yusuke1997/dblp-id-title huggingface dataset:
Dynamic balance between vesicle transport and microtubule growth enables neurite outgrowth
Structural Insights into the Inhibition of Cytosolic 5′-Nucleotidase II (cN-II) by Ribonucleoside 5′-Monophosphate Analogues
STREAK: A supervised cell surface receptor abundance estimation strategy for single cell RNA-sequencing data using feature selection and thresholded gene set scoring
Modeling sensory-motor decisions in natural behavior
Protein Complexes in Bacteria
Linking signal detection theory and encoding models to reveal independent neural representations from neuroimaging data
Regulators Associated with Clinical Outcomes Revealed by DNA Methylation Data in Breast Cancer
Using deep neural networks to evaluate object vision tasks in rats
Temporal specificity of the initial adaptive response in motor adaptation
A Dynamic Gene Regulatory Network Model That Recovers the Cyclic Behavior of Arabidopsis thaliana Cell Cycle
Deconvolving the contributions of cell-type heterogeneity on cortical gene expression
International Society for Computational Biology Honours Gunnar von Heijne and Ziv Bar-Joseph with Top Bioinformatics/Computational Biology Awards for 2012
Analysis of Combinatorial Regulation: Scaling of Partnerships between Regulators with the Number of Governed Targets
Hippocampal Remapping Is Constrained by Sparseness rather than Capacity
Interplay between the Localization and Kinetics of Phosphorylation in Flagellar Pole Development of the Bacterium Caulobacter crescentus
Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions
SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes
Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations
Human-like dissociations between confidence and accuracy in convolutional neural networks
A Reappraisal of How to Build Modular, Reusable Models of Biological Systems
Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning
Aggregating forecasts of multiple respiratory pathogens supports more accurate forecasting of influenza-like illness
Delayed global feedback in the genesis and stability of spatiotemporal excitation patterns in paced biological excitable media
Modeling Dynamic Regulatory Processes in Stroke
From Endosymbiont to Host-Controlled Organelle: The Hijacking of Mitochondrial Protein Synthesis and Metabolism
Full-length ribosome density prediction by a multi-input and multi-output model
Genome-Scale Reconstruction and Analysis of the Pseudomonas putid a KT2440 Metabolic Network Facilitates Applications in Biotechnology
Dopamine transporter oligomerization involves the scaffold domain, but spares the bundle domain
Ten quick tips for harnessing the power of ChatGPT in computational biology
Ligand-Induced Modulation of the Free-Energy Landscape of G Protein-Coupled Receptors Explored by Adaptive Biasing Techniques
Agent-based modeling of nuclear chromosome ensembles identifies determinants of homolog pairing during meiosis
2018 ISCB Innovator Award recognizes M. Madan Babu
Formation of Raft-Like Assemblies within Clusters of Influenza Hemagglutinin Observed by MD Simulations
An Information-Theoretic Characterization of the Optimal Gradient Sensing Response of Cells
Correction: A probabilistic model for the ultradian timing of REM sleep in mice
Bioinformatics and Computational Biology in Poland
Ascension of Chlamydia is moderated by uterine peristalsis and the neutrophil response to infection
Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin
Topology, Cross-Frequency, and Same-Frequency Band Interactions Shape the Generation of Phase-Amplitude Coupling in a Neural Mass Model of a Cortical Column
Diversity and Noise Effects in a Model of Homeostatic Regulation of the Sleep-Wake Cycle
Dynamical persistence in high-diversity resource-consumer communities
Correction: Foraging as sampling without replacement: A Bayesian statistical model for estimating biases in target selection
Initial-state-dependent, robust, transient neural dynamics encode conscious visual perception
Power Laws for Heavy-Tailed Distributions: Modeling Allele and Haplotype Diversity for the National Marrow Donor Program
Internal but not external noise frees working memory resources
Expansion of the Protein Repertoire in Newly Explored Environments: Human Gut Microbiome Specific Protein Families
Inferring Correlation Networks from Genomic Survey Data
Why Don't CD8+ T Cells Reduce the Lifespan of SIV-Infected Cells In Vivo?
Local Function Conservation in Sequence and Structure Space
Ten Simple Rules for writing algorithmic bioinformatics conference papers
Modeling opioid overdose events recurrence with a covariate-adjusted triggering point process
Library of Disordered Patterns in 3D Protein Structures
Numerical evaluation reveals the effect of branching morphology on vessel transport properties during angiogenesis
A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa
Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis
The role of training variability for model-based and model-free learning of an arbitrary visuomotor mapping
The Pathway Coexpression Network: Revealing pathway relationships
Life cycle synchronization is a viral drug resistance mechanism
A novel riboswitch classification based on imbalanced sequences achieved by machine learning
The empirical characteristics of human pattern vision defy theoretically-driven expectations
A comprehensive exploration of the druggable conformational space of protein kinases using AI-predicted structures
Accuracy Maximization Analysis for Sensory-Perceptual Tasks: Computational Improvements, Filter Robustness, and Coding Advantages for Scaled Additive Noise
Eleven quick tips for writing a Bioconductor package
Computationally-guided drug repurposing enables the discovery of kinase targets and inhibitors as new schistosomicidal agents
Spontaneous Reaction Silencing in Metabolic Optimization
PASA: Proteomic analysis of serum antibodies web server
Combining hypoxia-activated prodrugs and radiotherapy in silico: Impact of treatment scheduling and the intra-tumoural oxygen landscape
Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments
Environmental Statistics and Optimal Regulation
Interleaved single and bursting spiking resonance in neurons
A New Model for Pore Formation by Cholesterol-Dependent Cytolysins
Dual Coordination of Post Translational Modifications in Human Protein Networks
Systematic evaluation of NIPT aneuploidy detection software tools with clinically validated NIPT samples
A General Model for Toxin-Antitoxin Module Dynamics Can Explain Persister Cell Formation in E. coli
Neuron tracing and quantitative analyses of dendritic architecture reveal symmetrical three-way-junctions and phenotypes of git-1 in C. elegans
Learning about and from others' prudence, impatience or laziness: The computational bases of attitude alignment
RMDGCN: Prediction of RNA methylation and disease associations based on graph convolutional network with attention mechanism
Modeling HIV-1 Drug Resistance as Episodic Directional Selection
Virus Encoded MHC-Like Decoys Diversify the Inhibitory KIR Repertoire
Regulus infers signed regulatory relations from few samples' information using discretization and likelihood constraints
Ancestral haplotype reconstruction in endogamous populations using identity-by-descent
Deciphering the interplay between biology and physics with a finite element method-implemented vertex organoid model: A tool for the mechanical analysis of cell behavior on a spherical organoid shell
DeepMIB: User-friendly and open-source software for training of deep learning network for biological image segmentation
High Epitope Expression Levels Increase Competition between T Cells
Estimating Re and overdispersion in secondary cases from the size of identical sequence clusters of SARS-CoV-2
Connectivity Matrix Seriation via Relaxation
A Model for a Correlated Random Walk Based on the Ordered Extension of Pseudopodia
Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks
Impact of Adaptation Currents on Synchronization of Coupled Exponential Integrate-and-Fire Neurons
Motif-pattern dependence of biomolecular phase separation driven by specific interactions
A Model for Integrating Elementary Neural Functions into Delayed-Response Behavior
Optimizing the learning rate for adaptive estimation of neural encoding models
Stochastic colonization of hosts with a finite lifespan can drive individual host microbes out of equilibrium
Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes
Doubly Bayesian Analysis of Confidence in Perceptual Decision-Making
Mechanistic Model of Natural Killer Cell Proliferative Response to IL-15 Receptor Stimulation
Redundancy and the Evolution of Cis -Regulatory Element Multiplicity
Capturing the emergent dynamical structure in biophysical neural models
Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome
High-Precision, In Vitro Validation of the Sequestration Mechanism for Generating Ultrasensitive Dose-Response Curves in Regulatory Networks
Microarray Comparative Genomic Hybridisation Analysis Incorporating Genomic Organisation, and Application to Enterobacterial Plant Pathogens
Ten Simple Rules for Effective Online Outreach
Revealing the True Incidence of Pandemic A(H1N1)pdm09 Influenza in Finland during the First Two Seasons - An Analysis Based on a Dynamic Transmission Model
Finding the Way with a Noisy Brain
Fast adaptation to rule switching using neuronal surprise
EventEpi - A natural language processing framework for event-based surveillance
Drug-disease networks and drug repurposing
Depression-Biased Reverse Plasticity Rule Is Required for Stable Learning at Top-Down Connections
Aggressive or moderate drug therapy for infectious diseases? Trade-offs between different treatment goals at the individual and population levels
Inferring fungal growth rates from optical density data
Pore Structure and Synergy in Antimicrobial Peptides of the Magainin Family
Bonsai Trees in Your Head: How the Pavlovian System Sculpts Goal-Directed Choices by Pruning Decision Trees
LOTUS: A single- and multitask machine learning algorithm for the prediction of cancer driver genes
Effects of Ploidy and Recombination on Evolution of Robustness in a Model of the Segment Polarity Network
Excitatory Local Interneurons Enhance Tuning of Sensory Information
A real-time regional model for COVID-19: Probabilistic situational awareness and forecasting
Power Law Scaling in Human and Empty Room MEG Recordings
Reproduction of patterns in melanocytic proliferations by agent-based simulation and geometric modeling
A Combined Experimental and Mathematical Approach for Molecular-based Optimization of Irinotecan Circadian Delivery
Dynamical and Structural Analysis of a T Cell Survival Network Identifies Novel Candidate Therapeutic Targets for Large Granular Lymphocyte Leukemia
A generalized higher-order correlation analysis framework for multi-omics network inference
Motor Demands Constrain Cognitive Rule Structures
Temporal Expression-based Analysis of Metabolism
A global map of the protein shape universe
Polymorphic sites preferentially avoid co-evolving residues in MHC class I proteins
Comparing Bayesian and non-Bayesian accounts of human confidence reports
A Learning Theory for Reward-Modulated Spike-Timing-Dependent Plasticity with Application to Biofeedback
A Dynamical Model Reveals Gene Co-Localizations in Nucleus
Celebrating a body of work
Informing policy via dynamic models: Cholera in Haiti
Numerical Modelling Of The V-J Combinations Of The T Cell Receptor TRA/TRD Locus
Selective consistency of recurrent neural networks induced by plasticity as a mechanism of unsupervised perceptual learning
Internal cohesion gradient as a novel mechanism of collective cell migration
Ten simple rules for biologists initiating a collaboration with computer scientists
Spatial modelling for population replacement of mosquito vectors at continental scale
Identification of periodic attractors in Boolean networks using a priori information
Reactome graph database: Efficient access to complex pathway data
Detailed Contact Data and the Dissemination of Staphylococcus aureus in Hospitals
Modeling the impact of changes in day-care contact patterns on the dynamics of varicella transmission in France between 1991 and 2015
Remote homology search with hidden Potts models
Genome-wide cross-cancer analysis illustrates the critical role of bimodal miRNA in patient survival and drug responses to PI3K inhibitors
Computational approach to modeling microbiome landscapes associated with chronic human disease progression
A mammalian inferior colliculus model for sound source separation using interaural time differences
Model-based approach for predicting the impact of genetic modifications on product yield in biopharmaceutical manufacturing - Application to influenza vaccine production
In silico discovery and biological validation of ligands of FAD synthase, a promising new antimicrobial target
A Common Model for Cytokine Receptor Activation: Combined Scissor-Like Rotation and Self-Rotation of Receptor Dimer Induced by Class I Cytokine
Host contact dynamics shapes richness and dominance of pathogen strains
A Horizontal Alignment Tool for Numerical Trend Discovery in Sequence Data: Application to Protein Hydropathy
Use of chiral cell shape to ensure highly directional swimming in trypanosomes
Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces
A spatial vaccination strategy to reduce the risk of vaccine-resistant variants
Isolation-by-Distance and Outbreeding Depression Are Sufficient to Drive Parapatric Speciation in the Absence of Environmental Influences
Occurrence and Treatment of Bone Atrophic Non-Unions Investigated by an Integrative Approach
Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb
Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level
On the Zwitterionic Nature of Gas-Phase Peptides and Protein Ions
Active reinforcement learning versus action bias and hysteresis: control with a mixture of experts and nonexperts
The Laminar Cortex Model: A New Continuum Cortex Model Incorporating Laminar Architecture
An Integrative Method for Accurate Comparative Genome Mapping
Ten simple rules for responsible big data research
A computational framework for a Lyapunov-enabled analysis of biochemical reaction networks
A Bayesian model for repeated cross-sectional epidemic prevalence survey data
A mathematical, classical stratification modeling approach to disentangling the impact of weather on infectious diseases: A case study using spatio-temporally disaggregated Campylobacter surveillance data for England and Wales
Incorporating physics to overcome data scarcity in predictive modeling of protein function: A case study of BK channels
Modeling changes in probabilistic reinforcement learning during adolescence
Notch signaling and taxis mechanisms regulate early stage angiogenesis: A mathematical and computational model
Chemotaxis in external fields: Simulations for active magnetic biological matter
An End to Endless Forms: Epistasis, Phenotype Distribution Bias, and Nonuniform Evolution
Specificity and Affinity Quantification of Flexible Recognition from Underlying Energy Landscape Topography
metagene Profiles Analyses Reveal Regulatory Element's Factor-Specific Recruitment Patterns
From experimental clues to theoretical modeling: Evolution associated with the membrane-takeover at an early stage of life
Utilizing a Dynamical Description of IspH to Aid in the Development of Novel Antimicrobial Drugs
Modeling bee movement shows how a perceptual masking effect can influence flower discovery
HPV Clearance and the Neglected Role of Stochasticity
Analysis of systemic effects of dioxin on human health through template-and-anchor modeling
Successful Reconstruction of a Physiological Circuit with Known Connectivity from Spiking Activity Alone
SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework
Modeling HER2 Effects on Cell Behavior from Mass Spectrometry Phosphotyrosine Data
Modeling cell populations metabolism and competition under maximum power constraints
Correction: Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA
Homeostatic control of synaptic rewiring in recurrent networks induces the formation of stable memory engrams
Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference
Of Toasters and Molecular Ticker Tapes
A biophysical model of striatal microcircuits suggests gamma and beta oscillations interleaved at delta/theta frequencies mediate periodicity in motor control
Chemical graph generators
Brain2GAN: Feature-disentangled neural encoding and decoding of visual perception in the primate brain
Confronting the Ethical Challenges of Big Data in Public Health
Invariant neural responses for sensory categories revealed by the time-varying information for communication calls
Iterative point set registration for aligning scRNA-seq data
Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins
The Origins of Lactase Persistence in Europe
Delayed Response and Biosonar Perception Explain Movement Coordination in Trawling Bats
Integrating multiple spatial transcriptomics data using community-enhanced graph contrastive learning
Efficiency and Cost of Economical Brain Functional Networks
Modelling the Self-Assembly of Elastomeric Proteins Provides Insights into the Evolution of Their Domain Architectures
Computational joint action: Dynamical models to understand the development of joint coordination
T-Cell Epitope Prediction: Rescaling Can Mask Biological Variation between MHC Molecules
Repeated measures ASCA+ for analysis of longitudinal intervention studies with multivariate outcome data
Moth olfactory receptor neurons adjust their encoding efficiency to temporal statistics of pheromone fluctuations
GeneDrive.jl: A decision tool to optimize biological vector control strategies under climate change
Diverse and flexible behavioral strategies arise in recurrent neural networks trained on multisensory decision making
Cohesive versus Flexible Evolution of Functional Modules in Eukaryotes
Identification of avian flapping motion from non-volant winged dinosaurs based on modal effective mass analysis
Coupling between Catalytic Loop Motions and Enzyme Global Dynamics
Evolution of the Division of Labor between Genes and Enzymes in the RNA World
Interpreting tree ensemble machine learning models with endoR
The complexity of protein interactions unravelled from structural disorder
Towards Structural Systems Pharmacology to Study Complex Diseases and Personalized Medicine
Combining Network Modeling and Gene Expression Microarray Analysis to Explore the Dynamics of Th1 and Th2 Cell Regulation
Microbiome-based disease prediction with multimodal variational information bottlenecks
Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts
Probabilistic fluorescence-based synapse detection
Computational Investigation of the Changing Patterns of Subtype Specific NMDA Receptor Activation during Physiological Glutamatergic Neurotransmission
Competitive advantages of T-even phage lysis inhibition in response to secondary infection
Molecular Dynamics Simulations Suggest that Electrostatic Funnel Directs Binding of Tamiflu to Influenza N1 Neuraminidases
Oxygen-Driven Tumour Growth Model: A Pathology-Relevant Mathematical Approach
Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions
Bird song comparison using deep learning trained from avian perceptual judgments
Cytoskeletal Signaling: Is Memory Encoded in Microtubule Lattices by CaMKII Phosphorylation?
Learning the payoffs and costs of actions
Quantification of Interactions between Dynamic Cellular Network Functionalities by Cascaded Layering
HaSAPPy: A tool for candidate identification in pooled forward genetic screens of haploid mammalian cells
Correction: How pupil responses track value-based decision-making during and after reinforcement learning
Targeting Neuropilin-1 to Inhibit VEGF Signaling in Cancer: Comparison of Therapeutic Approaches
Topological Cluster Analysis Reveals the Systemic Organization of the Caenorhabditis elegans Connectome
Kernel machine tests of association using extrinsic and intrinsic cluster evaluation metrics
Non-trophic interactions strengthen the diversity - functioning relationship in an ecological bioenergetic network model
Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges
Ten simple rules for being a faculty advocate of first-year graduate students
Computational Prediction of Alanine Scanning and Ligand Binding Energetics in G-Protein Coupled Receptors
A mechanistic and data-driven reconstruction of the time-varying reproduction number: Application to the COVID-19 epidemic
A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens
Modeling ChIP Sequencing In Silico with Applications
Unsupervised logic-based mechanism inference for network-driven biological processes
Systems Analysis of Bioenergetics and Growth of the Extreme Halophile Halobacterium salinarum
Objects guide human gaze behavior in dynamic real-world scenes
The Interaction of Vinculin with Actin
Discriminating between negative cooperativity and ligand binding to independent sites using pre-equilibrium properties of binding curves
Ten Simple Rules for Selecting a Postdoctoral Position
Using Transcription Modules to Identify Expression Clusters Perturbed in Williams-Beuren Syndrome
Coping with Viral Diversity in HIV Vaccine Design: A Response to Nickle et al
Regression convolutional neural network models implicate peripheral immune regulatory variants in the predisposition to Alzheimer's disease
Imputation for transcription factor binding predictions based on deep learning
Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments
Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles
Delayed feedback embedded in perception-action coordination cycles results in anticipation behavior during synchronized rhythmic action: A dynamical systems approach
Understanding the high-order network plasticity mechanisms of ultrasound neuromodulation
Numerical analysis of the impact of cytoskeletal actin filament density alterations onto the diffusive vesicle-mediated cell transport
Computational exploration of treadmilling and protrusion growth observed in fire ant rafts
Novel metrics reveal new structure and unappreciated heterogeneity in Caenorhabditis elegans development
A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types
Correlated Inter-Domain Motions in Adenylate Kinase
A multi-scale clutch model for adhesion complex mechanics
Emergent spatial goals in an integrative model of the insect central complex
K + Block Is the Mechanism of Functional Asymmetry in Bacterial Na v Channels
Complex Spatial Dynamics of Oncolytic Viruses In Vitro: Mathematical and Experimental Approaches
Tracking calcium dynamics from individual neurons in behaving animals
Effect of synchronization of firings of different motor unit types on the force variability in a model of the rat medial gastrocnemius muscle
The automatic parameter-exploration with a machine-learning-like approach: Powering the evolutionary modeling on the origin of life
Breaking the Ice and Forging Links: The Importance of Socializing in Research
Correlated Mutations: A Hallmark of Phenotypic Amino Acid Substitutions
Distinguishing multiple roles of T cell and macrophage involvement in determining lymph node fates during Mycobacterium tuberculosis infection