, and nerve fiber parameters. 1011833 - Derek E. Moulton
A multiscale computational framework for the development of spines in molluscan shells. 1011835 - Benjamin S. M. Barlow
Impact on backpropagation of the spatial heterogeneity of sodium channel kinetics in the axon initial segment. 1011846 - Yu Toyoshima
Ensemble dynamics and information flow deduction from whole-brain imaging data. 1011848 - Hendrik Reimann
The condition for dynamic stability in humans walking with feedback control. 1011861 - Mari Kawakatsu
When do stereotypes undermine indirect reciprocity? 1011862 - Elizabeth Seckel
Ten simple rules to leverage large language models for getting grants. 1011863 - Robert P. Gowers, Susanne Schreiber
How neuronal morphology impacts the synchronisation state of neuronal networks. 1011874 - Tadeusz Satlawa, Mateusz Tarkowski, Sonia Wróbel, Pawel Dudzic, Tomasz Gawlowski, Tomasz Klaus, Marek Orlowski
LAP: Liability Antibody Profiler by sequence & structural mapping of natural and therapeutic antibodies. 1011881 - Chenyu Wu
Using birth-death processes to infer tumor subpopulation structure from live-cell imaging drug screening data. 1011888 - András Ecker
Cortical cell assemblies and their underlying connectivity: An in silico study. 1011891 - Nora S. Martin
Bias in the arrival of variation can dominate over natural selection in Richard Dawkins's biomorphs. 1011893 - Kohei Ichikawa
Bayesian inference is facilitated by modular neural networks with different time scales. 1011897 - Jonas Denk
Tipping points emerge from weak mutualism in metacommunities. 1011899 - Yang Jiang
It is theoretically possible to avoid misfolding into non-covalent lasso entanglements using small molecule drugs. 1011901 - Maria Luisa Saggio
Bifurcations and bursting in the Epileptor. 1011903 - Yang Ping Kuo
Evolutionary graph theory beyond pairwise interactions: Higher-order network motifs shape times to fixation in structured populations. 1011905 - Cera W. Hassinan
Dimensionality of locomotor behaviors in developing C. elegans. 1011906 - Junjie Xia, Hoang Van Phan, Luke Vistain
Computational prediction of protein interactions in single cells by proximity sequencing. 1011915 - Nazanin Ahmadi Daryakenari
AI-Aristotle: A physics-informed framework for systems biology gray-box identification. 1011916 - Jessica S. Yu
Model design choices impact biological insight: Unpacking the broad landscape of spatial-temporal model development decisions. 1011917 - Nadin Haase, Wolf Holtkamp, Simon Christ, Dag Heinemann, Marina V. Rodnina, Sophia Rudorf
Decomposing bulk signals to reveal hidden information in processive enzyme reactions: A case study in mRNA translation. 1011918 - Luís Pedro Coelho
For long-term sustainable software in bioinformatics. 1011920 - Javier Galván Fraile, Franz Scherr, José J. Ramasco
Modeling circuit mechanisms of opposing cortical responses to visual flow perturbations. 1011921 - Minija Tamosiunaite
Unsupervised learning of perceptual feature combinations. 1011926 - Søren D. Petersen, Lucas Levassor
teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering. 1011929 - Md Nurul Anwar
Mathematical models of Plasmodium vivax transmission: A scoping review. 1011931 - Cameron Zachreson
Ethical frameworks should be applied to computational modelling of infectious disease interventions. 1011933 - Sofía Jijón, Peter Czuppon, François Blanquart, Florence Débarre
Using early detection data to estimate the date of emergence of an epidemic outbreak. 1011934 - Maximilian M. Mandl
Raising awareness of uncertain choices in empirical data analysis: A teaching concept toward replicable research practices. 1011936 - Manuel Razo-Mejia
Bayesian inference of relative fitness on high-throughput pooled competition assays. 1011937 - Moritz Ertelt
Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins. 1011939 - Chaitanya Chintaluri
kCSD-python, reliable current source density estimation with quality control. 1011941 - Hao-Ting Wang
Continuous evaluation of denoising strategies in resting-state fMRI connectivity using fMRIPrep and Nilearn. 1011942 - Peng Liu
Emergence of Emotion Selectivity in Deep Neural Networks Trained to Recognize Visual Objects. 1011943 - Pahala Gedara Jayathilake
Metabolic symbiosis between oxygenated and hypoxic tumour cells: An agent-based modelling study. 1011944 - Jaron T. Colas
Active reinforcement learning versus action bias and hysteresis: control with a mixture of experts and nonexperts. 1011950 - Timothy Hasse
Mechanistic insights into ligand dissociation from the SARS-CoV-2 spike glycoprotein. 1011955 - Büsra Atamer Balkan, You Chang, Martijn Sparnaaij
The multi-dimensional challenges of controlling respiratory virus transmission in indoor spaces: Insights from the linkage of a microscopic pedestrian simulation and SARS-CoV-2 transmission model. 1011956 - Rachael Pung
Detecting changes in generation and serial intervals under varying pathogen biology, contact patterns and outbreak response. 1011967 - Nicholas Markarian
Enrichment on steps, not genes, improves inference of differentially expressed pathways. 1011968 - Jialiang Sun, Jun Guo, Jian Liu
CRISPR-M: Predicting sgRNA off-target effect using a multi-view deep learning network. 1011972 - Sarah A. Vollert
Unlocking ensemble ecosystem modelling for large and complex networks. 1011976 - Kati Hyvärinen
A machine-learning method for biobank-scale genetic prediction of blood group antigens. 1011977 - Jonas Simoens
Learning environment-specific learning rates. 1011978 - Yitong Lv, He Gong, Xuechao Liu, Jia Hao, Lei Xu, Zhiwei Sun, Changyuan Yu
A dual computational and experimental strategy to enhance TSLP antibody affinity for improved asthma treatment. 1011984 - Ann Osi
Parameter estimation in behavioral epidemic models with endogenous societal risk-response. 1011992 - Boaz Shvartzman, Yoav Ram
Self-replicating artificial neural networks give rise to universal evolutionary dynamics. 1012004 - Jakub Svoboda
Amplifiers of selection for the Moran process with both Birth-death and death-Birth updating. 1012008
Volume 20, Number 4, 2024
- Irena Balzekas
Method for cycle detection in sparse, irregularly sampled, long-term neuro-behavioral timeseries: Basis pursuit denoising with polynomial detrending of long-term, inter-ictal epileptiform activity. 1011152 - Beren Millidge, Mufeng Tang, Mahyar Osanlouy, Nicol S. Harper, Rafal Bogacz
Predictive coding networks for temporal prediction. 1011183 - Alice Geminiani
Mesoscale simulations predict the role of synergistic cerebellar plasticity during classical eyeblink conditioning. 1011277 - Chaoyue Sun
DeepDynaForecast: Phylogenetic-informed graph deep learning for epidemic transmission dynamic prediction. 1011351 - Rabea Link, Mona Jaggy, Martin Bastmeyer, Ulrich S. Schwarz
Modelling cell shape in 3D structured environments: A quantitative comparison with experiments. 1011412 - Carolin Zitzmann, Ruian Ke, Ruy M. Ribeiro, Alan S. Perelson
How robust are estimates of key parameters in standard viral dynamic models? 1011437 - Arco Bast
Network-neuron interactions underlying sensory responses of layer 5 pyramidal tract neurons in barrel cortex. 1011468 - Vineeth Gutta
UNNT: A novel Utility for comparing Neural Net and Tree-based models. 1011504 - Yuhao Wang
Dopamine encoding of novelty facilitates efficient uncertainty-driven exploration. 1011516 - Anastasis Oulas
Ranking of cell clusters in a single-cell RNA-sequencing analysis framework using prior knowledge. 1011550 - Scott Boebinger
Precise cortical contributions to sensorimotor feedback control during reactive balance. 1011562 - Judith A. Bouman
Bayesian workflow for time-varying transmission in stratified compartmental infectious disease transmission models. 1011575 - Alex D. Richardson
Learning spatio-temporal patterns with Neural Cellular Automata. 1011589 - Adam Husár, Mariam Ordyan, Guadalupe C. Garcia, Joel G. Yancey, Ali Sinan Saglam, James R. Faeder, Thomas M. Bartol, Mary B. Kennedy
MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface. 1011800 - Jinghao Chen, Jesse R. Holt, Elizabeth L. Evans, John S. Lowengrub
PIEZO1 regulates leader cell formation and cellular coordination during collective keratinocyte migration. 1011855 - Dong Ouyang, Yong Liang
HGCLAMIR: Hypergraph contrastive learning with attention mechanism and integrated multi-view representation for predicting miRNA-disease associations. 1011927 - Chang Liu
A probabilistic knowledge graph for target identification. 1011945 - Tianhe Wang
Perturbation Variability Does Not Influence Implicit Sensorimotor Adaptation. 1011951 - Kenneth Kay
Emergent neural dynamics and geometry for generalization in a transitive inference task. 1011954 - Christian Donner
Ensemble learning and ground-truth validation of synaptic connectivity inferred from spike trains. 1011964 - Danica Despotovic
Encoding surprise by retinal ganglion cells. 1011965 - Shiro Kato, Yukiko Himeno, Akira Amano
Mathematical analysis of left ventricular elastance with respect to afterload change during ejection phase. 1011974 - Rui Meng, Kristofer E. Bouchard
Bayesian inference of structured latent spaces from neural population activity with the orthogonal stochastic linear mixing model. 1011975 - Bryce Morsky
Indirect reciprocity with Bayesian reasoning and biases. 1011979 - Carla S. Griffiths, Jules M. Lebert, Joseph Sollini, Jennifer K. Bizley
Gradient boosted decision trees reveal nuances of auditory discrimination behavior. 1011985 - Yixiao Zhai, Jiannan Chao, Yizheng Wang, Pinglu Zhang
TPMA: A two pointers meta-alignment tool to ensemble different multiple nucleic acid sequence alignments. 1011988 - Yiyang Shi
SubGE-DDI: A new prediction model for drug-drug interaction established through biomedical texts and drug-pairs knowledge subgraph enhancement. 1011989 - Yajas Shah
Benchmarking multi-ancestry prostate cancer polygenic risk scores in a real-world cohort. 1011990 - Christopher N. Davis
Comparison of stochastic and deterministic models for gambiense sleeping sickness at different spatial scales: A health area analysis in the DRC. 1011993 - Kje Hickman, Geoffrey Zahn
Ten simple rules for leading a successful undergraduate-intensive research lab. 1011994 - Patrick Gemmell, Timothy B. Sackton
A phylogenetic method linking nucleotide substitution rates to rates of continuous trait evolution. 1011995 - Adam Lampert
Optimizing strategies for slowing the spread of invasive species. 1011996 - Alejandro Tlaie
What does the mean mean? A simple test for neuroscience. 1012000 - Christian Cammarota, Nicole S. Dawney, Philip M. Bellomio, Maren Jüng
The mechanical influence of densification on epithelial architecture. 1012001 - Florian E. C. Blanc
A weak coupling mechanism for the early steps of the recovery stroke of myosin VI: A free energy simulation and string method analysis. 1012005 - Malek Senoussi, Thierry Artières
Partial label learning for automated classification of single-cell transcriptomic profiles. 1012006 - Emma Beniston, Jordan P. Skittrall
Locations and structures of influenza A virus packaging-associated signals and other functional elements via an in silico pipeline for predicting constrained features in RNA viruses. 1012009 - Hui Liu, Feng Wang
DBDNMF: A Dual Branch Deep Neural Matrix Factorization method for drug response prediction. 1012012 - Kamil Wolos
Non-invasive assessment of stroke volume and cardiovascular parameters based on peripheral pressure waveform. 1012013 - Kevin Zhang, Junhao Zhu, Dehan Kong, Zhaolei Zhang
Modeling single cell trajectory using forward-backward stochastic differential equations. 1012015 - Satyaki Roy
CoVar: A generalizable machine learning approach to identify the coordinated regulators driving variational gene expression. 1012016 - Jennifer A. Flegg
Spatio-temporal spread of artemisinin resistance in Southeast Asia. 1012017 - Adrian Lison
Generative Bayesian modeling to nowcast the effective reproduction number from line list data with missing symptom onset dates. 1012021 - Luca Giudice
StellarPath: Hierarchical-vertical multi-omics classifier synergizes stable markers and interpretable similarity networks for patient profiling. 1012022 - Puranjan Ghimire, Mo Motamedi, Richard I. Joh
Mathematical model for the role of multiple pericentromeric repeats on heterochromatin assembly. 1012027 - Marc D. Singleton
Evolutionary analyses of intrinsically disordered regions reveal widespread signals of conservation. 1012028 - Bingxian Xu
Temperature-driven coordination of circadian transcriptional regulation. 1012029 - Sami Mollard
Recurrent neural networks that learn multi-step visual routines with reinforcement learning. 1012030 - Tracy J. Kuper
Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment. 1012031 - Jesse Wheeler
Informing policy via dynamic models: Cholera in Haiti. 1012032 - Florian G. Pflug
Neutral competition explains the clonal composition of neural organoids. 1012054 - Lucy Lai
Human decision making balances reward maximization and policy compression. 1012057 - Sarah L. Master
Wagers for work: Decomposing the costs of cognitive effort. 1012060 - Robert Challen
Combined multiplex panel test results are a poor estimate of disease prevalence without adjustment for test error. 1012062 - Jong Hyuk Byun
Validity conditions of approximations for a target-mediated drug disposition model: A novel first-order approximation and its comparison to other approximations. 1012066 - Naiqian Zhang
A novel hypergraph model for identifying and prioritizing personalized drivers in cancer. 1012068 - Carla Alejandre
Synergistic epistasis among cancer drivers can rescue early tumors from the accumulation of deleterious passengers. 1012081 - H. Robert Frost
Reconstruction Set Test (RESET): A computationally efficient method for single sample gene set testing based on randomized reduced rank reconstruction error. 1012084
Volume 20, Number 5, 2024
- Yifei Ren, Pouya Bashivan
How well do models of visual cortex generalize to out of distribution samples? 1011145 - Velma K. Lopez
Challenges of COVID-19 Case Forecasting in the US, 2020-2021. 1011200 - Paulina Clara Dagnino
Re-awakening the brain: Forcing transitions in disorders of consciousness by external in silico perturbation. 1011350 - Sean M. Cascarina
Identification of Low-Complexity Domains by Compositional Signatures Reveals Class-Specific Frequencies and Functions Across the Domains of Life. 1011372 - Sanjeevani Choudhery
A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens. 1011408 - Ariana Chriss
Agent-based modeling of nuclear chromosome ensembles identifies determinants of homolog pairing during meiosis. 1011416 - Eric R. Snyder
Where's Whaledo: A software toolkit for array localization of animal vocalizations. 1011456 - Evan D. Gorman, Manuel E. Lladser
Interpretable metric learning in comparative metagenomics: The adaptive Haar-like distance. 1011543 - Shoutik Mukherjee
Adaptive modeling and inference of higher-order coordination in neuronal assemblies: A dynamic greedy estimation approach. 1011605 - Luke Trinity
Tying the knot: Unraveling the intricacies of the coronavirus frameshift pseudoknot. 1011787 - Moo K. Chung
Topological state-space estimation of functional human brain networks. 1011869 - David Pastor-Alonso, Maxime Berg, Franck Boyer, Natalie Fomin-Thunemann, Michel Quintard, Yohan Davit, Sylvie Lorthois
Modeling oxygen transport in the brain: An efficient coarse-grid approach to capture perivascular gradients in the parenchyma. 1011973 - Keiji Ota
Dissecting Bayes: Using influence measures to test normative use of probability density information derived from a sample. 1011999 - Andriana Manousidaki
Clustering and visualization of single-cell RNA-seq data using path metrics. 1012014 - Ava M. Hoffman
Ten simple rules for teaching an introduction to R. 1012018 - Hong Yang, Ying Shi
PESSA: A web tool for pathway enrichment score-based survival analysis in cancer. 1012024 - Fleur Zeldenrust
The tuning of tuning: How adaptation influences single cell information transfer. 1012043 - Raphael Sonabend
FAIR-USE4OS: Guidelines for creating impactful open-source software. 1012045 - Héctor M. Sánchez C.
MGSurvE: A framework to optimize trap placement for genetic surveillance of mosquito populations. 1012046 - Blox Bloxham
Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches. 1012049 - Yves Dumont
On the impact of re-mating and residual fertility on the Sterile Insect Technique efficacy: Case study with the medfly, Ceratitis capitata. 1012052 - Benjamin Antin
Removing direct photocurrent artifacts in optogenetic connectivity mapping data via constrained matrix factorization. 1012053 - Santiago A. Cadena
Diverse task-driven modeling of macaque V4 reveals functional specialization towards semantic tasks. 1012056 - Thirza Dado
Brain2GAN: Feature-disentangled neural encoding and decoding of visual perception in the primate brain. 1012058 - Jason M. Müller, Katharina Moos, Till Baar
Nuclear export is a limiting factor in eukaryotic mRNA metabolism. 1012059 - Richard Michael
A systematic analysis of regression models for protein engineering. 1012061 - Daniel L. Barton
Data-driven modelling makes quantitative predictions regarding bacteria surface motility. 1012063 - Nezar Abdennur, Sameer Abraham, Geoffrey Fudenberg
Cooltools: Enabling high-resolution Hi-C analysis in Python. 1012067 - Charles Mullon
The evolution of environmentally mediated social interactions and posthumous spite under isolation by distance. 1012071 - Yuchao Li, Difan Deng, Chris Tina Höfer, Jihye Kim, Won Do Heo, Quanbin Xu, Xuedong Liu, Zhike Zi
Liebig's law of the minimum in the TGF-β/SMAD pathway. 1012072 - Kanyarat Jitmana
Mathematical modeling of the evolution of resistance and aggressiveness of high-grade serous ovarian cancer from patient CA-125 time series. 1012073 - Valdemar Kargård Olsen
The quality and complexity of pairwise maximum entropy models for large cortical populations. 1012074 - James Ryu, Amin Nejatbakhsh, Mahdi Torkashvand
Versatile multiple object tracking in sparse 2D/3D videos via deformable image registration. 1012075 - Yasuhiro Mochizuki
Foraging in a non-foraging task: Fitness maximization explains human risk preference dynamics under changing environment. 1012080 - An Qi Zhang, Martin R. Ralph, Adam R. Stinchcombe
A mathematical model for the role of dopamine-D2 self-regulation in the production of ultradian rhythms. 1012082 - Udaysankar Chockanathan
Differential disruptions in population coding along the dorsal-ventral axis of CA1 in the APP/PS1 mouse model of Aβ pathology. 1012085 - Tianqi Wei, Qinghai Guo, Barbara Webb
Learning with sparse reward in a gap junction network inspired by the insect mushroom body. 1012086 - David Mezey
Visual social information use in collective foraging. 1012087 - Sébastien Benzekry
Machine-learning and mechanistic modeling of metastatic breast cancer after neoadjuvant treatment. 1012088 - Tanmoy Sarkar, Matej Krajnc
Graph topological transformations in space-filling cell aggregates. 1012089 - Hazal Koptagel
Scuphr: A probabilistic framework for cell lineage tree reconstruction. 1012094 - Vishal Rana, Jianhao Peng, Chao Pan, Hanbaek Lyu, Albert Cheng, Minji Kim, Olgica Milenkovic
Interpretable online network dictionary learning for inferring long-range chromatin interactions. 1012095 - Phoebe Asplin
Epidemiological and health economic implications of symptom propagation in respiratory pathogens: A mathematical modelling investigation. 1012096 - Tomas Ferreira Amaro Freire, Zhijian Hu, Kevin B. Wood, Erida Gjini
Modeling spatial evolution of multi-drug resistance under drug environmental gradients. 1012098 - Alexander Kroll, Sahasra Ranjan, Martin J. Lercher
A multimodal Transformer Network for protein-small molecule interactions enhances predictions of kinase inhibition and enzyme-substrate relationships. 1012100 - Nikhil Phaniraj
Marmosets mutually compensate for differences in rhythms when coordinating vigilance. 1012104 - Tara Hameed
Inferring fungal growth rates from optical density data. 1012105 - Martina Conte
Structural and practical identifiability of contrast transport models for DCE-MRI. 1012106 - István Oszoli, István Zachar
Group-selection via aggregative propagule-formation enables cooperative multicellularity in an individual based, spatial model. 1012107 - Albert Albesa-González
Learning with filopodia and spines: Complementary strong and weak competition lead to specialized, graded, and protected receptive fields. 1012110 - Claudia Pascovich
Dorsal and median raphe neuronal firing dynamics characterized by nonlinear measures. 1012111 - Meng Wang
Machine learning and multi-omics data reveal driver gene-based molecular subtypes in hepatocellular carcinoma for precision treatment. 1012113 - Feng Jiao, Jing Li, Ting Liu, Yifeng Zhu, Wenhao Che, Leonidas Bleris, Chen Jia
What can we learn when fitting a simple telegraph model to a complex gene expression model? 1012118 - Milena Rmus
Artificial neural networks for model identification and parameter estimation in computational cognitive models. 1012119 - Alexander Massey
Real-time forecasting of COVID-19-related hospital strain in France using a non-Markovian mechanistic model. 1012124 - Philippe Nguyen
Estimating receptive fields of simple and complex cells in early visual cortex: A convolutional neural network model with parameterized rectification. 1012127 - Thomas Hladish
Evaluating targeted COVID-19 vaccination strategies with agent-based modeling. 1012128 - Marko Sterk, Yaowen Zhang, Viljem Pohorec, Eva Paradiz Leitgeb, Jurij Dolensek, Richard K. P. Benninger, Andraz Stozer, Vira Kravets, Marko Gosak
Network representation of multicellular activity in pancreatic islets: Technical considerations for functional connectivity analysis. 1012130 - Andre J. Faure
An extension of the Walsh-Hadamard transform to calculate and model epistasis in genetic landscapes of arbitrary shape and complexity. 1012132 - Agastya Mondal
MGDrivE 3: A decoupled vector-human framework for epidemiological simulation of mosquito genetic control tools and their surveillance. 1012133 - Kerr Ding
Leveraging conformal prediction to annotate enzyme function space with limited false positives. 1012135 - Tong Liu
Learning Micro-C from Hi-C with diffusion models. 1012136 - Akseli Niemelä
Systematic evaluation of lecithin:cholesterol acyltransferase binding sites in apolipoproteins via peptide based nanodiscs: regulatory role of charged residues at positions 4 and 7. 1012137 - Zachary S. L. Foster, Andrew S. Tupper, Caroline M. Press, Niklaus J. Grünwald
Krisp: A Python package to aid in the design of CRISPR and amplification-based diagnostic assays from whole genome sequencing data. 1012139 - Maria J. Hagelaars
A computational analysis of the role of integrins and Rho-GTPases in the emergence and disruption of apical-basal polarization in renal epithelial cells. 1012140 - Thomas Rawson
The impact of health inequity on spatial variation of COVID-19 transmission in England. 1012141 - Giacomo Janson, Michael Feig
Transferable deep generative modeling of intrinsically disordered protein conformations. 1012144 - Xi Chen
Modelling midline shift and ventricle collapse in cerebral oedema following acute ischaemic stroke. 1012145 - Lucy Lansch-Justen
Estimating mutation rates under heterogeneous stress responses. 1012146 - Trini Nguyen
Competition between physical search and a weak-to-strong transition rate-limits kinesin binding times. 1012158 - Amber Marijn Brands
Temporal dynamics of short-term neural adaptation across human visual cortex. 1012161 - Nezar Abdennur, Geoffrey Fudenberg
Pairtools: From sequencing data to chromosome contacts. 1012164 - Garrick W. Bruening, Robert J. Courter, Shruthi Sukumar, Megan K. O'brien, Alaa A. Ahmed
Disentangling the effects of metabolic cost and accuracy on movement speed. 1012169 - Franz Wurm
Surprise-minimization as a solution to the structural credit assignment problem. 1012175 - Lulu Gong
Astrocytes as a mechanism for contextually-guided network dynamics and function. 1012186
Volume 20, Number 6, 2024
- Jeremy Vanderdoes
Using random forests to uncover the predictive power of distance-varying cell interactions in tumor microenvironments. 1011361 - Lu Zhang, Gang Xue, Xiaolin Zhou, Jiandong Huang, Zhiyuan Li
A mathematical framework for understanding the spontaneous emergence of complexity applicable to growing multicellular systems. 1011882 - Jared Adolf-Bryfogle
Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design. 1011895 - Joshua M. Mitchell
Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline. 1011912 - Bartosz Ambrozy Gren
Knotted artifacts in predicted 3D RNA structures. 1011959 - Jakob Jordan
Conductance-based dendrites perform Bayes-optimal cue integration. 1012047 - Joy M. O'Brien
Ten "simple" rules for non-Indigenous researchers engaging Indigenous communities in Arctic research. 1012093 - Pavel Sanda, Jaroslav Hlinka, Monica van den Berg, Antonín Skoch, Maxim Bazhenov, Georgios A. Keliris, Giri P. Krishnan
Cholinergic modulation supports dynamic switching of resting state networks through selective DMN suppression. 1012099 - Xiaoman Xie
Quantitative estimates of the regulatory influence of long non-coding RNAs on global gene expression variation using TCGA breast cancer transcriptomic data. 1012103 - Nikolaos M. Dimitriou
Cancer cell sedimentation in 3D cultures reveals active migration regulated by self-generated gradients and adhesion sites. 1012112 - Devon J. Boland
Cracking AlphaFold2: Leveraging the power of artificial intelligence in undergraduate biochemistry curriculums. 1012123 - Ellie Mainou
Modeling dynamics of acute HIV infection incorporating density-dependent cell death and multiplicity of infection. 1012129 - Jacqueline Wistuba-Hamprecht
Machine learning prediction of malaria vaccine efficacy based on antibody profiles. 1012131 - Christina M. P. Ray
Mechanistic computational modeling of monospecific and bispecific antibodies targeting interleukin-6/8 receptors. 1012157 - Seoyoung Ahn
The attentive reconstruction of objects facilitates robust object recognition. 1012159 - Justin Bellavance
Eight quick tips for including chromosome X in genome-wide association studies. 1012160 - Mingyi Wang, Jacob G. Scott, Alexander Vladimirsky
Threshold-awareness in adaptive cancer therapy. 1012165 - Roberto Efraín Díaz, Stephanie A. Wankowicz
Ten recommendations for hosting a Diversity, Equity, Inclusion, and Justice (DEIJ) journal club. 1012166 - Justine Vandendorpe
Ten simple rules for implementing electronic lab notebooks (ELNs). 1012170 - Genís Bayarri, Pau Andrio, Josep Lluis Gelpí, Adam Hospital
Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows. 1012173 - Mark D. Robinson
Ten simple rules for computational biologists collaborating with wet lab researchers. 1012174 - Alexandra M. Proca
Synergistic information supports modality integration and flexible learning in neural networks solving multiple tasks. 1012178 - Marisa Conte
Ten simple rules to make computable knowledge shareable and reusable. 1012179 - Mikhail Shubin
The influence of cross-border mobility on the COVID-19 epidemic in Nordic countries. 1012182 - Xiangting Li
Reliable ligand discrimination in stochastic multistep kinetic proofreading: First passage time vs. product counting strategies. 1012183 - Zijian Wang
Missing data in amortized simulation-based neural posterior estimation. 1012184 - Yuanchi Ha, Helena R. Ma
Data-driven learning of structure augments quantitative prediction of biological responses. 1012185 - Lindsey Perry, Rebecca L. Kelble, Valerie N. Brewer, Cara E. Christensen
Ten simple rules for implementing a successful field season. 1012189 - Caleb J. Holt
The stabilized supralinear network accounts for the contrast dependence of visual cortical gamma oscillations. 1012190 - Apolline Louvet
Assessing the extinction risk of the spontaneous flora in urban tree bases. 1012191 - Sebastian Salwig
Zero-shot denoising of microscopy images recorded at high-resolution limits. 1012192 - Yu Zhu
Revisiting the invasion paradox: Resistance-richness relationship is driven by augmentation and displacement trends. 1012193 - Md Zulfikar Ali
Regulatory properties of transcription factors with diverse mechanistic function. 1012194 - Matthew C. Perrone
Prioritizing drug targets by perturbing biological network response functions. 1012195 - Kris Sankaran
mbtransfer: Microbiome intervention analysis using transfer functions and mirror statistics. 1012196 - Roseline Dzekem Dine
Ten simple rules for successful and sustainable African research collaborations. 1012197 - Florian Bolenz
Older adults select different but not simpler strategies than younger adults in risky choice. 1012204 - Seolah Shin, Seok Joo Chae, Seunggyu Lee
Beyond homogeneity: Assessing the validity of the Michaelis-Menten rate law in spatially heterogeneous environments. 1012205 - Diego Andrés Contreras, Giulia Cencetti
Infection patterns in simple and complex contagion processes on networks. 1012206 - Lionel Rigoux, Klaas E. Stephan, Frederike Petzschner
Beliefs, compulsive behavior and reduced confidence in control. 1012207 - Lakshmipuram S. Swapna, Grant C. Stevens, Aline Sardinha-Silva, Lucas Zhongming Hu
ToxoNet: A high confidence map of protein-protein interactions in Toxoplasma gondii. 1012208 - Jente Willaert
Combined translational and rotational perturbations of standing balance reveal contributions of reduced reciprocal inhibition to balance impairments in children with cerebral palsy. 1012209 - Jack M. O'shea
Computational design of Periplasmic binding protein biosensors guided by molecular dynamics. 1012212 - Edward M. Hill, Stavros Petrou, Simon de Lusignan, Ivelina Yonova, Matt J. Keeling:
Correction: Seasonal influenza: Modelling approaches to capture immunity propagation. 1012213 - Shaked Bergman
Strong association between genomic 3D structure and CRISPR cleavage efficiency. 1012214 - Roberth Anthony Rojas Chávez
Mapping the Evolutionary Space of SARS-CoV-2 Variants to Anticipate Emergence of Subvariants Resistant to COVID-19 Therapeutics. 1012215 - Jannik Jauch
Differences in the consolidation by spontaneous and evoked ripples in the presence of active dendrites. 1012218 - Lars D'Hondt
A dynamic foot model for predictive simulations of human gait reveals causal relations between foot structure and whole-body mechanics. 1012219 - Lara S. Burchardt
A toolkit for the dynamic study of air sacs in siamang and other elastic circular structures. 1012222 - Audrey Duval, Quentin J. Leclerc
An algorithm to build synthetic temporal contact networks based on close-proximity interactions data. 1012227 - Chengwei Ai
MTMol-GPT: De novo multi-target molecular generation with transformer-based generative adversarial imitation learning. 1012229 - Tina Yao
Image2Flow: A proof-of-concept hybrid image and graph convolutional neural network for rapid patient-specific pulmonary artery segmentation and CFD flow field calculation from 3D cardiac MRI data. 1012231 - Soraya Mirzaei
GEM-based computational modeling for exploring metabolic interactions in a microbial community. 1012233 - Leopold Zehetner
Logistic PCA explains differences between genome-scale metabolic models in terms of metabolic pathways. 1012236 - Hyeonuk Woo, Yubeen Kim, Chaok Seok
Protein loop structure prediction by community-based deep learning and its application to antibody CDR H3 loop modeling. 1012239 - Qince Li, Zheng Yan, Zhen Wang, Cuiping Liang, Xiqian Wang, Xianghu Wu, Wei Wang, Yongfeng Yuan, Kuanquan Wang
A simulation study on the antiarrhythmic mechanisms of established agents in myocardial ischemia and infarction. 1012244 - Youcheng Li, Leann Lac, Qian Liu, Pingzhao Hu
ST-CellSeg: Cell segmentation for imaging-based spatial transcriptomics using multi-scale manifold learning. 1012254
Volume 20, Number 7, 2024
- Bin Liu
A variational autoencoder trained with priors from canonical pathways increases the interpretability of transcriptome data. 1011198 - Maud Delattre
Modeling soybean growth: A mixed model approach. 1011258 - Jesper J. Madsen
Elucidating the complex membrane binding of a protein with multiple anchoring domains using extHMMM. 1011421 - Paul Schmidt-Barbo
Detection of disease-specific signatures in B cell repertoires of lymphomas using machine learning. 1011570 - Florian Borse, Dovydas Kiciatovas, Teemu Kuosmanen
Quantifying massively parallel microbial growth with spatially mediated interactions. 1011585 - Gustavo Magaña López, Laurence Calzone
scBoolSeq: Linking scRNA-seq statistics and Boolean dynamics. 1011620 - David R. Penas, Meysam Hashemi, Viktor K. Jirsa
Parameter estimation in a whole-brain network model of epilepsy: Comparison of parallel global optimization solvers. 1011642 - Ghazaleh Ostovar, James Q. Boedicker
Phenotypic memory in quorum sensing. 1011696 - Jonas Verhellen, Kosio Beshkov
Multitask learning of a biophysically-detailed neuron model. 1011728 - Haocheng Zhu, Ulrik R. Beierholm
BCI Toolbox: An open-source python package for the Bayesian causal inference model. 1011791 - Wilfredo Blanco
Population bursts in a modular neural network as a mechanism for synchronized activity in KNDy neurons. 1011820 - Thomas Couppey, Louis Regnacq
NRV: An open framework for in silico evaluation of peripheral nerve electrical stimulation strategies. 1011826 - Matthieu Bouguéon, Vincent Legagneux, Octave Hazard, Jérémy Bomo, Anne Siegel, Jérôme Feret, Nathalie Théret:
A rule-based multiscale model of hepatic stellate cell plasticity: Critical role of the inactivation loop in fibrosis progression. 1011858 - Vivienne Leech, Fiona N. Kenny, Stefania Marcotti
Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment. 1011879 - Harry Saxton
Convergence, sampling and total order estimator effects on parameter orthogonality in global sensitivity analysis. 1011946 - Lu Hong
An integrative approach to protein sequence design through multiobjective optimization. 1011953 - Nathan J. Doyle
When should lockdown be implemented? Devising cost-effective strategies for managing epidemics amid vaccine uncertainty. 1012010 - Wentao Li
FedGMMAT: Federated generalized linear mixed model association tests. 1012142 - Samuel E. Hoff, F. Emil Thomasen, Kresten Lindorff-Larsen
Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference. 1012180 - Robyn M. Stuart
HPVsim: An agent-based model of HPV transmission and cervical disease. 1012181 - Xiaoyu Yang, Giancarlo La Camera
Co-existence of synaptic plasticity and metastable dynamics in a spiking model of cortical circuits. 1012220 - Luka Maisuradze
Identifying topologically associating domains using differential kernels. 1012221 - Pascal Grobecker
Identifying cell states in single-cell RNA-seq data at statistically maximal resolution. 1012224 - Sarah Schwöbel
Joint modeling of choices and reaction times based on Bayesian contextual behavioral control. 1012228 - Sara Stoudt
Ten simple rules for building and maintaining a responsible data science workflow. 1012232 - Vinoth Manivannan, Mandar M. Inamdar, Ranjith Padinhateeri
Role of diffusion and reaction of the constituents in spreading of histone modification marks. 1012235 - Mahshid Fardadi
Model-based analysis of the acute effects of transcutaneous magnetic spinal cord stimulation on micturition after spinal cord injury in humans. 1012237 - Chrysovalantou Kalaitzidou
Compressive instabilities enable cell-induced extreme densification patterns in the fibrous extracellular matrix: Discrete model predictions. 1012238 - Simone Blanco Malerba
Jointly efficient encoding and decoding in neural populations. 1012240 - Andrew A. Chen
PARE: A framework for removal of confounding effects from any distance-based dimension reduction method. 1012241 - Ulrik Hvid, Namiko Mitarai
Competitive advantages of T-even phage lysis inhibition in response to secondary infection. 1012242 - Xun Fu, Jack Withers, Juri A. Miyamae, Talia Y. Moore
ArborSim: Articulated, branching, OpenSim routing for constructing models of multi-jointed appendages with complex muscle-tendon architecture. 1012243 - Brianna Marsh
Emergent effects of synaptic connectivity on the dynamics of global and local slow waves in a large-scale thalamocortical network model of the human brain. 1012245 - Marcus Ghosh
Nonlinear fusion is optimal for a wide class of multisensory tasks. 1012246 - Simon K. S. Chu
Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset. 1012248 - David Moreau
Nine quick tips for open meta-analyses. 1012252 - Patrick Bryant
Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile. 1012253 - Shihan Ma, Irene Mendez Guerra, Arnault H. Caillet, Jiamin Zhao, Alexander Kenneth Clarke, Kostiantyn Maksymenko, Samuel Deslauriers-Gauthier, Xinjun Sheng, Xiangyang Zhu, Dario Farina
NeuroMotion: Open-source platform with neuromechanical and deep network modules to generate surface EMG signals during voluntary movement. 1012257 - Matthew Beauregard Smith
Estimating error rates for single molecule protein sequencing experiments. 1012258 - Pau Clusella
Modeling the impact of neuromorphological alterations in Down syndrome on fast neural oscillations. 1012259 - Kanishk Chauhan
Synaptic reorganization of synchronized neuronal networks with synaptic weight and structural plasticity. 1012261 - Elias Rosenblatt
Epidemiological modeling of SARS-CoV-2 in white-tailed deer (Odocoileus virginianus) reveals conditions for introduction and widespread transmission. 1012263 - Thomas Williams
Spatial information allows inference of the prevalence of direct cell-to-cell viral infection. 1012264 - Gisela Gabernet
nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework. 1012265 - Alexa Petrucciani, Alexis Hoerter, Leigh Kotze, Nelita Du Plessis, Elsje Pienaar
Agent-based model predicts that layered structure and 3D movement work synergistically to reduce bacterial load in 3D in vitro models of tuberculosis granuloma. 1012266 - Andres J. Nevarez
Using deep learning to decipher the impact of telomerase promoter mutations on the dynamic metastatic morpholome. 1012271 - Pierre Le Denmat
A low-dimensional approximation of optimal confidence. 1012273 - Ziyan Guo, Jialu Yu, Wenxin Wang, Patricia Lockwood, Zhen Wu
Reinforcement learning of altruistic punishment differs between cultures and across the lifespan. 1012274 - Virgile Andréani
Generating information-dense promoter sequences with optimal string packing. 1012276 - Hsun Chiang, Chih-Ang Chung
Simulation of Soluble and Bound VEGF-stimulated in vitro Capillary-like Network Formation on Deformed Substrate. 1012281 - Botond B. Antal, Anthony G. Chesebro, Helmut H. Strey, Lilianne R. Mujica-Parodi, Corey Weistuch
Achieving Occam's razor: Deep learning for optimal model reduction. 1012283 - Yingjun Ma
Kernel Bayesian logistic tensor decomposition with automatic rank determination for predicting multiple types of miRNA-disease associations. 1012287 - David A. Brewster, Martin A. Nowak, Josef Tkadlec
Fixation times on directed graphs. 1012299 - Diogo Melo
Reassessing the modularity of gene co-expression networks using the Stochastic Block Model. 1012300 - Noah B. Herrington
A comprehensive exploration of the druggable conformational space of protein kinases using AI-predicted structures. 1012302 - Eric Tatara, Qinyun Lin
Spatial inequities in access to medications for treatment of opioid use disorder highlight scarcity of methadone providers under counterfactual scenarios. 1012307 - Beth M. Tuschhoff
Detecting and quantifying heterogeneity in susceptibility using contact tracing data. 1012310 - Yiu Chung Lau, Songwei Shan, Dong Wang, Dongxuan Chen, Zhanwei Du, Eric H. Y. Lau, Daihai He, Linwei Tian, Peng Wu, Benjamin J. Cowling
Forecasting of influenza activity and associated hospital admission burden and estimating the impact of COVID-19 pandemic on 2019/20 winter season in Hong Kong. 1012311 - Nan Wu, Isabel Valera, Fabian H. Sinz, Alexander S. Ecker, Thomas Euler, Yongrong Qiu
Probabilistic neural transfer function estimation with Bayesian system identification. 1012354
Volume 20, Number 8, 2024
- Priscilla E. Greenwood, Lawrence M. Ward
Attentional selection and communication through coherence: Scope and limitations. 1011431 - Ayooluwa J. Bolaji
In silico analyses identify sequence contamination thresholds for Nanopore-generated SARS-CoV-2 sequences. 1011539 - William F. Dean
OOPS: Object-Oriented Polarization Software for analysis of fluorescence polarization microscopy images. 1011723 - Mahraz Behbood
The Na+/K+-ATPase generically enables deterministic bursting in class I neurons by shearing the spike-onset bifurcation structure. 1011751 - Robby Concha-Eloko, Michiel Stock, Bernard De Baets
DepoScope: Accurate phage depolymerase annotation and domain delineation using large language models. 1011831 - Fengdi Zhao
scaDA: A novel statistical method for differential analysis of single-cell chromatin accessibility sequencing data. 1011854 - Rachael Stentiford
Estimating orientation in natural scenes: A spiking neural network model of the insect central complex. 1011913 - Daniel Seeler
Novel mathematical approach to accurately quantify 3D endothelial cell morphology and vessel geometry based on fluorescently marked endothelial cell contours: Application to the dorsal aorta of wild-type and Endoglin-deficient zebrafish embryos. 1011924 - Catherine M. Byrne, Ana Citlali Márquez, Bing Cai, Daniel Coombs
Spatial kinetics and immune control of murine cytomegalovirus infection in the salivary glands. 1011940 - Simon Syga
Evolution of phenotypic plasticity leads to tumor heterogeneity with implications for therapy. 1012003 - Janani Ravi
Modeling the START transition in the budding yeast cell cycle. 1012048 - Alex T. Keeley, Jeffrey M. Lotthammer, Jacqueline F. Pelham
Rhythmidia: A modern tool for circadian period analysis of filamentous fungi. 1012167 - Chadi M. Saad-Roy
Impact of waning immunity against SARS-CoV-2 severity exacerbated by vaccine hesitancy. 1012211 - Einar Bjarki Gunnarsson, Seungil Kim, Brandon Choi, J. Karl Schmid
Understanding patient-derived tumor organoid growth through an integrated imaging and mathematical modeling framework. 1012256 - Quantitative drug susceptibility testing for Mycobacterium tuberculosis using unassembled sequencing data and machine learning. 1012260
- Teemu J. Rintala
COPS: A novel platform for multi-omic disease subtype discovery via robust multi-objective evaluation of clustering algorithms. 1012275 - Rune Höper
A quantitative description of light-limited cyanobacterial growth using flux balance analysis. 1012280 - Hiroto Murata
Protein superfolds are characterised as frustration-free topologies: A case study of pure parallel β-sheet topologies. 1012282 - Ulysse Rançon, Timothée Masquelier, Benoit R. Cottereau
A general model unifying the adaptive, transient and sustained properties of ON and OFF auditory neural responses. 1012288 - Pras Pathmanathan
Credibility assessment of in silico clinical trials for medical devices. 1012289 - Iratxe Puebla
Ten simple rules for recognizing data and software contributions in hiring, promotion, and tenure. 1012296 - Ye Chen
Decoding dynamic visual scenes across the brain hierarchy. 1012297 - Jiayi Lin
A proactive/reactive mass screening approach with uncertain symptomatic cases. 1012308 - Ioana Bouros
Prioritising older individuals for COVID-19 booster vaccination leads to optimal public health outcomes in a range of socio-economic settings. 1012309 - Honghan Li
Diffusion model predicts the geometry of actin cytoskeleton from cell morphology. 1012312 - Jose L. Alejo
Alternate conformational trajectories in ribosome translocation. 1012319 - Ksenia Guseva
Bacteria face trade-offs in the decomposition of complex biopolymers. 1012320 - Andrew A. Schmidt, Alexander Y. Grosberg, Anna Grosberg
A novel kinetic model to demonstrate the independent effects of ATP and ADP/Pi concentrations on sarcomere function. 1012321 - Alireza Zaeemzadeh
Upper bounds for integrated information. 1012323 - Jiaping Liu
rtestim: Time-varying reproduction number estimation with trend filtering. 1012324 - Jonathan S. Ramos, Ivo Henrique Provensi Vieira, Wan Song Rocha, Rosimar Pires Esquerdo, Carolina Yukari Veludo Watanabe, Fernando Berton Zanchi
A transfer learning approach to identify Plasmodium in microscopic images. 1012327 - Lies Zandberg
Bird song comparison using deep learning trained from avian perceptual judgments. 1012329 - Christoph Koch, Ondrej Zika
Influence of surprise on reinforcement learning in younger and older adults. 1012331 - David G. Pina
Ten simple rules for successfully managing EU research grants. 1012335 - Anubha Dey, Suresh Mudunuri, Manjari Kiran
MAGICAL: A multi-class classifier to predict synthetic lethal and viable interactions using protein-protein interaction network. 1012336 - Anton Suvorov
Reliable estimation of tree branch lengths using deep neural networks. 1012337 - Michael B. Sohn
An optimal normalization method for high sparse compositional microbiome data. 1012338 - Yuqing Qian
scRNMF: An imputation method for single-cell RNA-seq data by robust and non-negative matrix factorization. 1012339 - Vasyl V. Mykuliak
Molecular dynamics simulations reveal how vinculin refolds partially unfolded talin rod helices to stabilize them against mechanical force. 1012341 - Ján Antolík, Rémy Cagnol, Tibor Rózsa, Cyril Monier, Yves Frégnac, Andrew P. Davison
A comprehensive data-driven model of cat primary visual cortex. 1012342 - Seth Commichaux
Database size positively correlates with the loss of species-level taxonomic resolution for the 16S rRNA and other prokaryotic marker genes. 1012343 - Yicheng Tao
CNTools: A computational toolbox for cellular neighborhood analysis from multiplexed images. 1012344 - Yunfeng Xiong, Chuntian Wang, Yuan Zhang
Interacting particle models on the impact of spatially heterogeneous human behavioral factors on dynamics of infectious diseases. 1012345 - Lucas Rudelt
Signatures of hierarchical temporal processing in the mouse visual system. 1012355 - Easwaran Ramamurthy
Regression convolutional neural network models implicate peripheral immune regulatory variants in the predisposition to Alzheimer's disease. 1012356 - Gerardo J. Félix-Martínez, Diana Osorio-Londoño, J. Rafael Godínez-Fernández:
Impact of oxygen and glucose availability on the viability and connectivity of islet cells: A computational study of reconstructed avascular human islets. 1012357 - Scott L. Nuismer
Quantifying the risk of spillover reduction programs for human health. 1012358 - Daniel Schirmacher
aiSEGcell: User-friendly deep learning-based segmentation of nuclei in transmitted light images. 1012361 - Keyvan Mahjoory
Convolutional neural networks can identify brain interactions involved in decoding spatial auditory attention. 1012376 - Efrat Cohen-Davidi, Isana Veksler-Lublinsky
Benchmarking the negatives: Effect of negative data generation on the classification of miRNA-mRNA interactions. 1012385 - Diogo L. Pires
The rules of multiplayer cooperation in networks of communities. 1012388 - Peiting Shi, Junmin Han, Yinghao Zhang, Guanpu Li, Xionghui Zhou
IMI-driver: Integrating multi-level gene networks and multi-omics for cancer driver gene identification. 1012389 - Lin Yuan
iCRBP-LKHA: Large convolutional kernel and hybrid channel-spatial attention for identifying circRNA-RBP interaction sites. 1012399 - Tao Wang, Linlin Zhuo
ECD-CDGI: An efficient energy-constrained diffusion model for cancer driver gene identification. 1012400 - Alexander Ney, Nuno R. Nené
Identification of a serum proteomic biomarker panel using diagnosis specific ensemble learning and symptoms for early pancreatic cancer detection. 1012408
Volume 20, Number 9, 2024
- Joseph Shingleton
Backtracking: Improved methods for identifying the source of a deliberate release of Bacillus anthracis from the temporal and spatial distribution of cases. 1010817 - Annika Schmidt
Finding the rhythm: Humans exploit nonlinear intrinsic dynamics of compliant systems in periodic interaction tasks. 1011478 - Carlos Albors
Impact of occluder device configurations in in-silico left atrial hemodynamics for the analysis of device-related thrombus. 1011546 - Monica Golumbeanu
AnophelesModel: An R package to interface mosquito bionomics, human exposure and intervention effects with models of malaria intervention impact. 1011609 - Cécile Le Sueur
GPMelt: A hierarchical Gaussian process framework to explore the dark meltome of thermal proteome profiling experiments. 1011632 - G. Eric Bastien
Virus-host interactions predictor (VHIP): Machine learning approach to resolve microbial virus-host interaction networks. 1011649 - Silja Tammi
Accurate multi-population imputation of MICA, MICB, HLA-E, HLA-F and HLA-G alleles from genome SNP data. 1011718 - Janice Yang, Neil J. Daily
Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments. 1011806 - Israel Luis
Springs vs. motors: Ideal assistance in the lower limbs during walking at different speeds. 1011837 - Anis Ur Rahman
Accelerating joint species distribution modelling with Hmsc-HPC by GPU porting. 1011914 - Ilaria Granata
HELP: A computational framework for labelling and predicting human common and context-specific essential genes. 1012076 - Nicola Dietler, Alia Abbara, Subham Choudhury, Anne-Florence Bitbol
Impact of phylogeny on the inference of functional sectors from protein sequence data. 1012091 - Adrielli Tina Lopes Rego
Language models outperform cloze predictability in a cognitive model of reading. 1012117 - Kath Nicholls, Paul D. W. Kirk, Chris Wallace
Bayesian clustering with uncertain data. 1012301 - Yann Le Cunff, Laurent Chesneau
Unveiling inter-embryo variability in spindle length over time: Towards quantitative phenotype analysis. 1012330 - Yanpeng Yang, Yanyi Zheng, Quan Zou, Jian Li, Hailin Feng
Overcoming CRISPR-Cas9 off-target prediction hurdles: A novel approach with ESB rebalancing strategy and CRISPR-MCA model. 1012340 - Artemy Bakulin, Noam B. Teyssier, Martin Kampmann, Matvei Khoroshkin, Hani Goodarzi
pyPAGE: A framework for Addressing biases in gene-set enrichment analysis - A case study on Alzheimer's disease. 1012346 - Hannah Zoller
Measuring and understanding information storage and transfer in a simulated human gut microbiome. 1012359 - Gustavo Menesse
Information dynamics of in silico EEG Brain Waves: Insights into oscillations and functions. 1012369 - Steffen Krüppel
Applying Super-Resolution and Tomography Concepts to Identify Receptive Field Subunits in the Retina. 1012370 - Ariel Rokem
Ten simple rules for scientific code review. 1012375 - Yujin Goto, Keiichi Kitajo
Selective consistency of recurrent neural networks induced by plasticity as a mechanism of unsupervised perceptual learning. 1012378 - Hamza Giaffar, Sergey Shuvaev, Dmitry Rinberg, Alexei A. Koulakov
The primacy model and the structure of olfactory space. 1012379 - Laura Collesano
Energy landscapes of peptide-MHC binding. 1012380 - Seema B. Plaisier
Design and implementation of an asynchronous online course-based undergraduate research experience (CURE) in computational genomics. 1012384 - Breanne Sparta, Timothy Hamilton, Gunalan Natesan, Samuel D. Aragones
Binomial models uncover biological variation during feature selection of droplet-based single-cell RNA sequencing. 1012386 - Caterina Millevoi
A Physics-Informed Neural Network approach for compartmental epidemiological models. 1012387 - Olav N. L. Aga
HyperTraPS-CT: Inference and prediction for accumulation pathways with flexible data and model structures. 1012393 - Zhichao Zhu
Learning to integrate parts for whole through correlated neural variability. 1012401 - Wilson Wen Bin Goh
Ten quick tips for ensuring machine learning model validity. 1012402 - Clémence Bergerot
Moderate confirmation bias enhances decision-making in groups of reinforcement-learning agents. 1012404 - Hao Duan, Qingchen Zhang, Feifei Cui, Quan Zou
MVST: Identifying spatial domains of spatial transcriptomes from multiple views using multi-view graph convolutional networks. 1012409 - Kit Gallagher
Ten simple rules for training scientists to make better software. 1012410 - Israel Luis
Insights into muscle metabolic energetics: Modelling muscle-tendon mechanics and metabolic rates during walking across speeds. 1012411 - Jiaxin Jiang
Effect of aberrant fructose metabolism following SARS-CoV-2 infection on colorectal cancer patients' poor prognosis. 1012412 - Dong Yu
Maintenance of delay-period activity in working memory task is modulated by local network structure. 1012415 - Kirstin I. Oliveira Roster
Surveillance strategies for the detection of new pathogen variants across epidemiological contexts. 1012416 - Daniel Steiert
An exploration into CTEPH medications: Combining natural language processing, embedding learning, in vitro models, and real-world evidence for drug repurposing. 1012417 - Travis M. Blimkie
Facilitating pathway and network based analysis of RNA-Seq data with pathlinkR. 1012422 - Adrian J. Green
Deep autoencoder-based behavioral pattern recognition outperforms standard statistical methods in high-dimensional zebrafish studies. 1012423 - Alia Abbara, Lisa Pagani
Mutant fate in spatially structured populations on graphs: Connecting models to experiments. 1012424 - Michiel Stock
Hyperdimensional computing: A fast, robust, and interpretable paradigm for biological data. 1012426 - Justin Lin
Calibrating dimension reduction hyperparameters in the presence of noise. 1012427 - Nafiseh Atapour, Marcello G. P. Rosa, Shi Bai, Sylwia Bednarek, Agata Kulesza, Gabriela Saworska, Sadaf Teymornejad, Katrina H. Worthy, Piotr Majka
Distribution of calbindin-positive neurons across areas and layers of the marmoset cerebral cortex. 1012428 - Katharina Duecker
Oscillations in an artificial neural network convert competing inputs into a temporal code. 1012429 - Aakash Agrawal
Cracking the neural code for word recognition in convolutional neural networks. 1012430 - Diego A. Forero
Ten simple rules for successfully carrying out funded research projects. 1012431 - Maansi Desai, Alyssa M. Field, Liberty S. Hamilton
A comparison of EEG encoding models using audiovisual stimuli and their unimodal counterparts. 1012433 - Bharadwaj Vemparala
Antiviral capacity of the early CD8 T-cell response is predictive of natural control of SIV infection: Learning in vivo dynamics using ex vivo data. 1012434 - Ahmadou Sylla
Understanding the transmission of bacterial agents of sapronotic diseases using an ecosystem-based approach: A first spatially realistic metacommunity model. 1012435 - Elena Miu
The refinement paradox and cumulative cultural evolution: Complex products of collective improvement favor conformist outcomes, blind copying, and hyper-credulity. 1012436 - Jason A. Papin
Celebrating a body of work. 1012441 - Eslam Abousamra
Fitness models provide accurate short-term forecasts of SARS-CoV-2 variant frequency. 1012443 - Shuo Wang, Shanjin Wang, Wei Pan, Yuyang Yi, Junyan Lu
Construct prognostic models of multiple myeloma with pathway information incorporated. 1012444 - Tobias Pfennig
Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803. 1012445 - Constance Creux
Comparison and benchmark of deep learning methods for non-coding RNA classification. 1012446 - Juan Pablo Franco
The neural dynamics associated with computational complexity. 1012447 - Mario Grassi, Barbara Tarantino
SEMbap: Bow-free covariance search and data de-correlation. 1012448 - Matt J. Keeling
A retrospective assessment of forecasting the peak of the SARS-CoV-2 Omicron BA.1 wave in England. 1012452 - Kiesha Prem, Kevin van Zandvoort, Petra Klepac, Rosalind M. Eggo, Nicholas G. Davies:
Correction: Projecting contact matrices in 177 geographical regions: An update and comparison with empirical data for the COVID-19 era. 1012454 - Jolanda Malamud
Characterizing the dynamics, reactivity and controllability of moods in depression with a Kalman filter. 1012457 - Brian C. O'Meara
Noise leads to the perceived increase in evolutionary rates over short time scales. 1012458 - Anibal S. Amaral
The neglected giants: Uncovering the prevalence and functional groups of huge proteins in proteomes. 1012459 - Margherita Molaro
A new approach to Health Benefits Package design: an application of the Thanzi La Onse model in Malawi. 1012462 - Ke Li
Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections. 1012469 - Carlos A. Velazquez-Vargas
The role of training variability for model-based and model-free learning of an arbitrary visuomotor mapping. 1012471 - Ylva Katarina Wedmark, Jon Olav Vik
A hierarchy of metabolite exchanges in metabolic models of microbial species and communities. 1012472 - Yutaro Kumagai
BootCellNet, a resampling-based procedure, promotes unsupervised identification of cell populations via robust inference of gene regulatory networks. 1012480 - Jacopo Pasqualini
Emergent ecological patterns and modelling of gut microbiomes in health and in disease. 1012482 - Julien Roche, Mathieu Besson, François Allal, Pierrick Haffray, Pierre Patrice, Marc Vandeputte, Florence Phocas
GenoTriplo: A SNP genotype calling method for triploids. 1012483 - Helder Veras Ribeiro filho
Exploring the potential of structure-based deep learning approaches for T cell receptor design. 1012489 - Kevin Tsai, Zhen Zhou, Jiadong Yang, Zhiliang Xu, Shixin Xu, Roya Zandi, Nan Hao, Weitao Chen, Mark S. Alber
Study of impacts of two types of cellular aging on the yeast bud morphogenesis. 1012491 - Biao Tang, Kexin Ma, Yan Liu, Xia Wang
Managing spatio-temporal heterogeneity of susceptibles by embedding it into an homogeneous model: A mechanistic and deep learning study. 1012497 - Mengze Zhang
Integrating dynamic models and neural networks to discover the mechanism of meteorological factors on Aedes population. 1012499 - Ron Zeira
HIPI: Spatially resolved multiplexed protein expression inferred from H&E WSIs. 1012501
Volume 20, Number 10, 2024
- Michele Gentili
Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals. 1011079 - Abhishek Ranjan
3-D Visualization of Atlantic salmon skin through Ultrasound and Photoacoustic Microscopy. 1011709 - Cecilia de Vicariis
Computational joint action: Dynamical models to understand the development of joint coordination. 1011948 - Felix Ezequiel Gerbaldo, Emanuel Sonder
On the identification of differentially-active transcription factors from ATAC-seq data. 1011971 - Marie-Cécile Dupas
Spatial distribution of poultry farms using point pattern modelling: A method to address livestock environmental impacts and disease transmission risks. 1011980 - Jessica L. Gaines
Bayesian inference of state feedback control parameters for fo perturbation responses in cerebellar ataxia. 1011986 - Yushi Yang, Abdelwahab Kawafi, Qiao Tong, Erika Kague, Chrissy L. Hammond, C. Patrick Royall
Tuning collective behaviour in zebrafish with genetic modification. 1012034 - Xubin Zheng, Dian Meng, Duo Chen, Wan-Ki Wong, Ka-Ho To, Lei Zhu, Jiafei Wu, Yining Liang, Kwong-Sak Leung, Man Hon Wong, Lixin Cheng
scCaT: An explainable capsulating architecture for sepsis diagnosis transferring from single-cell RNA sequencing. 1012083 - Malin Ramne
A Computational Framework for Understanding the Impact of Prior Experiences on Pain Perception and Neuropathic Pain. 1012097 - Amanda Craine, Adarsh Krishnamurthy
Successful cardiac resynchronization therapy reduces negative septal work in patient-specific models of dyssynchronous heart failure. 1012150 - Haolin Jiang, Yulian Xu, Yunguang Tong, Dong Zhang
IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation. 1012293 - Raúl A. Reyes Hueros, Rodrigo A. Gier, Sydney M. Shaffer
Non-genetic differences underlie variability in proliferation among esophageal epithelial clones. 1012360 - Ted Moskovitz
Understanding dual process cognition via the minimum description length principle. 1012383 - Jan Lause
The art of seeing the elephant in the room: 2D embeddings of single-cell data do make sense. 1012403 - Colby Fronk
Bayesian polynomial neural networks and polynomial neural ordinary differential equations. 1012414 - Nicolai Kraus, Michael Aichem
TIBA: A web application for the visual analysis of temporal occurrences, interactions, and transitions of animal behavior. 1012425 - Ruipeng Wei
Quantitative evaluation of DNA damage repair dynamics to elucidate predictors of autism vs. cancer in individuals with germline PTEN variants. 1012449 - Francesco Poli
Autistic traits foster effective curiosity-driven exploration. 1012453 - Ankur Kamboj
Human motor learning dynamics in high-dimensional tasks. 1012455 - Dephney Mathebula
Modelling the impact of vaccination on COVID-19 in African countries. 1012456 - Alexis Bénichou, Jean-Baptiste Masson
Compression-based inference of network motif sets. 1012460 - Safiye Celik
Building, benchmarking, and exploring perturbative maps of transcriptional and morphological data. 1012463 - Lani Fox
Enhancing insights in sexually transmitted infection mapping: Syphilis in Forsyth County, North Carolina, a case study. 1012464 - Philip Greulich
Emergent order in epithelial sheets by interplay of cell divisions and cell fate regulation. 1012465 - Diana C. de Oliveira
A flexible generative algorithm for growing in silico placentas. 1012470 - Adam M. Roth
Roles and interplay of reinforcement-based and error-based processes during reaching and gait in neurotypical adults and individuals with Parkinson's disease. 1012474 - Brandon J. Thio
Reverse-engineered models reveal differential membrane properties of autonomic and cutaneous unmyelinated fibers. 1012475 - Dmitry R. Lyamzin, Andrea Alamia, Mohammad Abdolrahmani, Ryo Aoki, Andrea Benucci
Regularizing hyperparameters of interacting neural signals in the mouse cortex reflect states of arousal. 1012478 - Elin K. Falla
Why aphid virus retention needs more attention: Modelling aphid behaviour and virus manipulation in non-persistent plant virus transmission. 1012479 - Chenxi Liao
Probing the link between vision and language in material perception using psychophysics and unsupervised learning. 1012481 - Nick Schafstall
Ten simple rules to bridge ecology and palaeoecology by publishing outside palaeoecological journals. 1012487 - Bertram Klinger
Quantitative modeling of signaling in aggressive B cell lymphoma unveils conserved core network. 1012488 - Lianghong Chen, Zi Huai Huang, Yan Sun, Mike Domaratzki, Qian Liu, Pingzhao Hu
Conditional probabilistic diffusion model driven synthetic radiogenomic applications in breast cancer. 1012490 - George Gabriel
De novo sensorimotor learning through reuse of movement components. 1012492 - Fan Xia, Yanni Xiao, Junling Ma
The optimal spatially-dependent control measures to effectively and economically eliminate emerging infectious diseases. 1012498 - Marta Mackowiak, Bartosz Adamczyk, Marta Szachniuk
RNAtango: Analysing and comparing RNA 3D structures via torsional angles. 1012500 - Jaspreet Ishar, Yee Man Tam
BoReMi: Bokeh-based jupyter-interface for registering spatio-molecular data to related microscopy images. 1012504 - Anika T. Löwe
Abrupt and spontaneous strategy switches emerge in simple regularised neural networks. 1012505 - Marta Sampaio
A diel multi-tissue genome-scale metabolic model of Vitis vinifera. 1012506 - Carrisa Cocuzza
Distributed network flows generate localized category selectivity in human visual cortex. 1012507 - Richard D. J. G. Ho
Dynamics of morphogen source formation in a growing tissue. 1012508 - Emmanouil Giannakakis
Structural influences on synaptic plasticity: The role of presynaptic connectivity in the emergence of E/I co-tuning. 1012510 - Wei Liu, Huaqin He, Davide Chicco
Gene signatures for cancer research: A 25-year retrospective and future avenues. 1012512 - Kelly Charniga
Best practices for estimating and reporting epidemiological delay distributions of infectious diseases. 1012520 - Giacomo Barzon
EEG microstate transition cost correlates with task demands. 1012521 - Jorge Fernandez-de-Cossío-Diaz
Inference and design of antibody specificity: From experiments to models and back. 1012522 - Alessio Andronico, Juliette Paireau
Integrating information from historical data into mechanistic models for influenza forecasting. 1012523 - Yujie Zhang, Mark Mao, Robert Zhang, Yen-Te Liao, Vivian C. H. Wu
DeepPL: A deep-learning-based tool for the prediction of bacteriophage lifecycle. 1012525 - Shaojun Yu
A novel classification framework for genome-wide association study of whole brain MRI images using deep learning. 1012527 - Ashima Keshava
Just-in-time: Gaze guidance in natural behavior. 1012529 - Ulisses Nunes da Rocha, Jonas Coelho Kasmanas, Rodolfo Toscan, Danilo Sipoli Sanches, Stefanía Magnúsdóttir, João Pedro Saraiva
Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery. 1012530 - Gaspard Oliviers
Learning probability distributions of sensory inputs with Monte Carlo predictive coding. 1012532 - Natchapon Srinak, Porntip Chiewchankaset, Saowalak Kalapanulak, Pornpan Panichnumsin, Treenut Saithong
Metabolic cross-feeding interactions modulate the dynamic community structure in microbial fuel cell under variable organic loading wastewaters. 1012533 - Lachlan Webb
Mapping the physiological changes in sleep regulation across infancy and young childhood. 1012541 - Yun Zuo
PreMLS: The undersampling technique based on ClusterCentroids to predict multiple lysine sites. 1012544 - Olga A. Nev
Metabolic modelling as a powerful tool to identify critical components of Pneumocystis growth medium. 1012545 - Anand V. Sastry
iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia. 1012546 - Mark C. W. van Rossum
Competitive plasticity to reduce the energetic costs of learning. 1012553 - Jiamu Jiang
Reinforcement learning when your life depends on it: A neuro-economic theory of learning. 1012554 - Saishi Cui
Mcadet: A feature selection method for fine-resolution single-cell RNA-seq data based on multiple correspondence analysis and community detection. 1012560 - Lingxia Qiao, Michael Getz, Ben Gross, Brian Tenner, Jin Zhang
Spatiotemporal orchestration of calcium-cAMP oscillations on AKAP/AC nanodomains is governed by an incoherent feedforward loop. 1012564 - Gabriel A. A. Silva
Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history. 1012566
Volume 20, Number 11, 2024
- Christian Jarvers
Teaching deep networks to see shape: Lessons from a simplified visual world. 1012019 - Jonathan Eden
During haptic communication, the central nervous system compensates distinctly for delay and noise. 1012037 - Martina Bukac, Suncica Canic
A computational algorithm for optimal design of a bioartificial organ scaffold architecture. 1012079 - Marte J. Sætra
An electrodiffusive network model with multicompartmental neurons and synaptic connections. 1012114 - Hong Yan Huang
A computational analysis of the oncogenic and anti-tumor immunity role of P4HA3 in human cancers. 1012284 - John H. Tay, Arthur Kocher, Sebastián Duchêne
Assessing the effect of model specification and prior sensitivity on Bayesian tests of temporal signal. 1012371 - Qing Wu
A deep learning model for prediction of autism status using whole-exome sequencing data. 1012468 - Michael Alexander Ramirez Sierra
AI-powered simulation-based inference of a genuinely spatial-stochastic gene regulation model of early mouse embryogenesis. 1012473 - Fabian Santiago
A new look at TFPI inhibition of factor X activation. 1012509 - Hugh O'Brien
A modular protein language modelling approach to immunogenicity prediction. 1012511 - Alexandria M. Jensen
Kernel machine tests of association using extrinsic and intrinsic cluster evaluation metrics. 1012524 - Boyan Xu, Alois Cerbu, Christopher J. Tralie, Daven Lim, Ksenia Krasileva
Structure-aware annotation of leucine-rich repeat domains. 1012526 - Ciara E. Judge
EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering. 1012528 - David Kappel
Synapses learn to utilize stochastic pre-synaptic release for the prediction of postsynaptic dynamics. 1012531 - Toshihito Umegaki
Molecular dynamics simulations of a multicellular model with cell-cell interactions and Hippo signaling pathway. 1012536 - Andrew Anderson
Deep-learning models reveal how context and listener attention shape electrophysiological correlates of speech-to-language transformation. 1012537 - Robert van Dijk, John Arevalo, Mehrtash Babadi, Anne E. Carpenter, Shantanu Singh
Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning. 1012547 - Alireza Rezvani-Sharif
A mechanistic model of in vitro plasma activation to evaluate therapeutic kallikrein-kinin system inhibitors. 1012552 - Rym Ben Boubaker
Mechanical stress and anionic lipids synergistically stabilize an atypical structure of the angiotensin II type 1 receptor (AT1). 1012559 - Jørgen Ankill, Zhi Zhao
Integrative pan-cancer analysis reveals a common architecture of dysregulated transcriptional networks characterized by loss of enhancer methylation. 1012565 - J. Roadnight Sheehan
Beyond IC50 - A computational dynamic model of drug resistance in enzyme inhibition treatment. 1012570 - Sven B. Gould
Reliability of plastid and mitochondrial localisation prediction declines rapidly with the evolutionary distance to the training set increasing. 1012575 - Zahra Razaghi-Moghadam
Harnessing the optimization of enzyme catalytic rates in engineering of metabolic phenotypes. 1012576 - Baptiste Ruiz
SPARTA: Interpretable functional classification of microbiomes and detection of hidden cumulative effects. 1012577 - Medha Shekhar
Human-like dissociations between confidence and accuracy in convolutional neural networks. 1012578 - Beren Millidge, Yuhang Song
Reward Bases: A simple mechanism for adaptive acquisition of multiple reward types. 1012580 - Lin Lin
GeM-LR: Discovering predictive biomarkers for small datasets in vaccine studies. 1012581 - Marta Kryven
Approximate planning in spatial search. 1012582 - Yuanchen Zhao
Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function. 1012590 - Aylin Bircan
Evolutionary history of calcium-sensing receptors unveils hyper/hypocalcemia-causing mutations. 1012591 - Evandro Konzen
Efficient modelling of infectious diseases in wildlife: A case study of bovine tuberculosis in wild badgers. 1012592 - Anna K. Leinheiser
A dynamical systems model for the total fission rate in Drp1-dependent mitochondrial fission. 1012596 - Dan Liu, Francesca Young, Kieran D. Lamb
Prediction of virus-host associations using protein language models and multiple instance learning. 1012597 - Salah Bazzi
Simplified internal models in human control of complex objects. 1012599 - Aaron R. Allred
Human perception of self-motion and orientation during galvanic vestibular stimulation and physical motion. 1012601 - Qiangwei Peng
Storm: Incorporating transient stochastic dynamics to infer the RNA velocity with metabolic labeling information. 1012606 - Chao Wang
MFPSP: Identification of fungal species-specific phosphorylation site using offspring competition-based genetic algorithm. 1012607 - Fei Cai, Yuehua Wei, Daniel Kirchhofer, Andrew Chang, Yingnan Zhang
Rapid prediction of key residues for foldability by machine learning model enables the design of highly functional libraries with hyperstable constrained peptide scaffolds. 1012609
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