Software

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  Subject Areas on Research

  • 10-year follow-up wear analysis of first-generation highly crosslinked polyethylene in primary total hip arthroplasty. 
  • 3D maps of RNA interhelical junctions. 
  • 4D XCAT phantom for multimodality imaging research. 
  • A Binaural Cochlear Implant Sound Coding Strategy Inspired by the Contralateral Medial Olivocochlear Reflex. 
  • A Flexible, Efficient Binomial Mixed Model for Identifying Differential DNA Methylation in Bisulfite Sequencing Data. 
  • A Self-Calibrating Radar Sensor System for Measuring Vital Signs. 
  • A Spatiotemporal-Constrained Sorting Method for Motion-Robust 4D-MRI: A Feasibility Study. 
  • A binary method for simple and accurate two-dimensional cursor control from EEG with minimal subject training. 
  • A case study comparing the relative benefit of optimizing beam weights, wedge angles, beam orientations and tomotherapy in stereotactic radiotherapy of the brain. 
  • A chartless record--is it adequate? 
  • A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. 
  • A combined explicit-implicit method for high accuracy reaction path integration. 
  • A comparative effectiveness study of eSource used for data capture for a clinical research registry. 
  • A computational framework to assess genome-wide distribution of polymorphic human endogenous retrovirus-K In human populations. 
  • A dose-volume-based tool for evaluating and ranking IMRT treatment plans. 
  • A framework for annotating human genome in disease context. 
  • A framework for optimising the radiographic technique in digital X-ray imaging. 
  • A framework phylogeny of the American oak clade based on sequenced RAD data. 
  • A functional analysis of the spacer of V(D)J recombination signal sequences. 
  • A general map of iron metabolism and tissue-specific subnetworks. 
  • A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments. 
  • A genome-wide association study of corneal astigmatism: The CREAM Consortium. 
  • A genomewide screen in multiplex rheumatoid arthritis families suggests genetic overlap with other autoimmune diseases. 
  • A hierarchical stepwise approach to evaluate nasal patency after virtual surgery for nasal airway obstruction. 
  • A kernel for open source drug discovery in tropical diseases. 
  • A kernel for the Tropical Disease Initiative. 
  • A large-scale survey of genetic copy number variations among Han Chinese residing in Taiwan. 
  • A mathematical model platform for optimizing a multiprojection breast imaging system. 
  • A mobile trauma database with charge capture. 
  • A model for fast axonal transport. 
  • A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families. 
  • A new analysis tool for individual-level allele frequency for genomic studies. 
  • A new fully automated approach for aligning and comparing shapes. 
  • A new generation of crystallographic validation tools for the protein data bank. 
  • A new method to measure peripheral retinal vascular caliber over an extended area. 
  • A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx). 
  • A novel application of the MIRC repository in medical education. 
  • A novel digital intervention for actively reducing severity of paediatric ADHD (STARS-ADHD): a randomised controlled trial. 
  • A pilot study using "ROPtool" to quantify plus disease in retinopathy of prematurity. 
  • A pilot study using ROPtool to measure retinal vascular dilation. 
  • A prospective multicenter validation study for a novel angiography-derived physiological assessment software: Rationale and design of the radiographic imaging validation and evaluation for Angio-iFR (ReVEAL iFR) study. 
  • A public resource facilitating clinical use of genomes. 
  • A randomized controlled trial on rehabilitation through caregiver-delivered nurse-organized service programs for disabled stroke patients in rural china (the RECOVER trial): design and rationale. 
  • A reliable and programmable acoustofluidic pump powered by oscillating sharp-edge structures. 
  • A robotics platform for automated batch fabrication of high density, microfluidics-based DNA microarrays, with applications to single cell, multiplex assays of secreted proteins. 
  • A robust and efficient method for estimating enzyme complex abundance and metabolic flux from expression data. 
  • A semi-automated tool for treatment plan-quality evaluation and clinical trial quality assurance. 
  • A set of 4D pediatric XCAT reference phantoms for multimodality research. 
  • A simple BASIC program allows the rapid entry of DNA nucleotide sequences into personal computers. 
  • A simplified method to measure choroidal thickness using adaptive compensation in enhanced depth imaging optical coherence tomography. 
  • A simulation environment for directional sensing as a phase separation process. 
  • A simulation test of Smith's "Degrees of freedom" correction for comparative studies. 
  • A strategy for the rapid identification of phosphorylation sites in the phosphoproteome. 
  • A system for the analysis of long-term electrocardiographic studies in clinical research and training. 
  • A tutorial on Bayesian multi-model linear regression with BAS and JASP. 
  • A vectorized Monte Carlo code for modeling photon transport in SPECT. 
  • AFLOW-CHULL: Cloud-Oriented Platform for Autonomous Phase Stability Analysis. 
  • Accelerating reconstruction of reference digital tomosynthesis using graphics hardware. 
  • Accounting for linkage in family-based tests of association with missing parental genotypes. 
  • Accuracy of mutational signature software on correlated signatures. 
  • Accurate fatty acid composition estimation of adipose tissue in the abdomen based on bipolar multi-echo MRI. 
  • Addressing biological uncertainties in engineering gene circuits. 
  • Adjusting for covariates on a slippery slope: linkage analysis of change over time. 
  • Advances to Bayesian network inference for generating causal networks from observational biological data. 
  • Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. 
  • All-atom contacts: a new approach to structure validation. 
  • American Association of Physicists in Medicine Task Group 263: Standardizing Nomenclatures in Radiation Oncology. 
  • American Society of Echocardiography Cardiovascular Technology and Research Summit: a roadmap for 2020. 
  • An 'electronic' extramural course in epidemiology and medical statistics. 
  • An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes. 
  • An automatic diagnosis system of nuclear cataract using slit-lamp images. 
  • An ensemble model of competitive multi-factor binding of the genome. 
  • An evaluation of copy number variation detection tools from whole-exome sequencing data. 
  • An exclusion map for facioscapulohumeral (Landouzy-Déjérine) disease. 
  • An investigation of the accuracy of an IMRT dose distribution using two- and three-dimensional dosimetry techniques. 
  • An object oriented user interface for analysis of biological data. 
  • An on-line archive of reconstructed hippocampal neurons. 
  • An overview of variance inflation factors for sample-size calculation. 
  • Analysis of 2-DG autoradiograms using image-averaging and image-differencing procedures for systems-level description of neurobehavioral function. 
  • Analysis of Huntington disease linkage and age-of-onset distributions. 
  • Analysis of allosteric signal transduction mechanisms in an engineered fluorescent maltose biosensor. 
  • Analysis of image quality for real-time target tracking using simultaneous kV-MV imaging. 
  • Analysis of repetitive sequence elements containing tRNA-like sequences. 
  • Analysis of the real EADGENE data set: comparison of methods and guidelines for data normalisation and selection of differentially expressed genes (open access publication). 
  • Analyzing animal behavior via classifying each video frame using convolutional neural networks. 
  • Annotating the human genome with Disease Ontology. 
  • Application description and policy model in collaborative environment for sharing of information on epidemiological and clinical research data sets. 
  • Application of a microcomputer-based system in the analysis of infection data at the emergency units of a large hospital. 
  • Application of the mutual information criterion for feature selection in computer-aided diagnosis. 
  • Approximating transcranial magnetic stimulation with electric stimulation in mouse: a simulation study. 
  • Artificial intelligence for automatic cerebral ventricle segmentation and volume calculation: a clinical tool for the evaluation of pediatric hydrocephalus. 
  • Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. 
  • Assessing clinical site readiness for electronic health record (EHR)-to-electronic data capture (EDC) automated data collection. 
  • Assessment of LD matrix measures for the analysis of biological pathway association. 
  • Assessment of PlanIQ Feasibility DVH for head and neck treatment planning. 
  • Assessment of display performance for medical imaging systems: executive summary of AAPM TG18 report. 
  • Association test for X-linked QTL in family-based designs. 
  • Atlas construction via dictionary learning and group sparsity. 
  • Atlas-based hippocampus segmentation in Alzheimer's disease and mild cognitive impairment. 
  • AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes. 
  • Automated Deep Brain Stimulation Programming for Tremor. 
  • Automated acuity scoring within a computer based medical record. 
  • Automated spectral analysis I: formation of a priori information by spectral simulation. 
  • Automated temperature scanning for hyperthermia treatment monitoring. 
  • Automatic detection of pathological myopia using variational level set. 
  • Automatic diagnosis of pathological myopia from heterogeneous biomedical data. 
  • Automatic glaucoma diagnosis through medical imaging informatics. 
  • Automatic segmentation of seven retinal layers in SDOCT images congruent with expert manual segmentation. 
  • BBK* (Branch and Bound Over K*): A Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity Over Large Sequence Spaces. 
  • BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells. 
  • Bayesian estimation of genetic regulatory effects in high-throughput reporter assays. 
  • Bayesian joint analysis of heterogeneous genomics data. 
  • Bayesian network-response regression. 
  • Benchmarking association analyses of continuous exposures with RNA-seq in observational studies. 
  • Benchmarking of Deformable Image Registration for Multiple Anatomic Sites Using Digital Data Sets With Ground-Truth Deformation Vector Fields. 
  • BioWarehouse: a bioinformatics database warehouse toolkit. 
  • Biochemistry. Exciting structures. 
  • Bootstrap calibration of TRANSMIT for informative missingness of parental genotype data. 
  • Building gold standard corpora for medical natural language processing tasks. 
  • CANEapp: a user-friendly application for automated next generation transcriptomic data analysis. 
  • CMINDS does not have identical tests to the CATIE and MATRICS batteries. Commentary on O'Halloran et al. 
  • CMOS-based carbon nanotube pass-transistor logic integrated circuits. 
  • CNR enhancement in the presence of multiple interfering processes using linear filters 
  • CONSTAX2: improved taxonomic classification of environmental DNA markers. 
  • COUGER--co-factors associated with uniquely-bound genomic regions. 
  • CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation. 
  • CPS analysis: self-contained validation of biomedical data clustering. 
  • CRP: Cleavage of Radiolabeled Phosphoproteins. 
  • CT colonography: investigation of the optimum reader paradigm by using computer-aided detection software. 
  • CT screening and follow-up of lung nodules: effects of tube current-time setting and nodule size and density on detectability and of tube current-time setting on apparent size. 
  • Calmodulin mediates Ca2+ sensitivity of sodium channels. 
  • Carbon sequestration in Synechococcus Sp.: from molecular machines to hierarchical modeling. 
  • Case-based reasoning computer algorithm that uses mammographic findings for breast biopsy decisions. 
  • Categorical data analysis in primary care research: log-linear models. 
  • Catheter ultrasound phased-array transducers for thermal ablation: a feasibility study. 
  • Causal network inference from gene transcriptional time-series response to glucocorticoids. 
  • Centralized immunogens as a vaccine strategy to overcome HIV-1 diversity. 
  • Characterization of spatial distortion in a 0.35 T MRI-guided radiotherapy system. 
  • Characterization of the surface topography and putative tertiary structure of the human CD7 molecule. 
  • Characterizing fishing effort and spatial extent of coastal fisheries 
  • Chemoinformatic identification of novel inhibitors against Mycobacterium tuberculosis L-aspartate α-decarboxylase. 
  • Choroidal vascularity index: a step towards software as a medical device. 
  • Classification and 3D averaging with missing wedge correction in biological electron tomography. 
  • Clinical data bases. Accomplishments and unrealized potential. 
  • Clinical pathways on a mobile device. 
  • Clinical utility of a patient-specific algorithm for simulating intracerebral drug infusions. 
  • Clinician-patient E-mail communication: challenges for reimbursement. 
  • Combining location and expression data for principled discovery of genetic regulatory network models. 
  • Comments about Joint Modeling of Cluster Size and Binary and Continuous Subunit-Specific Outcomes. 
  • Comparative Evaluation of MS-based Metabolomics Software and Its Application to Preclinical Alzheimer's Disease. 
  • Comparing Bayesian and frequentist approaches for multiple outcome mixed treatment comparisons. 
  • Comparing data mining methods on the VAERS database. 
  • Comparison of 2D and 3D gamma analyses. 
  • Comparison of Human Tissue Microarray to Human Pericyte Transcriptome Yields Novel Perivascular Cell Markers. 
  • Comparison of an automated thrombolytic predictive instrument to both diagnostic software and an expert cardiologist for diagnosis of an ST elevation acute myocardial infarction. 
  • Comparison of anterior segment optical tomography parameters measured using a semi-automatic software to standard clinical instruments. 
  • Comparison of conventional and simulated reduced-tube current MDCT for evaluation of suspected appendicitis in the pediatric population. 
  • Comparison of two high-resolution manometry software systems in evaluating esophageal motor function. 
  • Compartmental transport model of microbicide delivery by an intravaginal ring. 
  • Complete effect-profile assessment in association studies with multiple genetic and multiple environmental factors. 
  • Complexity reduction in context-dependent DNA substitution models. 
  • Compressive holography. 
  • Computational Methods for RNA Structure Validation and Improvement. 
  • Computational and experimental analyses reveal previously undetected coding exons of the KRIT1 (CCM1) gene. 
  • Computational design of protein antigens that interact with the CDR H3 loop of HIV broadly neutralizing antibody 2F5. 
  • Computational immunology--from bench to virtual reality. 
  • Computer programs for the concordance correlation coefficient. 
  • Computer-assisted design of an implantable, intrathoracic artificial lung. 
  • Computer-assisted measurement of retinal vascular width and tortuosity in retinopathy of prematurity. 
  • Computer-based evaluation of pediatric dental residents' clinical performance. 
  • Computer-based finite element modeling of insulated Tuohy needles used in regional anesthesia. 
  • Computerized medical records. A new resource for clinical decision making. 
  • Computing robustness and persistence for images. 
  • ConceFT for Time-Varying Heart Rate Variability Analysis as a Measure of Noxious Stimulation During General Anesthesia. 
  • Connection, a microcomputer program for storing and analyzing structural properties of neural circuits. 
  • Consensus guidelines on plasma cell myeloma minimal residual disease analysis and reporting. 
  • Conserved Residues Control Activation of Mammalian G Protein-Coupled Odorant Receptors. 
  • Consistent self-monitoring in a commercial app-based intervention for weight loss: results from a randomized trial. 
  • Constructing a multichannel electrocardiography system from a few standardized, high-level components. 
  • Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with pre-defined geometry. 
  • Conversion of a maltose receptor into a zinc biosensor by computational design. 
  • Conversion of manual to total computerized medical records. Experience with selected abstraction. 
  • Converting a legacy system database into relational format to enhance query efficiency. 
  • Correlation Between Macular Integrity Assessment and Optical Coherence Tomography Imaging of Ellipsoid Zone in Macular Telangiectasia Type 2. 
  • Creating and parameterizing patient-specific deep brain stimulation pathway-activation models using the hyperdirect pathway as an example. 
  • Creation of DICOM--aware applications using ImageJ. 
  • Critical assessment of automated flow cytometry data analysis techniques. 
  • Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution. 
  • DIG--a system for gene annotation and functional discovery. 
  • Data acquisition and analysis system for intracellular neuronal signals. 
  • Data and animal management software for large-scale phenotype screening. 
  • Decision model for the acute treatment of mania. 
  • Deep brain stimulation that abolishes Parkinsonian activity in basal ganglia improves thalamic relay fidelity in a computational circuit. 
  • Defining functional DNA elements in the human genome. 
  • Design and implementation of a comprehensive outpatient Results Manager. 
  • Design considerations, architecture, and use of the Mini-Sentinel distributed data system. 
  • Design, implementation, use, and preliminary evaluation of SEBASTIAN, a standards-based Web service for clinical decision support. 
  • Design, synthesis and discovery of picomolar selective α4β2 nicotinic acetylcholine receptor ligands. 
  • Detecting glaucomatous progression using GDx with variable and enhanced corneal compensation using Guided Progression Analysis. 
  • Detection of the JAK2 V617F mutation by LightCycler PCR and probe dissociation analysis. 
  • Developing a Real-Time Electroencephalogram-Guided Anesthesia-Management Curriculum for Educating Residents: A Single-Center Randomized Controlled Trial. 
  • Developing tailored instruments: item banking and computerized adaptive assessment. 
  • Development and reliability of retinal arteriolar central light reflex quantification system: a new approach for severity grading. 
  • Development and validation of XML-based calculations within order sets. 
  • Development and validation of a deep-learning algorithm for the detection of polyps during colonoscopy. 
  • Development and validation of an unsupervised scoring system (Autonomate) for skin conductance response analysis. 
  • Development and validation of the social information processing application: a Web-based measure of social information processing patterns in elementary school-age boys. 
  • Development of a computerized assessment of clinician adherence to a treatment guideline for patients with bipolar disorder. 
  • Development of a new patient-reported outcome measure in sarcopenia. 
  • Development of a telemedicine model for emerging countries: a case study on pediatric oncology in Brazil. 
  • Development of a virtual reality assessment of everyday living skills. 
  • Diagnostic accuracy of translucency rendering to differentiate polyps from pseudopolyps at 3D endoluminal CT colonography: a feasibility study. 
  • Differences in apolipoprotein E3/3 and E4/4 allele-specific gene expression in hippocampus in Alzheimer disease. 
  • Differential expression analysis for RNAseq using Poisson mixed models. 
  • Differentiation and classification of RNA motifs using small molecule-based pattern recognition. 
  • Digital image analysis: a reliable tool in the quantitative evaluation of cutaneous lesions and beyond. 
  • Digital pathology in nephrology clinical trials, research, and pathology practice. 
  • Digital synthesis of lung nodules. 
  • Direct comparison of a tablet computer and a personal digital assistant for point-of-care documentation in eye care. 
  • Discovery of Lipidome Alterations Following Traumatic Brain Injury via High-Resolution Metabolomics. 
  • Discretizing large traceable vessels and using DE-MRI perfusion maps yields numerical temperature contours that match the MR noninvasive measurements. 
  • Disease Ontology: a backbone for disease semantic integration. 
  • Distribution and determinants of choroidal thickness and volume using automated segmentation software in a population-based study. 
  • Does access modality matter? Evaluation of validity in reusing clinical care data. 
  • Does hormone replacement therapy influence retinal microvascular caliber? 
  • Domain prediction with probabilistic directional context. 
  • DukeSim: A Realistic, Rapid, and Scanner-Specific Simulation Framework in Computed Tomography. 
  • Dynamics of rural-urban migration in India: 1960-1981. 
  • E-Pedigrees: a large-scale automatic family pedigree prediction application. 
  • Early hominid diets from quantitative image analysis of dental microwear. 
  • Effective knowledge management in translational medicine. 
  • Effectiveness of automatic diagnostic test result feedback on outpatient laboratory and radiology testing in veterans. A controlled trial. 
  • Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples. 
  • Efficient estimation of grouped survival models. 
  • Efficient optic cup detection from intra-image learning with retinal structure priors. 
  • Efficient, Cost-Effective, High-Throughput, Multilocus Sequencing Typing (MLST) Method, NGMLST, and the Analytical Software Program MLSTEZ. 
  • Electronic toxicity monitoring and patient-reported outcomes. 
  • Enabling cross-platform clinical decision support through Web-based decision support in commercial electronic health record systems: proposal and evaluation of initial prototype implementations. 
  • Enabling high-throughput biology with flexible open-source automation. 
  • Enhancing communication between oncologists and patients with a computer-based training program: a randomized trial. 
  • Enhancing measurement in health outcomes research supported by Agencies within the US Department of Health and Human Services. 
  • Enhancing the use of EHR systems for pragmatic embedded research: lessons from the NIH Health Care Systems Research Collaboratory. 
  • Equalizing cDNA subtraction based on selective suppression of polymerase chain reaction: cloning of Jurkat cell transcripts induced by phytohemaglutinin and phorbol 12-myristate 13-acetate. 
  • Establishing a framework to implement 4D XCAT phantom for 4D radiotherapy research. 
  • Estimation of Radiation Dose in CT Based on Projection Data. 
  • Estimation of coefficients of individual agreement (CIAs) for quantitative and binary data using SAS and R. 
  • Estimation of immune cell content in tumor using single-cell RNA-seq reference data. 
  • EuroPhenome: a repository for high-throughput mouse phenotyping data. 
  • Evaluating measurement models in clinical research: covariance structure analysis of latent variable models of self-conception. 
  • Evaluation of Right Ventricular Myocardial Mechanics Using Velocity Vector Imaging of Cardiac MRI Cine Images in Transposition of the Great Arteries Following Atrial and Arterial Switch Operations. 
  • Evaluation of a commercial DIR platform for contour propagation in prostate cancer patients treated with IMRT/VMAT. 
  • Evaluation of a method to measure fluorescent cell burden in complex culture systems. 
  • Evaluation of antiviral drugs and neutralizing antibodies to human immunodeficiency virus by a rapid and sensitive microtiter infection assay. 
  • Evidence-based decision support for neurological diagnosis reduces errors and unnecessary workup. 
  • Evolution of plus disease in retinopathy of prematurity: quantification by ROPtool. 
  • Exploiting expression patterns across multiple tissues to map expression quantitative trait loci. 
  • Exploratory case method to determine the frequency of redundant orders within manually consolidated order lists. 
  • Exploring biological electron transfer pathway dynamics with the Pathways plugin for VMD. 
  • Exploring steric constraints on protein mutations using MAGE/PROBE. 
  • Extraction of spatial information for low-bandwidth telerehabilitation applications. 
  • Extrema-weighted feature extraction for functional data. 
  • F-Seq: a feature density estimator for high-throughput sequence tags. 
  • FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization. 
  • FDDI information management system for centralizing interactive, computerized multimedia clinical experiences in pediatric rheumatology/Immunology. 
  • Family health history: underused for actionable risk assessment. 
  • Fast and robust association tests for untyped SNPs in case-control studies. 
  • Fast reconstruction of digital tomosynthesis using on-board images. 
  • Feasibility and applicability of computer-assisted myocardial blush quantification after primary percutaneous coronary intervention for ST-segment elevation myocardial infarction. 
  • Fine mapping of the chromosome 12 late-onset Alzheimer disease locus: potential genetic and phenotypic heterogeneity. 
  • Finite-element modeling of compression and gravity on a population of breast phantoms for multimodality imaging simulation. 
  • Flow cytometric analysis of DNA content in budding yeast. 
  • FlowKit: A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows. 
  • FlyRNAi.org--the database of the Drosophila RNAi screening center: 2012 update. 
  • FlyRNAi: the Drosophila RNAi screening center database. 
  • Focal biologically inspired feature for glaucoma type classification. 
  • Free and open-source software application for the evaluation of coronary computed tomography angiography images. 
  • From lab to field, new approaches to phenotyping root system architecture. 
  • Fully automated system for three-dimensional bronchial morphology analysis using volumetric multidetector computed tomography of the chest. 
  • Fully automatic segmentation of fluorescein leakage in subjects with diabetic macular edema. 
  • Fully automatic software for retinal thickness in eyes with diabetic macular edema from images acquired by cirrus and spectralis systems. 
  • Functional analysis of novel SNPs and mutations in human and mouse genomes. 
  • GAVA: spectral simulation for in vivo MRS applications. 
  • GREAT improves functional interpretation of cis-regulatory regions. 
  • GWAS analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis. 
  • GenBlastA: enabling BLAST to identify homologous gene sequences. 
  • Gene prediction and verification in a compact genome with numerous small introns. 
  • Generalized linear mixed models: a practical guide for ecology and evolution. 
  • Generalized sampling using a compound-eye imaging system for multi-dimensional object acquisition. 
  • Genetic analysis of MRL-lpr mice: relationship of the Fas apoptosis gene to disease manifestations and renal disease-modifying loci. 
  • Genetic analysis workshop IV: Huntington disease linkage analysis summary. 
  • Genetic linkage studies in Alzheimer's disease families. 
  • Genetic mapping of a novel familial form of infantile hemangioma. 
  • Genetic simulation tools for post-genome wide association studies of complex diseases. 
  • Genetics and evolution: an iOS application to supplement introductory courses in transmission and evolutionary genetics. 
  • GenoWatch: a disease gene mining browser for association study. 
  • Genome engineering: the next genomic revolution. 
  • Genome-wide copy number analysis using copy number inferring tool (CNIT) and DNA pooling. 
  • Genome-wide prediction of imprinted murine genes. 
  • Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach. 
  • Geolocation of hospitalizations registered on the Brazilian National Health System's Hospital Information System: a solution based on the R Statistical Software. 
  • Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs. 
  • GiA Roots: software for the high throughput analysis of plant root system architecture. 
  • Glaucoma Progression Analysis software compared with expert consensus opinion in the detection of visual field progression in glaucoma. 
  • Global folds of proteins with low densities of NOEs using residual dipolar couplings: application to the 370-residue maltodextrin-binding protein. 
  • Glocal clinical registries: pacemaker registry design and implementation for global and local integration--methodology and case study. 
  • Glycemic response to stress is altered in euglycemic Pima Indians. 
  • Goodbye Electronic Health Record? 
  • Guidelines for Genome-Scale Analysis of Biological Rhythms. 
  • HASH: a program to accurately predict protein Hα shifts from neighboring backbone shifts. 
  • Hardware and software for tachistoscopy: how to make accurate measurements on any PC utilizing the Microsoft Windows operating system. 
  • Health Level 7. A protocol for the interchange of healthcare data. 
  • Hemodynamic consequences of right ventricular isolation: the contribution of the right ventricular free wall to cardiac performance. 
  • Hereditary prostate cancer in African American families: linkage analysis using markers that map to five candidate susceptibility loci. 
  • Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. 
  • High-side digitally current controlled biphasic bipolar microstimulator. 
  • High-throughput cardiac safety evaluation and multi-parameter arrhythmia profiling of cardiomyocytes using microelectrode arrays. 
  • High-throughput imaging and analysis of root system architecture in Brachypodium distachyon under differential nutrient availability. 
  • High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. 
  • High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology. 
  • Hippocampal atrophy confounds template-based functional MR imaging measures of hippocampal activation in patients with mild cognitive impairment. 
  • How does c-view image quality compare with conventional 2D FFDM? 
  • How the past teaches the future: ACMI distinguished lecture. 
  • How to Shoot and Edit High-Quality Surgical Videos for Hand and Upper Extremity Surgery. 
  • How to make more out of community data? A conceptual framework and its implementation as models and software. 
  • IRT health outcomes data analysis project: an overview and summary. 
  • Identification of Long Noncoding RNAs Associated to Human Disease Susceptibility. 
  • Identifying the macromolecular targets of de novo-designed chemical entities through self-organizing map consensus. 
  • Imagining a lean and agile digital health ecosystem - a measure of pandemic responsiveness. 
  • Impact of Game-Based Health Promotion Programs on Body Mass Index in Overweight/Obese Children and Adolescents: A Systematic Review and Meta-Analysis of Randomized Controlled Trials. 
  • Impact of missing data in evaluating artificial neural networks trained on complete data. 
  • Implementation of an Automated Radiology Recommendation-Tracking Engine for Abdominal Imaging Findings of Possible Cancer. 
  • Implementation of an accelerated iterative algorithm for cone-beam SPECT. 
  • Implementation of graphic user interface screen capture solution for workflow assessment of abdominal MR examinations valuable tool to analyze discrepancies in expected and experienced MR table time. 
  • Implementation of remote 3-dimensional image guided radiation therapy quality assurance for radiation therapy oncology group clinical trials. 
  • Implementation of the isocenter-shift technique for smoothing MLC field edge on a 3D treatment planning system. 
  • Implementation, adoption, and utility of family health history risk assessment in diverse care settings: evaluating implementation processes and impact with an implementation framework. 
  • Implementing diffusion-weighted MRI for body imaging in prospective multicentre trials: current considerations and future perspectives. 
  • Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix. 
  • Improved transcript isoform discovery using ORF graphs. 
  • Improving indel detection specificity of the Ion Torrent PGM benchtop sequencer. 
  • Improving information access with an emergency department system. 
  • Improving the application of imaging clinical decision support tools: making the complex simple. 
  • In situ measurements of phytoplankton fluorescence using low cost electronics. 
  • In vivo measurement of corneal angiogenesis with video data acquisition and computerized image analysis. 
  • InVEST: interactive and visual edge selection tool for constructing evolutionary trees. 
  • Incorporating Multiple Perspectives Into the Development of an Electronic Survivorship Platform for Head and Neck Cancer. 
  • Increasing productivity and reducing errors through usability analysis: a case study and recommendations. 
  • Infobuttons at Intermountain Healthcare: utilization and infrastructure. 
  • Information-theoretic CAD system in mammography: entropy-based indexing for computational efficiency and robust performance. 
  • Infrared imaging of trauma patients for detection of acute compartment syndrome of the leg. 
  • Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline. 
  • Initial clinical assessment of CT-MRI image fusion software in localization of the prostate for 3D conformal radiation therapy. 
  • Instructional PowerPoint presentations for cutaneous wound healing and tissue response to sutures. 
  • Instrumentation for multi-modal spectroscopic diagnosis of epithelial dysplasia. 
  • Integrated radio-frequency/wireless coil design for simultaneous MR image acquisition and wireless communication. 
  • Integrating technology into palliative care research. 
  • Integration of clinical decision support with on-line encounter documentation for well child care at the point of care. 
  • Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. 
  • Interpretation of electron density maps. 
  • Introduction of the Tools for Economic Analysis of Patient Management Interventions in Heart Failure Costing Tool: a user-friendly spreadsheet program to estimate costs of providing patient-centered interventions. 
  • Invasive hemodynamic evaluation in patients with mechanical aortic valves. 
  • Investigation of the support vector machine algorithm to predict lung radiation-induced pneumonitis. 
  • Investigations into the feasibility of optical-CT 3D dosimetry with minimal use of refractively matched fluids. 
  • Iodine quantification using dual-energy multidetector computed tomography imaging: phantom study assessing the impact of iterative reconstruction schemes and patient habitus on accuracy. 
  • Iterative aperture mask design in phase space using a rank constraint. 
  • KAT: a flexible XML-based knowledge authoring environment. 
  • KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program. 
  • Kernel Principal Component analysis through time for voice disorder classification. 
  • Kernel canonical correlation analysis for assessing gene-gene interactions and application to ovarian cancer. 
  • Knowledge discovery from structured mammography reports using inductive logic programming. 
  • LabKey Server NAb: a tool for analyzing, visualizing and sharing results from neutralizing antibody assays. 
  • Large-scale, three-dimensional tissue cytometry of the human kidney: a complete and accessible pipeline. 
  • Lateral and axial measurement differences between spectral-domain optical coherence tomography systems. 
  • Lateral lamella of the cribriform plate: software-enabled computed tomographic analysis and its clinical relevance in skull base surgery. 
  • Lessons on pattern formation from planet WATOR. 
  • Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells. 
  • Life after the screen: making sense of many P-values. 
  • Likelihood ratios, sensitivity, and specificity values can be back-calculated when the odds ratios are known. 
  • Limits in the detection of m6A changes using MeRIP/m6A-seq. 
  • Local encoding of computationally designed enzyme activity. 
  • Low-dose spiral CT: application to surface-rendered three-dimensional imaging of central airways. 
  • Luminance and contrast performance of liquid crystal displays for mammographic applications. 
  • MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome. 
  • MIN1PIPE: A Miniscope 1-Photon-Based Calcium Imaging Signal Extraction Pipeline. 
  • MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. 
  • MPDA: microarray pooled DNA analyzer. 
  • MSIseq: Software for Assessing Microsatellite Instability from Catalogs of Somatic Mutations. 
  • Managing clinical research data: software tools for hypothesis exploration. 
  • Managing research data with self-documenting files. 
  • Mapping and characterization of structural variation in 17,795 human genomes. 
  • Mapping strategies for multiple linked markers. 
  • Measurement of boundaries using a digitizer tablet. 
  • Measurement of macular fractal dimension using a computer-assisted program. 
  • Measuring similarity between dynamic ensembles of biomolecules. 
  • Medical physics 3.0 versus 1.0: A case study in digital radiography quality control. 
  • Meta-analysis of studies with bivariate binary outcomes: a marginal beta-binomial model approach. 
  • Metabomxtr: an R package for mixture-model analysis of non-targeted metabolomics data. 
  • Methodological issues for building item banks and computerized adaptive scales. 
  • Methods for transferring patient and plan data between radiotherapy treatment planning systems. 
  • Methods for using narrative text from injury reports to identify factors contributing to construction injury. 
  • Minimizing pulling geometry errors in atomic force microscope single molecule force spectroscopy. 
  • Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS). 
  • Mining terabytes of submillimeter-resolution ECoG datasets for neurophysiologic biomarkers. 
  • Mis-mappings between a producer's quantitative test codes and LOINC codes and an algorithm for correcting them. 
  • Mismodeled purines: implicit alternates and hidden Hoogsteens. 
  • Model of creation and evolution of stable electropores for DNA delivery. 
  • Modeling and superposition of multiple protein structures using affine transformations: analysis of the globins. 
  • Modeling biological systems using Dynetica--a simulator of dynamic networks. 
  • Modeling end-users' acceptance of a knowledge authoring tool. 
  • Modeling transcranial magnetic stimulation coil with magnetic cores. 
  • Modeling vectorcardiograms based on left ventricle papillary muscle position. 
  • Modelling covariance structure in the analysis of repeated measures data. 
  • MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. 
  • MolProbity: all-atom structure validation for macromolecular crystallography. 
  • Multi-system verification of registrations for image-guided radiotherapy in clinical trials. 
  • Multiple, conserved cryptic recombination signals in VH gene segments: detection of cleavage products only in pro B cells. 
  • Multiscale lens design. 
  • Multisphere phantom and analysis algorithm for PET image quality assessment. 
  • Multivariable prognostic models: issues in developing models, evaluating assumptions and adequacy, and measuring and reducing errors. 
  • Multivariate Curve Resolution for Signal Isolation from Fast-Scan Cyclic Voltammetric Data. 
  • NIfTI-MRS: A standard data format for magnetic resonance spectroscopy. 
  • NeXML: rich, extensible, and verifiable representation of comparative data and metadata. 
  • Neptune: an environment for the delivery of genomic medicine. 
  • Neural network analysis of quantitative histological factors to predict pathological stage in clinical stage I nonseminomatous testicular cancer. 
  • New techniques for DNA sequence classification. 
  • New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink "waters," and NGL Viewer to recapture online 3D graphics. 
  • Next generation multilocus sequence typing (NGMLST) and the analytical software program MLSTEZ enable efficient, cost-effective, high-throughput, multilocus sequencing typing. 
  • No association or linkage between an intronic polymorphism of presenilin-1 and sporadic or late-onset familial Alzheimer disease. 
  • Nonlinear phenomena in the vocalizations of North Atlantic right whales (Eubalaena glacialis) and killer whales (Orcinus orca). 
  • Normobaric hypoxia training: the effects of breathing-gas flow rate on symptoms. 
  • Novel anterior-chamber angle measurements by high-definition optical coherence tomography using the Schwalbe line as the landmark. 
  • Novel methodology for echocardiographic quantification of cardiac shape. 
  • Novel software strategy for glaucoma diagnosis: asymmetry analysis of retinal thickness. 
  • Nuclear quantum effects on an enzyme-catalyzed reaction with reaction path potential: proton transfer in triosephosphate isomerase. 
  • ORIGA(-light): an online retinal fundus image database for glaucoma analysis and research. 
  • OSPREY: protein design with ensembles, flexibility, and provable algorithms. 
  • Object technology: raising the standards for healthcare information systems. 
  • OligoCalc: an online oligonucleotide properties calculator. 
  • On the feasibility of optical-CT imaging in media of different refractive index. 
  • On the feasibility of polyurethane based 3D dosimeters with optical CT for dosimetric verification of low energy photon brachytherapy seeds. 
  • On the use of trajectory log files for machine & patient specific QA. 
  • Open source software for automatic detection of cone photoreceptors in adaptive optics ophthalmoscopy using convolutional neural networks. 
  • Open source tools and toolkits for bioinformatics: significance, and where are we? 
  • Open window: when easily identifiable genomes and traits are in the public domain. 
  • Opening the Duke electronic health record to apps: Implementing SMART on FHIR. 
  • Optimized mixed Markov models for motif identification. 
  • Optimized temporal pattern of brain stimulation designed by computational evolution. 
  • Ordered-subsets linkage analysis detects novel Alzheimer disease loci on chromosomes 2q34 and 15q22. 
  • Organ-based dose current modulation and thyroid shields: techniques of radiation dose reduction for neck CT. 
  • OrthoClusterDB: an online platform for synteny blocks. 
  • Outlier detection for multi-network data. 
  • Over-scanning in chest CT: Comparison of practice among six hospitals and its impact on radiation dose. 
  • PR-CALC: a program for the reconstruction of NMR spectra from projections. 
  • Palo: spatially aware color palette optimization for single-cell and spatial data. 
  • Parallel Multi-Omics in High-Risk Subjects for the Identification of Integrated Biomarker Signatures of Type 1 Diabetes. 
  • Parameter optimization of a computer-aided diagnosis scheme for the segmentation of microcalcification clusters in mammograms. 
  • Pathway analysis using random forests classification and regression. 
  • Patterns of variation within self-incompatibility loci. 
  • Pedigree generation for analysis of genetic linkage and association. 
  • Performance comparison of aperture codes for multimodal, multiplex spectroscopy. 
  • Performance of four computer-based diagnostic systems. 
  • Peripapillary choroidal thickness assessed using automated choroidal segmentation software in an Asian population. 
  • Permanently implantable diagnostic computerized devices: where is the regulatory rar? 
  • Pharmacokinetic model-driven infusion of fentanyl: assessment of accuracy. 
  • Phase aberration correction in two dimensions using a deformable array transducer. 
  • Phenex: ontological annotation of phenotypic diversity. 
  • Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes. 
  • Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools. 
  • Phylogenetic targeting of research effort in evolutionary biology. 
  • Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. 
  • Physiologically-Based Pharmacokinetic Modeling of Fluconazole Using Plasma and Cerebrospinal Fluid Samples From Preterm and Term Infants. 
  • Pitfalls in programming: The HV and VH intervals in his bundle pacing. 
  • Podcasting: making waves in millennial education. 
  • Point/Counterpoint. Universal implementation of automated treatment planning software will be detrimental to future generations of trainees. 
  • Polarized Fluorescence Microscopy to Study Cytoskeleton Assembly and Organization in Live Cells. 
  • Polymorphisms of CAK genes and risk for lung cancer: a case-control study in Chinese population. 
  • Poor drug distribution as a possible explanation for the results of the PRECISE trial. 
  • Population Pharmacokinetics and Exploratory Pharmacodynamics of Lorazepam in Pediatric Status Epilepticus. 
  • Postmortem validation of the automated coronary analysis (ACA) software package. 
  • Potential for expanded power in linkage studies using the ALLEGRO and MERLIN software programs. 
  • Power and sample size calculations for SNP association studies with censored time-to-event outcomes. 
  • Practical approach to determine sample size for building logistic prediction models using high-throughput data. 
  • Precise mapping of recombination breakpoints suggests a common parent of two BC recombinant HIV type 1 strains circulating in China. 
  • Predicting gene structure changes resulting from genetic variants via exon definition features. 
  • Predicting the need for laser treatment in retinopathy of prematurity using computer-assisted quantitative vascular analysis. 
  • Predictive Utility of Marketed Volumetric Software Tools in Subjects at Risk for Alzheimer Disease: Do Regions Outside the Hippocampus Matter? 
  • Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. 
  • Primer3--new capabilities and interfaces. 
  • PrimerZ: streamlined primer design for promoters, exons and human SNPs. 
  • Probabilities of Unranked and Ranked Anomaly Zones under Birth-Death Models. 
  • Progressive Cactus is a multiple-genome aligner for the thousand-genome era. 
  • Projected t-SNE for batch correction. 
  • Promoter prediction on a genomic scale--the Adh experience. 
  • Propagation of excitation in idealized anisotropic two-dimensional tissue. 
  • Prophage Hunter: an integrative hunting tool for active prophages. 
  • Proposal for fulfilling strategic objectives of the U.S. Roadmap for national action on clinical decision support through a service-oriented architecture leveraging HL7 services. 
  • Prospective validation of a prediction tool for identifying patients at high risk for chemotherapy-induced nausea and vomiting. 
  • Prostate Cancer Detection Rate of Freehand versus 3-Dimensional Template Mapping Biopsy Using a Magnetic Resonance Imaging-Ultrasound Fusion Device in Biopsy Naïve Men. 
  • Prostate biopsy protocols: 3D visualization-based evaluation and clinical correlation. 
  • Protein fabrication automation. 
  • Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data. 
  • Protein-Protein Docking Benchmark 2.0: an update. 
  • Protein-protein docking: overview and performance analysis. 
  • Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT. 
  • Prototype for real-time adaptive sampling using the fan algorithm. 
  • Puzzle pieces defined: locating common packing units in tertiary protein contacts. 
  • QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants. 
  • Quadratic string method for determining the minimum-energy path based on multiobjective optimization. 
  • Quality assurance and training procedures for computer-aided detection and diagnosis systems in clinical use. 
  • Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform. 
  • Quantification of intravenous contrast-enhanced Doppler power spectrum in the rabbit carotid artery. 
  • Quantitation of corneal neovascularization using computerized image analysis. 
  • Quantitative CT: technique dependence of volume estimation on pulmonary nodules. 
  • Quantitative and qualitative coronary angiographic analysis: review of methods, utility, and limitations. 
  • Quantitative assessment of the time course of infarct signal intensity on diffusion-weighted images. 
  • Quantitative mouse brain phenotyping based on single and multispectral MR protocols. 
  • Quantitative neuromorphometry using magnetic resonance histology. 
  • Quantitative spatial analysis of transcripts in multinucleate cells using single-molecule FISH. 
  • Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface. 
  • R package to estimate intracluster correlation coefficient with confidence interval for binary data. 
  • REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants. 
  • RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone. 
  • Racial Differences of Pigmentation in the Human Vestibular Organs. 
  • Rapid Golgi analysis method for efficient and unbiased classification of dendritic spines. 
  • Rapid determination of protein folds using residual dipolar couplings. 
  • Real-time fMRI paradigm control, physiology, and behavior combined with near real-time statistical analysis. 
  • Real-time graphics display of mass variation or elemental concentration during electron beam microanalysis using a general purpose computer. 
  • Real-time quantitative elemental analysis and mapping: microchemical imaging in cell physiology. 
  • Rebuttal to Hasan and Pedraza in comments and controversies: "Improving the reliability of manual and automated methods for hippocampal and amygdala volume measurements". 
  • RecDraw: a software package for the representation of HIV-1 recombinant structures. 
  • Recommendations towards standards for quantitative MRI (qMRI) and outstanding needs. 
  • Redefining the Autonomic Nerve Distribution of the Bladder Using 3-Dimensional Image Reconstruction. 
  • Redesigned HIV antibodies exhibit enhanced neutralizing potency and breadth. 
  • Reformatted images improve the detection rate of acute traumatic subdural hematomas on brain CT compared with axial images alone. 
  • Registration of three-dimensional magnetic resonance and radionuclide skeletal images. 
  • Registry. 
  • Regression models in clinical studies: determining relationships between predictors and response. 
  • Relaxed constraint and evolutionary rate variation between basic helix-loop-helix floral anthocyanin regulators in Ipomoea. 
  • Reliability analysis framework for computer-assisted medical decision systems. 
  • Reliability of a preliminary 3-D pain mapping program. 
  • Remote programming of cochlear implants: a telecommunications model. 
  • Repeat polymorphisms within gene regions: phenotypic and evolutionary implications. 
  • Report and abstracts of the sixth international workshop on human chromosome 1 mapping 2000. Iowa City, Iowa, USA. 30 September-3 October 2000. 
  • Report of AAPM Task Group 162: Software for planar image quality metrology. 
  • Reproducibility of the retinal vascular response to flicker light in Asians. 
  • Reproducible research in medical imaging. 
  • Respiratory system simulations and modeling. 
  • Responses to the 10 most frequently asked questions about perfusion CT. 
  • Retinal artery and venular caliber grading: a semi-automated evaluation tool. 
  • Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays. 
  • Right Ventricular Longitudinal Strain Reproducibility Using Vendor-Dependent and Vendor-Independent Software. 
  • Robust regression analysis of copy number variation data based on a univariate score. 
  • Round Trip: An Automated Pipeline for Experimental Design, Execution, and Analysis. 
  • SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data. 
  • SNPpy--database management for SNP data from genome wide association studies. 
  • SNPselector: a web tool for selecting SNPs for genetic association studies. 
  • SNiPA: an interactive, genetic variant-centered annotation browser. 
  • SVA: software for annotating and visualizing sequenced human genomes. 
  • Say it with multimedia: new presentation tools for the radiologist. 
  • Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. 
  • Scanning fiber angle-resolved low coherence interferometry. 
  • Scientific benchmarks for guiding macromolecular energy function improvement. 
  • Searching the literature is not for the faint of heart! 
  • Secondary prevention risk interventions via telemedicine and tailored patient education (SPRITE): a randomized trial to improve postmyocardial infarction management. 
  • Secure transmission of urologic images and records over the Internet. 
  • Secured medical imaging over the Internet. 
  • Segment and fit thresholding: a new method for image analysis applied to microarray and immunofluorescence data. 
  • Semiautomated segmentation of blood vessels using ellipse-overlap criteria: method and comparison to manual editing. 
  • Semiautomatic Segmentation of Rim Area Focal Hyperautofluorescence Predicts Progression of Geographic Atrophy Due to Dry Age-Related Macular Degeneration. 
  • Sensitivity of 3D Dose Verification to Multileaf Collimator Misalignments in Stereotactic Body Radiation Therapy of Spinal Tumor. 
  • SeqSIMLA2: simulating correlated quantitative traits accounting for shared environmental effects in user-specified pedigree structure. 
  • Sequential sib-pair and association studies to detect genes in quantitative traits. 
  • Serial dilution curve: a new method for analysis of reverse phase protein array data. 
  • SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events. 
  • Simplified skipped phase encoding and edge deghosting (SPEED) for imaging sparse objects with applications to MRA. 
  • Simultaneous multichannel cardiac mapping systems. 
  • Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics. 
  • Smooth nonparametric maximum likelihood estimation for population pharmacokinetics, with application to quinidine. 
  • Smooth operator: The effects of different 3D mesh retriangulation protocols on the computation of Dirichlet normal energy. 
  • Software for lattice light-sheet imaging of FRET biosensors, illustrated with a new Rap1 biosensor. 
  • Solid organ transplantation at the National Institutes of Health: development of a research-based transplantation practice. 
  • Some general estimation methods for nonlinear mixed-effects models. 
  • SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization. 
  • Spectroscopic diagnosis of esophageal cancer: new classification model, improved measurement system. 
  • SplicerAV: a tool for mining microarray expression data for changes in RNA processing. 
  • Statistical Code for Clinical Research Papers. 
  • Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser. 
  • Statistical considerations for analysis of microarray experiments. 
  • Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays. 
  • Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events. 
  • Stratification-score matching improves correction for confounding by population stratification in case-control association studies. 
  • Strong means slow: dynamic contributions to the bulk mechanical properties of supramolecular networks. 
  • Structural analysis of neural circuits using the theory of directed graphs. 
  • Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits. 
  • Synthetic Biology: Caught Between Property Rights, the Public Domain, and the Commons 
  • Systematic gene mapping in man: data management considerations. 
  • T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life. 
  • Targeting telestroke: benchmarking time performance in telestroke consultations. 
  • Technical note: Comparing dental topography software using platyrrhine molars. 
  • Technical note: rapid prototyping of 3D grid arrays for image guided therapy quality assurance. 
  • Technology-based cognitive training and rehabilitation interventions for individuals with mild cognitive impairment: a systematic review. 
  • Testing Rare-Variant Association without Calling Genotypes Allows for Systematic Differences in Sequencing between Cases and Controls. 
  • Testing gene-treatment interactions in pharmacogenetic studies. 
  • Testing morphological concepts of orders of pleurocarpous mosses (Bryophyta) using phylogenetic reconstructions based on TRNL-TRNF and RPS4 sequences. 
  • Testing the optimal defense hypothesis in nature: Variation for glucosinolate profiles within plants. 
  • Text data extraction for a prospective, research-focused data mart: implementation and validation. 
  • The 2013 Novitski Prize: Jonathan Pritchard. 
  • The Association of a classical left bundle Branch Block Contraction Pattern by vendor-independent strain echocardiography and outcome after cardiac resynchronization therapy. 
  • The B56 family of protein phosphatase 2A (PP2A) regulatory subunits encodes differentiation-induced phosphoproteins that target PP2A to both nucleus and cytoplasm. 
  • The BLUEPRINT Data Analysis Portal. 
  • The Bioperl toolkit: Perl modules for the life sciences. 
  • The DEDUCE Guided Query tool: providing simplified access to clinical data for research and quality improvement. 
  • The ECG Belt for CRT response trial: Design and clinical protocol. 
  • The Gene Ontology (GO) database and informatics resource. 
  • The Gene Ontology (GO) project in 2006. 
  • The Gene Ontology in 2010: extensions and refinements. 
  • The Household Registration System: computer software for the rapid dissemination of demographic surveillance systems. 
  • The LabFlow system for workflow management in large scale biology research laboratories. 
  • The Need for Targeted Labeling of Machine Learning-Based Software as a Medical Device. 
  • The Phenix software for automated determination of macromolecular structures. 
  • The Reference Image Database to Evaluate Response to therapy in lung cancer (RIDER) project: a resource for the development of change-analysis software. 
  • The SSV Evaluation System: A Tool to Prioritize Short Structural Variants for Studies of Possible Regulatory and Causal Variants. 
  • The U.S. Food and Drug Administration's Mini-Sentinel program: status and direction. 
  • The US National Comorbidity Survey: overview and future directions. 
  • The backrub motion: how protein backbone shrugs when a sidechain dances. 
  • The bootstrap and identification of prognostic factors via Cox's proportional hazards regression model. 
  • The cancer translational research informatics platform. 
  • The clinical document architecture and the continuity of care record: a critical analysis. 
  • The effect of ambient pressure on well chamber response: Monte Carlo calculated results for the HDR 1000 plus. 
  • The effect of respiratory motion variability and tumor size on the accuracy of average intensity projection from four-dimensional computed tomography: an investigation based on dynamic MRI. 
  • The evaluation of screening methods to identify medically unnecessary hospital stay for patients with pneumonia. 
  • The future of endoscopy simulation: a Duke perspective. 
  • The genetics of hybrid male sterility between the allopatric species pair Drosophila persimilis and D. pseudoobscura bogotana: dominant sterility alleles in collinear autosomal regions. 
  • The hazard of software updates to clinical workstations: a natural experiment. 
  • The importance of residue-level filtering and the Top2018 best-parts dataset of high-quality protein residues. 
  • The integrity of a cholesterol-binding pocket in Niemann-Pick C2 protein is necessary to control lysosome cholesterol levels. 
  • The kinemage: a tool for scientific communication. 
  • The optimisation of wedge filters in radiotherapy of the prostate. 
  • The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models. 
  • The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI. 
  • The role of standards in creating a health information infrastructure. 
  • The small subunit of the mammalian mitochondrial ribosome. Identification of the full complement of ribosomal proteins present. 
  • The smallest membrane anchoring subunit (QPs3) of bovine heart mitochondrial succinate-ubiquinone reductase. Cloning, sequencing, topology, and Q-binding domain. 
  • The time course of segmentation and cue-selectivity in the human visual cortex. 
  • Theoretical and practical advances in genome halving. 
  • Thinking outside the gate: single-cell assessments in multiple dimensions. 
  • Three-dimensional computed tomographic analysis of the relationship between the arcuate eminence and the superior semicircular canal. 
  • Toward a standard for the evaluation of PET-Auto-Segmentation methods following the recommendations of AAPM task group No. 211: Requirements and implementation. 
  • Towards an integrated ecosystem of R packages for the analysis of population genetic data. 
  • Tracking procedure outcomes using Epic SmartText and SmartData Elements following minor dermatologic procedures in the ambulatory setting. 
  • Training software using virtual-reality technology and pre-calculated effective dose data. 
  • Transcriptional pausing in a region important for plasmid NR1 replication control. 
  • Triangulating differential nonresponse by race in a telephone survey. 
  • Trust but verify: the introduction of plagiarism detection software. 
  • Ultrasonic Shear Wave Elasticity Imaging Sequencing and Data Processing Using a Verasonics Research Scanner. 
  • Usability and Acceptability of the QDACT-PC, an Electronic Point-of-Care System for Standardized Quality Monitoring in Palliative Care. 
  • Usability evaluation at the point-of-care: a method to identify user information needs in CPOE applications. 
  • Use of Machine Learning-Based Software for the Screening of Thyroid Cytopathology Whole Slide Images. 
  • Use of MindMapper software for research domain mapping. 
  • Use of a non-monetary incentive to improve physician responses to a mail survey. 
  • Use of an electronic patient-reported outcome measurement system to improve distress management in oncology. 
  • Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. 
  • Use of normalized prediction distribution errors for assessing population physiologically-based pharmacokinetic model adequacy. 
  • Use of patient registries and administrative datasets for the study of pediatric cancer. 
  • User Experience Evaluation of a Smoking Cessation App in People With Serious Mental Illness. 
  • Using DNase digestion data to accurately identify transcription factor binding sites. 
  • Using a wiki in nursing education and research. 
  • Using bibliographic software to appraise and code data in educational systematic review research. 
  • Using the bioconductor GeneAnswers package to interpret gene lists. 
  • Validity of a new optic disc grading software for use in clinical and epidemiological research. 
  • Variability in the analysis of a single neuroimaging dataset by many teams. 
  • Variability of global left ventricular deformation analysis using vendor dependent and independent two-dimensional speckle-tracking software in adults. 
  • VarioWatch: providing large-scale and comprehensive annotations on human genomic variants in the next generation sequencing era. 
  • Verification of a novel method for tube voltage constancy measurement of orthovoltage x-ray irradiators. 
  • Vessel noise affects beaked whale behavior: results of a dedicated acoustic response study. 
  • Virtual reality in surgical education. 
  • Virtual septoplasty: a method to predict surgical outcomes for patients with nasal airway obstruction. 
  • VirtualDose: a software for reporting organ doses from CT for adult and pediatric patients. 
  • Visual annotation of the gene database. 
  • Visual presentation as a welcome alternative to textual presentation of gene annotation information. 
  • Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. 
  • Volumetric quantification of lung nodules in CT with iterative reconstruction (ASiR and MBIR). 
  • WASABI: an automated sequence processing system for multigene phylogenies. 
  • WebGLORE: a web service for Grid LOgistic REgression. 
  • What is segmented sleep? Actigraphy field validation for daytime sleep and nighttime wake. 
  • What works. Surgeons generate "clean bills" from the point of care. 
  • Whole-brain activity mapping onto a zebrafish brain atlas. 
  • WormSizer: high-throughput analysis of nematode size and shape. 
  • Wound healing PowerPoint presentations for introductory biomaterials education. 
  • X-ray structure of cytidine-5'-O-dimethylphosphate. Novel stacking between the ribosyl O(2') hydroxyl oxygen atom and the base. 
  • Y2K: effects on pacemaker and implantable defibrillator programmers. 
  • ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. 
  • ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. 
  • [A system for computer visualization of excitation wave propagation in the myocardium] 
  • [Computer programs SAN and EPID: family analysis and epidemiology of multifactorial diseases] 
  • [Current perspectives of orthogonal polarization spectral imaging in plastic surgery]. 
  • apex: phylogenetics with multiple genes. 
  • bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens. 
  • cis element/transcription factor analysis (cis/TF): a method for discovering transcription factor/cis element relationships. 
  • dictyBase, the model organism database for Dictyostelium discoideum. 
  • eSource-Enabled vs. Traditional Clinical Trial Data Collection Methods: A Site-Level Economic Analysis. 
  • hemaClass.org: Online One-By-One Microarray Normalization and Classification of Hematological Cancers for Precision Medicine. 
  • lumi: a pipeline for processing Illumina microarray. 
  • maplet: an extensible R toolbox for modular and reproducible metabolomics pipelines. 
  • meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays. 
  • minotaur: A platform for the analysis and visualization of multivariate results from genome scans with R Shiny. 
  • permGPU: Using graphics processing units in RNA microarray association studies. 
  • rqt: an R package for gene-level meta-analysis. 
  • scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data. 
• 

  Keywords of People

  • Craciunescu, Oana, Professor of Radiation Oncology, Radiation Oncology
  • Dodge, Kenneth A., William McDougall Distinguished Professor of Public Policy Studies, Duke Science & Society
  • Farsiu, Sina, Professor in the Department of Biomedical Engineering, Electrical and Computer Engineering
  • Ferrari, Guido, Professor in Surgery, Molecular Genetics and Microbiology
  • Gordan, Raluca Mihaela, Associate Professor in Biostatistics & Bioinformatics, Computer Science
  • Grambow, Steven C., Associate Professor of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics
  • Hartemink, Alexander J., Professor in the Department of Computer Science, Biology
  • Johnson, G. Allan, Charles E. Putman University Distinguished Professor of Radiology, Biomedical Engineering
  • Katz, David F., Nello L. Teer, Jr. Distinguished Professor of Biomedical Engineering, in the Edmund T. Pratt, Jr. School of Engineering, Biomedical Engineering
  • Kibbe, Warren Alden, Professor in Biostatistics & Bioinformatics, Biostatistics & Bioinformatics
  • Lee, Walter T, Professor of Head and Neck Surgery & Communication Sciences, Radiation Oncology
  • Muir, Kelly Walton, Associate Professor of Ophthalmology, Ophthalmology, Glaucoma
  • Pang, Herbert, Adjunct Assistant Professor in the Department of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics
  • Richardson, David C., Professor Emeritus of Biochemistry, Biochemistry
  • Sampson, John Howard, Robert H., M.D. and Gloria Wilkins Professor of Neurosurgery, in the School of Medicine, Biomedical Engineering
  • Segars, William Paul, Associate Professor in Radiology, Radiology
  • Starmer, Charles Franklin, Professor Emeritus of Computer Science, Computer Science
  • Turkington, Timothy Garvey, Associate Professor in Radiology, Radiology