yusuke1997/dblp-id-title huggingface dataset:
Ten simple rules for conducting a mendelian randomization study
Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset
2018 ISCB Overton Prize awarded to Cole Trapnell
Parameter Trajectory Analysis to Identify Treatment Effects of Pharmacological Interventions
Gene Expression of Caenorhabditis elegans Neurons Carries Information on Their Synaptic Connectivity
Evolutionary model for the unequal segregation of high copy plasmids
Explaining distortions in metacognition with an attractor network model of decision uncertainty
Trade-off and flexibility in the dynamic regulation of the cullin-RING ubiquitin ligase repertoire
Connecting a Connectome to Behavior: An Ensemble of Neuroanatomical Models of C. elegans Klinotaxis
Ten quick tips for making things findable
Chemotactic Migration of T Cells towards Dendritic Cells Promotes the Detection of Rare Antigens
Taste of time: A porous-medium model for human tongue surface with implications for early taste perception
What do Eulerian and Hamiltonian cycles have to do with genome assembly?
Network Receptive Field Modeling Reveals Extensive Integration and Multi-feature Selectivity in Auditory Cortical Neurons
Computational phenotyping of brain-behavior dynamics underlying approach-avoidance conflict in major depressive disorder
A general model unifying the adaptive, transient and sustained properties of ON and OFF auditory neural responses
Computable early Caenorhabditis elegans embryo with a phase field model
Ten simple rules to cultivate belonging in collaborative data science research teams
Multiscale Modeling of Influenza A Virus Infection Supports the Development of Direct-Acting Antivirals
ADEMA: An Algorithm to Determine Expected Metabolite Level Alterations Using Mutual Information
Retrospective Parameter Estimation and Forecast of Respiratory Syncytial Virus in the United States
redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models
Regional mutational signature activities in cancer genomes
Mouse and human striatal projection neurons compared - somatodendritic arbor, spines and in silico analyses
MetaGSCA: A tool for meta-analysis of gene set differential coexpression
Potential Role of a Bistable Histidine Kinase Switch in the Asymmetric Division Cycle of Caulobacter crescentus
A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers
How to Get the Most out of Your Curation Effort
Hierarchical marker genes selection in scRNA-seq analysis
A Tunable Coarse-Grained Model for Ligand-Receptor Interaction
Ten simple rules for queer data collection and analysis by STEM researchers
Noise propagation in an integrated model of bacterial gene expression and growth
Using mixture density networks to emulate a stochastic within-host model of Francisella tularensis infection
Stochastic optimal open-loop control as a theory of force and impedance planning via muscle co-contraction
Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks
GeneCOCOA: Detecting context-specific functions of individual genes using co-expression data
Structured random receptive fields enable informative sensory encodings
To Lyse or Not to Lyse: Transient-Mediated Stochastic Fate Determination in Cells Infected by Bacteriophages
Biased placement of Mitochondria fission facilitates asymmetric inheritance of protein aggregates during yeast cell division
Plant Classification from Bat-Like Echolocation Signals
Spatial Learning and Action Planning in a Prefrontal Cortical Network Model
An integrated model for predicting KRAS dependency
Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks
Sparse RNNs can support high-capacity classification
Adaptation to Different Human Populations by HIV-1 Revealed by Codon-Based Analyses
Feature reliability determines specificity and transfer of perceptual learning in orientation search
Bayesian modeling of the impact of antibiotic resistance on the efficiency of MRSA decolonization
Nowcasting reported covid-19 hospitalizations using de-identified, aggregated medical insurance claims data
Estimating the Hidden Burden of Bovine Tuberculosis in Great Britain
A novel algorithm identifies stress-induced alterations in mitochondrial connectivity and inner membrane structure from confocal images
Depressive symptoms are associated with blunted reward learning in social contexts
A composite network of conserved and tissue specific gene interactions reveals possible genetic interactions in glioma
Optimal Serotype Compositions for Pneumococcal Conjugate Vaccination under Serotype Replacement
TAMMiCol: Tool for analysis of the morphology of microbial colonies
Gauge fixing for sequence-function relationships
Memorization bias impacts modeling of alternative conformational states of solute carrier membrane proteins with methods from deep learning
Disease Prevention versus Data Privacy: Using Landcover Maps to Inform Spatial Epidemic Models
Providing new insights on the biphasic lifestyle of the predatory bacterium Bdellovibrio bacteriovorus through genome-scale metabolic modeling
Learning and executing goal-directed choices by internally generated sequences in spiking neural circuits
Cell Sorting and Noise-Induced Cell Plasticity Coordinate to Sharpen Boundaries between Gene Expression Domains
Stability and Responsiveness in a Self-Organized Living Architecture
Phasic Firing in Vasopressin Cells: Understanding Its Functional Significance through Computational Models
OCIAD2 as a novel prognostic and therapeutic biomarker for pancreatic cancer: A study based on transcriptomic signature and bioinformatics analysis
Viral and Latent Reservoir Persistence in HIV-1-Infected Patients on Therapy
Effects of persistent sodium current blockade in respiratory circuits depend on the pharmacological mechanism of action and network dynamics
Attractor neural networks with double well synapses
Molecular Mechanism of Cyclodextrin Mediated Cholesterol Extraction
Dynamics of SIN Asymmetry Establishment
The Role of Membrane-Mediated Interactions in the Assembly and Architecture of Chemoreceptor Lattices
Role of neutrophil extracellular traps in regulation of lung cancer invasion and metastasis: Structural insights from a computational model
A multiscale computational framework for the development of spines in molluscan shells
Multiple bumps can enhance robustness to noise in continuous attractor networks
Correction: Hybrid predictive coding: Inferring, fast and slow
Integrating dynamic models and neural networks to discover the mechanism of meteorological factors on Aedes population
Prediction of the P. falciparum Target Space Relevant to Malaria Drug Discovery
The Evolution of Robust Development and Homeostasis in Artificial Organisms
A Multi-Component Model of the Developing Retinocollicular Pathway Incorporating Axonal and Synaptic Growth
Fine scale prediction of ecological community composition using a two-step sequential Machine Learning ensemble
A systematic atlas of chaperome deregulation topologies across the human cancer landscape
How People Use Social Information to Find out What to Want in the Paradigmatic Case of Inter-temporal Preferences
The Spatiotemporal Pattern of Src Activation at Lipid Rafts Revealed by Diffusion-Corrected FRET Imaging
Order-Based Representation in Random Networks of Cortical Neurons
Skilled motor control of an inverted pendulum implies low entropy of states but high entropy of actions
Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling
Priority-based transformations of stimulus representation in visual working memory
AutoClickChem: Click Chemistry in Silico
MFPSP: Identification of fungal species-specific phosphorylation site using offspring competition-based genetic algorithm
When and why direct transmission models can be used for environmentally persistent pathogens
A Review of 2010 for PLoS Computational Biology
Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale
Maximizing the reusability of gene expression data by predicting missing metadata
Getting Started in Text Mining: Part Two
Collaboration leads to cooperation on sparse networks
Stern-Judging: A Simple, Successful Norm Which Promotes Cooperation under Indirect Reciprocity
A Mathematical Model of Neonatal Rat Atrial Monolayers with Constitutively Active Acetylcholine-Mediated K+ Current
Emergence of a complex network structure on a Spatial Prisoner's Dilemma
Social Interaction, Noise and Antibiotic-Mediated Switches in the Intestinal Microbiota
Frequency Response of a Protein to Local Conformational Perturbations
Minimal biophysical model of combined antibiotic action
Effects of segmentation errors on downstream-analysis in highly-multiplexed tissue imaging
Syntrophy emerges spontaneously in complex metabolic systems
Memory replay in balanced recurrent networks
Cultured Cortical Neurons Can Perform Blind Source Separation According to the Free-Energy Principle
Dynamic Modeling of Vaccinating Behavior as a Function of Individual Beliefs
Bioinformatics in Sudan: Status and challenges case study: The National University-Sudan
Associating Genes and Protein Complexes with Disease via Network Propagation
Molecular Dynamics Simulations of the Bacterial UraA H + -Uracil Symporter in Lipid Bilayers Reveal a Closed State and a Selective Interaction with Cardiolipin
Ten Simple Rules for organizing a non-real-time web conference
MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions
Simulation Predicts IGFBP2-HIF1α Interaction Drives Glioblastoma Growth
Metabolic and Demographic Feedbacks Shape the Emergent Spatial Structure and Function of Microbial Communities
Broad CTL Response in Early HIV Infection Drives Multiple Concurrent CTL Escapes
Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images
An integrative transcriptome analysis framework for drug efficacy and similarity reveals drug-specific signatures of anti-TNF treatment in a mouse model of inflammatory polyarthritis
Formation, collective motion, and merging of macroscopic bacterial aggregates
Efficient and robust coding in heterogeneous recurrent networks
Ten simple rules to increase computational skills among biologists with Code Clubs
PenDA, a rank-based method for personalized differential analysis: Application to lung cancer
Kinetic Memory Based on the Enzyme-Limited Competition
An In-Silico Model of Lipoprotein Metabolism and Kinetics for the Evaluation of Targets and Biomarkers in the Reverse Cholesterol Transport Pathway
Neural spiking for causal inference and learning
Integration of partially observed multimodal and multiscale neural signals for estimating a neural circuit using dynamic causal modeling
Real-time decision-making during emergency disease outbreaks
A model of head direction and landmark coding in complex environments
Zika virus dynamics: Effects of inoculum dose, the innate immune response and viral interference
Integrating Hi-C links with assembly graphs for chromosome-scale assembly
On the Accessibility of Adaptive Phenotypes of a Bacterial Metabolic Network
Fluid and solute transport by cells and a model of systemic circulation
Modeling individual time courses of thrombopoiesis during multi-cyclic chemotherapy
Analysing pneumococcal invasiveness using Bayesian models of pathogen progression rates
Integrative multi-omics framework for causal gene discovery in Long COVID
Changing cognitive chimera states in human brain networks with age: Variations in cognitive integration and segregation
A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design
Feature Selection Methods for Identifying Genetic Determinants of Host Species in RNA Viruses
Reconciling Estimates of Cell Proliferation from Stable Isotope Labeling Experiments
Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes
Mathematical modeling of plus-strand RNA virus replication to identify broad-spectrum antiviral treatment strategies
Biophysical attributes that affect CaMKII activation deduced with a novel spatial stochastic simulation approach
Graph topological transformations in space-filling cell aggregates
resevol: An R package for spatially explicit models of pesticide resistance given evolving pest genomes
SBMLNetwork: A framework for standards-based visualization of biochemical models
Geometry can provide long-range mechanical guidance for embryogenesis
Accurate Bayesian phylogenetic point estimation using a tree distribution parameterized by clade probabilities
Corresponding Functional Dynamics across the Hsp90 Chaperone Family: Insights from a Multiscale Analysis of MD Simulations
Multiscale model of integrin adhesion assembly
Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks
Dynamic Excitatory and Inhibitory Gain Modulation Can Produce Flexible, Robust and Optimal Decision-making
From reaction kinetics to dementia: A simple dimer model of Alzheimer's disease etiology
Neural signatures of arbitration between Pavlovian and instrumental action selection
Designing combination therapies with modeling chaperoned machine learning
Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective
Exploiting glycan topography for computational design of Env glycoprotein antigenicity
Reconciling ASPP-p53 binding mode discrepancies through an ensemble binding framework that bridges crystallography and NMR data
Ten Simple Rules for Getting Involved in Your Scientific Community
Very Slow Search and Reach: Failure to Maximize Expected Gain in an Eye-Hand Coordination Task
Changes in parasite traits, rather than intensity, affect the dynamics of infection under external perturbation
A Probabilistic Palimpsest Model of Visual Short-term Memory
Fast and accurate Ab Initio Protein structure prediction using deep learning potentials
Revisiting chemoaffinity theory: Chemotactic implementation of topographic axonal projection
How the spleen reshapes and retains young and old red blood cells: A computational investigation
Emergence of qualitative states in synthetic circuits driven by ultrasensitive growth feedback
Correction: On the evolution and development of morphological complexity: A view from gene regulatory networks
Emergence of Metastable State Dynamics in Interconnected Cortical Networks with Propagation Delays
Metabolic pathway inference using multi-label classification with rich pathway features
Fast protein structure comparison through effective representation learning with contrastive graph neural networks
Shape-to-graph mapping method for efficient characterization and classification of complex geometries in biological images
Opponent processes in visual memories: A model of attraction and repulsion in navigating insects' mushroom bodies
Targeted modification of the Per2 clock gene alters circadian function in mPer2luciferase (mPer2Luc) mice
Discovery of Influenza A Virus Sequence Pairs and Their Combinations for Simultaneous Heterosubtypic Targeting that Hedge against Antiviral Resistance
Detection of gene cis-regulatory element perturbations in single-cell transcriptomes
Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model
The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications
Mapping the Structural and Dynamical Features of Kinesin Motor Domains
Disentangling signal and noise in neural responses through generative modeling
Rapid Transition towards the Division of Labor via Evolution of Developmental Plasticity
Deconvolution of calcium imaging data using marked point processes
Representing Where along with What Information in a Model of a Cortical Patch
Changes of Mind in an Attractor Network of Decision-Making
Prioritization of causal genes from genome-wide association studies by Bayesian data integration across loci
A Generative Statistical Algorithm for Automatic Detection of Complex Postures
Quantifying expression and metabolic activity of genes regulated by pregnane X receptor in primary human hepatocyte spheroids
E(3) equivariant graph neural networks for robust and accurate protein-protein interaction site prediction
Molecular Basis for Evolving Modularity in the Yeast Protein Interaction Network
Extracting Diffusive States of Rho GTPase in Live Cells: Towards In Vivo Biochemistry
Tracheal branching in ants is area-decreasing, violating a central assumption of network transport models
APAV: An advanced pangenome analysis and visualization toolkit
PreTIS: A Tool to Predict Non-canonical 5' UTR Translational Initiation Sites in Human and Mouse
Predicting precision grip grasp locations on three-dimensional objects
Interactions between attributions and beliefs at trial-by-trial level: Evidence from a novel computer game task
Bayesian Integration and Non-Linear Feedback Control in a Full-Body Motor Task
Selective Adaptation in Networks of Heterogeneous Populations: Model, Simulation, and Experiment
Multicellular spatial model of RNA virus replication and interferon responses reveals factors controlling plaque growth dynamics
Fifteen quick tips for success with HPC, i.e., responsibly BASHing that Linux cluster
Modelling motility of Trypanosoma brucei
Tuning network dynamics from criticality to an asynchronous state
A quantitative model for human neurovascular coupling with translated mechanisms from animals
Molecular noise of innate immunity shapes bacteria-phage ecologies
Unlocking ensemble ecosystem modelling for large and complex networks
Binomial models uncover biological variation during feature selection of droplet-based single-cell RNA sequencing
SDImpute: A statistical block imputation method based on cell-level and gene-level information for dropouts in single-cell RNA-seq data
Neural networks for self-adjusting mutation rate estimation when the recombination rate is unknown
Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate
Accounting for multiple imputation-induced variability for differential analysis in mass spectrometry-based label-free quantitative proteomics
Synchronization dependent on spatial structures of a mesoscopic whole-brain network
Leaky or polarised immunity: Non-Markovian modelling highlights the impact of immune memory assumptions
An algorithm to build synthetic temporal contact networks based on close-proximity interactions data
Probabilistic Inference of Biochemical Reactions in Microbial Communities from Metagenomic Sequences
A simple model of the attentional blink and its modulation by mental training
Diffusion controls local versus dispersed inheritance of histones during replication and shapes epigenomic architecture
A Systems Biology Approach Identifies Molecular Networks Defining Skeletal Muscle Abnormalities in Chronic Obstructive Pulmonary Disease
Tracking causal pathways in TMS-evoked brain responses
Expression of Concern: HiSV: A control-free method for structural variation detection from Hi-C data
Modelling midline shift and ventricle collapse in cerebral oedema following acute ischaemic stroke
Role of Mechanical Factors in the Morphology of the Primate Cerebral Cortex
Modelling Virus and Antibody Dynamics during Dengue Virus Infection Suggests a Role for Antibody in Virus Clearance
Understanding the impact of third-party species on pairwise coexistence
Problem-based learning in clinical bioinformatics education: Does it help to create communities of practice?
Modelling Circulating Tumour Cells for Personalised Survival Prediction in Metastatic Breast Cancer
COVID-19 modeling and non-pharmaceutical interventions in an outpatient dialysis unit
The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch
Assessment of the cardiovascular adverse effects of drug-drug interactions through a combined analysis of spontaneous reports and predicted drug-target interactions
Mathematical Modeling of Bacterial Kinetics to Predict the Impact of Antibiotic Colonic Exposure and Treatment Duration on the Amount of Resistant Enterobacteria Excreted
Analysis of targeted and whole genome sequencing of PacBio HiFi reads for a comprehensive genotyping of gene-proximal and phenotype-associated Variable Number Tandem Repeats
Algorithms to reconstruct past indels: The deletion-only parsimony problem
RETINA: Reconstruction-based pre-trained enhanced TransUNet for electron microscopy segmentation on the CEM500K dataset
Cross-species regulatory sequence activity prediction
Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals
FindAdapt: A python package for fast and accurate adapter detection in small RNA sequencing
Hands-on training about data clustering with orange data mining toolbox
A role for cortical interneurons as adversarial discriminators
Noradrenaline and acetylcholine shape functional connectivity organization of NREM substages: An empirical and simulation study
Hippocampal and medial prefrontal cortices encode structural task representations following progressive and interleaved training schedules
Modelling the spatial and temporal constrains of the GABAergic influence on neuronal excitability
Blind Predictions of DNA and RNA Tweezers Experiments with Force and Torque
Molecular Structures of Quiescently Grown and Brain-Derived Polymorphic Fibrils of the Alzheimer Amyloid Aβ 9-40 Peptide: A Comparison to Agitated Fibrils
Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells
Spatial close-kin mark-recapture methods to estimate dispersal parameters and barrier strength for mosquitoes
Classifying sex and strain from mouse ultrasonic vocalizations using deep learning
A Bayesian approach to modeling phytoplankton population dynamics from size distribution time series
GCAEMDA: Predicting miRNA-disease associations via graph convolutional autoencoder
Individual Rules for Trail Pattern Formation in Argentine Ants ( Linepithema humile )
Excitatory-inhibitory tone shapes decision strategies in a hierarchical neural network model of multi-attribute choice
LAILAPS-QSM: A RESTful API and JAVA library for semantic query suggestions
Model-inferred mechanisms of liver function from magnetic resonance imaging data: Validation and variation across a clinically relevant cohort
Semantic Similarity in Biomedical Ontologies
Introduction to the Quantitative Analysis of Two-Dimensional Fluorescence Microscopy Images for Cell-Based Screening
A Dual Receptor Crosstalk Model of G-Protein-Coupled Signal Transduction
The Hamiltonian Brain: Efficient Probabilistic Inference with Excitatory-Inhibitory Neural Circuit Dynamics
Deprotonation by Dehydration: The Origin of Ammonium Sensing in the AmtB Channel
Bridging cell-scale simulations and radiologic images to explain short-time intratumoral oxygen fluctuations
Defining the Product Chemical Space of Monoterpenoid Synthases
Uncoupling the roles of firing rates and spike bursts in shaping the STN-GPe beta band oscillations
Novel modelling approaches to predict the role of antivirals in reducing influenza transmission
Characterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor Design
A Model for an Angular Velocity-Tuned Motion Detector Accounting for Deviations in the Corridor-Centering Response of the Bee
Project-based learning course on metabolic network modelling in computational systems biology
Predicting microbial growth dynamics in response to nutrient availability
Extended graphical lasso for multiple interaction networks for high dimensional omics data
Support Vector Machines and Kernels for Computational Biology
Cytosolic proteins can exploit membrane localization to trigger functional assembly
TastepepAI: An artificial intelligence platform for taste peptide de novo design
Self-organization in brain tumors: How cell morphology and cell density influence glioma pattern formation