yusuke1997/dblp-id-title huggingface dataset:
Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations
Computational Identification of Genomic Features That Influence 3D Chromatin Domain Formation
Scabies in residential care homes: Modelling, inference and interventions for well-connected population sub-units
Cell Patterns Emerge from Coupled Chemical and Physical Fields with Cell Proliferation Dynamics: The Arabidopsis thaliana Root as a Study System
Estimation of neural network model parameters from local field potentials (LFPs)
A multiscale model of the action of a capsid assembly modulator for the treatment of chronic hepatitis B
A model of naturalistic decision making in preference tests
Thunderstruck: The ACDC model of flexible sequences and rhythms in recurrent neural circuits
A compiler for biological networks on silicon chips
Malaria's Missing Number: Calculating the Human Component of R 0 by a Within-Host Mechanistic Model of Plasmodium falciparum Infection and Transmission
Correction: Emergence of Protein Fold Families through Rational Design
SWIFT: A deep learning approach to prediction of hypoxemic events in critically-Ill patients using SpO2 waveform prediction
The activity of human enhancers is modulated by the splicing of their associated lncRNAs
A dynamic genetic-hormonal regulatory network model explains multiple cellular behaviors of the root apical meristem of Arabidopsis thaliana
Collective Dynamics Differentiates Functional Divergence in Protein Evolution
A modeling study of budding yeast colony formation and its relationship to budding pattern and aging
An objective criterion to evaluate sequence-similarity networks helps in dividing the protein family sequence space
Noradrenergic deficits contribute to apathy in Parkinson's disease through the precision of expected outcomes
Stability Depends on Positive Autoregulation in Boolean Gene Regulatory Networks
From imaging to computational domains for physics-driven molecular biology simulations: Hindered diffusion in platelet masses
Reconstructing promoter activity from Lux bioluminescent reporters
graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture
Understanding Variation in Transcription Factor Binding by Modeling Transcription Factor Genome-Epigenome Interactions
The neural dynamics associated with computational complexity
Correcting for batch effects in case-control microbiome studies
Optimal Census by Quorum Sensing
Engaging biological oscillators through second messenger pathways permits emergence of a robust gastric slow-wave during peristalsis
Ten simple rules to cultivate transdisciplinary collaboration in data science
Variability of Metabolite Levels Is Linked to Differential Metabolic Pathways in Arabidopsis's Responses to Abiotic Stresses
Intrinsic Stability of Temporally Shifted Spike-Timing Dependent Plasticity
IgStrand: A universal residue numbering scheme for the immunoglobulin-fold (Ig-fold) to study Ig-proteomes and Ig-interactomes
Signatures of criticality arise from random subsampling in simple population models
A bacterial size law revealed by a coarse-grained model of cell physiology
Computing the Dynamic Supramolecular Structural Proteome
IDP-LM: Prediction of protein intrinsic disorder and disorder functions based on language models
The invasion of de-differentiating cancer cells into hierarchical tissues
Scaling up data curation using deep learning: An application to literature triage in genomic variation resources
Hexagons all the way down: grid cells as a conformal isometric map of space
Kinome inhibition states and multiomics data enable prediction of cell viability in diverse cancer types
Enrichment on steps, not genes, improves inference of differentially expressed pathways
Genome-wide identification and characterization of DNA enhancers with a stacked multivariate fusion framework
Accurate multi-population imputation of MICA, MICB, HLA-E, HLA-F and HLA-G alleles from genome SNP data
Role of water-bridged interactions in metal ion coupled protein allostery
Identifying (un)controllable dynamical behavior in complex networks
On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report
Multiscale modeling of human cerebrovasculature: A hybrid approach using image-based geometry and a mathematical algorithm
Do Ants Need to Estimate the Geometrical Properties of Trail Bifurcations to Find an Efficient Route? A Swarm Robotics Test Bed
Personalized prediction for multiple chronic diseases by developing the multi-task Cox learning model
Fusing multisensory signals across channels and time
Machine-Learning Approaches for Classifying Haplogroup from Y Chromosome STR Data
Ten simple rules to complete successfully a computational MSc thesis project
Modelling daily weight variation in honey bee hives
The Emergence of Environmental Homeostasis in Complex Ecosystems
Exploring Bacterial Organelle Interactomes: A Model of the Protein-Protein Interaction Network in the Pdu Microcompartment
Human Inferences about Sequences: A Minimal Transition Probability Model
A systematic analysis of regression models for protein engineering
Large-scale simulations of biological cell sorting driven by differential adhesion follow diffusion-limited domain coalescence regime
GEM-based computational modeling for exploring metabolic interactions in a microbial community
Maturation of GABAergic Inhibition Promotes Strengthening of Temporally Coherent Inputs among Convergent Pathways
Orientation processing by synaptic integration across first-order tactile neurons
Integrated information theory (IIT) 4.0: Formulating the properties of phenomenal existence in physical terms
Chapter 14: Cancer Genome Analysis
Predicting Odor Pleasantness with an Electronic Nose
Different Evolutionary Paths to Complexity for Small and Large Populations of Digital Organisms
A new look at TFPI inhibition of factor X activation
Circadian Rhythmicity by Autocatalysis
Spatial Pattern Switching Enables Cyclic Evolution in Spatial Epidemics
Messages Do Diffuse Faster than Messengers: Reconciling Disparate Estimates of the Morphogen Bicoid Diffusion Coefficient
A Differential Wiring Analysis of Expression Data Correctly Identifies the Gene Containing the Causal Mutation
Reliability of plastid and mitochondrial localisation prediction declines rapidly with the evolutionary distance to the training set increasing
ProteinVR: Web-based molecular visualization in virtual reality
Feedback Signals in Myelodysplastic Syndromes: Increased Self-Renewal of the Malignant Clone Suppresses Normal Hematopoiesis
Neural networks with optimized single-neuron adaptation uncover biologically plausible regularization
Understanding glioblastoma invasion using physically-guided neural networks with internal variables
Discovery of Regulatory Elements is Improved by a Discriminatory Approach
Anatomy of the first six months of COVID-19 vaccination campaign in Italy
Modeling the role of gap junctions between excitatory neurons in the developing visual cortex
Deep mendelian randomization: Investigating the causal knowledge of genomic deep learning models
Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples
Zero-shot denoising of microscopy images recorded at high-resolution limits
The Role of Multiple Marks in Epigenetic Silencing and the Emergence of a Stable Bivalent Chromatin State
Pattern Recognition Software and Techniques for Biological Image Analysis
Deciphering regulatory architectures of bacterial promoters from synthetic expression patterns
A Voltage-Based STDP Rule Combined with Fast BCM-Like Metaplasticity Accounts for LTP and Concurrent "Heterosynaptic" LTD in the Dentate Gyrus In Vivo
PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories
The role of the encapsulated cargo in microcompartment assembly
Ligand-Dependent Conformations and Dynamics of the Serotonin 5-HT 2A Receptor Determine Its Activation and Membrane-Driven Oligomerization Properties
Interconversion of Functional Motions between Mesophilic and Thermophilic Adenylate Kinases
Image-based model of the spectrin cytoskeleton for red blood cell simulation
Simulations of tumor growth and response to immunotherapy by coupling a spatial agent-based model with a whole-patient quantitative systems pharmacology model
BOSO: A novel feature selection algorithm for linear regression with high-dimensional data
Assessing the effect of model specification and prior sensitivity on Bayesian tests of temporal signal
A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a Consensus Approach
Stimulus-Driven Population Activity Patterns in Macaque Primary Visual Cortex
Risk-Sensitive Optimal Feedback Control Accounts for Sensorimotor Behavior under Uncertainty
Signal neutrality, scalar property, and collapsing boundaries as consequences of a learned multi-timescale strategy
Using Phylogeny to Improve Genome-Wide Distant Homology Recognition
A biophysical mechanism for preferred direction enhancement in fly motion vision
Dendritic normalisation improves learning in sparsely connected artificial neural networks
Detailed Per-residue Energetic Analysis Explains the Driving Force for Microtubule Disassembly
Humans use multi-objective control to regulate lateral foot placement when walking
SuperFreq: Integrated mutation detection and clonal tracking in cancer
G-quadruplex forming sequences in the genome of all known human viruses: A comprehensive guide
Dynamical network analysis reveals key microRNAs in progressive stages of lung cancer
A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs
Estimation of Parent Specific DNA Copy Number in Tumors using High-Density Genotyping Arrays
Density-dependent effects are the main determinants of variation in growth dynamics between closely related bacterial strains
Forecasting Human African Trypanosomiasis Prevalences from Population Screening Data Using Continuous Time Models
Cooperative Binding
NbIT - A New Information Theory-Based Analysis of Allosteric Mechanisms Reveals Residues that Underlie Function in the Leucine Transporter LeuT
Editorial Note: In silico knockout studies of xenophagic capturing of Salmonella
Simulating flow induced migration in vascular remodelling
Effect of Interaction between Chromatin Loops on Cell-to-Cell Variability in Gene Expression
De-Novo Discovery of Differentially Abundant Transcription Factor Binding Sites Including Their Positional Preference
PyHIST: A Histological Image Segmentation Tool
Quantifying pluripotency landscape of cell differentiation from scRNA-seq data by continuous birth-death process
Marginal effects of public health measures and COVID-19 disease burden in China: A large-scale modelling study
Unified thalamic model generates multiple distinct oscillations with state-dependent entrainment by stimulation
Ten Simple Rules for Chairing a Scientific Session
The rules of multiplayer cooperation in networks of communities
Discrete Element Framework for Modelling Extracellular Matrix, Deformable Cells and Subcellular Components
Exploration and stabilization of Ras1 mating zone: A mechanism with positive and negative feedbacks
Estimating the epidemic reproduction number from temporally aggregated incidence data: A statistical modelling approach and software tool
Ethical frameworks should be applied to computational modelling of infectious disease interventions
The language of geometry: Fast comprehension of geometrical primitives and rules in human adults and preschoolers
Cortical Resonance Frequencies Emerge from Network Size and Connectivity
Ten simple rules for good model-sharing practices
Mechanism of Action of Cyclophilin A Explored by Metadynamics Simulations
G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation
Linking multiple serological assays to infer dengue virus infections from paired samples using mixture models
What Is the Most Realistic Single-Compartment Model of Spike Initiation?
Heterogeneity, Mixing, and the Spatial Scales of Mosquito-Borne Pathogen Transmission
Mechanistic within-host mathematical model of inhalational anthrax
Computational Model Explains High Activity and Rapid Cycling of Rho GTPases within Protein Complexes
miRWoods: Enhanced precursor detection and stacked random forests for the sensitive detection of microRNAs
Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis
Examining the dynamics of Epstein-Barr virus shedding in the tonsils and the impact of HIV-1 coinfection on daily saliva viral loads
TAPES: A tool for assessment and prioritisation in exome studies
A Protein Turnover Signaling Motif Controls the Stimulus-Sensitivity of Stress Response Pathways
Target Inhibition Networks: Predicting Selective Combinations of Druggable Targets to Block Cancer Survival Pathways
Drug2ways: Reasoning over causal paths in biological networks for drug discovery
Dynamic inference of cell developmental complex energy landscape from time series single-cell transcriptomic data
Inclusion of maintenance energy improves the intracellular flux predictions of CHO
Targeting TMPRSS2 and Cathepsin B/L together may be synergistic against SARS-CoV-2 infection
Rule-based and stimulus-based cues bias auditory decisions via different computational and physiological mechanisms
Hyperdimensional computing: A fast, robust, and interpretable paradigm for biological data
A Statistical Framework for Modeling HLA-Dependent T Cell Response Data
The Free Energy Profile of Tubulin Straight-Bent Conformational Changes, with Implications for Microtubule Assembly and Drug Discovery
From time-series transcriptomics to gene regulatory networks: A review on inference methods
Adjudicating between face-coding models with individual-face fMRI responses
Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases
Inheritable cell-states shape drug-persister correlations and population dynamics in cancer cells
Chromosome Driven Spatial Patterning of Proteins in Bacteria
Complex Dynamics of Virus Spread from Low Infection Multiplicities: Implications for the Spread of Oncolytic Viruses
Exploration of Multi-State Conformational Dynamics and Underlying Global Functional Landscape of Maltose Binding Protein
Is it selfish to be filamentous in biofilms? Individual-based modeling links microbial growth strategies with morphology using the new and modular iDynoMiCS 2.0
An exploration into CTEPH medications: Combining natural language processing, embedding learning, in vitro models, and real-world evidence for drug repurposing
Modeling Within-Host Dynamics of Influenza Virus Infection Including Immune Responses
Insights into Protein-DNA Interactions through Structure Network Analysis
Can Monkeys Choose Optimally When Faced with Noisy Stimuli and Unequal Rewards?
Beyond the E -Value: Stratified Statistics for Protein Domain Prediction
ZnT2 is an electroneutral proton-coupled vesicular antiporter displaying an apparent stoichiometry of two protons per zinc ion
Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics
Learning spatiotemporal signals using a recurrent spiking network that discretizes time
Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer
Interspike interval correlations in neuron models with adaptation and correlated noise
Distinct Neurogenomic States in Basal Ganglia Subregions Relate Differently to Singing Behavior in Songbirds
Bayesian data assimilation for estimating instantaneous reproduction numbers during epidemics: Applications to COVID-19
Vector genetics, insecticide resistance and gene drives: An agent-based modeling approach to evaluate malaria transmission and elimination
Cryo-EM ligand building using AlphaFold3-like model and molecular dynamics
The Activity Reaction Core and Plasticity of Metabolic Networks
The mechanism of dynamic steady states in lamellipodia
fingeRNAt - A novel tool for high-throughput analysis of nucleic acid-ligand interactions
HormoneBayes: A novel Bayesian framework for the analysis of pulsatile hormone dynamics
A mathematical model suggests collectivity and inconstancy enhance the efficiency of neuronal migration in the adult brain
The Ion Channel Inverse Problem: Neuroinformatics Meets Biophysics
Transient Calcium and Dopamine Increase PKA Activity and DARPP-32 Phosphorylation
Hosts mobility and spatial spread of Rickettsia rickettsii
Synthesizing developmental trajectories
Defining the Plasticity of Transcription Factor Binding Sites by Deconstructing DNA Consensus Sequences: The PhoP-Binding Sites among Gamma/Enterobacteria
Computational Modelling of Metastasis Development in Renal Cell Carcinoma
Transcriptomic Coordination in the Human Metabolic Network Reveals Links between n-3 Fat Intake, Adipose Tissue Gene Expression and Metabolic Health
DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex's Dynamics
Environments that Induce Synthetic Microbial Ecosystems
Unveiling dynamic metabolic signatures in human induced pluripotent and neural stem cells
Drug combination sensitivity scoring facilitates the discovery of synergistic and efficacious drug combinations in cancer
Microbial communities display alternative stable states in a fluctuating environment
Population modeling of tumor growth curves and the reduced Gompertz model improve prediction of the age of experimental tumors
DNA Exit Ramps Are Revealed in the Binding Landscapes Obtained from Simulations in Helical Coordinates
Untangling the Interplay between Epidemic Spread and Transmission Network Dynamics
The Brain Ages Optimally to Model Its Environment: Evidence from Sensory Learning over the Adult Lifespan
Representational Switching by Dynamical Reorganization of Attractor Structure in a Network Model of the Prefrontal Cortex
Binding of DNA-bending non-histone proteins destabilizes regular 30-nm chromatin structure
Near-term forecasting of Covid-19 cases and hospitalisations in Aotearoa New Zealand
Estimating time of HIV-1 infection from next-generation sequence diversity
A mechanistic framework for a priori pharmacokinetic predictions of orally inhaled drugs
Types of anomalies in two-dimensional video-based gait analysis in uncontrolled environments
Varying molecular interactions explain aspects of crowder-dependent enzyme function of a viral protease
Using mobility data in the design of optimal lockdown strategies for the COVID-19 pandemic
Phenotypic Heterogeneity and the Evolution of Bacterial Life Cycles
Spectral Signatures of Reorganised Brain Networks in Disorders of Consciousness
Heterogeneous CD8 + T Cell Migration in the Lymph Node in the Absence of Inflammation Revealed by Quantitative Migration Analysis
Selective Constraint on Noncoding Regions of Hominid Genomes
Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses
Wildlife vaccination strategies for eliminating bovine tuberculosis in white-tailed deer populations
DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies
Correction: Time to revisit the endpoint dilution assay and to replace the TCID50 as a measure of a virus sample's infection concentration
Combined Role of Seizure-Induced Dendritic Morphology Alterations and Spine Loss in Newborn Granule Cells with Mossy Fiber Sprouting on the Hyperexcitability of a Computer Model of the Dentate Gyrus
Estimating information in time-varying signals
Intragenomic Matching Reveals a Huge Potential for miRNA-Mediated Regulation in Plants
Cooperative Adaptive Responses in Gene Regulatory Networks with Many Degrees of Freedom
Removing contaminants from databases of draft genomes
CSMET: Comparative Genomic Motif Detection via Multi-Resolution Phylogenetic Shadowing
Towards a comprehensive view of the pocketome universe - biological implications and algorithmic challenges
Transcriptional and Post-Transcriptional Regulation of Thrombospondin-1 Expression: A Computational Model
A Combinatorial Approach to Detect Coevolved Amino Acid Networks in Protein Families of Variable Divergence
RCFGL: Rapid Condition adaptive Fused Graphical Lasso and application to modeling brain region co-expression networks
Correction: (A)Symmetric Stem Cell Replication and Cancer
Efficacy of Synaptic Inhibition Depends on Multiple, Dynamically Interacting Mechanisms Implicated in Chloride Homeostasis
Modeling Reveals Bistability and Low-Pass Filtering in the Network Module Determining Blood Stem Cell Fate
Anticipating epidemic transitions with imperfect data
Virus Replication Strategies and the Critical CTL Numbers Required for the Control of Infection
Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment
A Power-Law Dependence of Bacterial Invasion on Mammalian Host Receptors
Epidemic prevalence information on social networks can mediate emergent collective outcomes in voluntary vaccine schemes
Neuronal Avalanches Differ from Wakefulness to Deep Sleep - Evidence from Intracranial Depth Recordings in Humans
Causal Modeling Using Network Ensemble Simulations of Genetic and Gene Expression Data Predicts Genes Involved in Rheumatoid Arthritis
Mechanistic insight into spontaneous transition from cellular alternans to arrhythmia - A simulation study
Emerging Object Representations in the Visual System Predict Reaction Times for Categorization
Anticancer drug response prediction integrating multi-omics pathway-based difference features and multiple deep learning techniques
Noise correlations in the human brain and their impact on pattern classification
Cell adhesion and fluid flow jointly initiate genotype spatial distribution in biofilms
A Computational Model of the Rainbow Trout Hypothalamus-Pituitary-Ovary-Liver Axis
The p7 Protein of Hepatitis C Virus Forms Structurally Plastic, Minimalist Ion Channels
Identifying nonlinear dynamical systems via generative recurrent neural networks with applications to fMRI
Accurate Prediction of the Dynamical Changes within the Second PDZ Domain of PTP1e
A machine-learning method for biobank-scale genetic prediction of blood group antigens
An integrative systems biology approach to overcome venetoclax resistance in acute myeloid leukemia
Modelling Co-Infection with Malaria and Lymphatic Filariasis
Global Mapping of DNA Conformational Flexibility on Saccharomyces cerevisiae
Method to determine whether sleep phenotypes are driven by endogenous circadian rhythms or environmental light by combining longitudinal data and personalised mathematical models
FedGMMAT: Federated generalized linear mixed model association tests
Sarc-Graph: Automated segmentation, tracking, and analysis of sarcomeres in hiPSC-derived cardiomyocytes
Learning to use past evidence in a sophisticated world model
Bias in the arrival of variation can dominate over natural selection in Richard Dawkins's biomorphs
Deep learning predicts short non-coding RNA functions from only raw sequence data
Correction: A prediction tool for plaque progression based on patient-specific multi-physical modeling
Community-based benchmarking improves spike rate inference from two-photon calcium imaging data
Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision
Inference and dynamic simulation of malaria using a simple climate-driven entomological model of malaria transmission
Implications of differential size-scaling of cell-cycle regulators on cell size homeostasis
Language models outperform cloze predictability in a cognitive model of reading
CINS: Cell Interaction Network inference from Single cell expression data
Health inequities in influenza transmission and surveillance
Correction: Bang-Bang Control of Feeding: Role of Hypothalamic and Satiety Signals
Inferring the Structure of Social Contacts from Demographic Data in the Analysis of Infectious Diseases Spread
Drug-induced liver injury prediction based on graph convolutional networks and toxicogenomics
A Looping-Based Model for Quenching Repression