yusuke1997/dblp-id-title huggingface dataset:
De Novo Design and Experimental Characterization of Ultrashort Self-Associating Peptides
Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle
Systematic comparison and prediction of the effects of missense mutations on protein-DNA and protein-RNA interactions
Estimating the contribution of HIV-infected adults to household pneumococcal transmission in South Africa, 2016-2018: A hidden Markov modelling study
Elements and evolutionary determinants of genomic divergence between paired primary and metastatic tumors
Brain Connectivity Dissociates Responsiveness from Drug Exposure during Propofol-Induced Transitions of Consciousness
Nano-scale solution of the Poisson-Nernst-Planck (PNP) equations in a fraction of two neighboring cells reveals the magnitude of intercellular electrochemical waves
Metadynamics Simulations Reveal a Na + Independent Exiting Path of Galactose for the Inward-Facing Conformation of vSGLT
Leukocyte Motility Models Assessed through Simulation and Multi-objective Optimization-Based Model Selection
How cortico-basal ganglia-thalamic subnetworks can shift decision policies to increase reward rate
Development of a hybrid model for a partially known intracellular signaling pathway through correction term estimation and neural network modeling
The art of seeing the elephant in the room: 2D embeddings of single-cell data do make sense
Non-Additive Coupling Enables Propagation of Synchronous Spiking Activity in Purely Random Networks
Efficient and flexible representation of higher-dimensional cognitive variables with grid cells
Deciphering the molecular mechanism of the cancer formation by chromosome structural dynamics
Closely related, yet unique: Distinct homo- and heterodimerization patterns of G protein coupled chemokine receptors and their fine-tuning by cholesterol
Insights into the Evolution and Emergence of a Novel Infectious Disease
Spatial considerations in the resolution of inflammation: Elucidating leukocyte interactions via an experimentally-calibrated agent-based model
Using Pre-existing Microarray Datasets to Increase Experimental Power: Application to Insulin Resistance
Investigating CTL Mediated Killing with a 3D Cellular Automaton
Thermodynamic Selection of Steric Zipper Patterns in the Amyloid Cross- β Spine
A computational analysis of in vivo VEGFR activation by multiple co-expressed ligands
Interconnected Cavernous Structure of Bacterial Fruiting Bodies
Characterizing the Relationship between Steady State and Response Using Analytical Expressions for the Steady States of Mass Action Models
A fast machine-learning-guided primer design pipeline for selective whole genome amplification
Blind demixing methods for recovering dense neuronal morphology from barcode imaging data
Integrating multiscale mathematical modeling and multidimensional data reveals the effects of epigenetic instability on acquired drug resistance in cancer
Objective quantification of nerves in immunohistochemistry specimens of thyroid cancer utilising deep learning
Deep reinforcement learning for the control of microbial co-cultures in bioreactors
Bridging Mechanistic and Phenomenological Models of Complex Biological Systems
Latent goal models for dynamic strategic interaction
Detecting change in stochastic sound sequences
"Fluctuograms" Reveal the Intermittent Intra-Protein Communication in Subtilisin Carlsberg and Correlate Mechanical Coupling with Co-Evolution
A Sensory-Driven Trade-Off between Coordinated Motion in Social Prey and a Predator's Visual Confusion
Structural Identifiability of Dynamic Systems Biology Models
A Theoretical Justification for Single Molecule Peptide Sequencing
A Multi-Scale Model of Hepcidin Promoter Regulation Reveals Factors Controlling Systemic Iron Homeostasis
Modelling Trial-by-Trial Changes in the Mismatch Negativity
Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials
Quantifying the Molecular Origins of Opposite Solvent Effects on Protein-Protein Interactions
DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network
Performance-gated deliberation: A context-adapted strategy in which urgency is opportunity cost
Stochasticity of replication forks' speeds plays a key role in the dynamics of DNA replication
Beam search decoder for enhancing sequence decoding speed in single-molecule peptide sequencing data
Graph-based description of tertiary lymphoid organs at single-cell level
Chemotaxis in Escherichia coli : A Molecular Model for Robust Precise Adaptation
Forecasting Influenza Epidemics in Hong Kong
Rhythmic Dynamics and Synchronization via Dimensionality Reduction: Application to Human Gait
Accounting for red blood cell accessibility reveals distinct invasion strategies in Plasmodium falciparum strains
Impact of Dimensionality and Network Disruption on Microrheology of Cancer Cells in 3D Environments
CGG toolkit: Software components for computational genomics
QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks
The Protective Role of Symmetric Stem Cell Division on the Accumulation of Heritable Damage
Robust and brain-like working memory through short-term synaptic plasticity
COBRAme: A computational framework for genome-scale models of metabolism and gene expression
pMD-Membrane: A Method for Ligand Binding Site Identification in Membrane-Bound Proteins
Model-Based Hypothesis Testing of Key Mechanisms in Initial Phase of Insulin Signaling
Trial-by-trial predictions of subjective time from human brain activity
SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data
Network Analysis of Global Influenza Spread
Predicting cell lineages using autoencoders and optimal transport
From affinity selection to kinetic selection in Germinal Centre modelling
Metabolic symbiosis between oxygenated and hypoxic tumour cells: An agent-based modelling study
Enhancing oscillations in intracranial electrophysiological recordings with data-driven spatial filters
The impact of climate change on ecology of tick associated with tick-borne diseases
Robustness of the Dorsal morphogen gradient with respect to morphogen dosage
Mechanical coupling in the nitrogenase complex
Impact of phylogeny on the inference of functional sectors from protein sequence data
A model of human motor sequence learning explains facilitation and interference effects based on spike-timing dependent plasticity
Chapter 15: Disease Gene Prioritization
A Race between Tumor Immunoescape and Genome Maintenance Selects for Optimum Levels of (epi)genetic Instability
Laminar and Dorsoventral Molecular Organization of the Medial Entorhinal Cortex Revealed by Large-scale Anatomical Analysis of Gene Expression
Computational Ecology: From the Complex to the Simple and Back
Graph-enhanced deep learning for diabetic retinopathy diagnosis: A quality-aware and uncertainty-driven approach
Hybrid dedicated and distributed coding in PMd/M1 provides separation and interaction of bilateral arm signals
Mouth-clicks used by blind expert human echolocators - signal description and model based signal synthesis
PremPDI estimates and interprets the effects of missense mutations on protein-DNA interactions
Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods
Modelling Cell Polarization Driven by Synthetic Spatially Graded Rac Activation
Modeling the temporal dynamics of master regulators and CtrA proteolysis in Caulobacter crescentus cell cycle
New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
Network analysis of patterns and relevance of enteric pathogen co-infections among infants in a diarrhea-endemic setting
The Origins of Time-Delay in Template Biopolymerization Processes
Chemotaxis when Bacteria Remember: Drift versus Diffusion
Many roads to minimizing regret: A comparison of Wang et al (2024) and OpAL* models of adaptive striatal dopamine
TimeTeller: A tool to probe the circadian clock as a multigene dynamical system
Ten Simple Rules for Online Learning
Activity Dependent Degeneration Explains Hub Vulnerability in Alzheimer's Disease
Computational mechanisms underlying cortical responses to the affordance properties of visual scenes
The Problem with Phi: A Critique of Integrated Information Theory
A Bayesian Partition Method for Detecting Pleiotropic and Epistatic eQTL Modules
A computational analysis of the oncogenic and anti-tumor immunity role of P4HA3 in human cancers
Mathematical modeling of the evolution of resistance and aggressiveness of high-grade serous ovarian cancer from patient CA-125 time series
Understanding the structure of cognitive noise
Assessing the feasibility and effectiveness of household-pooled universal testing to control COVID-19 epidemics
Will a Biological Database Be Different from a Biological Journal?
Control of tissue homeostasis, tumorigenesis, and degeneration by coupled bidirectional bistable switches
Ribosome reinitiation can explain length-dependent translation of messenger RNA
Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties
Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles
Null models for comparing information decomposition across complex systems
rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison
Bayesian clustering with uncertain data
Distributions of Transposable Elements Reveal Hazardous Zones in Mammalian Introns
An HIV Epidemic Model Based on Viral Load Dynamics: Value in Assessing Empirical Trends in HIV Virulence and Community Viral Load
Modeling the adenosine system as a modulator of cognitive performance and sleep patterns during sleep restriction and recovery
Cortical Surround Interactions and Perceptual Salience via Natural Scene Statistics
How Can PLOS Computational Biology Help the Biological Sciences?
Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling
Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways
Look twice: A generalist computational model predicts return fixations across tasks and species
Transcription factor interactions explain the context-dependent activity of CRX binding sites
Biologically-informed neural networks guide mechanistic modeling from sparse experimental data
Ten simple rules for scientists engaging in science communication
Shrinking Bouma's window: How to model crowding in dense displays
Four Distances between Pairs of Amino Acids Provide a Precise Description of their Interaction
High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED
Choice history effects in mice and humans improve reward harvesting efficiency
Two Birds with One Stone? Possible Dual-Targeting H1N1 Inhibitors from Traditional Chinese Medicine
Construction and Modelling of an Inducible Positive Feedback Loop Stably Integrated in a Mammalian Cell-Line
Multiplexing rhythmic information by spike timing dependent plasticity
For long-term sustainable software in bioinformatics
Getting Started in Text Mining
How can computation advance microbiome research?
Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis
Model diagnostics and refinement for phylodynamic models
2018 ISCB accomplishments by a senior scientist award
Smart epidemic control: A hybrid model blending ODEs and agent-based simulations for optimal, real-world intervention planning
A Gestalt inference model for auditory scene segregation
Clinical progression parameters associated with SARS-CoV-2, influenza, and respiratory syncytial virus infections in a large US integrated healthcare population
Inferring Pathway Activity toward Precise Disease Classification
Bayesian inference of metabolic kinetics from genome-scale multiomics data
The impact of individual perceptual and cognitive factors on collective states in a data-driven fish school model
Ultrafast population coding and axo-somatic compartmentalization
Don't Wear Your New Shoes (Yet): Taking the Right Steps to Become a Successful Principal Investigator
Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia
Ten simple rules for teaching applied programming in an authentic and immersive online environment
Shaping Neuronal Network Activity by Presynaptic Mechanisms
Flux Imbalance Analysis and the Sensitivity of Cellular Growth to Changes in Metabolite Pools
CNTools: A computational toolbox for cellular neighborhood analysis from multiplexed images
Functional Connectivity in Islets of Langerhans from Mouse Pancreas Tissue Slices
Modeling Planarian Regeneration: A Primer for Reverse-Engineering the Worm
Oroxylin A Inhibits Hemolysis via Hindering the Self-Assembly of α-Hemolysin Heptameric Transmembrane Pore
Coarse-Grained Molecular Simulation of Epidermal Growth Factor Receptor Protein Tyrosine Kinase Multi-Site Self-Phosphorylation
SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps
A Comparative Study and a Phylogenetic Exploration of the Compositional Architectures of Mammalian Nuclear Genomes
Including population and environmental dynamic heterogeneities in continuum models of collective behaviour with applications to locust foraging and group structure
Optimal Reaction Coordinate as a Biomarker for the Dynamics of Recovery from Kidney Transplant
Computational modeling of ketamine-induced changes in gamma-band oscillations: The contribution of parvalbumin and somatostatin interneurons
Use of Angiotensin-Converting Enzyme Inhibitors and Angiotensin II Receptor Blockers During the COVID-19 Pandemic: A Modeling Analysis
Predicting Functional Alternative Splicing by Measuring RNA Selection Pressure from Multigenome Alignments
Bayesian Estimation of Conditional Independence Graphs Improves Functional Connectivity Estimates
Experimentally Verified Parameter Sets for Modelling Heterogeneous Neocortical Pyramidal-Cell Populations
Gene Circuit Analysis of the Terminal Gap Gene huckebein
Eleven quick tips for finding research data
From policy to practice: Lessons learned from an open science funding initiative
Predicting organoid morphology through a phase field model: Insights into cell division and lumenal pressure
Risk factors for fluoroquinolone- and macrolide-resistance among swine Campylobacter coli using multi-layered chain graphs
Bayesian inference is facilitated by modular neural networks with different time scales
Measuring the Evolutionary Rewiring of Biological Networks
A novel classification framework for genome-wide association study of whole brain MRI images using deep learning
Personalizing physical exercise in a computational model of fuel homeostasis
Whole-body iron transport and metabolism: Mechanistic, multi-scale model to improve treatment of anemia in chronic kidney disease
Detecting behavioural changes in human movement to inform the spatial scale of interventions against COVID-19
Changes-of-mind in the absence of new post-decision evidence
Transient amplifiers of selection and reducers of fixation for death-Birth updating on graphs
The Individualized Genetic Barrier Predicts Treatment Response in a Large Cohort of HIV-1 Infected Patients
Population variability in the generation and selection of T-cell repertoires
Properties of MHC Class I Presented Peptides That Enhance Immunogenicity
Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue
Representational models: A common framework for understanding encoding, pattern-component, and representational-similarity analysis
Early visual signatures and benefits of intra-saccadic motion streaks
Probabilistic program inference in network-based epidemiological simulations
Local field potentials in a pre-motor region predict learned vocal sequences
TranSynergy: Mechanism-driven interpretable deep neural network for the synergistic prediction and pathway deconvolution of drug combinations
Changes in Spo0A~P pulsing frequency control biofilm matrix deactivation
Trial-Type Dependent Frames of Reference for Value Comparison
Estimating mutation rates under heterogeneous stress responses
Uncovering MicroRNA and Transcription Factor Mediated Regulatory Networks in Glioblastoma
Automatic Annotation of Spatial Expression Patterns via Sparse Bayesian Factor Models
Network propagation of rare variants in Alzheimer's disease reveals tissue-specific hub genes and communities
Mechanisms of ventricular arrhythmias elicited by coexistence of multiple electrophysiological remodeling in ischemia: A simulation study
Determinants of Brain Cell Metabolic Phenotypes and Energy Substrate Utilization Unraveled with a Modeling Approach
Statistical Use of Argonaute Expression and RISC Assembly in microRNA Target Identification
Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules
Developing Computational Biology
Simultaneous Identification of Multiple Driver Pathways in Cancer
Binding Leverage as a Molecular Basis for Allosteric Regulation
Mathematical model studies of the comprehensive generation of major and minor phyllotactic patterns in plants with a predominant focus on orixate phyllotaxis
Rich-club connectivity, diverse population coupling, and dynamical activity patterns emerging from local cortical circuits
Irrelevance by inhibition: Learning, computation, and implications for schizophrenia
Modeling and Measuring Signal Relay in Noisy Directed Migration of Cell Groups
Multi-scale computational modeling towards efficacy in radiopharmaceutical therapies while minimizing side effects: Modeling of amino acid infusion
Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2
Adapting to time: Why nature may have evolved a diverse set of neurons
Modeling an Excitable Biosynthetic Tissue with Inherent Variability for Paired Computational-Experimental Studies
Computational modelling of muscle fibre operating ranges in the hindlimb of a small ground bird (Eudromia elegans), with implications for modelling locomotion in extinct species
Modeling the Evolution of Beliefs Using an Attentional Focus Mechanism
Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil
Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering
The spinal cord facilitates cerebellar upper limb motor learning and control; inputs from neuromusculoskeletal simulation
Cell Type Specific Alterations in Interchromosomal Networks across the Cell Cycle
Ten simple rules for annotating sequencing experiments
2017 ISCB Overton Prize awarded to Christoph Bock
Codon Usage Domains over Bacterial Chromosomes
Bayesian accounts of perceptual decisions in the nonclinical continuum of psychosis: Greater imprecision in both top-down and bottom-up processes
Ten simple rules for large-scale data processing
Molecular Simulation-Based Structural Prediction of Protein Complexes in Mass Spectrometry: The Human Insulin Dimer
Residual Viremia in Treated HIV + Individuals
Bioinformatics in China: A Personal Perspective
Modeling decision-making under uncertainty with qualitative outcomes
Unsupervised manifold learning of collective behavior
Identifying longevity associated genes by integrating gene expression and curated annotations
Hebbian plasticity in parallel synaptic pathways: A circuit mechanism for systems memory consolidation
Ten quick tips for bioinformatics analyses using an Apache Spark distributed computing environment
Modulation of the Disordered Conformational Ensembles of the p53 Transactivation Domain by Cancer-Associated Mutations
Differential T cell response against BK virus regulatory and structural antigens: A viral dynamics modelling approach
Replication Timing: A Fingerprint for Cell Identity and Pluripotency
Localization, epidemic transitions, and unpredictability of multistrain epidemics with an underlying genotype network
Stytra: An open-source, integrated system for stimulation, tracking and closed-loop behavioral experiments
Correction: Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
Omnidirectional propulsion in a metachronal swimmer
The Role of Local Backrub Motions in Evolved and Designed Mutations
Brownian Dynamics Simulation of Nucleocytoplasmic Transport: A Coarse-Grained Model for the Functional State of the Nuclear Pore Complex
Curation of the Mammalian Palmitoylome Indicates a Pivotal Role for Palmitoylation in Diseases and Disorders of the Nervous System and Cancers
Development of a physiologically-based pharmacokinetic pediatric brain model for prediction of cerebrospinal fluid drug concentrations and the influence of meningitis
Sequence-based prediction of protein binding mode landscapes
An Evolutionary Trace method defines functionally important bases and sites common to RNA families
Mapping the Evolutionary Space of SARS-CoV-2 Variants to Anticipate Emergence of Subvariants Resistant to COVID-19 Therapeutics
Excitability Constraints on Voltage-Gated Sodium Channels
A hybrid stochastic-deterministic approach to explore multiple infection and evolution in HIV
nAdder: A scale-space approach for the 3D analysis of neuronal traces
ScalaFlux: A scalable approach to quantify fluxes in metabolic subnetworks
Integrative pan-cancer analysis reveals a common architecture of dysregulated transcriptional networks characterized by loss of enhancer methylation
Integrating Statistical Predictions and Experimental Verifications for Enhancing Protein-Chemical Interaction Predictions in Virtual Screening
Classification of T lymphocyte motility behaviors using a machine learning approach
Ten simple rules for running and managing virtual internships
Modeling the three-dimensional connectivity of in vitro cortical ensembles coupled to Micro-Electrode Arrays
Programming co-assembled peptide nanofiber morphology via anionic amino acid type: Insights from molecular dynamics simulations
Task-induced neural covariability as a signature of approximate Bayesian learning and inference
Network Analysis of Intrinsic Functional Brain Connectivity in Alzheimer's Disease
An uncertainty-based model of the effects of fixation on choice
Topological data analysis reveals core heteroblastic and ontogenetic programs embedded in leaves of grapevine (Vitaceae) and maracuyá (Passifloraceae)
On the Importance of Polar Interactions for Complexes Containing Intrinsically Disordered Proteins
Label-free imaging and classification of live P. falciparum enables high performance parasitemia quantification without fixation or staining
The intrinsic dimension of protein sequence evolution
Receptor dimerization enables ligand discrimination through tunable response heterogeneity
New Universal Rules of Eukaryotic Translation Initiation Fidelity
Engineering recurrent neural networks from task-relevant manifolds and dynamics
Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy
Genetic Signatures in the Envelope Glycoproteins of HIV-1 that Associate with Broadly Neutralizing Antibodies
The Peri-Saccadic Perception of Objects and Space
VolPy: Automated and scalable analysis pipelines for voltage imaging datasets
WormPose: Image synthesis and convolutional networks for pose estimation in C. elegans
Theory of Choice in Bandit, Information Sampling and Foraging Tasks
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
Disease evolution in reaction networks: Implications for a diagnostic problem
Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome
Which of Our Modeling Predictions Are Robust?
Balrog: A universal protein model for prokaryotic gene prediction
STDP Allows Fast Rate-Modulated Coding with Poisson-Like Spike Trains
pSSAlib: The partial-propensity stochastic chemical network simulator
Simulated actin reorganization mediated by motor proteins
Cloud computing applications for biomedical science: A perspective