yusuke1997/dblp-id-title huggingface dataset:
'HypothesisFinder: ' A Strategy for the Detection of Speculative Statements in Scientific Text
Ten simple rules for empowering women in STEM
Antibiotic Restriction Might Facilitate the Emergence of Multi-drug Resistance
Modeling Signal Propagation Mechanisms and Ligand-Based Conformational Dynamics of the Hsp90 Molecular Chaperone Full-Length Dimer
Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations
Feed-Forward versus Feedback Inhibition in a Basic Olfactory Circuit
Identifying Changes in Selective Constraints: Host Shifts in Influenza
How public can public goods be? Environmental context shapes the evolutionary ecology of partially private goods
A comprehensive overview and evaluation of circular RNA detection tools
No increased circular inference in adults with high levels of autistic traits or autism
Protein Domain-Level Landscape of Cancer-Type-Specific Somatic Mutations
sc2MeNetDrug: A computational tool to uncover inter-cell signaling targets and identify relevant drugs based on single cell RNA-seq data
A genome-scale metabolic model for the denitrifying bacterium Thauera sp. MZ1T accurately predicts degradation of pollutants and production of polymers
How effective were Australian Quarantine Stations in mitigating transmission aboard ships during the influenza pandemic of 1918-19?
Lipidated apolipoprotein E4 structure and its receptor binding mechanism determined by a combined cross-linking coupled to mass spectrometry and molecular dynamics approach
Adaptive landscape flattening allows the design of both enzyme: Substrate binding and catalytic power
kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
Ten simple rules for creating a brand-new virtual academic meeting (even amid a pandemic)
Mutational Analysis of the High-Affinity Zinc Binding Site Validates a Refined Human Dopamine Transporter Homology Model
Analysis of Hepatitis C Virus Decline during Treatment with the Protease Inhibitor Danoprevir Using a Multiscale Model
Integrative Analysis of Deep Sequencing Data Identifies Estrogen Receptor Early Response Genes and Links ATAD3B to Poor Survival in Breast Cancer
Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation
Searching through functional space reveals distributed visual, auditory, and semantic coding in the human brain
GDI-Mediated Cell Polarization in Yeast Provides Precise Spatial and Temporal Control of Cdc42 Signaling
Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data
NAVIP: Unraveling the influence of neighboring small sequence variants on functional impact prediction
Improved transcriptome assembly using a hybrid of long and short reads with StringTie
Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic
Combining Structural Connectivity and Response Latencies to Model the Structure of the Visual System
Major depressive disorder and bistability in an HPA-CNS toggle switch
A Bayesian neural ordinary differential equations framework to study the effects of chemical mixtures on survival
Fine-Tuning Tomato Agronomic Properties by Computational Genome Redesign
When Less Is More: Non-monotonic Spike Sequence Processing in Neurons
A Computational Model of the Fetal Circulation to Quantify Blood Redistribution in Intrauterine Growth Restriction
Crowd control: Reducing individual estimation bias by sharing biased social information
Assessing the public health impact of tolerance-based therapies with mathematical models
Quantitative Epistasis Analysis and Pathway Inference from Genetic Interaction Data
The Effect of Farmers' Decisions on Pest Control with Bt Crops: A Billion Dollar Game of Strategy
Direct Solution of the Chemical Master Equation Using Quantized Tensor Trains
A Dynamic Model of Interactions of Ca 2+ , Calmodulin, and Catalytic Subunits of Ca 2+ /Calmodulin-Dependent Protein Kinase II
Stochastic dynamics of Type-I interferon responses
Inference of trajectory presence by tree dimension and subset specificity by subtree cover
A Computational Framework for 3D Mechanical Modeling of Plant Morphogenesis with Cellular Resolution
Correcting the hebbian mistake: Toward a fully error-driven hippocampus
Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties
Computer simulations of Template-Directed RNA Synthesis driven by temperature cycling in diverse sequence mixtures
Encoding surprise by retinal ganglion cells
A novel machine learning based approach for iPS progenitor cell identification
Trade-off between Responsiveness and Noise Suppression in Biomolecular System Responses to Environmental Cues
Modeling dynamics of acute HIV infection incorporating density-dependent cell death and multiplicity of infection
Charge as a Selection Criterion for Translocation through the Nuclear Pore Complex
Reinforcement Learning Explains Conditional Cooperation and Its Moody Cousin
Theta-gamma phase amplitude coupling in a hippocampal CA1 microcircuit
Feedback between motion and sensation provides nonlinear boost in run-and-tumble navigation
Ensemble learning-based predictor for driver synonymous mutation with sequence representation
Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data
"Simple Rules for Editors"? Here is One Rule to Tackle Neglected Problems of Publishing
Linking Changes in Epithelial Morphogenesis to Cancer Mutations Using Computational Modeling
Multiscale modeling of presynaptic dynamics from molecular to mesoscale
Statistical prediction of microbial metabolic traits from genomes
CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer
Alpha blocking and 1/fβ spectral scaling in resting EEG can be accounted for by a sum of damped alpha band oscillatory processes
Choice of method of place cell classification determines the population of cells identified
MOSAIC: A Multiscale Model of Osteogenesis and Sprouting Angiogenesis with Lateral Inhibition of Endothelial Cells
Orientation control strategies and adaptation to a visuomotor perturbation in rotational hand movements
Benchmarking residue-resolution protein coarse-grained models for simulations of biomolecular condensates
Buildup and bistability in auditory streaming as an evidence accumulation process with saturation
Brain-inspired model for early vocal learning and correspondence matching using free-energy optimization
Curated single cell multimodal landmark datasets for R/Bioconductor
Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights
In the Body's Eye: The computational anatomy of interoceptive inference
Correction: Most Undirected Random Graphs Are Amplifiers of Selection for Birth-Death Dynamics, but Suppressors of Selection for Death-Birth Dynamics
DOGS: Reaction-Driven de novo Design of Bioactive Compounds
Ten quick tips for developing a reproducible Shiny application
Improving the coverage of credible sets in Bayesian genetic fine-mapping
Moving in on human motor cortex. Characterizing the relationship between body parts with non-rigid population response fields
Spatio-Temporal Dynamics of Yeast Mitochondrial Biogenesis: Transcriptional and Post-Transcriptional mRNA Oscillatory Modules
Iterative sure independence screening EM-Bayesian LASSO algorithm for multi-locus genome-wide association studies
Large-Scale Conformational Changes of Trypanosoma cruzi Proline Racemase Predicted by Accelerated Molecular Dynamics Simulation
Use It and Improve It or Lose It: Interactions between Arm Function and Use in Humans Post-stroke
How Landscape Heterogeneity Frames Optimal Diffusivity in Searching Processes
VASP-E: Specificity Annotation with a Volumetric Analysis of Electrostatic Isopotentials
Gain control with A-type potassium current: IA as a switch between divisive and subtractive inhibition
Human-like face pareidolia emerges in deep neural networks optimized for face and object recognition
De novo sensorimotor learning through reuse of movement components
Ten Simple Rules of Live Tweeting at Scientific Conferences
Group-selection via aggregative propagule-formation enables cooperative multicellularity in an individual based, spatial model
Epiclomal: Probabilistic clustering of sparse single-cell DNA methylation data
The respiratory cycle modulates distinct dynamics of affective and perceptual decision-making
A Mathematical Framework for Estimating Pathogen Transmission Fitness and Inoculum Size Using Data from a Competitive Mixtures Animal Model
Inferred regulons are consistent with regulator binding sequences in E. coli
The topology of synergy: Linking topological and information-theoretic approaches to higher-order interactions in complex systems
Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting
Ten simple rules for success as a trainee-led outreach organization in computational biology education
Baseline CD4 + T Cell Counts Correlates with HIV-1 Synonymous Rate in HLA-B*5701 Subjects with Different Risk of Disease Progression
A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation
Modelling response strategies for controlling gonorrhoea outbreaks in men who have sex with men in Australia
Linking statistical shape models and simulated function in the healthy adult human heart
Predicting Novel Binding Modes of Agonists to β Adrenergic Receptors Using All-Atom Molecular Dynamics Simulations
Regional sequence expansion or collapse in heterozygous genome assemblies
Data-driven method to infer the seizure propagation patterns in an epileptic brain from intracranial electroencephalography
Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate
Helix 8 in chemotactic receptors of the complement system
Bistability and Oscillations in the Huang-Ferrell Model of MAPK Signaling
Modelling membrane reshaping by staged polymerization of ESCRT-III filaments
Building and experimenting with an agent-based model to study the population-level impact of CommunityRx, a clinic-based community resource referral intervention
The Complexity of Dynamics in Small Neural Circuits
Identification of Entry Factors Involved in Hepatitis C Virus Infection Based on Host-Mimicking Short Linear Motifs
Heterogeneous synaptic homeostasis: A novel mechanism boosting information propagation in the cortex
Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models
Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer's disease
Enzyme sequestration by the substrate: An analysis in the deterministic and stochastic domains
Extracting Behaviorally Relevant Traits from Natural Stimuli: Benefits of Combinatorial Representations at the Accessory Olfactory Bulb
M-current modulation of cortical slow oscillations: Network dynamics and computational modeling
Modelling Feedback Excitation, Pacemaker Properties and Sensory Switching of Electrically Coupled Brainstem Neurons Controlling Rhythmic Activity
Simple model for encoding natural images by retinal ganglion cells with nonlinear spatial integration
Expansion of epileptogenic networks via neuroplasticity in neural mass models
Multi-Scaled Explorations of Binding-Induced Folding of Intrinsically Disordered Protein Inhibitor IA3 to its Target Enzyme
Quantifying model evidence for yellow fever transmission routes in Africa
Ten simple rules for starting FAIR discussions in your community
Hidden variable models reveal the effects of infection from changes in host survival
Path integration in large-scale space and with novel geometries: Comparing vector addition and encoding-error models
The G Protein-Coupled Receptor Subset of the Chicken Genome
Bowhead: Bayesian modelling of cell velocity during concerted cell migration
Extracting individual characteristics from population data reveals a negative social effect during honeybee defence
Emergence of cooperative bistability and robustness of gene regulatory networks
Computing Biology
Neural circuit mechanisms of hierarchical sequence learning tested on large-scale recording data
Statistical signature of subtle behavioral changes in large-scale assays
Social Norms of Cooperation in Small-Scale Societies
Gene signatures for cancer research: A 25-year retrospective and future avenues
Dissociating error-based and reinforcement-based loss functions during sensorimotor learning
Superspreading and the evolution of virulence
Operational response simulation tool for epidemics within refugee and IDP settlements: A scenario-based case study of the Cox's Bazar settlement
Human decision making balances reward maximization and policy compression
How good are pathogenicity predictors in detecting benign variants?
Changes in morphogen kinetics and pollen grain size are potential mechanisms of aberrant pollen aperture patterning in previously observed and novel mutants of Arabidopsis thaliana
Correction: Time to Organize the Bioinformatics Resourceome
Gentle and fast all-atom model refinement to cryo-EM densities via a maximum likelihood approach
Gradient boosted decision trees reveal nuances of auditory discrimination behavior
Integrated Text Mining and Chemoinformatics Analysis Associates Diet to Health Benefit at Molecular Level
Literature Based Drug Interaction Prediction with Clinical Assessment Using Electronic Medical Records: Novel Myopathy Associated Drug Interactions
Computational and Empirical Studies Predict Mycobacterium tuberculosis-Specific T Cells as a Biomarker for Infection Outcome
BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods
An Allosteric Mechanism for Switching between Parallel Tracks in Mammalian Sulfur Metabolism
Unpacking the V1 map: Differential covariation of preferred spatial frequency and cortical magnification across spatial dimensions
Friendly-rivalry solution to the iterated n-person public-goods game
Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals
Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth
Properties of Neurons in External Globus Pallidus Can Support Optimal Action Selection
Multiscale modeling of tumor growth and angiogenesis: Evaluation of tumor-targeted therapy
Penalized regression and model selection methods for polygenic scores on summary statistics
PoreWalker: A Novel Tool for the Identification and Characterization of Channels in Transmembrane Proteins from Their Three-Dimensional Structure
Exome Sequencing and Prediction of Long-Term Kidney Allograft Function
Filament Depolymerization Can Explain Chromosome Pulling during Bacterial Mitosis
Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics
Feedback, Mass Conservation and Reaction Kinetics Impact the Robustness of Cellular Oscillations
Impact of occluder device configurations in in-silico left atrial hemodynamics for the analysis of device-related thrombus
Prediction of Drug-Target Interactions for Drug Repositioning Only Based on Genomic Expression Similarity
Remodeling and Tenacity of Inhibitory Synapses: Relationships with Network Activity and Neighboring Excitatory Synapses
A Motor-Gradient and Clustering Model of the Centripetal Motility of MTOCs in Meiosis I of Mouse Oocytes
A multi-scale study of thalamic state-dependent responsiveness
Versatile multiple object tracking in sparse 2D/3D videos via deformable image registration
Functional Classification Using Phylogenomic Inference
Understanding molecular mechanisms and predicting phenotypic effects of pathogenic tubulin mutations
Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy
Predictors of Hepatitis B Cure Using Gene Therapy to Deliver DNA Cleavage Enzymes: A Mathematical Modeling Approach
State-dependent protein-lipid interactions of a pentameric ligand-gated ion channel in a neuronal membrane
Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes
Mouse Cognition-Related Behavior in the Open-Field: Emergence of Places of Attraction
Topic Pages: PLoS Computational Biology Meets Wikipedia
Microstimulation in a spiking neural network model of the midbrain superior colliculus
The Association of Tetrameric Acetylcholinesterase with ColQ Tail: A Block Normal Mode Analysis
Multitask deep learning for the emulation and calibration of an agent-based malaria transmission model
Prediction of infectious disease epidemics via weighted density ensembles
EPINEST, an agent-based model to simulate epidemic dynamics in large-scale poultry production and distribution networks
Cattle transport network predicts endemic and epidemic foot-and-mouth disease risk on farms in Turkey
Data-driven modelling captures dynamics of the circadian clock of Neurospora crassa
ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements
Modeling Phenotypic Metabolic Adaptations of Mycobacterium tuberculosis H37Rv under Hypoxia
Mechanisms underlying different onset patterns of focal seizures
A Curvature-Mediated Mechanism for Localization of Lipids to Bacterial Poles
Evolutionary dynamics of hyperbolic language
Structure and Age Jointly Influence Rates of Protein Evolution
The accuracy of absolute differential abundance analysis from relative count data
A comprehensive data-driven model of cat primary visual cortex
The refinement paradox and cumulative cultural evolution: Complex products of collective improvement favor conformist outcomes, blind copying, and hyper-credulity
The role of feedforward and feedback inhibition in modulating theta-gamma cross-frequency interactions in neural circuits
Pairing statistics and melting of random DNA oligomers: Finding your partner in superdiverse environments
Behavioral discrimination and time-series phenotyping of birdsong performance
Candidate correlates of protection in the HVTN505 HIV-1 vaccine efficacy trial identified by positive-unlabeled learning
Large vessels as a tree of transmission lines incorporated in the CircAdapt whole-heart model: A computational tool to examine heart-vessel interaction
Discovering Motifs in Ranked Lists of DNA Sequences
Statistical Analysis of Molecular Signal Recording
Lack of Ecological and Life History Context Can Create the Illusion of Social Interactions in Dictyostelium discoideum
Correction: Decentralized control of insect walking: A simple neural network explains a wide range of behavioral and neurophysiological results
A Minimal Regulatory Network of Extrinsic and Intrinsic Factors Recovers Observed Patterns of CD4+ T Cell Differentiation and Plasticity
Membrane thinning and lateral gating are consistent features of BamA across multiple species
Ten simple rules for optimal and careful use of generative AI in science
A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins
Identification of Potent EGFR Inhibitors from TCM Database@Taiwan
Using stochastic cellular automata to model and define sufficient conditions for the survival of Enterococcus faecalis biofilms with the pCF10 plasmid under erythromycin treatment
Directed Mammalian Gene Regulatory Networks Using Expression and Comparative Genomic Hybridization Microarray Data from Radiation Hybrids
The 2015 Bioinformatics Open Source Conference (BOSC 2015)
Dynamic divisive normalization circuits explain and predict change detection in monkey area MT
Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens
Discovering Biological Progression Underlying Microarray Samples
Correction: Ten Simple Rules for Selecting a Postdoctoral Position
Metabolic reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: A hybrid modeling approach
Bias-free estimation of information content in temporally sparse neuronal activity
Targeted modulation of protein liquid-liquid phase separation by evolution of amino-acid sequence
Correction: Uncoupling the roles of firing rates and spike bursts in shaping the STN-GPe beta band oscillations
Elucidating reaction dynamics in a model of human brain energy metabolism
An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes
Evolution of foraging behaviour induces variable complexity-stability relationships in mutualist-exploiter-predator communities
Fundamental limits on inferring epidemic resurgence in real time using effective reproduction numbers
Vulnerabilities in the Tau Network and the Role of Ultrasensitive Points in Tau Pathophysiology
Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm
An approximate diffusion process for environmental stochasticity in infectious disease transmission modelling
sourceR: Classification and source attribution of infectious agents among heterogeneous populations
Thermodynamics-Based Models of Transcriptional Regulation by Enhancers: The Roles of Synergistic Activation, Cooperative Binding and Short-Range Repression
A zero inflated log-normal model for inference of sparse microbial association networks
Role of Histone Tails in Structural Stability of the Nucleosome
Development of Accurate Long-lead COVID-19 Forecast
CystAnalyser: A new software tool for the automatic detection and quantification of cysts in Polycystic Kidney and Liver Disease, and other cystic disorders
Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection
Angiogenic Activity of Breast Cancer Patients' Monocytes Reverted by Combined Use of Systems Modeling and Experimental Approaches
Use of Data-Biased Random Walks on Graphs for the Retrieval of Context-Specific Networks from Genomic Data
Machine Learning based histology phenotyping to investigate the epidemiologic and genetic basis of adipocyte morphology and cardiometabolic traits
Predictability in process-based ensemble forecast of influenza
Effect of depth information on multiple-object tracking in three dimensions: A probabilistic perspective
A multiscale model of epigenetic heterogeneity-driven cell fate decision-making
Comprehensive Annotation of Bidirectional Promoters Identifies Co-Regulation among Breast and Ovarian Cancer Genes
Elucidation of genome-wide understudied proteins targeted by PROTAC-induced degradation using interpretable machine learning
Differential quantification of alternative splicing events on spliced pangenome graphs
Marked point process variational autoencoder with applications to unsorted spiking activities
dcGOR: An R Package for Analysing Ontologies and Protein Domain Annotations
The SH2 Domain Regulates c-Abl Kinase Activation by a Cyclin-Like Mechanism and Remodulation of the Hinge Motion
A circuit model of auditory cortex
Unsupervised machine learning predicts future sexual behaviour and sexually transmitted infections among HIV-positive men who have sex with men
Selective control of synaptic plasticity in heterogeneous networks through transcranial alternating current stimulation (tACS)
Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections
A Mechanistic Understanding of Allosteric Immune Escape Pathways in the HIV-1 Envelope Glycoprotein
Misuse of the Michaelis-Menten rate law for protein interaction networks and its remedy
Prediction and classification in equation-free collective motion dynamics
ENQUIRE automatically reconstructs, expands, and drives enrichment analysis of gene and Mesh co-occurrence networks from context-specific biomedical literature
Evolutionary History of Mammalian Transposons Determined by Genome-Wide Defragmentation
Quantifying microbial interactions based on compositional data using an iterative approach for solving generalized Lotka-Volterra equations
The impact of phenotypic heterogeneity of tumour cells on treatment and relapse dynamics