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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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OCplus Resource Report Resource Website 1+ mentions |
OCplus (RRID:SCR_001342) | OCplus | software resource | Software package that allows to characterize the operating characteristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes). | differential expression, microarray, multiple comparison |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:16368770 | Free, Available for download, Freely available | OMICS_01999 | SCR_001342 | Ocplus - Operating characteristics plus sample size and local fdr for microarray experiments | 2026-02-07 02:05:30 | 1 | ||||||
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bridge Resource Report Resource Website 100+ mentions |
bridge (RRID:SCR_001343) | bridge | software resource | Software package to test for differentially expressed genes with microarray data. It can be used with both cDNA microarrays or Affymetrix chip. The packge fits a robust Bayesian hierarchical model for testing for differential expression. Outliers are modeled explicitly using a $t$-distribution. The model includes an exchangeable prior for the variances which allow different variances for the genes but still shrink extreme empirical variances. The model can be used for testing for differentially expressed genes among multiple samples, and can distinguish between the different possible patterns of differential expression when there are three or more samples. Parameter estimation is carried out using a novel version of Markov Chain Monte Carlo that is appropriate when the model puts mass on subspaces of the full parameter space. | cdna microarray, affymetrix chip, differential expression, microarray, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:16542223 | Free, Available for download, Freely available | OMICS_01996, biotools:bridge | http://www.bioconductor.org/packages/release/bioc/html/bridge.html | SCR_001343 | Bayesian Robust Inference for Differential Gene Expression | 2026-02-07 02:05:31 | 154 | |||||
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CALIB Resource Report Resource Website 100+ mentions |
CALIB (RRID:SCR_001338) | CALIB | software resource | Software package that contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estimated from external control spikes. | microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:17485432 | Free, Available for download, Freely available | OMICS_02003 | http://www.bioconductor.org/packages/release/bioc/html/CALIB.html | SCR_001338 | 2026-02-07 02:05:36 | 131 | ||||||
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aroma.light Resource Report Resource Website 1+ mentions |
aroma.light (RRID:SCR_001312) | aroma.light | software resource | Light-weight software package for normalization and visualization of microarray data using only basic R data types. Software can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes. | infrastructure, microarray, preprocessing, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
DOI:10.1186/1471-2105-11-245 | Free, Available for download, Freely available | OMICS_01998, biotools:aroma.light | https://bio.tools/aroma.light https://sources.debian.org/src/r-bioc-aroma.light/ |
SCR_001312 | 2026-02-07 02:05:29 | 1 | ||||||
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OLIN Resource Report Resource Website 10+ mentions |
OLIN (RRID:SCR_001304) | OLIN | software resource | Software functions for normalization of two-color microarrays by optimised local regression and for detection of artifacts in microarray data. | r, normalization, visualization, quality control, two-channel, microarray, preprocessing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Humboldt University of Berlin; Berlin; Germany has parent organization: Bioconductor |
PMID:15585527 | Free, Available for download, Freely available | biotools:olin, OMICS_02029 | http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN/index.html | SCR_001304 | Optimised Local Intensity-dependent Normalisation | 2026-02-07 02:05:35 | 18 | |||||
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qcmetrics Resource Report Resource Website 1+ mentions |
qcmetrics (RRID:SCR_001303) | qcmetrics | software resource | Software package that provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats. | mass spectrometry, microarray, proteomics, quality control, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02032, biotools:qcmetrics, BioTools:qcmetrics | https://bio.tools/qcmetrics https://bio.tools/qcmetrics https://bio.tools/qcmetrics |
SCR_001303 | qcmetrics - A Framework for Quality Control | 2026-02-07 02:05:30 | 1 | ||||||
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DEXUS Resource Report Resource Website 1+ mentions |
DEXUS (RRID:SCR_001309) | DEXUS | software resource | Software package that identifies differentially expressed genes in RNA-Seq data under all possible study designs such as studies without replicates, without sample groups, and with unknown conditions. It works also for known conditions, for example for RNA-Seq data with two or multiple conditions. RNA-Seq read count data can be provided both by the S4 class Count Data Set and by read count matrices. Differentially expressed transcripts can be visualized by heatmaps, in which unknown conditions, replicates, and samples groups are also indicated. This software is fast since the core algorithm is written in C. For very large data sets, a parallel version of DEXUS is provided in this package. DEXUS is a statistical model that is selected in a Bayesian framework by an EM algorithm. It does not need replicates to detect differentially expressed transcripts, since the replicates (or conditions) are estimated by the EM method for each transcript. The method provides an informative/non-informative value to extract differentially expressed transcripts at a desired significance level or power. | classification, differential expression, gene expression, hapmap, quality control, rna-seq, sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24049071 | Free, Available for download, Freely available | biotools:dexus, OMICS_02024 | http://www.bioconductor.org/packages/release/bioc/html/dexus.html | SCR_001309 | DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates | 2026-02-07 02:05:30 | 1 | |||||
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James Cook University; Townsville; Australia Resource Report Resource Website 1+ mentions |
James Cook University; Townsville; Australia (RRID:SCR_001420) | JCU | university | Public university in Townsville, Australia that functions as a research and teaching institution. Some well-known divisions of the university include the division of Tropical Environments and Societies, Tropical Health and Medicine, and Research and Innovation. | public, university, teaching, research, tropical health, environment, medicine | is parent organization of: Australian ResearCH Enabling enviRonment | Free, Freely Available | ISNI:0000 0004 0474 1797, nlx_62328, Wikidata:Q536512, Crossref funder ID:501100008451, grid.1011.1 | https://ror.org/04gsp2c11 | SCR_001420 | James Cook University | 2026-02-07 02:05:37 | 5 | ||||||
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Computer Integrated Systems for Microscopy and Manipulation Resource Report Resource Website 1+ mentions |
Computer Integrated Systems for Microscopy and Manipulation (RRID:SCR_001413) | CISMM | training resource | Biomedical technology research center that develops force technologies applicable over a wide range of biological settings, from the single molecule to the tissue, with integrated systems that orchestrate facile instrument control, multimodal imaging, and analysis through visualization and modeling. The Force Microscope Technologies Core designs instruments in an area of science where there are unusual opportunities: the measurement of forces and the integration with optical microscopy. Force technologies play the obvious role of both measuring events in the sample and modifying the sample during the experiment. It is through the microscope that the force data is correlated with simultaneous 3D optical images. The force technology development includes the magnetic bead technology in the 3D Force Microscope project, Atomic Force Microscopy in the nanoManipulator project, and Control Software to drive the instrumentation. This core is focused on providing the physical capability to perform the experiments and probe structure/property correlations. The Ideal User Interfaces core makes the connection between the user and the instrument, the model building, and the data. This includes control systems that allow the user to move the bead inside the cell culture with a handheld pen and the visualization techniques to view the optical microscope data as a rendered 3D image collocated with the force data. Using data to create, change, and understand a model is the focus of the Advanced Model Fitting and Analysis core. The quantitative reduction of images to structural, shape, and velocity parameters is the goal of Image Analysis. The immediate understanding of correlations across image fields and between data sets in the challenge of Visualization. The power of combining the strength of a computer science graphics group with a microscopy technology group is most evident in the Graphics Hardware Acceleration project, which seeks to harness the speed of graphics processors for microscope data analysis and simulation. The Advanced Technology core pushes the boundaries of the Human Computer Interface through the investigation of improved techniques for the interaction of users with virtual environments, the real time lighting of virtual settings, and the enabling of multi-person collaboration. These techniques are validated and evaluated through physiological measures in virtual environments effectiveness evaluation studies. | microscope, visual analytics, image analysis, biomedical, bioinstrumatics, scanning electron microscope, light microscope, microscopy | has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA | Thrombosis, Lung disease, Cancer | NIBIB 5-P41-EB002025 | Freely Available | nlx_152648 | http://cismm.cs.unc.edu/ | SCR_001413 | UNC Chapel Hill Computer Integrated Systems for Microscopy and Manipulation | 2026-02-07 02:05:32 | 8 | ||||
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Center for Biomedical OCT Research Resource Report Resource Website 1+ mentions |
Center for Biomedical OCT Research (RRID:SCR_001418) | CBORT | training resource | Biomedical technology research center that pioneers and provides access to microscopic imaging instruments for biologic and clinical research. Optical coherence tomography (OCT) has evolved over the last two decades to become a standard of care for diagnostic ophthalmic imaging and is poised to make significant impact in the fields of cardiology and gastrointestinal endoscopy. Access to state-of-the-art instrumentation, however, has been limited to a relatively few research laboratories and the optimization of instruments for new biomedical applications has hindered the investigation of new opportunities. A major focus of CBORT will be to cultivate strategic research collaborations and respond to a pressing need for application-specific OCT instrumentation and hardware. | imaging, optical coherence tomography, microscope, catheter, endoscopy, near infrared fluorescence | has parent organization: Harvard Medical School; Massachusetts; USA | NIBIB P41EB015903 | Free, Freely Available | nlx_152640 | SCR_001418 | Center for Biomedical OCT Research and Translation | 2026-02-07 02:05:32 | 2 | ||||||
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BioMEMS Resource Center Resource Report Resource Website 1+ mentions |
BioMEMS Resource Center (RRID:SCR_001417) | BMRC | training resource | Biomedical technology research center that provides biomedical investigators with novel microsystems engineering tools for biological discovery, diagnostic, prognostic, and therapeutic applications. Thrust areas of interest are the development of novel living cell-based, lab-on-a-chip type devices for sorting blood cells, for high-throughput biochemistry in small volumes, and for studying cellular behavior in controlled microenvironments. | cell, tissue, microengineering, diagnostics, chip | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | NIBIB 5P41EB002503-12 | Free, Freely Available | nlx_152639 | SCR_001417 | Bio MicroElectroMechanical Systems (BioMEMS) Resource Center, Biomicroelectromechanical Systems (BioMEMS) Resource Center, BioMEMS, Bio MicroElectroMechanical Systems Resource Center | 2026-02-07 02:05:31 | 4 | ||||||
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CisGenome Resource Report Resource Website 50+ mentions |
CisGenome (RRID:SCR_001558) | data analysis tool | Integrated software tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis. | sequencing software, chip seq, downstream analysis, chip analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian works with: TileMap |
PMID:18978777 | Free, Available for download, Freely available | OMICS_00423, biotools:cisgenome | https://bio.tools/cisgenome | http://biogibbs.stanford.edu/~jihk/CisGenome/index.htm | SCR_001558 | CisGenome v2.0 | 2026-02-07 02:05:39 | 81 | |||||
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vsn Resource Report Resource Website 1+ mentions |
vsn (RRID:SCR_001459) | vsn | software resource | Software package that implements a method for normalizing microarray intensities, both between colours within array, and between arrays. The method uses a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references. The model incorporates data calibration (a.k.a. normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation. Differences between transformed intensities are analogous to normalized log-ratios. However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription. | microarray, preprocessing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: European Bioinformatics Institute |
Free, Available for download, Freely available | OMICS_01977, biotools:vsn | https://bio.tools/vsn | SCR_001459 | vsn - Variance stabilization and calibration for microarray data | 2026-02-07 02:05:32 | 5 | ||||||
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CytoSPADE Resource Report Resource Website 1+ mentions |
CytoSPADE (RRID:SCR_001457) | software resource | Cytoscape plugin that provides a high-performance implementation of an interface for the Spanning-tree Progression Analysis of Density-normalized Events (SPADE) algorithm for tree-based analysis and visualization of high-dimensional cytometry data. | plugin, mac os x, unix/linux, windows, c++, java, r |
uses: Cytoscape is listed by: OMICtools has parent organization: Stanford University; Stanford; California is a plug in for: Cytoscape |
PMID:22782546 | Free, Available for download, Freely available | OMICS_05644 | http://cytospade.org/ | SCR_001457 | CytoSPADE: Cytoscape-driven Spanning tree Progression of Density normalized Events, CytoSPADE Cytoscape Plugin for SPADE, Cytoscape-driven Spanning tree Progression of Density normalized Events | 2026-02-07 02:05:38 | 2 | ||||||
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BARI 2D Resource Report Resource Website 1+ mentions |
BARI 2D (RRID:SCR_001496) | BARI 2D, BARI-2D | clinical trial | A multicenter randomized clinical trial that aims to determine the best therapies for people with type 2 diabetes and moderately severe cardiovascular disease. 2368 participants were randomized at 49 sites in 6 countries. All subjects were given intensive medical therapy to control cholesterol and blood pressure and given counseling, if needed, to quit smoking and to lose weight. Beyond that, they compared whether prompt revascularization, either bypass surgery or angioplasty, e.g. stents, was more effective than medical therapy alone. At the same time, they also looked at which of two diabetes treatment strategies resulted in better outcomes����??insulin-providing versus insulin-sensitizing - that is, increasing the amount of insulin or making the insulin work better. Only patients with known type 2 diabetes and heart disease that could be treated appropriately with a revascularization OR medical therapy alone were eligible for the trial. Patients entered the study between January 2001 ����?? March 2005 and were followed for an average of five years. When a patient entered the study, physicians first decided whether that patient should receive stenting or bypass surgery. The patient then received their randomization assignment. All patients were treated in BARI 2D for both their diabetes and heart disease, as well as other risk factors that might effect those diseases, regardless of which group they were in. Diabetes-specific complications including retinopathy, nephropathy, neuropathy, and peripheral vascular disease were monitored regularly. Tests, blood samples, urine samples, and treatment cost data were obtained periodically through the trial and examined by experts at 7 central laboratories and other research partners. Experts on risk factors routinely oversaw treatments of all patients at 4 central management centers. A panel of independent experts reviewed data every six months to make sure that all patients were receiving safe care. | clinical, cholesterol, blood pressure, counseling, insulin, epidemiology, longitudinal, stenting, bypass surgery, standard-of-care study, standard-of-care, treatment, medication, outcome, medical cost, blood, urine, biomaterial supply resource |
is listed by: One Mind Biospecimen Bank Listing is listed by: NIDDK Information Network (dkNET) has parent organization: University of Pittsburgh; Pennsylvania; USA |
Type 2 diabetes, Cardiovascular disease, Heart attack, Stroke | NCRR 5M01RR000847-36 | PMID:23757426 PMID:23735723 PMID:23500245 PMID:23067918 PMID:23008442 PMID:22527794 PMID:22496082 PMID:21958742 |
Free, Freely available | nlx_152754 | SCR_001496 | Bypass Angioplasty Revascularization Investigation (BARI) 2 Diabetes, Bypass Angioplasty Revascularization Investigation 2 Diabetes | 2026-02-07 02:05:38 | 1 | ||||
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Juvenile Diabetes Research Foundation Resource Report Resource Website 50+ mentions |
Juvenile Diabetes Research Foundation (RRID:SCR_001522) | JDRF | institution | Global funder of type 1 diabetes (T1D) research that aims to progressively remove the impact of T1D from people's lives until a world without T1D is achieved. JDRF collaborates with a wide spectrum of partners and is the only organization with the scientific resources, regulatory influence, and a working plan to better treat, prevent, and eventually cure T1D. More than 80 percent of JDRF's expenditures directly support research and research-related education. In 2012 Forbes magazine named JDRF one of its five All-Star charities, citing the organization's efficiency and effectiveness. The organization awards research grants for laboratory and clinical investigations and sponsors a variety of career development and research training programs for new and established investigators. JDRF also sponsors international workshops and conferences for biomedical researchers. Individual chapters offer support groups and other activities for families affected by diabetes. | treatment, prevention, cure, research, education |
is listed by: NIDDK Information Network (dkNET) is affiliated with: Helmsley Cellular Research Hub is related to: JDRF Artificial Pancreas Project Consortium is related to: Kidney Health Initiative |
Type 1 diaberes, Diabetes | Free, Freely available | grid.429307.b, nlx_152841, Crossref funder ID: 100008871, Wikidata: Q6107958, ISNI: 0000 0004 0575 6413 | https://ror.org/00vqxjy61 | SCR_001522 | JDRF International, Juvenile Diabetes Research Foundation International | 2026-02-07 02:05:33 | 64 | |||||
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Multiple-Path Particle Dosimetry Model Resource Report Resource Website 10+ mentions |
Multiple-Path Particle Dosimetry Model (RRID:SCR_001486) | MPPD | software resource | Computational model that can be used for estimating human and rat airway particle dosimetry. The model is applicable to risk assessment, research, and education. The MPPD model calculates the deposition and clearance of monodisperse and polydisperse aerosols in the respiratory tracts of rats and human adults and children (deposition only) for particles ranging in size from ultrafine (0.01 micrometers) to coarse (20 micrometers). The models are based on single-path and multiple-path methods for tracking air flow and calculating aerosol deposition in the lung. The single-path method calculates deposition in a typical path per airway generation, while the multiple-path method calculates particle deposition in all airways of the lung and provides lobar-specific and airway-specific information. Within each airway, deposition is calculated using theoretically derived efficiencies for deposition by diffusion, sedimentation, and impaction within the airway or airway bifurcation. Filtration of aerosols by the nose and mouth is determined using empirical efficiency functions. The MPPD model includes calculations of particle clearance in the lung following deposition. | model, computational model, particle dosimetry, risk assessment, adult human, child, aerosol, deposition, clearance, lung | is related to: The Hamner Institute for Health Sciences: BMDExpress and The multiple-path particle dosimetry | PMID:8566482 | Free, Freely available | nlx_152744 | http://www.ara.com/products/mppd.htm | SCR_001486 | Multiple Path Particle Dosimetry Model | 2026-02-07 02:05:31 | 11 | |||||
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Jaeb Center for Health Research Resource Report Resource Website 1+ mentions |
Jaeb Center for Health Research (RRID:SCR_001513) | JCHR | institution | Freestanding, nonprofit coordinating center for multi-center clinical trials and epidemiologic research that focus on projects involving eye disorders or type 1 diabetes. | epidemiologic research, epidemiology, clinical, disease, clinical trial, eye |
is parent organization of: Diabetes Research in Children Network is parent organization of: Diabetic Retinopathy Clinical Research Network is parent organization of: JDRF Artificial Pancreas Project Consortium |
Type 1 diabetes, Multiple sclerosis, Eye disorder, Diabetes | Free, Freely available | ISNI: 0000 0004 0586 473X, nlx_152815, grid.414912.b | https://ror.org/04ezjnq35 | SCR_001513 | 2026-02-07 02:05:33 | 4 | ||||||
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WordPress Resource Report Resource Website 50+ mentions |
WordPress (RRID:SCR_001518) | software resource | Web software which helps users create a website or blog. WordPress software can be downloaded and installed with an appropriate web host and minimum requirements. There is also a service called WordPress.com which allows users to get started with a new and free WordPress-based blog in seconds, though it varies in several ways and is less flexible than the self-installed WordPress. An array of plugins and themes are available to further customize a site. | software application, web software, content management system |
is related to: Wordpress for Scientists is related to: Commons In A Box is related to: Code4Lib Journal WordPress Customizations is related to: Poetica is related to: Knowledge Blog is parent organization of: Cassandras Tears is parent organization of: Beautiful Brain is parent organization of: neurosphere is parent organization of: WordPress Plugin Directory is parent organization of: Brains Lab has plug in: Commentpress |
Free, Freely available | nlx_152818 | SCR_001518 | WordPress.org | 2026-02-07 02:05:39 | 85 | ||||||||
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TRIGR Resource Report Resource Website 1+ mentions |
TRIGR (RRID:SCR_001550) | TRIGR | clinical trial | International, randomized, double-blinded trial to determine whether weaning to a casein hydrolysate formula during the first 6-8 months of life in place of cow milk based formula reduces the incidence of autoimmunity and type 1 diabetes in genetically susceptible newborn infants. 2160 eligible infants were randomized to test or control formulas when mothers decide to wean from exclusive breastfeeding. The participants will be monitored up to the age of 10 years for the appearance of diabetes-predictive autoantibodies and clinical type 1 diabetes. The TRIGR trial will determine whether delayed exposure to intact food proteins will reduce the chances of developing type 1 diabetes later in life. All babies in the study received the recommendation to breastfeed for at least the first six months of life. If a mother was unable to exclusively breastfeed before the baby was 8 months of age, her child was randomly assigned to one of two groups. One group of these babies received a trial formula based on extensively hydrolyzed protein; the other group received another trial formula containing a smaller amount of hydrolyzed protein. In the hydrolyzed formula, the big protein molecules have been split into very small fragments to provide a source of nutritional amino acids, but the fragments are likely too small to stimulate the immune system. The TRIGR trial will also be able to analyze whether exclusive breastfeeding per se can reduce the risk of the children to develop type 1 diabetes. | casein hydrolysate formula, newborn, hydrolyzed infant formula, genetically susceptible, insulin, cow's milk, infant, feeding, diet, intervention, genetic risk, bibliography, dietary intervention, wean, prevention, nutrition, nonhydrolyzed infant formula, breast feeding, infant formula |
is listed by: ClinicalTrials.gov is listed by: NIDDK Research Resources is listed by: NIDDK Information Network (dkNET) has parent organization: University of South Florida; Florida; USA |
Type 1 diabetes, Diabetes | NICHD HD040364; NICHD HD042444; NICHD HD051997; RTD programme Quality of Life and Management of Living Resources contract QLK1-2002-00372 |
PMID:21153533 PMID:17550422 |
Free, Freely available | nlx_152860 | http://trigr.epi.usf.edu/ http://clinicaltrials.gov/show/NCT00179777 |
SCR_001550 | TRIGR - Trial to Reduce IDDM in the Genetically at Risk, Trial to Reduce IDDM in the Genetically at Risk, TRIGR trial | 2026-02-07 02:05:32 | 1 |
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