yusuke1997/dblp-id-title huggingface dataset:
Beyond Bouma's window: How to explain global aspects of crowding?
Assessing variant effect predictors and disease mechanisms in intrinsically disordered proteins
Cavities and Atomic Packing in Protein Structures and Interfaces
Frontal cortex tracks surprise separately for different sensory modalities but engages a common inhibitory control mechanism
An optimal strategy for epilepsy surgery: Disruption of the rich-club?
Integrated information structure collapses with anesthetic loss of conscious arousal in Drosophila melanogaster
Reconstructing noisy gene regulation dynamics using extrinsic-noise-driven neural stochastic differential equations
Phylogenetic Gaussian Process Model for the Inference of Functionally Important Regions in Protein Tertiary Structures
Sequence dependence of transient Hoogsteen base pairing in DNA
An extension of the Walsh-Hadamard transform to calculate and model epistasis in genetic landscapes of arbitrary shape and complexity
Model-Based Design of Growth-Attenuated Viruses
Optimal Experimental Design for Parameter Estimation of a Cell Signaling Model
A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase
Non-linear archetypal analysis of single-cell RNA-seq data by deep autoencoders
Quantifying and Analyzing the Network Basis of Genetic Complexity
Heterogeneous responses to low level death receptor activation are explained by random molecular assembly of the Caspase-8 activation platform
Whom do we prefer to learn from in observational reinforcement learning?
One-carbon metabolism during the menstrual cycle and pregnancy
Transformation of Stimulus Correlations by the Retina
Genome-Wide Association between Branch Point Properties and Alternative Splicing
BIITE: A Tool to Determine HLA Class II Epitopes from T Cell ELISpot Data
Bioinspired figure-ground discrimination via visual motion smoothing
Ten Simple Rules for Starting a Company
nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework
Astrocytic Kir4.1 channels and gap junctions account for spontaneous epileptic seizure
Predictive modelling of a novel anti-adhesion therapy to combat bacterial colonisation of burn wounds
The Computational Properties of a Simplified Cortical Column Model
A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval
A 2D model to study how secondary growth affects the self-supporting behaviour of climbing plants
Training Excitatory-Inhibitory Recurrent Neural Networks for Cognitive Tasks: A Simple and Flexible Framework
Novelty is not surprise: Human exploratory and adaptive behavior in sequential decision-making
Monte Carlo Analysis of Neck Linker Extension in Kinesin Molecular Motors
Modeling the Slow CD4+ T Cell Decline in HIV-Infected Individuals
Correction: Modeling differentiation-state transitions linked to therapeutic escape in triple-negative breast cancer
Computational Resources in Infectious Disease: Limitations and Challenges
An enormous potential for niche construction through bacterial cross-feeding in a homogeneous environment
Implementing Arithmetic and Other Analytic Operations By Transcriptional Regulation
SubGE-DDI: A new prediction model for drug-drug interaction established through biomedical texts and drug-pairs knowledge subgraph enhancement
Modeling Co-Expression across Species for Complex Traits: Insights to the Difference of Human and Mouse Embryonic Stem Cells
Quantitative Analysis of Axonal Branch Dynamics in the Developing Nervous System
Cytoplasmic convection currents and intracellular temperature gradients
Uncertainty-driven regulation of learning and exploration in adolescents: A computational account
Regulation of transcription reactivation dynamics exiting mitosis
The value of confidence: Confidence prediction errors drive value-based learning in the absence of external feedback
Remeshing flexible membranes under the control of free energy
An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes
Historical Pedigree Reconstruction from Extant Populations Using PArtitioning of RElatives (PREPARE)
Binding of the general anesthetic sevoflurane to ion channels
Bacterial surface colonization, preferential attachment and fitness under periodic stress
Correction: Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources
DART-ID increases single-cell proteome coverage
Ten simple rules for starting research in your late teens
Interrogating the topological robustness of gene regulatory circuits by randomization
A dynamic network model of temporal receptive fields in primary auditory cortex
Predicted impact of the viral mutational landscape on the cytotoxic response against SARS-CoV-2
Eleven quick tips for running an interdisciplinary short course for new graduate students
Blood and brain gene expression signatures of chronic intermittent ethanol consumption in mice
Leadership in Moving Human Groups
Integrating Diverse Datasets Improves Developmental Enhancer Prediction
Emergent Systems Energy Laws for Predicting Myosin Ensemble Processivity
A Quantitative Model of the GIRK1/2 Channel Reveals That Its Basal and Evoked Activities Are Controlled by Unequal Stoichiometry of Gα and Gβγ
A Kinetic Platform to Determine the Fate of Hydrogen Peroxide in Escherichia coli
Kinetic Modeling of ABCG2 Transporter Heterogeneity: A Quantitative, Single-Cell Analysis of the Side Population Assay
Mapping of promoter usage QTL using RNA-seq data reveals their contributions to complex traits
Ensemble learning and ground-truth validation of synaptic connectivity inferred from spike trains
Analysis of Stop-Gain and Frameshift Variants in Human Innate Immunity Genes
Biosynthetic Potentials of Metabolites and Their Hierarchical Organization
From homeostasis to behavior: Balanced activity in an exploration of embodied dynamic environmental-neural interaction
Model checking via testing for direct effects in Mendelian Randomization and transcriptome-wide association studies
Mathematical models of Plasmodium vivax transmission: A scoping review
Predicting bioprocess targets of chemical compounds through integration of chemical-genetic and genetic interactions
Inferring Epidemic Contact Structure from Phylogenetic Trees
Predicting proprioceptive cortical anatomy and neural coding with topographic autoencoders
Defining the Estimated Core Genome of Bacterial Populations Using a Bayesian Decision Model
Measuring uncertainty in human visual segmentation
Minimal Mesoscale Model for Protein-Mediated Vesiculation in Clathrin-Dependent Endocytosis
Identification of Synaptic Targets of Drosophila Pumilio
Characterizing non-exponential growth and bimodal cell size distributions in fission yeast: An analytical approach
Molecular Mechanisms of Glutamine Synthetase Mutations that Lead to Clinically Relevant Pathologies
Highly Loaded Behavior of Kinesins Increases the Robustness of Transport Under High Resisting Loads
PLoS Computational Biology Conference Postcard from PSB 2011
Correction: Identifying influential neighbors in animal flocking
Characterization of K-Complexes and Slow Wave Activity in a Neural Mass Model
Sequence-Based Prediction for Vaccine Strain Selection and Identification of Antigenic Variability in Foot-and-Mouth Disease Virus
Multiscale Coarse-Graining of the Protein Energy Landscape
PDKit: A data science toolkit for the digital assessment of Parkinson's Disease
Mechanistic models of PLC/PKC signaling implicate phosphatidic acid as a key amplifier of chemotactic gradient sensing
A Logical Model Provides Insights into T Cell Receptor Signaling
Repetitive transcranial magnetic stimulation (rTMS) triggers dose-dependent homeostatic rewiring in recurrent neuronal networks
Using ephaptic coupling to estimate the synaptic cleft resistivity of the calyx of Held synapse
A unified mechanism for innate and learned visual landmark guidance in the insect central complex
Spatial Heterogeneity in Drug Concentrations Can Facilitate the Emergence of Resistance to Cancer Therapy
Regulation of Pom cluster dynamics in Myxococcus xanthus
Uncertainty quantification and sensitivity analysis of COVID-19 exit strategies in an individual-based transmission model
Polyamine Sharing between Tubulin Dimers Favours Microtubule Nucleation and Elongation via Facilitated Diffusion
Bioinformatics analysis of whole slide images reveals significant neighborhood preferences of tumor cells in Hodgkin lymphoma
Cardiogenic and chronobiological mechanisms in seizure-induced sinus arrhythmias
Hierarchical Post-transcriptional Regulation of Colicin E2 Expression in Escherichia coli
Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers
Protein Interaction Networks - More Than Mere Modules
Predicting three-dimensional genome organization with chromatin states
HLA class I haplotype diversity is consistent with selection for frequent existing haplotypes
Identifying the drivers of multidrug-resistant Klebsiella pneumoniae at a European level
PLoS Computational Biology Conference Postcards from PSB 2010
A kinetic model for Brain-Derived Neurotrophic Factor mediated spike timing-dependent LTP
Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering
Correction of Distortion in Flattened Representations of the Cortical Surface Allows Prediction of V1-V3 Functional Organization from Anatomy
A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar
The research and development process for multiscale models of infectious disease systems
Modeling cortical synaptic effects of anesthesia and their cholinergic reversal
Application of a bioinformatics training delivery method for reaching dispersed and distant trainees
Sub-diffraction Limit Localization of Proteins in Volumetric Space Using Bayesian Restoration of Fluorescence Images from Ultrathin Specimens
Molecular recognition and packing frustration in a helical protein
Improving the accuracy of automated labeling of specimen images datasets via a confidence-based process
Context-Specific Metabolic Networks Are Consistent with Experiments
Inferring the structures of signaling motifs from paired dynamic traces of single cells
Iliski, a software for robust calculation of transfer functions
The stabilized supralinear network accounts for the contrast dependence of visual cortical gamma oscillations
Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)
Characterising antibody kinetics from multiple influenza infection and vaccination events in ferrets
Mitochondrial Variability as a Source of Extrinsic Cellular Noise
FOCAL3D: A 3-dimensional clustering package for single-molecule localization microscopy
Temperature manipulation of neuronal dynamics in a forebrain motor control nucleus
Graph-theoretical formulation of the generalized epitope-based vaccine design problem
Experiment level curation of transcriptional regulatory interactions in neurodevelopment
Beyond IC50 - A computational dynamic model of drug resistance in enzyme inhibition treatment
Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays
Model-based Traction Force Microscopy Reveals Differential Tension in Cellular Actin Bundles
Building, benchmarking, and exploring perturbative maps of transcriptional and morphological data
When to wake up? The optimal waking-up strategies for starvation-induced persistence
A comprehensive investigation of intracortical and corticothalamic models of the alpha rhythm
Is the Conformational Ensemble of Alzheimer's Aβ10-40 Peptide Force Field Dependent?
Multi-layer network utilizing rewarded spike time dependent plasticity to learn a foraging task
Mouse-Specific Single cell cytokine activity prediction and Estimation (MouSSE)
Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology
Determining clinically relevant features in cytometry data using persistent homology
Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data
A Computational Framework for Analyzing Stochasticity in Gene Expression
A Threshold Equation for Action Potential Initiation
Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations
DNA methylation-based classifier and gene expression signatures detect BRCAness in osteosarcoma
φ-evo: A program to evolve phenotypic models of biological networks
A new approach to Health Benefits Package design: an application of the Thanzi La Onse model in Malawi
Effect of transcription factor resource sharing on gene expression noise
Identifying Single Copy Orthologs in Metazoa
Are There Laws of Genome Evolution?
A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data
Molecular characterization of breast and lung tumors by integration of multiple data types with functional sparse-factor analysis
A fully joint Bayesian quantitative trait locus mapping of human protein abundance in plasma
Population dynamics of engineered underdominance and killer-rescue gene drives in the control of disease vectors
Multimodal CustOmics: A unified and interpretable multi-task deep learning framework for multimodal integrative data analysis in oncology
Methods for computing the maximum performance of computational models of fMRI responses
Classification and analysis of a large collection of in vivo bioassay descriptions
Malaria Elimination Campaigns in the Lake Kariba Region of Zambia: A Spatial Dynamical Model
A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs)
Mitochondrial mRNA localization is governed by translation kinetics and spatial transport
Intra-ripple frequency accommodation in an inhibitory network model for hippocampal ripple oscillations
A Neurophysiologically Plausible Population Code Model for Feature Integration Explains Visual Crowding
Interspecies Translation of Disease Networks Increases Robustness and Predictive Accuracy
A Genomewide Functional Network for the Laboratory Mouse
Computational models reveal how chloride dynamics determine the optimal distribution of inhibitory synapses to minimise dendritic excitability
Modeling full-scale leaf venation networks
Molecular dynamics simulations of a multicellular model with cell-cell interactions and Hippo signaling pathway
BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions
A Hierarchical Neuronal Model for Generation and Online Recognition of Birdsongs
Neural field model to reconcile structure with function in primary visual cortex
iPRESTO: Automated discovery of biosynthetic sub-clusters linked to specific natural product substructures
Nonidentifiability of the Source of Intrinsic Noise in Gene Expression from Single-Burst Data
Modelling African horse sickness emergence and transmission in the South African control area using a deterministic metapopulation approach
Biochemical Competition Makes Fatty-Acid β-Oxidation Vulnerable to Substrate Overload
Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes
A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness
Deconvolution of heterogeneous tumor samples using partial reference signals
Surprise response as a probe for compressed memory states
Viral Capsid Proteins Are Segregated in Structural Fold Space
An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer
BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale
Connecting mass-action models and network models for infectious diseases
Evaluating spatially adaptive guidelines for the treatment of gonorrhea to reduce the incidence of gonococcal infection and increase the effective lifespan of antibiotics
Polymorphisms in the F8 Gene and MHC-II Variants as Risk Factors for the Development of Inhibitory Anti-Factor VIII Antibodies during the Treatment of Hemophilia A: A Computational Assessment
Wiggle - Predicting Functionally Flexible Regions from Primary Sequence
Mathematical model for the role of multiple pericentromeric repeats on heterochromatin assembly
The Kinematics of Plant Nutation Reveals a Simple Relation between Curvature and the Orientation of Differential Growth
ASSET: Analysis of Sequences of Synchronous Events in Massively Parallel Spike Trains
Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes
Latent environment allocation of microbial community data
Does Sex Speed Up Evolutionary Rate and Increase Biodiversity?
Movement and conformity interact to establish local behavioural traditions in animal populations
Locust Dynamics: Behavioral Phase Change and Swarming
Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges
THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites
The influence of red blood cell deformability on hematocrit profiles and platelet margination
A validation framework for neuroimaging software: The case of population receptive fields
Mechanistic Basis of Branch-Site Selection in Filamentous Bacteria
Protein-Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks
Strategies for Controlling Non-Transmissible Infection Outbreaks Using a Large Human Movement Data Set
Information and Efficiency in the Nervous System - A Synthesis
How to Estimate Epidemic Risk from Incomplete Contact Diaries Data?
Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species
Mitochondrial depolarization promotes calcium alternans: Mechanistic insights from a ventricular myocyte model
WhichTF is functionally important in your open chromatin data?
Role of path information in visual perception of joint stiffness
Non-invasive assessment of stroke volume and cardiovascular parameters based on peripheral pressure waveform
The risks of using the chi-square periodogram to estimate the period of biological rhythms
Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway
Quantifying epidemiological drivers of gambiense human African Trypanosomiasis across the Democratic Republic of Congo
A Whole-Body Model for Glycogen Regulation Reveals a Critical Role for Substrate Cycling in Maintaining Blood Glucose Homeostasis
Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design
Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis
The DIOS framework for optimizing infectious disease surveillance: Numerical methods for simulation and multi-objective optimization of surveillance network architectures
Structural Disorder Provides Increased Adaptability for Vesicle Trafficking Pathways
Suboptimal human inference can invert the bias-variance trade-off for decisions with asymmetric evidence
OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities
Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142
A Bayesian method for detecting pairwise associations in compositional data
Network-Assisted Investigation of Combined Causal Signals from Genome-Wide Association Studies in Schizophrenia
Chloride dynamics alter the input-output properties of neurons
Executable pathway analysis using ensemble discrete-state modeling for large-scale data
Accurate Structural Correlations from Maximum Likelihood Superpositions
General Relationship of Global Topology, Local Dynamics, and Directionality in Large-Scale Brain Networks
Dynamic brain connectivity predicts emotional arousal during naturalistic movie-watching
Paradoxical phase response of gamma rhythms facilitates their entrainment in heterogeneous networks
PrMFTP: Multi-functional therapeutic peptides prediction based on multi-head self-attention mechanism and class weight optimization
Modeling invasion patterns in the glioblastoma battlefield
Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors
Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration
Measuring genetic diversity across populations
Towards a category theory approach to analogy: Analyzing re-representation and acquisition of numerical knowledge
Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model
MetMap Enables Genome-Scale Methyltyping for Determining Methylation States in Populations
Detection of latent brain states from spontaneous neural activity in the amygdala
Locating the Route of Entry and Binding Sites of Benzocaine and Phenytoin in a Bacterial Voltage Gated Sodium Channel
Striated myocyte structural integrity: Automated analysis of sarcomeric z-discs
Novel Methods for Analysing Bacterial Tracks Reveal Persistence in Rhodobacter sphaeroides
External Drive to Inhibitory Cells Induces Alternating Episodes of High- and Low-Amplitude Oscillations
Near-term forecasting of companion animal tick paralysis incidence: An iterative ensemble model
From Inverse Problems in Mathematical Physiology to Quantitative Differential Diagnoses
Theta Coordinated Error-Driven Learning in the Hippocampus
CBEA: Competitive balances for taxonomic enrichment analysis
Alternative Splicing in the Differentiation of Human Embryonic Stem Cells into Cardiac Precursors
Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM
An Integrative Model of Ion Regulation in Yeast
Computational epitope map of SARS-CoV-2 spike protein
Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations
Forcing Versus Feedback: Epidemic Malaria and Monsoon Rains in Northwest India
How Recent History Affects Perception: The Normative Approach and Its Heuristic Approximation
Stability and Competition in Multi-spike Models of Spike-Timing Dependent Plasticity
Epistasis in a Model of Molecular Signal Transduction
Switching state-space modeling of neural signal dynamics
Modeling human intuitions about liquid flow with particle-based simulation
The Context-Dependence of Mutations: A Linkage of Formalisms
Decoding biomolecular condensate dynamics: an energy landscape approach
Understanding the Molecular Determinants Driving the Immunological Specificity of the Protective Pilus 2a Backbone Protein of Group B Streptococcus
Intronic Alternative Splicing Regulators Identified by Comparative Genomics in Nematodes
Aggregative cycles evolve as a solution to conflicts in social investment
Power Efficiency of Outer Hair Cell Somatic Electromotility
Direct Inference of SNP Heterozygosity Rates and Resolution of LOH Detection
Melanoma Cell Colony Expansion Parameters Revealed by Approximate Bayesian Computation
Evolution of Complex Modular Biological Networks
Modeling of the Dorsal Gradient across Species Reveals Interaction between Embryo Morphology and Toll Signaling Pathway during Evolution
The role of glutamate in neuronal ion homeostasis: A case study of spreading depolarization
An agent-based model of leukocyte transendothelial migration during atherogenesis
Virus Neutralisation: New Insights from Kinetic Neutralisation Curves
Presynaptic inhibition rapidly stabilises recurrent excitation in the face of plasticity
Polar or Apolar - The Role of Polarity for Urea-Induced Protein Denaturation
Innate Visual Learning through Spontaneous Activity Patterns
Modelling the impact of clot fragmentation on the microcirculation after thrombectomy