yusuke1997/dblp-id-title huggingface dataset:
Classifying dynamic transitions in high dimensional neural mass models: A random forest approach
Dynamics of the Heat Stress Response of Ceramides with Different Fatty-Acyl Chain Lengths in Baker's Yeast
Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++
Ligand-Target Prediction by Structural Network Biology Using nAnnoLyze
A Peptide-Based Method for 13 C Metabolic Flux Analysis in Microbial Communities
Disordered Flanks Prevent Peptide Aggregation
A Bipolar Clamp Mechanism for Activation of Jak-Family Protein Tyrosine Kinases
Ten "simple" rules for non-Indigenous researchers engaging Indigenous communities in Arctic research
Assessing Vaccination Sentiments with Online Social Media: Implications for Infectious Disease Dynamics and Control
A Report of the Curriculum Task Force of the ISCB Education Committee
The Effects of NR2 Subunit-Dependent NMDA Receptor Kinetics on Synaptic Transmission and CaMKII Activation
Fast Reconstruction of Compact Context-Specific Metabolic Network Models
A Human Platelet Calcium Calculator Trained by Pairwise Agonist Scanning
AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression
A Quick Guide to Large-Scale Genomic Data Mining
Ten Simple Rules for Developing a MOOC
Native Contact Density and Nonnative Hydrophobic Effects in the Folding of Bacterial Immunity Proteins
Direct prediction of regulatory elements from partial data without imputation
Gene Expression Switching of Receptor Subunits in Human Brain Development
A Cell-Based Model for Quorum Sensing in Heterogeneous Bacterial Colonies
Mechanisms of Magnetic Stimulation of Central Nervous System Neurons
HillTau: A fast, compact abstraction for model reduction in biochemical signaling networks
Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification
Multiview learning for understanding functional multiomics
Single-molecule protein identification by sub-nanopore sensors
Ten Years of PLoS ‡ Computational Biology: A Decade of Appreciation and Innovation
RBC-GEM: A genome-scale metabolic model for systems biology of the human red blood cell
Are V1 Simple Cells Optimized for Visual Occlusions? A Comparative Study
Image-Based Modeling Reveals Dynamic Redistribution of DNA Damage into Nuclear Sub-Domains
The formation of preference in risky choice
Generative AI extracts ecological meaning from the complex three dimensional shapes of bird bills
Transient Resetting: A Novel Mechanism for Synchrony and Its Biological Examples
Inverse Stochastic Resonance in Cerebellar Purkinje Cells
The Sense of Confidence during Probabilistic Learning: A Normative Account
Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion
Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system
Integrating systemic and molecular levels to infer key drivers sustaining metabolic adaptations
Two-step mechanism of J-domain action in driving Hsp70 function
Regulated CRISPR Modules Exploit a Dual Defense Strategy of Restriction and Abortive Infection in a Model of Prokaryote-Phage Coevolution
The gradient clusteron: A model neuron that learns to solve classification tasks via dendritic nonlinearities, structural plasticity, and gradient descent
Ultra-Fast Evaluation of Protein Energies Directly from Sequence
Systems approach for congruence and selection of cancer models towards precision medicine
Quantitative mechanistic model reveals key determinants of placental IgG transfer and informs prenatal immunization strategies
Ten simple rules for using entrepreneurship skills to improve research careers and culture
Optimizing interneuron circuits for compartment-specific feedback inhibition
PUMA: A Unified Framework for Penalized Multiple Regression Analysis of GWAS Data
Precision of Readout at the hunchback Gene: Analyzing Short Transcription Time Traces in Living Fly Embryos
Annotating functional effects of non-coding variants in neuropsychiatric cell types by deep transfer learning
An integrative approach to protein sequence design through multiobjective optimization
Computational analysis of memory consolidation following inhibitory avoidance (IA) training in adult and infant rats: Critical roles of CaMKIIα and MeCP2
The Differential Response of Proteins to Macromolecular Crowding
Uncovering the organization of neural circuits with Generalized Phase Locking Analysis
A Computational Approach to the Functional Screening of Genomes
Active Nuclear Receptors Exhibit Highly Correlated AF-2 Domain Motions
Bayesian inference of neuronal assemblies
A fully autonomous terrestrial bat-like acoustic robot
Examination of the Effects of Heterogeneous Organization of RyR Clusters, Myofibrils and Mitochondria on Ca 2+ Release Patterns in Cardiomyocytes
Metagenome and Metatranscriptome Analyses Using Protein Family Profiles
The Vast, Conserved Mammalian lincRNome
Binding free energy decomposition and multiple unbinding paths of buried ligands in a PreQ1 riboswitch
Multiplexing information flow through dynamic signalling systems
A Dynamic Neural Field Model of Mesoscopic Cortical Activity Captured with Voltage-Sensitive Dye Imaging
Learning Multisensory Integration and Coordinate Transformation via Density Estimation
Improving deep models of protein-coding potential with a Fourier-transform architecture and machine translation task
Prospective Coding by Spiking Neurons
Spike and burst coding in thalamocortical relay cells
Approximating complex musculoskeletal biomechanics using multidimensional autogenerating polynomials
Bayesian parameter estimation for dynamical models in systems biology
Neuronal population model of globular bushy cells covering unit-to-unit variability
Dynamic Network Drivers of Seizure Generation, Propagation and Termination in Human Neocortical Epilepsy
OSCAR: Optimal subset cardinality regression using the L0-pseudonorm with applications to prognostic modelling of prostate cancer
Evaluation and comparison of multi-omics data integration methods for cancer subtyping
Cortico-Cortical Interactions during Acquisition and Use of a Neuroprosthetic Skill
A framework for integrating directed and undirected annotations to build explanatory models of cis-eQTL data
Protein and DNA Sequence Determinants of Thermophilic Adaptation
Model certainty in cellular network-driven processes with missing data
Evolution under Fluctuating Environments Explains Observed Robustness in Metabolic Networks
Large-Scale Turnover of Functional Transcription Factor Binding Sites in Drosophila
Leveraging heterogeneity for neural computation with fading memory in layer 2/3 cortical microcircuits
A Bayesian Approach to Quantifying the Effects of Mass Poultry Vaccination upon the Spatial and Temporal Dynamics of H5N1 in Northern Vietnam
Smoothing of, and Parameter Estimation from, Noisy Biophysical Recordings
Mesoscale, long-time mixing of chromosomes and its connection to polymer dynamics
Modeling the activation of the alternative complement pathway and its effects on hemolysis in health and disease
Predicted Role of NAD Utilization in the Control of Circadian Rhythms during DNA Damage Response
Addressing erroneous scale assumptions in microbe and gene set enrichment analysis
Shunting Inhibition Controls the Gain Modulation Mediated by Asynchronous Neurotransmitter Release in Early Development
Predicting Phenotypic Diversity and the Underlying Quantitative Molecular Transitions
Inferring Nonlinear Neuronal Computation Based on Physiologically Plausible Inputs
Negative Example Selection for Protein Function Prediction: The NoGO Database
Incremental Mutual Information: A New Method for Characterizing the Strength and Dynamics of Connections in Neuronal Circuits
Structural prediction of chimeric immunogen candidates to elicit targeted antibodies against betacoronaviruses
Measuring and understanding information storage and transfer in a simulated human gut microbiome
Overexpression of Heat Shock Protein 72 Attenuates NF-κB Activation Using a Combination of Regulatory Mechanisms in Microglia
Biosensor Approach to Psychopathology Classification
Computation predicts rapidly adapting mechanotransduction currents cannot account for tactile encoding in Merkel cell-neurite complexes
ISMB 2008 Toronto
Model-based decoupling of evoked and spontaneous neural activity in calcium imaging data
Critical Dynamics in the Evolution of Stochastic Strategies for the Iterated Prisoner's Dilemma
Intriguing effects of selection intensity on the evolution of prosocial behaviors
Antioxidant Properties of Kynurenines: Density Functional Theory Calculations
A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing
Mechanisms underlying attraction to odors in walking Drosophila
Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling
Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism
Scoring epidemiological forecasts on transformed scales
Structure-Based Statistical Mechanical Model Accounts for the Causality and Energetics of Allosteric Communication
A Comparative Analysis of Drug-Induced Hepatotoxicity in Clinically Relevant Situations
Dimensionality, information and learning in prefrontal cortex
Inferring the immune response from repertoire sequencing
Linkage of Viral Sequences among HIV-Infected Village Residents in Botswana: Estimation of Linkage Rates in the Presence of Missing Data
Why SIT Works: Normal Function Despite Typical Myofiber Pattern in Situs Inversus Totalis (SIT) Hearts Derived by Shear-induced Myofiber Reorientation
Population coding strategies in human tactile afferents
Trade-Offs and Constraints in Allosteric Sensing
An error-tuned model for sensorimotor learning
The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes
BinaryCIF and CIFTools - Lightweight, efficient and extensible macromolecular data management
Influence of confinement on the spreading of bacterial populations
Epigenome-based splicing prediction using a recurrent neural network
Mechano-biological and bio-mechanical pathways in cutaneous wound healing
Detecting Network Communities: An Application to Phylogenetic Analysis
Correction: Extracellular loops of BtuB facilitate transport of vitamin B12 through the outer membrane of E. coli
Co-occurring protein phosphorylation are functionally associated
Toward a Detailed Description of the Thermally Induced Dynamics of the Core Promoter
The Virtuous Cycle of a Data Ecosystem
Efficient Sparse Coding in Early Sensory Processing: Lessons from Signal Recovery
Adaptation and Selective Information Transmission in the Cricket Auditory Neuron AN2
Analysis of Initial Cell Spreading Using Mechanistic Contact Formulations for a Deformable Cell Model
Superinfection exclusion: A viral strategy with short-term benefits and long-term drawbacks
Correction: Catalyst: Fast and flexible modeling of reaction networks
Network Topologies and Dynamics Leading to Endotoxin Tolerance and Priming in Innate Immune Cells
Inferring Host Gene Subnetworks Involved in Viral Replication
Adaptation towards scale-free dynamics improves cortical stimulus discrimination at the cost of reduced detection
ENCORE: Software for Quantitative Ensemble Comparison
Bridging the gap: Using reservoir ecology and human serosurveys to estimate Lassa virus spillover in West Africa
Active inference unifies intentional and conflict-resolution imperatives of motor control
A Design Principle of Group-level Decision Making in Cell Populations
Evidence for Sequential and Increasing Activation of Replication Origins along Replication Timing Gradients in the Human Genome
Stochastic resonance enhances the rate of evidence accumulation during combined brain stimulation and perceptual decision-making
Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models
Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins
ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data
NextVir: Enabling classification of tumor-causing viruses with genomic foundation models
Phylogenetic correlations can suffice to infer protein partners from sequences
Interkinetic nuclear movements promote apical expansion in pseudostratified epithelia at the expense of apicobasal elongation
MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
The SONATA data format for efficient description of large-scale network models
Extracting temporal relationships between weakly coupled peptidergic and motoneuronal signaling: Application to Drosophila ecdysis behavior
Mapping the physiological changes in sleep regulation across infancy and young childhood
Strain design optimization using reinforcement learning
Balance of mechanical forces drives endothelial gap formation and may facilitate cancer and immune-cell extravasation
State transitions through inhibitory interneurons in a cortical network model
Vicus: Exploiting local structures to improve network-based analysis of biological data
On State-Space Reduction in Multi-Strain Pathogen Models, with an Application to Antigenic Drift in Influenza A
Energetic costs of cellular and therapeutic control of stochastic mitochondrial DNA populations
A diel multi-tissue genome-scale metabolic model of Vitis vinifera
Mutational analysis of SARS-CoV-2 variants of concern reveals key tradeoffs between receptor affinity and antibody escape
Correction: Synthetic method of analogues for emerging infectious disease forecasting
Thermodynamic Costs of Information Processing in Sensory Adaptation
Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences
Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability
Emergent decision-making behaviour and rhythm generation in a computational model of the ventromedial nucleus of the hypothalamus
HippoUnit: A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data
A single Markov-type kinetic model accounting for the macroscopic currents of all human voltage-gated sodium channel isoforms
Multiple patterns of persistent inward currents with multiple types of repetitive firings in medullary serotonergic neurons of mice: An experimental and modeling study
Lysine120 Interactions with p53 Response Elements can Allosterically Direct p53 Organization
Estimation of the force of infection and infectious period of skin sores in remote Australian communities using interval-censored data
Gaussian curvature and the budding kinetics of enveloped viruses
High-throughput Computer Method for 3D Neuronal Structure Reconstruction from the Image Stack of the Drosophila Brain and Its Applications
An Exclusion Zone for Ca 2+ Channels around Docked Vesicles Explains Release Control by Multiple Channels at a CNS Synapse
A simulation study on the antiarrhythmic mechanisms of established agents in myocardial ischemia and infarction
Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling
Structural and Energetic Characterization of the Ankyrin Repeat Protein Family
Editorial Note: Mathematical modeling of the molecular switch of TNFR1-mediated signaling pathways applying Petri net formalism and in silico knockout analysis
Optimism and pessimism in optimised replay
EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos
Identification of Crosstalk between Phosphoprotein Signaling Pathways in RAW 264.7 Macrophage Cells
Ten Simple Rules to Enable Multi-site Collaborations through Data Sharing
Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial
Ten simple rules for acing virtual interviews
Activation of the DNA-repair mechanism through NBS1 and MRE11 diffusion
Covalent docking and molecular dynamics simulations reveal the specificity-shifting mutations Ala237Arg and Ala237Lys in TEM beta-lactamase
A Digital Atlas to Characterize the Mouse Brain Transcriptome
Model guided trait-specific co-expression network estimation as a new perspective for identifying molecular interactions and pathways
Ten simple rules for early-career researchers supervising short-term student projects
Diversity and evolution of computationally predicted T cell epitopes against human respiratory syncytial virus
CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing
Posterior Probability Matching and Human Perceptual Decision Making
Chemical, Target, and Bioactive Properties of Allosteric Modulation
Inferring pathway activity from single-cell and spatial transcriptomics data with PaaSc
TRANSIT - A Software Tool for Himar1 TnSeq Analysis
A proposed workflow for proactive virus surveillance and prediction of variants for vaccine design
Interference with HIV infection of the first cell is essential for viral clearance at sub-optimal levels of drug inhibition
Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots
Comparison of Detailed and Simplified Models of Human Atrial Myocytes to Recapitulate Patient Specific Properties
Performance and Scalability of Discriminative Metrics for Comparative Gene Identification in 12 Drosophila Genomes
Nucleotide context models outperform protein language models for predicting antibody affinity maturation
A simulation-based method to inform serosurvey design for estimating the force of infection using existing blood samples
MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments
Biophysical network modeling of the dLGN circuit: Effects of cortical feedback on spatial response properties of relay cells
Using pseudoalignment and base quality to accurately quantify microbial community composition
Spatial Simulations of Myxobacterial Development
A Generic Mechanism for Adaptive Growth Rate Regulation
Flexible Cognitive Strategies during Motor Learning
A Self-Organizing State-Space-Model Approach for Parameter Estimation in Hodgkin-Huxley-Type Models of Single Neurons
How to Understand the Cell by Breaking It: Network Analysis of Gene Perturbation Screens
Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement
Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology
Prediction of Co-Receptor Usage of HIV-1 from Genotype
Chapter 16: Text Mining for Translational Bioinformatics
Bistable, Irregular Firing and Population Oscillations in a Modular Attractor Memory Network
Forecasting Influenza Outbreaks in Boroughs and Neighborhoods of New York City
Antibody Responses during Hepatitis B Viral Infection
The HIV Mutation Browser: A Resource for Human Immunodeficiency Virus Mutagenesis and Polymorphism Data
FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms
War of Ontology Worlds: Mathematics, Computer Code, or Esperanto?
Intramolecular Cohesion of Coils Mediated by Phenylalanine-Glycine Motifs in the Natively Unfolded Domain of a Nucleoporin
Dissecting Bayes: Using influence measures to test normative use of probability density information derived from a sample
Adhesion Failures Determine the Pattern of Choroidal Neovascularization in the Eye: A Computer Simulation Study
Discovering the Phylodynamics of RNA Viruses
Apoptotic Lymphocytes of H. sapiens Lose Nucleosomes in GC-Rich Promoters
Searching algorithm for Type IV effector proteins (S4TE) 2.0: Improved tools for Type IV effector prediction, analysis and comparison in proteobacteria
Spatial organisation of the mesoscale connectome: A feature influencing synchrony and metastability of network dynamics
Transitions in information processing dynamics at the whole-brain network level are driven by alterations in neural gain
Memories in a network with excitatory and inhibitory plasticity are encoded in the spiking irregularity
Modeling visual performance differences 'around' the visual field: A computational observer approach
Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data
Developing a Physiologically-Based Pharmacokinetic Model Knowledgebase in Support of Provisional Model Construction
Experimental and Computational Analysis of Polyglutamine-Mediated Cytotoxicity
Modeling of the axon membrane skeleton structure and implications for its mechanical properties
Evidence for Gene-Specific Rather Than Transcription Rate-Dependent Histone H3 Exchange in Yeast Coding Regions
2016 ISCB Innovator Award: Serafim Batzoglou
Securing the future of research computing in the biosciences
Understanding Auditory Spectro-Temporal Receptive Fields and Their Changes with Input Statistics by Efficient Coding Principles
Spatio-Temporal Simulation of First Pass Drug Perfusion in the Liver
NHE Inhibition Does Not Improve Na + or Ca 2+ Overload During Reperfusion: Using Modeling to Illuminate the Mechanisms Underlying a Therapeutic Failure
Multiscale representations of community structures in attractor neural networks
Close-kin mark-recapture methods to estimate demographic parameters of mosquitoes
Internal Representations of Temporal Statistics and Feedback Calibrate Motor-Sensory Interval Timing
Error-Robust Modes of the Retinal Population Code
Multiple-target tracking in human and machine vision
3D structure and stability prediction of DNA with multi-way junctions in ionic solutions
Correction: Opponent learning with different representations in the cortico-basal ganglia pathways can develop obsession-compulsion cycle
In Silico Evidence for Gluconeogenesis from Fatty Acids in Humans
Likelihood-ratio test statistic for the finite-sample case in nonlinear ordinary differential equation models
A practical application of generative adversarial networks for RNA-seq analysis to predict the molecular progress of Alzheimer's disease
Conservation of conformational dynamics across prokaryotic actins
Survival analysis of pathway activity as a prognostic determinant in breast cancer
Weak coupling between intracellular feedback loops explains dissociation of clock gene dynamics
Ten simple rules for hitting a home run with your elevator pitch
How To Advance Open International Scientific Exchange
Individual versus superensemble forecasts of seasonal influenza outbreaks in the United States
Exploring O 2 Diffusion in A-Type Cytochrome c Oxidases: Molecular Dynamics Simulations Uncover Two Alternative Channels towards the Binuclear Site
Combined model-free and model-sensitive reinforcement learning in non-human primates
Automatic Extraction of Protein Point Mutations Using a Graph Bigram Association
Metabomatching: Using genetic association to identify metabolites in proton NMR spectroscopy
In Silico Oncology: Quantification of the In Vivo Antitumor Efficacy of Cisplatin-Based Doublet Therapy in Non-Small Cell Lung Cancer (NSCLC) through a Multiscale Mechanistic Model
The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber
Explainable multi-task learning improves the parallel estimation of polygenic risk scores for many diseases through shared genetic basis
Recovery of Dynamics and Function in Spiking Neural Networks with Closed-Loop Control
Informed Switching Strongly Decreases the Prevalence of Antibiotic Resistance in Hospital Wards
Unveiling functions of the visual cortex using task-specific deep neural networks
RNA velocity unraveled
Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening
Implications of alternative routes to APC/C inhibition by the mitotic checkpoint complex
Quantifying Clonal and Subclonal Passenger Mutations in Cancer Evolution
Ten simple rules for finding and selecting R packages
Some Work and Some Play: Microscopic and Macroscopic Approaches to Labor and Leisure
Modelling and analysis of cAMP-induced mixed-mode oscillations in cortical neurons: Critical roles of HCN and M-type potassium channels