Software PubMed MeSh Term

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subject area of

• A COMPARATIVE-EVALUATION OF HEART-RATE REACTIVITY DURING MATH AND A STANDARD MENTAL ARITHMETIC TASK  Journal Article
• A Computational Workflow for the Automated Generation of Models of Genetic Designs  Journal Article
• A Method for High Fidelity Optogenetic Control of Individual Pyramidal Neurons In vivo  Journal Article
• A Methodology to Annotate Systems Biology Markup Language Models with the Synthetic Biology Open Language  Journal Article
• A NUMERICAL FRAMEWORK FOR COMPUTING STEADY STATES OF STRUCTURED POPULATION MODELS AND THEIR STABILITY  Journal Article
• A Real-Time Capable Software-Defined Receiver Using GPU for Adaptive Anti-Jam GPS Sensors  Journal Article
• A Simple Method for Estimating Informative Node Age Priors for the Fossil Calibration of Molecular Divergence Time Analyses  Journal Article
• A Simulated MS/MS Library for Spectrum-to-spectrum Searching in Large Scale Identification of Proteins  Journal Article
• A Validator and Converter for the Synthetic Biology Open Language  Journal Article
• A fast and accurate method for detection of IBD shared haplotypes in genome-wide SNP data  Journal Article
• A generative model for the behavior of RNA polymerase  Journal Article
• A method of mapping protein sumoylation sites by mass spectrometry using a modified small ubiquitin-like modifier 1 (SUMO-1) and a computational program  Journal Article
• A new open-source tool for measuring 3D osteocyte lacunar geometries from confocal laser scanning microscopy reveals age-related changes to lacunar size and shape in cortical mouse bone  Journal Article
• A standard-enabled workflow for synthetic biology  Journal Article
• Advancing Our Understanding of the Human Microbiome Using QIIME  Journal Article
• An Interlaboratory Comparison on the Characterization of a Sub-micrometer Polydisperse Particle Dispersion  Journal Article
• Analysis of MAP Kinases by Hydrogen Exchange Mass Spectrometry  Journal Article
• Analytical Ultracentrifugation (AUC): An Overview of the Application of Fluorescence and Absorbance AUC to the Study of Biological Macromolecules.  Journal Article
• Applying eye movement miscue analysis to the reading patterns of children with language impairment  Journal Article
• Applying knowledge-driven mechanistic inference to toxicogenomics  Conference Proceeding
• Automated discovery of functional generality of human gene expression programs.  Journal Article
• Behavior change interventions: the potential of ontologies for advancing science and practice  Journal Article
• BioSimulators: a central registry of simulation engines and services for recommending specific tools  Journal Article
• CTF determination and correction for low dose tomographic tilt series  Journal Article
• Call for transparency of COVI D-19 models  Journal Article
• CodaChrome: a tool for the visualization of proteome conservation across all fully sequenced bacterial genomes  Journal Article
• Communicating Structure and Function in Synthetic Biology Diagrams  Journal Article
• Comparison of label-free methods for quantifying human proteins by shotgun proteomics  Journal Article
• Computational Modeling for Biomimetic Sensors  Journal Article
• ConFind: a robust tool for conserved sequence identification  Journal Article
• Contributions of episodic retrieval and mentalizing to autobiographical thought: Evidence from functional neuroimaging, resting-state connectivity, and fMRI meta-analyses  Journal Article
• Creased hydrogels as active platforms for mechanical deformation of cultured cells  Journal Article
• Designing a Collaborative Visual Analytics Tool for Social and Technological Change Prediction  Journal Article
• Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks  Journal Article
• Direct Estimation of Parameters in ODE Models Using WENDy: Weak-Form Estimation of Nonlinear Dynamics  Journal Article
• Dynamic Modeling of Cellular Populations within iBioSim  Journal Article
• Efficient Analysis of Systems Biology Markup Language Models of Cellular Populations Using Arrays  Conference Proceeding
• Efficient estimation of sensory thresholds with ML-PEST  Journal Article
• Engineering genetic circuits: advancements in genetic design automation tools and standards for synthetic biology  Journal Article
• Evidence for Association Between Low Frequency Variants in CHRNA6/CHRNB3 and Antisocial Drug Dependence  Journal Article
• Excel-SBOL Converter: Creating SBOL from Excel Templates and Vice Versa  Journal Article
• Experimental Data Connector (XDC): Integrating the Capture of Experimental Data and Metadata Using Standard Formats and Digital Repositories  Journal Article
• Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data  Journal Article
• Extending SynBioHub's Functionality with Plugins  Journal Article
• FITTING GENETIC MODELS WITH LISREL - HYPOTHESIS-TESTING  Journal Article
• FOLDING OF CIRCULARLY PERMUTED TRANSFER-RNAS  Journal Article
• Face templates for the Chicago Face Database  Journal Article
• Fast-Find: A novel computational approach to analyzing combinatorial motifs  Journal Article
• Forgetting of Foreign-Language Skills: A Corpus-Based Analysis of Online Tutoring Software  Journal Article
• GIGGLE: a search engine for large-scale integrated genome analysis.  Journal Article
• GRADED MENTAL ARITHMETIC AS AN ACTIVE PSYCHOLOGICAL CHALLENGE  Journal Article
• GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit  Journal Article
• GeneEvolve: a fast and memory efficient forward-time simulator of realistic whole-genome sequence and SNP data  Journal Article
• Genetic circuit design automation with Cello 2.0  Journal Article
• Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering  Journal Article
• Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample  Journal Article
• Grow Where You Thrive, or Where Only You Can Survive? An Analysis of Performance Curve Evolution in a Clade with Diverse Habitat Affinities  Journal Article
• HUMAN NONMUSCLE MYOSIN HEAVY-CHAIN MESSENGER-RNA - GENERATION OF DIVERSITY THROUGH ALTERNATIVE POLYADENYLYLATION  Journal Article
• Harmonizing semantic annotations for computational models in biology  Journal Article
• Harnessing technology to improve formative assessment of student conceptions in STEM: forging a national network.  Journal Article
• Hierarchical Partial Matching and Segmentation of Interacting Cells  Journal Article
• Human Proteinpedia enables sharing of human protein data  Journal Article
• IWBDA 2012 Special Issue  Journal Article
• Improved validation of peptide MS/MS assignments using spectral intensity prediction  Journal Article
• Improving Students' Long-Term Knowledge Retention Through Personalized Review  Journal Article
• Influence of Distal Resistance and Proximal Stiffness on Hemodynamics and RV Afterload in Progression and Treatments of Pulmonary Hypertension: A Computational Study with Validation Using Animal Models  Journal Article
• Instant spectral assignment for advanced decision tree-driven mass spectrometry  Journal Article
• IsoformResolver: A Peptide-Centric Algorithm for Protein Inference  Journal Article
• JSBML 1.0: providing a smorgasbord of options to encode systems biology models  Journal Article
• LIMITED SAMPLING OF CONFORMATIONAL SPACE BY THE DISTANCE GEOMETRY ALGORITHM - IMPLICATIONS FOR STRUCTURES GENERATED FROM NMR DATA  Journal Article
• Large area mass analyzer instrument for the chemical analysis of interstellar dust particles  Journal Article
• Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset  Journal Article
• Machine learning models for segmentation and classification of cyanobacterial cells  Journal Article
• Mapping and characterization of structural variation in 17,795 human genomes  Journal Article
• Measuring the Absolute Abundance of the Smad Transcription Factors Using Quantitative Immunoblotting  Journal Article
• Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications  Journal Article
• Modeling 3-D compliant blood flow with fosls  Journal Article
• Modeling Extended Twin Family Data II: Power Associated With Different Family Structures  Journal Article
• MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifs  Journal Article
• Motion Tracker: Camera-Based Monitoring of Bodily Movements Using Motion Silhouettes  Journal Article
• ParSe 2.0: A web tool to identify drivers of protein phase separation at the proteome level  Journal Article
• Plant community responses to experimental warming across the tundra biome  Journal Article
• Practical methods for deuterium exchange/mass spectrometry.  Journal Article
• PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers  Journal Article
• Proposed Data Model for the Next Version of the Synthetic Biology Open Language  Journal Article
• QIIME allows analysis of high-throughput community sequencing data  Journal Article
• Quantifying Yeast Microtubules and Spindles Using the Toolkit for Automated Microtubule Tracking (TAMiT)  Journal Article
• Quantifying incoherence in speech:: An automated methodology and novel application to schizophrenia  Journal Article
• Quantifying the Impact of Chimera MS/MS Spectra on Peptide Identification in Large-Scale Proteomics Studies  Journal Article
• RNA-Puzzles Round V: blind predictions of 23 RNA structures  Journal Article
• Rebranding Exercise: There's an App for That  Journal Article
• Recommendations for utilizing and reporting population genetic analyses: the reproducibility of genetic clustering using the program STRUCTURE  Journal Article
• Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.  Journal Article
• Review of ozone and temperature lidar validations performed within the framework of the Network for the Detection of Stratospheric Change  Journal Article
• Robust sequence selection method used to develop the FluChip diagnostic microarray for influenza virus  Journal Article
• Role of a heterogeneous free state in the formation of a specific RNA-theophylline complex  Journal Article
• Round Trip: An Automated Pipeline for Experimental Design, Execution, and Analysis  Journal Article
• SBML Level 3: an extensible format for the exchange and reuse of biological models  Journal Article
• SBOL Visual: A Graphical Language for Genetic Designs  Journal Article
• SBOL-OWL: An Ontological Approach for Formal and Semantic Representation of Synthetic Biology Information  Journal Article
• SBOLDesigner 2: An Intuitive Tool for Structural Genetic Design  Journal Article
• SBOLExplorer: Data Infrastructure and Data Mining for Genetic Design Repositories  Journal Article
• SITEHOUND-web: a server for ligand binding site identification in protein structures  Journal Article
• SV-plaudit: A cloud-based framework for manually curating thousands of structural variants  Journal Article
• Samplot: a platform for structural variant visual validation and automated filtering  Journal Article
• Science Concierge: A Fast Content-Based Recommendation System for Scientific Publications  Journal Article
• Searching for and predicting the activity of sites for DNA binding proteins: compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF).  Journal Article
• Searching thousands of genomes to classify somatic and novel structural variants using STIX  Journal Article
• Self-assembly of a metal-ion-bound monolayer of trigonal connectors on mercury: An electrochemical Langmuir trough  Journal Article
• SeqImprove: Machine-Learning-Assisted Curation of Genetic Circuit Sequence Information  Journal Article
• Sequence-Based Searching for SynBioHub Using VSEARCH  Journal Article
• Sexual infidelity in a national survey of American women: Differences in prevalence and correlates as a function of method of assessment  Journal Article
• Sharing Structure and Function in Biological Design with SBOL 2.0  Journal Article
• SitePainter: a tool for exploring biogeographical patterns  Journal Article
• Solution structure of tRNA(Val) from refinement of homology model against residual dipolar coupling and SAXS data  Journal Article
• Specifications of standards in systems and synthetic biology: status and developments in 2021  Journal Article
• Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022  Journal Article
• Specifying Combinatorial Designs with the Synthetic Biology Open Language (SBOL)  Journal Article
• Stabilization of an optical microscope to 0.1 nm in three dimensions  Journal Article
• Stochastic Lanczos estimation of genomic variance components for linear mixed-effects models  Journal Article
• Structure of the BamC Two-Domain Protein Obtained by Rosetta with a Limited NMR Data Set  Journal Article
• SynBioSuite: A Tool for Improving the Workflow for Genetic Design and Modeling  Journal Article
• Synthetic Biology Curation Tools (SYNBICT)  Journal Article
• Synthetic Biology Open Language (SBOL) Version 2.2.0  Journal Article
• Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0  Journal Article
• Synthetic biology open language (SBOL) version 3.0.0  Journal Article
• Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1  Journal Article
• TESTING STRUCTURAL EQUATION MODELS FOR TWIN DATA USING LISREL  Journal Article
• TF Profiler: a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networks.  Journal Article
• THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures  Journal Article
• Testing for physical validity in molecular simulations  Journal Article
• The Development of a Novel High Throughput Computational Tool for Studying Individual and Collective Cellular Migration  Journal Article
• The Distributed Annotation System  Journal Article
• The GPlates Portal: Cloud-Based Interactive 3D Visualization of Global Geophysical and Geological Data in a Web Browser  Journal Article
• The MiPACQ clinical question answering system.  Conference Proceeding
• The National Longitudinal Study of Adolescent to Adult Health (Add Health) Sibling Pairs Genome-Wide Data  Journal Article
• The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology  Journal Article
• The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core  Journal Article
• The adjoint of CMAQ  Journal Article
• The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE).  Journal Article
• The mathematics of SELEX against complex targets  Journal Article
• Three dimensional tracking of fluorescent microparticles using a photon-limited double-helix response system  Journal Article
• Three-Dimensional Root Phenotyping with a Novel Imaging and Software Platform  Journal Article
• UniFrac: an effective distance metric for microbial community comparison  Journal Article
• Using Internet search engines to estimate word frequency  Journal Article
• Using parentage analysis to examine gene flow and spatial genetic structure  Journal Article
• Using the nucleotide substitution rate matrix to detect horizontal gene transfer  Journal Article
• Variability in the analysis of a single neuroimaging dataset by many teams  Journal Article
• VisBOL2-Improving Web-Based Visualization for Synthetic Biology Designs  Journal Article
• dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication  Journal Article
• iBioSim 3: A Tool for Model-Based Genetic Circuit Design  Journal Article
• iBioSim: a tool for the analysis and design of genetic circuits  Journal Article
• pySBOL: A Python Package for Genetic Design Automation and Standardization  Journal Article
• sboljs: Bringing the Synthetic Biology Open Language to the Web Browser  Journal Article
• svtools: population-scale analysis of structural variation  Journal Article

broader concept

• Computing Methodologies  PubMed MeSh Term

narrower concept

• Hypermedia  PubMed MeSh Term
• Mobile Applications  PubMed MeSh Term
• Programming Languages  PubMed MeSh Term
• Software - Database Management Systems  PubMed MeSh Term
• Software - User-Centered Design  PubMed MeSh Term
• Software - Video Games  PubMed MeSh Term
• Software - Web Browser  PubMed MeSh Term
• Software Design  PubMed MeSh Term
• User-Computer Interface  PubMed MeSh Term