yusuke1997/dblp-id-title huggingface dataset:
Nuclear deformation by microtubule molecular motors
Protein-Protein Docking with Dynamic Residue Protonation States
RNA-Seq is not required to determine stable reference genes for qPCR normalization
Electrostatic and bending energies predict staggering and splaying in nonmuscle myosin II minifilaments
Surveillance strategies for the detection of new pathogen variants across epidemiological contexts
Accounting for non-stationarity in epidemiology by embedding time-varying parameters in stochastic models
Evaluating a large language model's ability to solve programming exercises from an introductory bioinformatics course
Identifying and Tracking Simulated Synaptic Inputs from Neuronal Firing: Insights from In Vitro Experiments
Cholinergic modulation of neural networks supports sequential and complementary roles for NREM and REM states in memory consolidation
Batch normalization followed by merging is powerful for phenotype prediction integrating multiple heterogeneous studies
Correction: Limits of Feedback Control in Bacterial Chemotaxis
A Scalable Approach for Discovering Conserved Active Subnetworks across Species
Quantifying HiPSC-CM structural organization at scale with deep learning-enhanced SarcGraph
Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis
The Layer-Oriented Approach to Declarative Languages for Biological Modeling
Vocalization with semi-occluded airways is favorable for optimizing sound production
Artificial Neural Networks Trained to Detect Viral and Phage Structural Proteins
Inference of Protein Complex Activities from Chemical-Genetic Profile and Its Applications: Predicting Drug-Target Pathways
Discovering Relations Between Mind, Brain, and Mental Disorders Using Topic Mapping
Open collaborative writing with Manubot
Cell Fate Reprogramming by Control of Intracellular Network Dynamics
Kinetics of Amyloid Aggregation: A Study of the GNNQQNY Prion Sequence
Learning Gene Networks under SNP Perturbations Using eQTL Datasets
SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions
Interpretable machine learning for high-dimensional trajectories of aging health
Endogenous Cholinergic Inputs and Local Circuit Mechanisms Govern the Phasic Mesolimbic Dopamine Response to Nicotine
Modeling historic incidence trends implies early field cancerization in esophageal squamous cell carcinoma
Mapping the semi-nested community structure of 3D chromosome contact networks
Ten recommendations for hosting a Diversity, Equity, Inclusion, and Justice (DEIJ) journal club
PSAMM: A Portable System for the Analysis of Metabolic Models
Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data
Genome Trees from Conservation Profiles
The PLOS Computational Biology Software Section
Deep Learning-driven research for drug discovery: Tackling Malaria
Policy Resistance Undermines Superspreader Vaccination Strategies for Influenza
Dynamic interactions of influenza viruses in Hong Kong during 1998-2018
Dynamic Conformational Changes in MUNC18 Prevent Syntaxin Binding
Cortical Factor Feedback Model for Cellular Locomotion and Cytofission
Imitating Manual Curation of Text-Mined Facts in Biomedicine
Comparative Analysis of Human Tissue Interactomes Reveals Factors Leading to Tissue-Specific Manifestation of Hereditary Diseases
BoReMi: Bokeh-based jupyter-interface for registering spatio-molecular data to related microscopy images
Evidence for spreading seizure as a cause of theta-alpha activity electrographic pattern in stereo-EEG seizure recordings
Ten simple rules for successfully hosting an intern at a scientific software company
Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations
Quantitative Test of the Barrier Nucleosome Model for Statistical Positioning of Nucleosomes Up- and Downstream of Transcription Start Sites
BCI Toolbox: An open-source python package for the Bayesian causal inference model
Automated evaluation of quaternary structures from protein crystals
A Computational Approach for Identifying Synergistic Drug Combinations
Optimization of surgical intervention outside the epileptogenic zone in the Virtual Epileptic Patient (VEP)
A Review of 2009 for PLoS Computational Biology
Estimation of Thalamocortical and Intracortical Network Models from Joint Thalamic Single-Electrode and Cortical Laminar-Electrode Recordings in the Rat Barrel System
Endothelial Cell Capture of Heparin-Binding Growth Factors under Flow
Stochastic Dynamics Underlying Cognitive Stability and Flexibility
Deciphering clock cell network morphology within the biological master clock, suprachiasmatic nucleus: From the perspective of circadian wave dynamics
Optimal sampling frequency and site selection for wastewater and environmental surveillance of infectious pathogens: A value of information assessment
With an eye on uncertainty: Modelling pupillary responses to environmental volatility
Examining B-cell dynamics and responsiveness in different inflammatory milieus using an agent-based model
Collective States, Multistability and Transitional Behavior in Schooling Fish
Graph-based algorithms for Laplace transformed coalescence time distributions
Assessing parameter identifiability of a hemodynamics PDE model using spectral surrogates and dimension reduction
Close spatial arrangement of mutants favors and disfavors fixation
Predictions of COVID-19 dynamics in the UK: Short-term forecasting and analysis of potential exit strategies
Mixed recurrent connectivity in primate prefrontal cortex
Modeling oxygen transport in the brain: An efficient coarse-grid approach to capture perivascular gradients in the parenchyma
Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data
History-dependent switch-like differentiation of keratinocytes in response to skin barrier damage
Cortical Composition Hierarchy Driven by Spine Proportion Economical Maximization or Wire Volume Minimization
3D computational models explain muscle activation patterns and energetic functions of internal structures in fish swimming
A Real-Time All-Atom Structural Search Engine for Proteins
Linking Transcriptional Changes over Time in Stimulated Dendritic Cells to Identify Gene Networks Activated during the Innate Immune Response
A probabilistic knowledge graph for target identification
Poisson-Like Spiking in Circuits with Probabilistic Synapses
The Physiological Molecular Shape of Spectrin: A Compact Supercoil Resembling a Chinese Finger Trap
Emergence of directional bias in tau deposition from axonal transport dynamics
A Genome-Scale Integration and Analysis of Lactococcus lactis Translation Data
Adaptive, Fast Walking in a Biped Robot under Neuronal Control and Learning
Random Field Model Reveals Structure of the Protein Recombinational Landscape
The Homeostasis of Plasmodium falciparum -Infected Red Blood Cells
Evolutionary Models for Formation of Network Motifs and Modularity in the Saccharomyces Transcription Factor Network
A Bayesian mixture modelling approach for spatial proteomics
The Presence of VEGF Receptors on the Luminal Surface of Endothelial Cells Affects VEGF Distribution and VEGF Signaling
Learning Micro-C from Hi-C with diffusion models
Geometric Interpretation of Gene Coexpression Network Analysis
A Multi-Variant, Viral Dynamic Model of Genotype 1 HCV to Assess the in vivo Evolution of Protease-Inhibitor Resistant Variants
Quantitative estimates of the regulatory influence of long non-coding RNAs on global gene expression variation using TCGA breast cancer transcriptomic data
A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis
Validation and tuning of in situ transcriptomics image processing workflows with crowdsourced annotations
Federated privacy-protected meta- and mega-omics data analysis in multi-center studies with a fully open-source analytic platform
Thousands of Rab GTPases for the Cell Biologist
Evaluating Gene Expression Dynamics Using Pairwise RNA FISH Data
Reading wild minds: A computational assay of Theory of Mind sophistication across seven primate species
Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases
Eight quick tips for including chromosome X in genome-wide association studies
Patient-specific pulse wave propagation model identifies cardiovascular risk characteristics in hemodialysis patients
Dopamine depletion leads to pathological synchronization of distinct basal ganglia loops in the beta band
Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective
Behavioral Lateralization and Optimal Route Choice in Flying Budgerigars
RMPJ: An ImageJ plugin for morphological information processing in biomedical images
Analyzing the Functional Properties of the Creatine Kinase System with Multiscale 'Sloppy' Modeling
A Computational Framework for Understanding the Impact of Prior Experiences on Pain Perception and Neuropathic Pain
Catalyzing computational biology research at an academic institute through an interest network
A review of active learning approaches to experimental design for uncovering biological networks
Correction: Adaptive, Fast Walking in a Biped Robot under Neuronal Control and Learning
Investigating the mitochondrial genomic landscape of Arabidopsis thaliana by long-read sequencing
Monte Carlo samplers for efficient network inference
Ten simple rules for doing a postdoc in pharma
Long-range correlation in protein dynamics: Confirmation by structural data and normal mode analysis
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
Normalization by orientation-tuned surround in human V1-V3
Modeling enamel matrix secretion in mammalian teeth
Implications of Heterogeneous Biting Exposure and Animal Hosts on Trypanosomiasis brucei gambiense Transmission and Control
Shaping Embodied Neural Networks for Adaptive Goal-directed Behavior
Predicting regional somatic mutation rates using DNA motifs
lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites
Quantifying and Predicting the Effect of Exogenous Interleukin-7 on CD4 + T Cells in HIV-1 Infection
Role of dynamic nuclear deformation on genomic architecture reorganization
HMFGraph: Novel Bayesian approach for recovering biological networks
DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning
Stochastic Computations in Cortical Microcircuit Models
High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE
Elucidation of Genetic Interactions in the Yeast GATA-Factor Network Using Bayesian Model Selection
Alternative Protein-Protein Interfaces Are Frequent Exceptions
Statistical tests for intra-tumour clonal co-occurrence and exclusivity
Hypertrophy and/or Hyperplasia: Dynamics of Adipose Tissue Growth
An electrodiffusive network model with multicompartmental neurons and synaptic connections
Omitting age-dependent mosquito mortality in malaria models underestimates the effectiveness of insecticide-treated nets
Hard real-time closed-loop electrophysiology with the Real-Time eXperiment Interface (RTXI)
Alu Exonization Events Reveal Features Required for Precise Recognition of Exons by the Splicing Machinery
Analysis of Single Locus Trajectories for Extracting In Vivo Chromatin Tethering Interactions
One model fits all: Combining inference and simulation of gene regulatory networks
Novel insights from the Plasmodium falciparum sporozoite-specific proteome by probabilistic integration of 26 studies
Prior expectations guide multisensory integration during face-to-face communication
Inference on dengue epidemics with Bayesian regime switching models
Transcriptome and Proteome Exploration to Model Translation Efficiency and Protein Stability in Lactococcus lactis
Inferring Function Using Patterns of Native Disorder in Proteins
Evolution of Taxis Responses in Virtual Bacteria: Non-Adaptive Dynamics
Novel feature selection methods for construction of accurate epigenetic clocks
Extracting interpretable signatures of whole-brain dynamics through systematic comparison
Adaptive modeling and inference of higher-order coordination in neuronal assemblies: A dynamic greedy estimation approach
Fast online deconvolution of calcium imaging data
Study of impacts of two types of cellular aging on the yeast bud morphogenesis
Ten simple rules for designing and running a computing minor for bio/chem students
Antibody Watch: Text mining antibody specificity from the literature
Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins
Optimized phylogenetic clustering of HIV-1 sequence data for public health applications
The detection of algebraic auditory structures emerges with self-supervised learning
Prioritizing interventions for preventing COVID-19 outbreaks in military basic training
Free energy landscape of RNA binding dynamics in start codon recognition by eukaryotic ribosomal pre-initiation complex
Network-based Survival Analysis Reveals Subnetwork Signatures for Predicting Outcomes of Ovarian Cancer Treatment
A Universal Trend among Proteomes Indicates an Oily Last Common Ancestor
Ten simple rules for defining a computational biology project
A novel artificial intelligence-based approach for identification of deoxynucleotide aptamers
Balancing Feed-Forward Excitation and Inhibition via Hebbian Inhibitory Synaptic Plasticity
The confidence-noise confidence-boost (CNCB) model of confidence rating data
Detection of Mixed Infection from Bacterial Whole Genome Sequence Data Allows Assessment of Its Role in Clostridium difficile Transmission
Modelling the first wave of COVID-19 in India
Risk, Unexpected Uncertainty, and Estimation Uncertainty: Bayesian Learning in Unstable Settings
Correction: Inferring transmission heterogeneity using virus genealogies: Estimation and targeted prevention
Coupled feedback loops maintain synaptic long-term potentiation: A computational model of PKMzeta synthesis and AMPA receptor trafficking
Protein - protein binding supersites
Patch formation driven by stochastic effects of interaction between viruses and defective interfering particles
Whole brain functional connectivity: Insights from next generation neural mass modelling incorporating electrical synapses
Spatial information allows inference of the prevalence of direct cell-to-cell viral infection
The Pharmacodynamics of the p53-Mdm2 Targeting Drug Nutlin: The Role of Gene-Switching Noise
Dissecting cascade computational components in spiking neural networks
KinPred: A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions
Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates
How cells tame noise while maintaining ultrasensitive transcriptional responses
Getting Started in Computational Mass Spectrometry-Based Proteomics
A multiscale modelling approach to assess the impact of metabolic zonation and microperfusion on the hepatic carbohydrate metabolism
DLoopCaller: A deep learning approach for predicting genome-wide chromatin loops by integrating accessible chromatin landscapes
Social mates dynamically coordinate aggressive behavior to produce strategic territorial defense
Clique of Functional Hubs Orchestrates Population Bursts in Developmentally Regulated Neural Networks
Nowcasting by Bayesian Smoothing: A flexible, generalizable model for real-time epidemic tracking
Effect of aberrant fructose metabolism following SARS-CoV-2 infection on colorectal cancer patients' poor prognosis
First passage time analysis of spatial mutation patterns reveals sub-clonal evolutionary dynamics in colorectal cancer
ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun
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
PathVisio 3: An Extendable Pathway Analysis Toolbox
Robust Signal Processing in Living Cells
Forecasting dengue and influenza incidences using a sparse representation of Google trends, electronic health records, and time series data
Discovering individual-specific gait signatures from data-driven models of neuromechanical dynamics
Direct Measurements of Local Coupling between Myosin Molecules Are Consistent with a Model of Muscle Activation
Contact tracing efficiency, transmission heterogeneity, and accelerating COVID-19 epidemics
Temporal Sensitivity of Protein Kinase A Activation in Late-Phase Long Term Potentiation
Informational structures: A dynamical system approach for integrated information
Phosphorylation of the Retinoic Acid Receptor Alpha Induces a Mechanical Allosteric Regulation and Changes in Internal Dynamics
Estimating Copy Number and Allelic Variation at the Immunoglobulin Heavy Chain Locus Using Short Reads
Learning of Chunking Sequences in Cognition and Behavior
Evolution of Evolvability in Gene Regulatory Networks
Stimulation-Based Control of Dynamic Brain Networks
Antenna Mechanism of Length Control of Actin Cables
Correction: Limits on reliable information flows through stochastic populations
Identifying prognostic pairwise relationships among bacterial species in microbiome studies
Binding-Induced Folding of a Natively Unstructured Transcription Factor
Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities
Predicting colorectal cancer risk from adenoma detection via a two-type branching process model
Predicting gastrointestinal drug effects using contextualized metabolic models
Mendel, MD: A user-friendly open-source web tool for analyzing WES and WGS in the diagnosis of patients with Mendelian disorders
Combining the dynamic model and deep neural networks to identify the intensity of interventions during COVID-19 pandemic
3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries
PLOS Computational Biology 2018 Reviewer and Editorial Board Thank You
A Reaction-Diffusion Model of Cholinergic Retinal Waves
Modeling Mechanisms of In Vivo Variability in Methotrexate Accumulation and Folate Pathway Inhibition in Acute Lymphoblastic Leukemia Cells
Designing diverse and high-performance proteins with a large language model in the loop
A mathematical model of the metastatic bottleneck predicts patient outcome and response to cancer treatment
Optimal Drug Synergy in Antimicrobial Treatments
Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks
Joint estimation of hand-foot-mouth disease model and prediction in korea using the ensemble kalman filter
Reproducibility of biophysical in silico neuron states and spikes from event-based partial histories
AI-Assisted chemical probe discovery for the understudied Calcium-Calmodulin Dependent Kinase, PNCK
Stochastic model of lignocellulosic material saccharification
Concentration fluctuations in growing and dividing cells: Insights into the emergence of concentration homeostasis
Archetypal Analysis for population genetics
Mathematical modeling identifies optimum lapatinib dosing schedules for the treatment of glioblastoma patients
Models of heterogeneous dopamine signaling in an insect learning and memory center
Modulation of Calmodulin Lobes by Different Targets: An Allosteric Model with Hemiconcerted Conformational Transitions
Ten simple rules for building and maintaining a responsible data science workflow
Structurally-Constrained Relationships between Cognitive States in the Human Brain
Colonization times in Moran process on graphs
MODMatcher: Multi-Omics Data Matcher for Integrative Genomic Analysis
The effect of natural selection on the propagation of protein expression noise to bacterial growth
Correction: Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action
Correction: Stability of spontaneous, correlated activity in mouse auditory cortex
Alcoholic liver disease: A registry view on comorbidities and disease prediction
Signaling Domain of Sonic Hedgehog as Cannibalistic Calcium-Regulated Zinc-Peptidase
Exploiting Gene-Expression Deconvolution to Probe the Genetics of the Immune System
A quantitative modelling approach for DNA repair on a population scale
A statistical model for describing and simulating microbial community profiles
Network Plasticity as Bayesian Inference
Accounting for isoform expression increases power to identify genetic regulation of gene expression
The gradient of the reinforcement landscape influences sensorimotor learning
Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters
ISCB Honors Temple F. Smith and Eran Segal
A Disorder-Induced Domino-Like Destabilization Mechanism Governs the Folding and Functional Dynamics of the Repeat Protein IκBα
Leveraging infectious disease models to interpret randomized controlled trials: Controlling enteric pathogen transmission through water, sanitation, and hygiene interventions
Network supporting contextual fear learning after dorsal hippocampal damage has increased dependence on retrosplenial cortex
Passenger mutations accurately classify human tumors
On the Origins of the Weak Folding Cooperativity of a Designed ββα Ultrafast Protein FSD-1
MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface
The preferred nucleotide contexts of the AID/APOBEC cytidine deaminases have differential effects when mutating retrotransposon and virus sequences compared to host genes
Ten simple rules for scientific code review
On the importance of evolving phenotype distributions on evolutionary diversification
Forecasting influenza in Europe using a metapopulation model incorporating cross-border commuting and air travel
Flocking in complex environments - Attention trade-offs in collective information processing
A time-series analysis of blood-based biomarkers within a 25-year longitudinal dolphin cohort
Phenotypic pliancy and the breakdown of epigenetic polycomb mechanisms
Modularity Induced Gating and Delays in Neuronal Networks
The Per2 Negative Feedback Loop Sets the Period in the Mammalian Circadian Clock Mechanism
scSDNE: A semi-supervised method for inferring cell-cell interactions based on graph embedding
Ten simple rules to create biological network figures for communication
Plato's Cave Algorithm: Inferring Functional Signaling Networks from Early Gene Expression Shadows
Testing microbiome associations with survival times at both the community and individual taxon levels
SPARTA: Interpretable functional classification of microbiomes and detection of hidden cumulative effects
Spatiotemporal dynamics of human high gamma discriminate naturalistic behavioral states
Simple models of quantitative firing phenotypes in hippocampal neurons: Comprehensive coverage of intrinsic diversity
JSOM: Jointly-evolving self-organizing maps for alignment of biological datasets and identification of related clusters
AGouTI-Flexible Annotation of Genomic and Transcriptomic Intervals
Distinctive Behaviors of Druggable Proteins in Cellular Networks
Benchmarking Ontologies: Bigger or Better?
Epitope profiling using computational structural modelling demonstrated on coronavirus-binding antibodies
A model for brain life history evolution
Analytical and computational solution for the estimation of SNP-heritability in biobank-scale and distributed datasets
Cleavage Entropy as Quantitative Measure of Protease Specificity
Ten simple rules for effective presentation slides
In silico biophysics and rheology of blood and red blood cells in Gaucher Disease
Interaction between games give rise to the evolution of moral norms of cooperation
Detecting Mild Traumatic Brain Injury Using Resting State Magnetoencephalographic Connectivity
The Effect of Stochasticity on the Lac Operon: An Evolutionary Perspective