yusuke1997/dblp-id-title huggingface dataset:
Calibrating dimension reduction hyperparameters in the presence of noise
Identification of a Topological Characteristic Responsible for the Biological Robustness of Regulatory Networks
Using Fluorescence Recovery After Photobleaching data to uncover filament dynamics
Ion channel noise shapes the electrical activity of endocrine cells
Introduction to Translational Bioinformatics Collection
Modeling of Large-Scale Functional Brain Networks Based on Structural Connectivity from DTI: Comparison with EEG Derived Phase Coupling Networks and Evaluation of Alternative Methods along the Modeling Path
Hierarchical Bayesian inference for concurrent model fitting and comparison for group studies
The proportion of resistant hosts in mixtures should be biased towards the resistance with the lowest breaking cost
Inflammatory Aetiology of Human Myometrial Activation Tested Using Directed Graphs
Predicting Signatures of "Synthetic Associations" and "Natural Associations" from Empirical Patterns of Human Genetic Variation
The Transcriptional Regulator CBP Has Defined Spatial Associations within Interphase Nuclei
Two dynamic regimes in the human gut microbiome
Joint Analysis of Multiple Metagenomic Samples
Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods
IMI-driver: Integrating multi-level gene networks and multi-omics for cancer driver gene identification
Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits
SARAH Domain-Mediated MST2-RASSF Dimeric Interactions
Investigating the ability of astrocytes to drive neural network synchrony
Evidence accumulation is biased by motivation: A computational account
Expanding signaling-molecule wavefront model of cell polarization in the Drosophila wing primordium
Insights to HIV-1 coreceptor usage by estimating HLA adaptation with Bayesian generalized linear mixed models
Mammalian Rest/Activity Patterns Explained by Physiologically Based Modeling
ISCB Public Policy Statement on Open Access to Scientific and Technical Research Literature
An evolutionary model of rhythmic accelerando in animal vocal signalling
A weighted constraint satisfaction approach to human goal-directed decision making
Exploring the Free Energy Landscape: From Dynamics to Networks and Back
FastTrack: An open-source software for tracking varying numbers of deformable objects
Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes
Harnessing the optimization of enzyme catalytic rates in engineering of metabolic phenotypes
Can Transgenic Maize Affect Soil Microbial Communities?
A Dynamical Systems Model for Combinatorial Cancer Therapy Enhances Oncolytic Adenovirus Efficacy by MEK-Inhibition
A network model of the barrel cortex combined with a differentiator detector reproduces features of the behavioral response to single-neuron stimulation
Inherent High Correlation of Individual Motility Enhances Population Dispersal in a Heterotrophic, Planktonic Protist
Categorial Compositionality II: Universal Constructions and a General Theory of (Quasi-)Systematicity in Human Cognition
A Sequential Vesicle Pool Model with a Single Release Sensor and a Ca 2+ -Dependent Priming Catalyst Effectively Explains Ca 2+ -Dependent Properties of Neurosecretion
Decoding Complex Chemical Mixtures with a Physical Model of a Sensor Array
Ten simple rules for successfully completing a graduate degree in Latin America
Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions
Nucleosome Presence at AML-1 Binding Sites Inversely Correlates with Ly49 Expression: Revelations from an Informatics Analysis of Nucleosomes and Immune Cell Transcription Factors
Thalamo-cortical spiking model of incremental learning combining perception, context and NREM-sleep
Herpes Simplex Virus-2 Genital Tract Shedding Is Not Predictable over Months or Years in Infected Persons
Predicting the effects of deep brain stimulation using a reduced coupled oscillator model
Non-monotonic Response to Monotonic Stimulus: Regulation of Glyoxylate Shunt Gene-Expression Dynamics in Mycobacterium tuberculosis
Sequence Motifs in MADS Transcription Factors Responsible for Specificity and Diversification of Protein-Protein Interaction
Learning Contrast-Invariant Cancellation of Redundant Signals in Neural Systems
Latent Dirichlet Allocation modeling of environmental microbiomes
Funneled potential and flux landscapes dictate the stabilities of both the states and the flow: Fission yeast cell cycle
Optimal Information Transfer in the Cortex through Synchronization
Decoupling of interacting neuronal populations by time-shifted stimulation through spike-timing-dependent plasticity
Thermal Stabilization of Dihydrofolate Reductase Using Monte Carlo Unfolding Simulations and Its Functional Consequences
Efficient sentinel surveillance strategies for preventing epidemics on networks
Probing T-cell response by sequence-based probabilistic modeling
Inactivation mode of sodium channels defines the different maximal firing rates of conventional versus atypical midbrain dopamine neurons
ISMB 2005 Conference Report
Phenotypic Robustness and the Assortativity Signature of Human Transcription Factor Networks
Long-time analytic approximation of large stochastic oscillators: Simulation, analysis and inference
MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis -Regulatory Modules
Data Sharing in the Post-Genomic World: The Experience of the International Cancer Genome Consortium (ICGC) Data Access Compliance Office (DACO)
Ensemble Models of Neutrophil Trafficking in Severe Sepsis
Advanced Genomic Data Mining
Optimal timing of one-shot interventions for epidemic control
Variations within Class-A β-Lactamase Physiochemical Properties Reflect Evolutionary and Environmental Patterns, but not Antibiotic Specificity
Human Leg Model Predicts Muscle Forces, States, and Energetics during Walking
Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces
The Overlap of Small Molecule and Protein Binding Sites within Families of Protein Structures
Predicting the infecting dengue serotype from antibody titre data using machine learning
Robustness of respiratory rhythm generation across dynamic regimes
De novo mutational signature discovery in tumor genomes using SparseSignatures
Correction: Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism
Similarity-based transfer learning with deep learning networks for accurate CRISPR-Cas9 off-target prediction
Connecting Macroscopic Observables and Microscopic Assembly Events in Amyloid Formation Using Coarse Grained Simulations
A k-mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria
Correction: Constructing Benchmark Test Sets for Biological Sequence Analysis Using Independent Set Algorithms
Systematic Analysis of Compositional Order of Proteins Reveals New Characteristics of Biological Functions and a Universal Correlate of Macroevolution
Mapping parameter spaces of biological switches
Notice of Republication: Simulating Cortical Development as a Self Constructing Process: A Novel Multi-Scale Approach Combining Molecular and Physical Aspects
Optimization-based framework with flux balance analysis (FBA) and metabolic pathway analysis (MPA) for identifying metabolic objective functions
Transcriptional bursts explain autosomal random monoallelic expression and affect allelic imbalance
Activation of Parallel Fiber Feedback by Spatially Diffuse Stimuli Reduces Signal and Noise Correlations via Independent Mechanisms in a Cerebellum-Like Structure
Somitogenesis Clock-Wave Initiation Requires Differential Decay and Multiple Binding Sites for Clock Protein
Revisiting the "satisfaction of spatial restraints" approach of MODELLER for protein homology modeling
Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins
Perspective: Dimensions of the scientific method
A probabilistic, distributed, recursive mechanism for decision-making in the brain
The Signal in the Genomes
Sparse multitask group Lasso for genome-wide association studies
Ten simple rules for launching an academic research career
Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield
Stochastic Delay Accelerates Signaling in Gene Networks
Atomistic fingerprint of hyaluronan-CD44 binding
SPF: A spatial and functional data analytic approach to cell imaging data
A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces
Regional heterogeneity in left atrial stiffness impacts passive deformation in a cohort of patient-specific models
The AmP project: Comparing species on the basis of dynamic energy budget parameters
Circadian regulation of sinoatrial nodal cell pacemaking function: Dissecting the roles of autonomic control, body temperature, and local circadian rhythmicity
The exclusive effects of chaperonin on the behavior of proteins with 52 knot
Dynamical Adaptation in Photoreceptors
Resource acquisition in diel cycles and the cost of growing quickly
iCVS - Inferring Cardio-Vascular hidden States from physiological signals available at the bedside
Correction: How Does Cross-Reactive Stimulation Affect the Longevity of CD8+ T Cell Memory?
Cortical propagation tracks functional recovery after stroke
Fungal feature tracker (FFT): A tool for quantitatively characterizing the morphology and growth of filamentous fungi
A thermodynamically consistent model of the post-translational Kai circadian clock
Efficient pedigree recording for fast population genetics simulation
Distilling identifiable and interpretable dynamic models from biological data
Isotope-assisted metabolic flux analysis as an equality-constrained nonlinear program for improved scalability and robustness
Social dynamics modeling of chrono-nutrition
Systems biology informed deep learning for inferring parameters and hidden dynamics
Challenges and New Approaches to Proving the Existence of Muscle Synergies of Neural Origin
LRT: Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity
Understanding the Sub-Cellular Dynamics of Silicon Transportation and Synthesis in Diatoms Using Population-Level Data and Computational Optimization
Dual-use capabilities of concern of biological AI models
Limitations and optimizations of cellular lineages tracking
Positional Bias of MHC Class I Restricted T-Cell Epitopes in Viral Antigens Is Likely due to a Bias in Conservation
Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas
Adaptive immunity selects against malaria infection blocking mutations
A Stochastic Multiscale Model That Explains the Segregation of Axonal Microtubules and Neurofilaments in Neurological Diseases
Energy Efficient Sparse Connectivity from Imbalanced Synaptic Plasticity Rules
APDCA: An accurate and effective method for predicting associations between RBPs and AS-events during epithelial-mesenchymal transition
Optimal noise level for coding with tightly balanced networks of spiking neurons in the presence of transmission delays
Bimodality in E. coli gene expression: Sources and robustness to genome-wide stresses
Correction: New Maximum Likelihood Estimators for Eukaryotic Intron Evolution
Leveraging conformal prediction to annotate enzyme function space with limited false positives
A New Take on John Maynard Smith's Concept of Protein Space for Understanding Molecular Evolution
Specific Entrainment of Mitral Cells during Gamma Oscillation in the Rat Olfactory Bulb
One dimensional approximations of neuronal dynamics reveal computational strategy
Posterior Association Networks and Functional Modules Inferred from Rich Phenotypes of Gene Perturbations
Ergodicity-breaking reveals time optimal decision making in humans
TPMA: A two pointers meta-alignment tool to ensemble different multiple nucleic acid sequence alignments
Asymmetric Genome Organization in an RNA Virus Revealed via Graph-Theoretical Analysis of Tomographic Data
Real-time structural motif searching in proteins using an inverted index strategy
Ten simple rules on writing clean and reliable open-source scientific software
An initial 'snapshot' of sensory information biases the likelihood and speed of subsequent changes of mind
Learning poly-synaptic paths with traveling waves
Active degradation of MarA controls coordination of its downstream targets
Aberrant computational mechanisms of social learning and decision-making in schizophrenia and borderline personality disorder
A Monte Carlo Study of Knots in Long Double-Stranded DNA Chains
MD/DPD Multiscale Framework for Predicting Morphology and Stresses of Red Blood Cells in Health and Disease
Sensory Information and Encounter Rates of Interacting Species
In Silico Detection of Sequence Variations Modifying Transcriptional Regulation
The 20S Proteasome Splicing Activity Discovered by SpliceMet
Binding mechanism of oseltamivir and influenza neuraminidase suggests perspectives for the design of new anti-influenza drugs
Operating Regimes of Signaling Cycles: Statics, Dynamics, and Noise Filtering
Conductance Ratios and Cellular Identity
Impact of Different Oseltamivir Regimens on Treating Influenza A Virus Infection and Resistance Emergence: Insights from a Modelling Study
Implicit Value Updating Explains Transitive Inference Performance: The Betasort Model
Unraveling the mechanism of the cadherin-catenin-actin catch bond
Evidence for Functional Groupings of Vibrissae across the Rodent Mystacial Pad
Wikipedia Usage Estimates Prevalence of Influenza-Like Illness in the United States in Near Real-Time
Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility
Time to revisit the endpoint dilution assay and to replace the TCID50 as a measure of a virus sample's infection concentration
A New Algorithm to Diagnose Atrial Ectopic Origin from Multi Lead ECG Systems - Insights from 3D Virtual Human Atria and Torso
Detecting Statistically Significant Common Insertion Sites in Retroviral Insertional Mutagenesis Screens
Near-Native Protein Loop Sampling Using Nonparametric Density Estimation Accommodating Sparcity
Quantification of nematic cell polarity in three-dimensional tissues
Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics
Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance
Detecting Functional Divergence after Gene Duplication through Evolutionary Changes in Posttranslational Regulatory Sequences
Coordinated Optimization of Visual Cortical Maps (II) Numerical Studies
High fidelity epigenetic inheritance: Information theoretic model predicts threshold filling of histone modifications post replication
ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach
Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach
Perfusion estimation using synthetic MRI-based measurements and a porous media flow model
Resting-State Temporal Synchronization Networks Emerge from Connectivity Topology and Heterogeneity
Notice of Republication: Ten simple rules for organizing a webinar series
Categorial Compositionality: A Category Theory Explanation for the Systematicity of Human Cognition
Estimating effective population size changes from preferentially sampled genetic sequences
Bidirectional Control of Absence Seizures by the Basal Ganglia: A Computational Evidence
Strategies and opportunities for promoting bioinformatics in Zimbabwe
Ten simple rules for hosting artists in a scientific lab
A Virtual Infection Model Quantifies Innate Effector Mechanisms and Candida albicans Immune Escape in Human Blood
Discovering Anti-platelet Drug Combinations with an Integrated Model of Activator-Inhibitor Relationships, Activator-Activator Synergies and Inhibitor-Inhibitor Synergies
Individual Differences in Dynamic Functional Brain Connectivity across the Human Lifespan
Ecological landscapes guide the assembly of optimal microbial communities
PRER: A patient representation with pairwise relative expression of proteins on biological networks
Improving Pharmacokinetic-Pharmacodynamic Modeling to Investigate Anti-Infective Chemotherapy with Application to the Current Generation of Antimalarial Drugs
A Model-Based Bayesian Estimation of the Rate of Evolution of VNTR Loci in Mycobacterium tuberculosis
Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling
Proteome-scale relationships between local amino acid composition and protein fates and functions
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
Estimating Transfer Entropy in Continuous Time Between Neural Spike Trains or Other Event-Based Data
Rosetta: MSF: a modular framework for multi-state computational protein design
Characterizing the variation in chromosome structure ensembles in the context of the nuclear microenvironment
Correction: Modeling multi-sensory feedback control of zebrafish in a flow
The relationship between anxious traits and learning about changes in stochasticity and volatility
Estimation of neuron parameters from imperfect observations
Deciphering conformational selectivity in the A2A adenosine G protein-coupled receptor by free energy simulations
PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions
Deep geometric representations for modeling effects of mutations on protein-protein binding affinity
IUSMMT: Survival mediation analysis of gene expression with multiple DNA methylation exposures and its application to cancers of TCGA
A Dynamical Model of Oocyte Maturation Unveils Precisely Orchestrated Meiotic Decisions
Temporal resolution of spike coding in feedforward networks with signal convergence and divergence
Pathway Switching Explains the Sharp Response Characteristic of Hypoxia Response Network
Abstract concept learning in a simple neural network inspired by the insect brain
Correction: A unifying Bayesian account of contextual effects in value-based choice
Entropic Tension in Crowded Membranes
Small Regulatory RNAs May Sharpen Spatial Expression Patterns
Ten simple rules for students navigating summer research experiences for undergraduates (REU) programs: From application to program completion
The specious art of single-cell genomics
High-frequency oscillations and sequence generation in two-population models of hippocampal region CA1
Propagation of orientation selectivity in a spiking network model of layered primary visual cortex
Computational modeling of multiscale collateral blood supply in a whole-brain-scale arterial network
A data-driven characterisation of natural facial expressions when giving good and bad news
Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing
Ten principles for machine-actionable data management plans
Spike-based Decision Learning of Nash Equilibria in Two-Player Games
Modeling resistance to the broadly neutralizing antibody PGT121 in people living with HIV-1
Accuracy of Protein-Protein Binding Sites in High-Throughput Template-Based Modeling
M-band wavelet-based multi-view clustering of cells
Data-Driven Prediction and Design of bZIP Coiled-Coil Interactions
Systems Modeling of Anti-apoptotic Pathways in Prostate Cancer: Psychological Stress Triggers a Synergism Pattern Switch in Drug Combination Therapy
Ten simple rules for quick and dirty scientific programming
The Environment Shapes the Inner Vestibule of LeuT
Real time structural search of the Protein Data Bank
A novel logical model of COVID-19 intracellular infection to support therapies development
Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations
What to know before forecasting the flu
Spatial Transmission of 2009 Pandemic Influenza in the US
Nonlinear mixed selectivity supports reliable neural computation
Maximizing Sensory Dynamic Range by Tuning the Cortical State to Criticality
Network-Free Inference of Knockout Effects in Yeast
Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications
Sequence similarity governs generalizability of de novo deep learning models for RNA secondary structure prediction
Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms
A Two-Dimensional Model of the Colonic Crypt Accounting for the Role of the Basement Membrane and Pericryptal Fibroblast Sheath
Correction: Linking statistical shape models and simulated function in the healthy adult human heart
Integrative modeling of the HIV-1 ribonucleoprotein complex
The Brain's Router: A Cortical Network Model of Serial Processing in the Primate Brain
Meta-Analysis of Drosophila Circadian Microarray Studies Identifies a Novel Set of Rhythmically Expressed Genes
A model of colour appearance based on efficient coding of natural images
Comprehensive analysis of structural and sequencing data reveals almost unconstrained chain pairing in TCRαβ complex
Integrative Analysis of Many Weighted Co-Expression Networks Using Tensor Computation
Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes
MAUI (MBI Analysis User Interface) - An image processing pipeline for Multiplexed Mass Based Imaging
A case study in the functional consequences of scaling the sizes of realistic cortical models
Structural and molecular insight into the pH-induced low-permeability of the voltage-gated potassium channel Kv1.2 through dewetting of the water cavity
A New Approach for Determining Phase Response Curves Reveals that Purkinje Cells Can Act as Perfect Integrators
Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion
Transmembrane Helix Dynamics of Bacterial Chemoreceptors Supports a Piston Model of Signalling
A Causal Inference Model Explains Perception of the McGurk Effect and Other Incongruent Audiovisual Speech
Modeling Brain Resonance Phenomena Using a Neural Mass Model
Bayesian classification of OXPHOS deficient skeletal myofibres
Evolution of cooperation in multichannel games on multiplex networks
Genome-Wide Prediction of SH2 Domain Targets Using Structural Information and the FoldX Algorithm
Performance and scaling behavior of bioinformatic applications in virtualization environments to create awareness for the efficient use of compute resources
On the Conservation of the Slow Conformational Dynamics within the Amino Acid Kinase Family: NAGK the Paradigm
Integrative analysis of ATAC-seq and RNA-seq for cells infected by human T-cell leukemia virus type 1
Beliefs, compulsive behavior and reduced confidence in control
Enhancing insights in sexually transmitted infection mapping: Syphilis in Forsyth County, North Carolina, a case study
Performance of convolutional neural networks for identification of bacteria in 3D microscopy datasets
Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes
Individual risk perception and empirical social structures shape the dynamics of infectious disease outbreaks
Encoder-Decoder Optimization for Brain-Computer Interfaces
Krisp: A Python package to aid in the design of CRISPR and amplification-based diagnostic assays from whole genome sequencing data
Bacterial age distribution in soil - Generational gaps in adjacent hot and cold spots
A dynamical systems model for the total fission rate in Drp1-dependent mitochondrial fission
Synaptic Scaling Enables Dynamically Distinct Short- and Long-Term Memory Formation
Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function
Conservation in Mammals of Genes Associated with Aggression-Related Behavioral Phenotypes in Honey Bees
Eco-evolutionary agriculture: Host-pathogen dynamics in crop rotations