yusuke1997/dblp-id-title huggingface dataset:
Tracking the Sleep Onset Process: An Empirical Model of Behavioral and Physiological Dynamics
A Structural Model of the Pore-Forming Region of the Skeletal Muscle Ryanodine Receptor (RyR1)
Automatic Assignment of EC Numbers
Real-time forecasting of data revisions in epidemic surveillance streams
Ten Simple Rules for Curating and Facilitating Small Workshops
Ten simple rules for maximizing summer research experiences for students, mentors, and research groups
Theoretical investigation of active listening behavior based on the echolocation of CF-FM bats
Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data
A mechanism for epithelial-mesenchymal heterogeneity in a population of cancer cells
Correction: An efficient and flexible framework for inferring global sensitivity of agent-based model parameters
LSD-induced increase of Ising temperature and algorithmic complexity of brain dynamics
FAMoS: A Flexible and dynamic Algorithm for Model Selection to analyse complex systems dynamics
An inelastic quadrupedal model discovers four-beat walking, two-beat running, and pseudo-elastic actuation as energetically optimal
SozRank: A new approach for localizing the epileptic seizure onset zone
Robustness in Glyoxylate Bypass Regulation
How Do Efficient Coding Strategies Depend on Origins of Noise in Neural Circuits?
Cell Invasion Dynamics into a Three Dimensional Extracellular Matrix Fibre Network
The Eps8/IRSp53/VASP Network Differentially Controls Actin Capping and Bundling in Filopodia Formation
A compact model of Escherichia coli core and biosynthetic metabolism
Speed/Accuracy Trade-Off between the Habitual and the Goal-Directed Processes
Genome-Wide Modeling of Transcription Preinitiation Complex Disassembly Mechanisms using ChIP-chip Data
Atomistic mechanism of transmembrane helix association
Nucleotide Binding Switches the Information Flow in Ras GTPases
Gene Expression Divergence is Coupled to Evolution of DNA Structure in Coding Regions
Merging short and stranded long reads improves transcript assembly
How to Distinguish Conformational Selection and Induced Fit Based on Chemical Relaxation Rates
Teaching Bioinformatics at the Secondary School Level
Theta-Gamma Coding Meets Communication-through-Coherence: Neuronal Oscillatory Multiplexing Theories Reconciled
Perturbing low dimensional activity manifolds in spiking neuronal networks
Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations
CAMAP: Artificial neural networks unveil the role of codon arrangement in modulating MHC-I peptides presentation
Heterogeneity coordinates bacterial multi-gene expression in single cells
Similarity Queries for Temporal Toxicogenomic Expression Profiles
Hierarchical Modeling for Rare Event Detection and Cell Subset Alignment across Flow Cytometry Samples
Characterizing Changes in the Rate of Protein-Protein Dissociation upon Interface Mutation Using Hotspot Energy and Organization
Reliable estimation of membrane curvature for cryo-electron tomography
DeepHiC: A generative adversarial network for enhancing Hi-C data resolution
Distinct Allelic Patterns of Nanog Expression Impart Embryonic Stem Cell Population Heterogeneity
A new model of Notch signalling: Control of Notch receptor cis-inhibition via Notch ligand dimers
Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism
DBDNMF: A Dual Branch Deep Neural Matrix Factorization method for drug response prediction
Mitochondrial respiration and ROS emission during β-oxidation in the heart: An experimental-computational study
The successor representation subserves hierarchical abstraction for goal-directed behavior
Identification of a serum proteomic biomarker panel using diagnosis specific ensemble learning and symptoms for early pancreatic cancer detection
Identifying reproducible transcription regulator coexpression patterns with single cell transcriptomics
ADP is the dominant controller of AMP-activated protein kinase activity dynamics in skeletal muscle during exercise
Orientation Selectivity in Inhibition-Dominated Networks of Spiking Neurons: Effect of Single Neuron Properties and Network Dynamics
Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks
A Kirchhoff-Nernst-Planck framework for modeling large scale extracellular electrodiffusion surrounding morphologically detailed neurons
Application of Biomarkers in Cancer Risk Management: Evaluation from Stochastic Clonal Evolutionary and Dynamic System Optimization Points of View
The role of memory in non-genetic inheritance and its impact on cancer treatment resistance
Hybrid Spreading Mechanisms and T Cell Activation Shape the Dynamics of HIV-1 Infection
Patterns of selection against centrosome amplification in human cell lines
Neural Coding of Natural Stimuli: Information at Sub-Millisecond Resolution
Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling
Reconciling emergences: An information-theoretic approach to identify causal emergence in multivariate data
RNA length has a non-trivial effect in the stability of biomolecular condensates formed by RNA-binding proteins
Learning the Optimal Control of Coordinated Eye and Head Movements
A crowdsourced set of curated structural variants for the human genome
Collective Cell Motion in an Epithelial Sheet Can Be Quantitatively Described by a Stochastic Interacting Particle Model
Mechanisms of generation of membrane potential resonance in a neuron with multiple resonant ionic currents
Brain network eigenmodes provide a robust and compact representation of the structural connectome in health and disease
Rapid prediction of key residues for foldability by machine learning model enables the design of highly functional libraries with hyperstable constrained peptide scaffolds
Evaluation and comparison of methods for neuronal parameter optimization using the Neuroptimus software framework
Genome-wide analysis of lncRNA stability in human
Correction: Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses
Tunable Stochastic Pulsing in the Escherichia coli Multiple Antibiotic Resistance Network from Interlinked Positive and Negative Feedback Loops
CAPE: An R Package for Combined Analysis of Pleiotropy and Epistasis
Inference of coevolutionary dynamics and parameters from host and parasite polymorphism data of repeated experiments
Theoretical Analysis of Pre-Receptor Image Conditioning in Weakly Electric Fish
Learning with sparse reward in a gap junction network inspired by the insect mushroom body
A Computational Framework for Influenza Antigenic Cartography
Neural control of body-plan axis in regenerating planaria
Competition between physical search and a weak-to-strong transition rate-limits kinesin binding times
Recurrent somatic mutations reveal new insights into consequences of mutagenic processes in cancer
Ten quick tips for fuzzy logic modeling of biomedical systems
Stochastic Dynamics of Interacting Haematopoietic Stem Cell Niche Lineages
Quantitative single cell analysis uncovers the life/death decision in CD95 network
Correction: Modelling locust foraging: How and why food affects group formation
Inferring rates of metastatic dissemination using stochastic network models
Learning to predict future locations with internally generated theta sequences
Coordinated Concentration Changes of Transcripts and Metabolites in Saccharomyces cerevisiae
Bistable Perception Modeled as Competing Stochastic Integrations at Two Levels
Image-based force inference by biomechanical simulation
NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis
A general framework for predicting the transcriptomic consequences of non-coding variation and small molecules
Epidemiologically Optimal Static Networks from Temporal Network Data
Orchestrating privacy-protected big data analyses of data from different resources with R and DataSHIELD
Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data
Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster
Attention Increases the Temporal Precision of Conscious Perception: Verifying the Neural-ST 2 Model
Embryonic Stem Cell Specific "Master" Replication Origins at the Heart of the Loss of Pluripotency
Olfactory coding in the turbulent realm
The multiscale self-similarity of the weighted human brain connectome
Nine quick tips for analyzing network data
Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM)
An application of nowcasting methods: Cases of norovirus during the winter 2023/2024 in England
3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients
Near real-time surveillance of the SARS-CoV-2 epidemic with incomplete data
Patterns of HIV-1 Protein Interaction Identify Perturbed Host-Cellular Subsystems
Instantaneous Non-Linear Processing by Pulse-Coupled Threshold Units
Metheor: Ultrafast DNA methylation heterogeneity calculation from bisulfite read alignments
Dynamical anchoring of distant arrhythmia sources by fibrotic regions via restructuring of the activation pattern
A Discrete Model of Drosophila Eggshell Patterning Reveals Cell-Autonomous and Juxtacrine Effects
Sequence determinants of protein phase behavior from a coarse-grained model
On the Number of Neurons and Time Scale of Integration Underlying the Formation of Percepts in the Brain
The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time - An Ultra-Deep Approach
Quantifying the Role of Population Subdivision in Evolution on Rugged Fitness Landscapes
Cortical state contributions to neuronal response variability in the early visual cortex: A system identification approach
Detection and analysis of spatiotemporal patterns in brain activity
Bayesian hypothesis testing and experimental design for two-photon imaging data
The roles of feedback loops in the Caenorhabditis elegans rhythmic forward locomotion
Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant
Analysis of Accuracy in Pointing with Redundant Hand-held Tools: A Geometric Approach to the Uncontrolled Manifold Method
Mutations in tumor signaling, metastases, and synthetic lethality establish distinct patterns
Foraging as an evidence accumulation process
A sensory integration account for time perception
The effect of cell geometry on polarization in budding yeast
Quantifying the Impact and Extent of Undocumented Biomedical Synonymy
Multiscale affinity maturation simulations to elicit broadly neutralizing antibodies against HIV
Comprehensive Analyses of Ventricular Myocyte Models Identify Targets Exhibiting Favorable Rate Dependence
The Impact of Phenotypic Switching on Glioblastoma Growth and Invasion
Early warning signals in motion inference
Prediction of Mutational Tolerance in HIV-1 Protease and Reverse Transcriptase Using Flexible Backbone Protein Design
Using neural networks to mine text and predict metabolic traits for thousands of microbes
Systematic evaluation of lecithin:cholesterol acyltransferase binding sites in apolipoproteins via peptide based nanodiscs: regulatory role of charged residues at positions 4 and 7
Emergent mechanics of actomyosin drive punctuated contractions and shape network morphology in the cell cortex
Uncoupled Analysis of Stochastic Reaction Networks in Fluctuating Environments
Tensor Analysis Reveals Distinct Population Structure that Parallels the Different Computational Roles of Areas M1 and V1
Soma-axon coupling configurations that enhance neuronal coincidence detection
Robust and consistent measures of pattern separation based on information theory and demonstrated in the dentate gyrus
Kinetic Modeling of the Assembly, Dynamic Steady State, and Contraction of the FtsZ Ring in Prokaryotic Cytokinesis
IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform
Predicting Positive p53 Cancer Rescue Regions Using Most Informative Positive (MIP) Active Learning
Electrodiffusive Model for Astrocytic and Neuronal Ion Concentration Dynamics
NESmapper: Accurate Prediction of Leucine-Rich Nuclear Export Signals Using Activity-Based Profiles
Secondary indoor air pollution and passive smoking associated with cannabis smoking using electric cigarette device-demonstrative in silico study
Mathematical modeling to understand the role of bivalent thrombin-fibrin binding during polymerization
Ten quick tips for biocuration
Microbial Co-occurrence Relationships in the Human Microbiome
ISCB Computational Biology Wikipedia Competition
Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database
Random time-shift approximation enables hierarchical Bayesian inference of mechanistic within-host viral dynamics models on large datasets
A Dendritic Mechanism for Decoding Traveling Waves: Principles and Applications to Motor Cortex
Adaptive Remodeling of Achilles Tendon: A Multi-scale Computational Model
Functional Roles for Synaptic-Depression within a Model of the Fly Antennal Lobe
Correction: The role of oscillations in grid cells' toroidal topology
Uncovering functional signature in neural systems via random matrix theory
Multi-omics data integration reveals metabolome as the top predictor of the cervicovaginal microenvironment
Studentsourcing - Aggregating and reusing data from a practical cell biology course
Facilitating the propagation of spiking activity in feedforward networks by including feedback
Short-Range Guiding Can Result in the Formation of Circular Aggregates in Myxobacteria Populations
Cross-scale excitability in networks of quadratic integrate-and-fire neurons
Correction: Long Non-Coding RNA and Alternative Splicing Modulations in Parkinson's Leukocytes Identified by RNA Sequencing
Systematic Approximations to Susceptible-Infectious-Susceptible Dynamics on Networks
Emergent ecological patterns and modelling of gut microbiomes in health and in disease
Active Learning to Understand Infectious Disease Models and Improve Policy Making
Conserved Substitution Patterns around Nucleosome Footprints in Eukaryotes and Archaea Derive from Frequent Nucleosome Repositioning through Evolution
Robust deep learning object recognition models rely on low frequency information in natural images
Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model
The role of intracellular interactions in the collective polarization of tissues and its interplay with cellular geometry
Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics
Prediction of Gene Expression in Embryonic Structures of Drosophila melanogaster
How well do rudimentary plasticity rules predict adult visual object learning?
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
Statistical analysis supports the size control mechanism of Chlamydia development
General differential Hebbian learning: Capturing temporal relations between events in neural networks and the brain
Modelling the dynamics of tuberculosis lesions in a virtual lung: Role of the bronchial tree in endogenous reinfection
Near-optimal combination of disparity across a log-polar scaled visual field
INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation
On the Role of Aggregation Prone Regions in Protein Evolution, Stability, and Enzymatic Catalysis: Insights from Diverse Analyses
A simple, scalable approach to building a cross-platform transcriptome atlas
Computational optimization of associative learning experiments
Exhaustive Sampling of Docking Poses Reveals Binding Hypotheses for Propafenone Type Inhibitors of P-Glycoprotein
Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails
Whole-genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming
Balancing prior knowledge and sensory data in a predictive coding model of coherent motion detection
A kinetic model of iron trafficking in growing Saccharomyces cerevisiae cells; applying mathematical methods to minimize the problem of sparse data and generate viable autoregulatory mechanisms
Chapter 6: Structural Variation and Medical Genomics
Correction: A quantitative modelling approach for DNA repair on a population scale
From Hub Proteins to Hub Modules: The Relationship Between Essentiality and Centrality in the Yeast Interactome at Different Scales of Organization
Probabilistic edge weights fine-tune Boolean network dynamics
From decision to action: Detailed modelling of frog tadpoles reveals neuronal mechanisms of decision-making and reproduces unpredictable swimming movements in response to sensory signals
miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data
Inferring on the Intentions of Others by Hierarchical Bayesian Learning
Amino acid variants of SARS-CoV-2 papain-like protease have impact on drug binding
Crossing Over...Markov Meets Mendel
Dopamine release, diffusion and uptake: A computational model for synaptic and volume transmission
Topography of Extracellular Matrix Mediates Vascular Morphogenesis and Migration Speeds in Angiogenesis
Conflicting Selection Pressures Will Constrain Viral Escape from Interfering Particles: Principles for Designing Resistance-Proof Antivirals
Optimizing COVID-19 testing strategies on college campuses: Evaluation of the health and economic costs
Repulsive expansion dynamics in colony growth and gene expression
Evolutionary and Topological Properties of Genes and Community Structures in Human Gene Regulatory Networks
Bayesian workflow for time-varying transmission in stratified compartmental infectious disease transmission models
Brain connectivity meets reservoir computing
How to Grow a Computational Biology Lab
Evolutionary Tradeoffs between Economy and Effectiveness in Biological Homeostasis Systems
Genotype-phenotype relations of the von Hippel-Lindau tumor suppressor inferred from a large-scale analysis of disease mutations and interactors
Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?
Improved Measures of Integrated Information
Machine learning augmented diagnostic testing to identify sources of variability in test performance
Computational Reconstruction of Iron- and Manganese-Responsive Transcriptional Networks in α-Proteobacteria
Shaping the Dynamics of a Bidirectional Neural Interface
Modelling Odor Decoding in the Antennal Lobe by Combining Sequential Firing Rate Models with Bayesian Inference
Imaging of neural oscillations with embedded inferential and group prevalence statistics
Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources
A Balanced Memory Network
Mathematical Modeling Identifies Inhibitors of Apoptosis as Mediators of Positive Feedback and Bistability
Phenotypic memory in quorum sensing
Aggregation of Aβ40/42 chains in the presence of cyclic neuropeptides investigated by molecular dynamics simulations
Integrated experimental-computational analysis of a HepaRG liver-islet microphysiological system for human-centric diabetes research
Allostery in the dengue virus NS3 helicase: Insights into the NTPase cycle from molecular simulations
Multi-scale modeling of macrophage - T cell interactions within the tumor microenvironment
Evidence for the emergence of β-trefoils by 'Peptide Budding' from an IgG-like β-sandwich
A zero-agnostic model for copy number evolution in cancer
Development of a scoring function for comparing simulated and experimental tumor spheroids
Why are different estimates of the effective reproductive number so different? A case study on COVID-19 in Germany
Chromosomal neighbourhoods allow identification of organ specific changes in gene expression
Non-linear auto-regressive models for cross-frequency coupling in neural time series
Infectivity and fatality of influenza in pre- and post-COVID-19 pandemic year
RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State
Parsimonious Higher-Order Hidden Markov Models for Improved Array-CGH Analysis with Applications to Arabidopsis thaliana
Factors influencing estimates of HIV-1 infection timing using BEAST
A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines
Communication Routes in ARID Domains between Distal Residues in Helix 5 and the DNA-Binding Loops
A Predictive Model of the Oxygen and Heme Regulatory Network in Yeast
Network analyses to quantify effects of host movement in multilevel disease transmission models using foot and mouth disease in Cameroon as a case study
Mechanistic model of hormonal contraception
Prioritizing drug targets by perturbing biological network response functions
Logistical constraints lead to an intermediate optimum in outbreak response vaccination
Metabolic dynamics restricted by conserved carriers: Jamming and feedback
Long-Range Signaling in MutS and MSH Homologs via Switching of Dynamic Communication Pathways
A Human-Specific De Novo Protein-Coding Gene Associated with Human Brain Functions
Identification of recurrent dynamics in distributed neural populations
scAmpi - A versatile pipeline for single-cell RNA-seq analysis from basics to clinics
The Interaction between Seasonality and Pulsed Interventions against Malaria in Their Effects on the Reproduction Number
A systems-biology approach to molecular machines: Exploration of alternative transporter mechanisms
PseudoknotVisualizer: Visualization of pseudoknots on three-dimensional RNA structures
A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks
Dynamic Effective Connectivity of Inter-Areal Brain Circuits
Identifying enhancer properties associated with genetic risk for complex traits using regulome-wide association studies
Alpha Helices Are More Robust to Mutations than Beta Strands
Relationships between Gene Expression and Brain Wiring in the Adult Rodent Brain
Synonymous Constraint Elements Show a Tendency to Encode Intrinsically Disordered Protein Segments
Modeling single cell trajectory using forward-backward stochastic differential equations
Genome-Scale Computational Biology and Bioinformatics in Australia
Shape-driven deep neural networks for fast acquisition of aortic 3D pressure and velocity flow fields
Conductance-based dendrites perform Bayes-optimal cue integration
Ten simple rules for researchers while in isolation from a pandemic
Metacoder: An R package for visualization and manipulation of community taxonomic diversity data
A human judgment approach to epidemiological forecasting
Clustering and visualization of single-cell RNA-seq data using path metrics
Spontaneous Excitation Patterns Computed for Axons with Injury-like Impairments of Sodium Channels and Na/K Pumps
Functional Modules, Structural Topology, and Optimal Activity in Metabolic Networks
Feeling lucky? Prospective and retrospective cues for sensorimotor confidence
Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens
The evolutionary history of topological variations in the CPA/AT transporters
A generalized theoretical framework to investigate multicomponent actin dynamics
Dynamic decorrelation as a unifying principle for explaining a broad range of brightness phenomena
RESCRIPt: Reproducible sequence taxonomy reference database management
Multi-scale phylodynamic modelling of rapid punctuated pathogen evolution
Systems Analysis of Chaperone Networks in the Malarial Parasite Plasmodium falciparum
The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics
A kinetic mechanism for enhanced selectivity of membrane transport
Seizure pathways: A model-based investigation