yusuke1997/dblp-id-title huggingface dataset:
Integration of Evolutionary Features for the Identification of Functionally Important Residues in Major Facilitator Superfamily Transporters
Establishing effective cross-disciplinary collaboration: Combining simple rules for reproducible computational research, a good data management plan, and good research practice
Modelling the effects of adult emergence on the surveillance and age distribution of medically important mosquitoes
Identifiability of phenotypic adaptation from low-cell-count experiments and a stochastic model
Recognition of Unknown Conserved Alternatively Spliced Exons
Base-resolution prediction of transcription factor binding signals by a deep learning framework
Temperature-amplitude coupling for stable biological rhythms at different temperatures
iPiDA-GCN: Identification of piRNA-disease associations based on Graph Convolutional Network
Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks
Using Matrix and Tensor Factorizations for the Single-Trial Analysis of Population Spike Trains
Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper
Mechanical Stress Induces Remodeling of Vascular Networks in Growing Leaves
Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome
An extended catalogue of tandem alternative splice sites in human tissue transcriptomes
Transcriptomic profiling in canines and humans reveals cancer specific gene modules and biological mechanisms common to both species
AlbaTraDIS: Comparative analysis of large datasets from parallel transposon mutagenesis experiments
Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components
Synaptic self-organization of spatio-temporal pattern selectivity
A general model for metabolic scaling in self-similar asymmetric networks
Neurogranin stimulates Ca2+/calmodulin-dependent kinase II by suppressing calcineurin activity at specific calcium spike frequencies
Zero-shot segmentation using embeddings from a protein language model identifies functional regions in the human proteome
TFOFinder: Python program for identifying purine-only double-stranded stretches in the predicted secondary structure(s) of RNA targets
Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes
Determinants of Heterogeneity, Excitation and Conduction in the Sinoatrial Node: A Model Study
Filopodial-Tension Model of Convergent-Extension of Tissues
Data-Derived Modeling Characterizes Plasticity of MAPK Signaling in Melanoma
Evolutionary divergence of induced versus constitutive antiviral gene expression levels between primates and rodents
An agent-based model of metabolic signaling oscillations in Bacillus subtilis biofilms
Automatic extraction of actin networks in plants
A Hybrid Model of Mammalian Cell Cycle Regulation
Spatio-temporal spread of artemisinin resistance in Southeast Asia
How Does Cross-Reactive Stimulation Affect the Longevity of CD8+ T Cell Memory?
Dual Coding with STDP in a Spiking Recurrent Neural Network Model of the Hippocampus
Optimal vaccine allocation for COVID-19 in the Netherlands: A data-driven prioritization
Motion, fixation probability and the choice of an evolutionary process
Branch-specific gene discovery in cell differentiation using multi-omics graph attention
Dopamine, Affordance and Active Inference
Rhythmic modulation of prediction errors: A top-down gating role for the beta-range in speech processing
Biases in Visual, Auditory, and Audiovisual Perception of Space
A critical analysis of computational protein design with sparse residue interaction graphs
Differential Adhesion between Moving Particles as a Mechanism for the Evolution of Social Groups
Evaluating supervised and unsupervised background noise correction in human gut microbiome data
A Neural Mechanism for Background Information-Gated Learning Based on Axonal-Dendritic Overlaps
Effect of the Latent Reservoir on the Evolution of HIV at the Within- and Between-Host Levels
How the value of the environment controls persistence in visual search
Sensory coding and contrast invariance emerge from the control of plastic inhibition over emergent selectivity
Modeling the efficiency of filovirus entry into cells in vitro: Effects of SNP mutations in the receptor molecule
Universally Sloppy Parameter Sensitivities in Systems Biology Models
Spatial Bistability Generates hunchback Expression Sharpness in the Drosophila Embryo
Quantifying massively parallel microbial growth with spatially mediated interactions
A systems genomics approach uncovers molecular associates of RSV severity
Temporal evolution of hemodynamics in murine arteriovenous fistula: A micro-CT based CFD study
Large-Scale Genomic Analysis Suggests a Neutral Punctuated Dynamics of Transposable Elements in Bacterial Genomes
Estimating the Stochastic Bifurcation Structure of Cellular Networks
Measuring Integrated Information from the Decoding Perspective
Evidence from simulation studies for selective constraints on the codon usage of the Angiosperm psbA gene
Control of Cation Permeation through the Nicotinic Receptor Channel
Cost-Effective Control of Plant Disease When Epidemiological Knowledge Is Incomplete: Modelling Bahia Bark Scaling of Citrus
AIM: A network model of attention in auditory cortex
Unsupervised Learning in an Ensemble of Spiking Neural Networks Mediated by ITDP
Regimes and mechanisms of transient amplification in abstract and biological neural networks
Hedging Your Bets: Intermediate Movements as Optimal Behavior in the Context of an Incomplete Decision
Inference of mutability landscapes of tumors from single cell sequencing data
iPAR: A framework for modelling and inferring information about disease spread when the populations at risk are unknown
No Need for a Cognitive Map: Decentralized Memory for Insect Navigation
Data-Driven Modeling of Src Control on the Mitochondrial Pathway of Apoptosis: Implication for Anticancer Therapy Optimization
The Dynamics of DNA Methylation Covariation Patterns in Carcinogenesis
Using Steered Molecular Dynamics to Predict and Assess Hsp70 Substrate-Binding Domain Mutants that Alter Prion Propagation
Pseudocell Tracer - A method for inferring dynamic trajectories using scRNAseq and its application to B cells undergoing immunoglobulin class switch recombination
Generalized Michaelis-Menten rate law with time-varying molecular concentrations
Geometry Shapes Evolution of Early Multicellularity
A Systems Model for Immune Cell Interactions Unravels the Mechanism of Inflammation in Human Skin
Quantitative Modeling of a Gene's Expression from Its Intergenic Sequence
Electrophysiology of Heart Failure Using a Rabbit Model: From the Failing Myocyte to Ventricular Fibrillation
The contribution of the basal ganglia and cerebellum to motor learning: A neuro-computational approach
Specialization of Gene Expression during Mouse Brain Development
Identifying control ensembles for information processing within the cortico-basal ganglia-thalamic circuit
Integrated Information in Discrete Dynamical Systems: Motivation and Theoretical Framework
MAGPIE: Simplifying access and execution of computational models in the life sciences
Local Orientation and the Evolution of Foraging: Changes in Decision Making Can Eliminate Evolutionary Trade-offs
Systems-level identification of key transcription factors in immune cell specification
Early prediction of antigenic transitions for influenza A/H3N2
Evolutionary multiplayer games on graphs with edge diversity
Ten simple rules to leverage large language models for getting grants
Relating sparse and predictive coding to divisive normalization
Structural Biology by NMR: Structure, Dynamics, and Interactions
Ten simple rules for successful and sustainable African research collaborations
Stability and learning in excitatory synapses by nonlinear inhibitory plasticity
Generative Bayesian modeling to nowcast the effective reproduction number from line list data with missing symptom onset dates
Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection
Sensitivity analysis of closed-loop one-chamber and four-chamber models with baroreflex
Beyond ranking nodes: Predicting epidemic outbreak sizes by network centralities
Structural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage
Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human
Power-Law Input-Output Transfer Functions Explain the Contrast-Response and Tuning Properties of Neurons in Visual Cortex
Analyzing greedy vaccine allocation algorithms for metapopulation disease models
The Role of Medical Structural Genomics in Discovering New Drugs for Infectious Diseases
Logistic PCA explains differences between genome-scale metabolic models in terms of metabolic pathways
Recurrently connected and localized neuronal communities initiate coordinated spontaneous activity in neuronal networks
Adaptive control of movement deceleration during saccades
Structural Determinants of Misfolding in Multidomain Proteins
MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments
Correction: A Likelihood-Based Approach to Identifying Contaminated Food Products Using Sales Data: Performance and Challenges
Activation gating in HCN2 channels
Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA
Correction: Epistasis in genomic and survival data of cancer patients
Insight into the protein solubility driving forces with neural attention
Minimum Information About a Simulation Experiment (MIASE)
In silico analysis of hypoxia activated prodrugs in combination with anti angiogenic therapy through nanocell delivery
Performance Limitations of Relay Neurons
Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies
Cancer recurrence times from a branching process model
Googling Food Webs: Can an Eigenvector Measure Species' Importance for Coextinctions?
Assessing Concordance of Drug-Induced Transcriptional Response in Rodent Liver and Cultured Hepatocytes
Dynamics of Immune Escape during HIV/SIV Infection
Translational Systems Biology of Inflammation
Classical mathematical models for prediction of response to chemotherapy and immunotherapy
Context-Dependent Role of Mitochondrial Fusion-Fission in Clonal Expansion of mtDNA Mutations
Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction
Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction
Phylogenetic Quantification of Intra-tumour Heterogeneity
The synergy of damage repair and retention promotes rejuvenation and prolongs healthy lifespans in cell lineages
Essential Requirements for Robust Signaling in Hfq Dependent Small RNA Networks
Genes as Cues of Relatedness and Social Evolution in Heterogeneous Environments
Modeling the impact of neuromorphological alterations in Down syndrome on fast neural oscillations
Identification of Yeast Transcriptional Regulation Networks Using Multivariate Random Forests
Stimulus-specific adaptation in a recurrent network model of primary auditory cortex
BALDR: A Web-based platform for informed comparison and prioritization of biomarker candidates for type 2 diabetes mellitus
Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu
Catalyst: Fast and flexible modeling of reaction networks
Tonic exploration governs both flexibility and lapses
De novo spatiotemporal modelling of cell-type signatures in the developmental human heart using graph convolutional neural networks
Atrial arrhythmogenicity of KCNJ2 mutations in short QT syndrome: Insights from virtual human atria
Dynamical stability and mechanical impedance are optimized when manipulating uncertain dynamically complex objects
Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery
Thermodynamic State Ensemble Models of cis -Regulation
Prediction of virus-host associations using protein language models and multiple instance learning
Evidence for influenza and RSV interaction from 10 years of enhanced surveillance in Nha Trang, Vietnam, a modelling study
G2S3: A gene graph-based imputation method for single-cell RNA sequencing data
Predicting antibody kinetics and duration of protection against SARS-CoV-2 following vaccination from sparse serological data
Ten Simple Rules for a Community Computational Challenge
Spatial Regulation and the Rate of Signal Transduction Activation
The complex ecosystem in non small cell lung cancer invasion
Ten simple rules for pushing boundaries of inclusion at academic events
Species-specific wiring of cortical circuits for small-world networks in the primary visual cortex
Transat - A Method for Detecting the Conserved Helices of Functional RNA Structures, Including Transient, Pseudo-Knotted and Alternative Structures
A Scalable Computational Framework for Establishing Long-Term Behavior of Stochastic Reaction Networks
Theory on the Coupled Stochastic Dynamics of Transcription and Splice-Site Recognition
Sequence dependency of canonical base pair opening in the DNA double helix
Social imitation dynamics of vaccination driven by vaccine effectiveness and beliefs
A Statistical Method of Identifying Interactions in Neuron-Glia Systems Based on Functional Multicell Ca2+ Imaging
Interactions between the tumor and the blood systemic response of breast cancer patients
Levels of SARS-CoV-2 population exposure are considerably higher than suggested by seroprevalence surveys
Ten Simple Rules for a Successful Cross-Disciplinary Collaboration
The blossoming of methods and software in computational biology
Visualization and Analysis of 3D Microscopic Images
Predicting Odor Perceptual Similarity from Odor Structure
A stochastic-field description of finite-size spiking neural networks
Inferring Binding Energies from Selected Binding Sites
Quorum sensing via dynamic cytokine signaling comprehensively explains divergent patterns of effector choice among helper T cells
A modular model integrating metabolism, growth, and cell cycle predicts that fermentation is required to modulate cell size in yeast populations
Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems
Stochastic modeling reveals kinetic heterogeneity in post-replication DNA methylation
Ten simple rules for building a successful science start-up
Detection of disease-specific signatures in B cell repertoires of lymphomas using machine learning
Need for speed: An optimized gridding approach for spatially explicit disease simulations
SHRiMP: Accurate Mapping of Short Color-space Reads
Environmental Influence on the Evolution of Morphological Complexity in Machines
Dissolution of spiral wave's core using cardiac optogenetics
Correction: A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway
A model of the onset of the senescence associated secretory phenotype after DNA damage induced senescence
Structure-Function Discrepancy: Inhomogeneity and Delays in Synchronized Neural Networks
Representation of Dynamical Stimuli in Populations of Threshold Neurons
Ten simple rules for getting started on Twitter as a scientist
The Influence of Spatiotemporal Structure of Noisy Stimuli in Decision Making
A quick guide for using Microsoft OneNote as an electronic laboratory notebook
Pharmacodynamic Modeling of Anti-Cancer Activity of Tetraiodothyroacetic Acid in a Perfused Cell Culture System
ARACHNE: A neural-neuroglial network builder with remotely controlled parallel computing
Effective resistance against pandemics: Mobility network sparsification for high-fidelity epidemic simulations
Prediction of HIV-1 sensitivity to broadly neutralizing antibodies shows a trend towards resistance over time
Estimating the glutamate transporter surface density in distinct sub-cellular compartments of mouse hippocampal astrocytes
Enhanced Regulatory Sequence Prediction Using Gapped k -mer Features
Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection
Cost and Effects of Different Admission Screening Strategies to Control the Spread of Methicillin-resistant Staphylococcus aureus
New Methods Section in PLOS Computational Biology
Seeing what you hear: Compression of rat visual perceptual space by task-irrelevant sounds
AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework
A Viral Dynamic Model for Treatment Regimens with Direct-acting Antivirals for Chronic Hepatitis C Infection
Ten simple rules for navigating AI in science
Statistical investigations of protein residue direct couplings
ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways
Complexity and diversity in sparse code priors improve receptive field characterization of Macaque V1 neurons
The use of mixture density networks in the emulation of complex epidemiological individual-based models
Simulating Cortical Development as a Self Constructing Process: A Novel Multi-Scale Approach Combining Molecular and Physical Aspects
Mechanistic modelling of within-mosquito viral dynamics: Insights into infection and dissemination patterns
Fundamental Activity Constraints Lead to Specific Interpretations of the Connectome
Identifying Driver Genomic Alterations in Cancers by Searching Minimum-Weight, Mutually Exclusive Sets
Heat Shock Partially Dissociates the Overlapping Modules of the Yeast Protein-Protein Interaction Network: A Systems Level Model of Adaptation
Optimizing the deployment of ultra-low volume and targeted indoor residual spraying for dengue outbreak response
Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions
Kernel Architecture of the Genetic Circuitry of the Arabidopsis Circadian System
Dynamic estimation of auditory temporal response functions via state-space models with Gaussian mixture process noise
Time to Organize the Bioinformatics Resourceome
A New Method to Reconstruct Recombination Events at a Genomic Scale
Systematic inference of indirect transcriptional regulation by protein kinases and phosphatases
Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria
Patient Dossier: Healthcare queries over distributed resources
A convolutional neural network provides a generalizable model of natural sound coding by neural populations in auditory cortex
Multiscale model for forecasting Sabin 2 vaccine virus household and community transmission
Abrupt and spontaneous strategy switches emerge in simple regularised neural networks
Predicting anti-cancer drug combination responses with a temporal cell state network model
Coherent noise enables probabilistic sequence replay in spiking neuronal networks
Mechanistic model of nutrient uptake explains dichotomy between marine oligotrophic and copiotrophic bacteria
Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress
A cell-based probabilistic approach unveils the concerted action of miRNAs
Modeling of Gap Gene Expression in Drosophila Kruppel Mutants
Parameter Identifiability and Sensitivity Analysis Predict Targets for Enhancement of STAT1 Activity in Pancreatic Cancer and Stellate Cells
Ten simple rules for investigating (meta)genomic data from environmental ecosystems
Error-independent effect of sensory uncertainty on motor learning when both feedforward and feedback control processes are engaged
Noise-invariant Neurons in the Avian Auditory Cortex: Hearing the Song in Noise
Design Principles for Ligand-Sensing, Conformation-Switching Ribozymes
PLOS Computational Biology 2016 Reviewer and Editorial Board Thank You
Within- and Cross-Modal Distance Information Disambiguate Visual Size-Change Perception
The interplay between vaccination and social distancing strategies affects COVID19 population-level outcomes
Bistability, non-ergodicity, and inhibition in pairwise maximum-entropy models
Simulation of calcium signaling in fine astrocytic processes: Effect of spatial properties on spontaneous activity
Coherent chaos in a recurrent neural network with structured connectivity
Finding Novel Molecular Connections between Developmental Processes and Disease
The HAMP Signal Relay Domain Adopts Multiple Conformational States through Collective Piston and Tilt Motions
Sleep deprivation detected by voice analysis
Robustness of Circadian Clocks to Daylight Fluctuations: Hints from the Picoeucaryote Ostreococcus tauri
ArborSim: Articulated, branching, OpenSim routing for constructing models of multi-jointed appendages with complex muscle-tendon architecture
Metric information in cognitive maps: Euclidean embedding of non-Euclidean environments
Transient Accumulation of NO 2 - and N 2 O during Denitrification Explained by Assuming Cell Diversification by Stochastic Transcription of Denitrification Genes
Modeling the Excess Cell Surface Stored in a Complex Morphology of Bleb-Like Protrusions
Disrupted Calcium Release as a Mechanism for Atrial Alternans Associated with Human Atrial Fibrillation
Community detection in empirical kinase networks identifies new potential members of signalling pathways
Interplay between Chaperones and Protein Disorder Promotes the Evolution of Protein Networks
The role of intracellular signaling in the stripe formation in engineered Escherichia coli populations
Towards Complete Sets of Farnesylated and Geranylgeranylated Proteins
Static length changes of cochlear outer hair cells can tune low-frequency hearing
Multiple Model-Informed Open-Loop Control of Uncertain Intracellular Signaling Dynamics
Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model
A comparison of neuronal population dynamics measured with calcium imaging and electrophysiology
Rational metareasoning and the plasticity of cognitive control
Three-dimensional stochastic simulation of chemoattractant-mediated excitability in cells
Quantifying Two-Dimensional Filamentous and Invasive Growth Spatial Patterns in Yeast Colonies
DOT: Gene-set analysis by combining decorrelated association statistics
Inferring age-specific differences in susceptibility to and infectiousness upon SARS-CoV-2 infection based on Belgian social contact data
Three People Can Synchronize as Coupled Oscillators during Sports Activities
CASynergy: A causal attention model for interpretable prediction of cancer drug synergy
Incorporating metadata in HIV transmission network reconstruction: A machine learning feasibility assessment
Ten quick tips to build a Model Life Cycle
Exploring the potential of structure-based deep learning approaches for T cell receptor design
A knowledge-based T2-statistic to perform pathway analysis for quantitative proteomic data
A New Integrated Variable Based on Thermometry, Actimetry and Body Position (TAP) to Evaluate Circadian System Status in Humans
Diverse role of NMDA receptors for dendritic integration of neural dynamics
Insertions and deletions as phylogenetic signal in an alignment-free context
Assessing the extinction risk of the spontaneous flora in urban tree bases
The Efficiency of the Human CD8+ T Cell Response: How Should We Quantify It, What Determines It, and Does It Matter?
MultiCens: Multilayer network centrality measures to uncover molecular mediators of tissue-tissue communication
Optimal multi-source forecasting of seasonal influenza
The Structural Pathway of Interleukin 1 (IL-1) Initiated Signaling Reveals Mechanisms of Oncogenic Mutations and SNPs in Inflammation and Cancer
Steady-state measures of visual suppression
Two modes of fusogenic action for influenza virus fusion peptide
The Route of HIV Escape from Immune Response Targeting Multiple Sites Is Determined by the Cost-Benefit Tradeoff of Escape Mutations
A method to estimate the cellular composition of the mouse brain from heterogeneous datasets