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https://www.preventivemedicine.northwestern.edu/divisions/biostatistics/

Core where division members engage in statistical methods development and application, research design and statistical computing for health science research. Faculty interests encompass Bayesian methods, bioinformatics, causal inference, computational biology, clinical trials, diagnostic testing, longitudinal modeling, missing data modeling, observational data methods, semi-parametric models, spatial modeling, statistical genetics and survival analysis.

Proper citation: Northwestern University Biostatistics Collaborative Center (RRID:SCR_017943) Copy   

•   Source: SciCrunch Registry

https://neurobot.incf.org

Software tool for data management in clinical studies to improve care for patients with Traumatic Brain Injury (TBI). Used to search and find study variables with the associated information and export study data for further analysis.

Proper citation: INCF-Neurobot (RRID:SCR_017004) Copy   

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https://t1dexchange.org/research/biobank/

Collection of biological samples linked to participant medical data from individuals living with type 1 diabetes. Unifies samples and data from eight different clinical studies related to type 1 diabetes.

Proper citation: T1D Exchange Biobank (RRID:SCR_017195) Copy   

•   Source: SciCrunch Registry

https://glomcon.org

Consortium to bring together clinicians, pathologists, researchers, and biotech innovators to create scalable network of stakeholders interested in helping patients with glomerular kidney disease. Makes collective expertise of its members available for discussion of individual cases, provides infrastructure for biomarker studies, enables genomic research, and facilitates clinical trials.

Proper citation: Glomerular Disease Study & Trial Consortium (RRID:SCR_017264) Copy   

•   Source: SciCrunch Registry

https://www.daqcord.org/

Software tool for practical self assessment and reporting method for clinical research studies, to capture key information about data acquisition and quality control measures. Linked to dataset so that potential research collaborators can determine if data meets their needs and expectations.

Proper citation: DAQCORD (RRID:SCR_017395) Copy   

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https://bioconductor.org/packages/TCGAbiolinks/

Software R Bioconductor package for integrative analysis with TCGA data.TCGAbiolinks is able to access National Cancer Institute Genomic Data Commons thorough its GDC Application Programming Interface to search, download and prepare relevant data for analysis in R.

Proper citation: TCGAbiolinks (RRID:SCR_017683) Copy   

•   Source: SciCrunch Registry

http://mips.gsf.de/services/genomes/uwe25/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. This is the official database of the environmental chlamydia genome project. This resource provides access to finished sequence for Parachlamydia-related symbiont UWE25 and to a wide range of manual annotations, automatical analyses and derived datasets. Functional classification and description has been manually annotated according to the Annotation guidelines. Chlamydiae are the major cause of preventable blindness and sexually transmitted disease. Genome analysis of a chlamydia-related symbiont of free-living amoebae revealed that it is twice as large as any of the pathogenic chlamydiae and had few signs of recent lateral gene acquisition. We showed that about 700 million years ago the last common ancestor of pathogenic and symbiotic chlamydiae was already adapted to intracellular survival in early eukaryotes and contained many virulence factors found in modern pathogenic chlamydiae, including a type III secretion system. Ancient chlamydiae appear to be the originators of mechanisms for the exploitation of eukaryotic cells. Environmental chlamydiae have recently been recognized as obligate endosymbionts of free-living amoebae and have been implicated as potential human pathogens. Environmental chlamydiae form a deep branching evolutionary lineage within the medically important order Chlamydiales. Despite their high diversity and ubiquitous distribution in clinical and environmental samples only limited information about genetics and ecology of these microorganisms is available. The Parachlamydia-related Acanthamoeba symbiont UWE25 was therefore selected as representative environmental chlamydia strain for whole genome sequencing. Comparative genome analysis was performed using PEDANT and simap. Sponsors: The environmental chlamydia genome project was funded by the bmb+f (German Federal Ministry of Education and Research) and is part of the Competence Network PathoGenoMiK.

Proper citation: Protochlamydia amoebophila UWE25 (RRID:SCR_008222) Copy   

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http://dtp.nci.nih.gov/docs/3d_database/dis3d.html

The NCI DIS 3D database is a collection of 3D structures for over 400,000 drugs. The database is an extension of the NCI Drug Information System. The structural information stored in the DIS is only the connection table for each drug. The connection table is just a list of which atoms are connected and how they are connected. It is essentially a searcheable database of three-dimensional structures has been developed from the chemistry database of the NCI Drug Information System (DIS), a file of about 450,000 primarily organic compounds which have been tested by NCI for anticancer activity. The DIS database is very similar in size and content to the proprietary databases used in the pharmaceutical industry; its development began in the 1950s; and this history led to a number of problems in the generation of 3D structures. This information can be searched to find drugs that share similar patterns of connections, which can correlate with similar biological activity. But the cellular targets for drug action, as well as the drugs themselves, are 3 dimensional objects and advances in computer hardware and software have reached the point where they can be represented as such. In many cases the important points of interaction between a drug and its target can be represented by a 3D arrangement of a small number of atoms. Such a group of atoms is called a pharmacophore. The pharmacophore can be used to search 3D databases and drugs that match the pharmacophore could have similar biological activity, but have very different patterns of atomic connections. Having a diverse set of lead compounds increases the chances of finding an active compound with acceptable properties for clinical development. Sponsor: The ICBG are supported by the Cooperative Agreement mechanism, with funds from nine components of the NIH, the National Science Foundation, and the Foreign Agricultural Service of the USDA.

Proper citation: National Cancer Institute 3D Structure Database (RRID:SCR_008211) Copy   

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http://www.ohsu.edu/xd/research/centers-institutes/neurology/alzheimers/research/data-tissue/clinical-data.cfm

A database housing longitudinal relational research data from over 4,000 research subjects. The database includes the following types of data: physical and neurological exam findings, neurocognitive test scores, personal and family history of dementia, personal demographic genotypes (APOE, HLA), age at service evaluations, age at onset, age at death, clinical diagnosis, neuropathology diagnosis, tissue inventory information (when available), health status, medications, laboratory tests, and MRI data.

Proper citation: Layton Center Clinical Data Resources (RRID:SCR_008822) Copy   

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http://www.cnio.es/ES/grupos/plantillas/presentacion.asp?grupo=50004308

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The need to use human neoplastic tissue under ideal conditions is currently of particular importance due to the development molecular pathology techniques that allow large-scale studies of genetic expression that are also of clinical significance. The Tumour Bank Network (TBN), instigated and coordinated by the Molecular Pathology Programme (MMP) aims to respond to this need by the promoting of Tumour Banks in Spanish hospitals. This will be achieved through the application of homogeneous procedures for the collection, processing and storage of neoplastic and normal tissue samples in such a way as to make molecular studies possible, avoiding that avoid the intrinsic bias of multi-centre studies possible. These Hospital Tumour Banks are based within the Pathology Departments of the collaborating Hospitals, that are interconnected through a computer-based network. In this way, each Centre''s tissue remains in the Hospital itself, thereby playing a key role in the development of the welfare, teaching and research activities within the Hospital. At the same time, it represents a tool to encourage of multi-hospital cancer research and of cooperation between basic and clinical researchers, constituting important collaboration between biomedical disciplines. The design does not correspond to a Central Tumour Bank, but that of a cooperative and coordinated Network of Hospital Banks, based on simple, homogeneous and optimal tissue treatment protocols. This Network is promoted by the Centro Nacional de Investigaciones Oncologicas (CNIO), which thereby undertakes the work of coordinating the network, using and maintaining the database, adhering to quality control. The aim of the CNIO's TBN is to acquire neoplastic and control non-neoplastic material of all types of malignant neoplasias, in the form of tissue fixed in formalin and paraffin embedded, of samples that are unfixed or frozen according to conventional methods as set out in Annexe 1 and even, exceptionally as fresh tissue. When other types of samples are required to carry out a specific project, the central office of the TBN will draw up a protocol with the group leading the project for the collection and maintenance of the tissue and clinicopathological data required for the proposed research. These protocols will be disseminated among the Associated Hospitals in order to gather the previously agreed number cases. Basic data surrounding the processing and preservation conditions for each case will be sent to the central office of the Bank, which under no circumstances will reveal the identity of the patient. Any Spanish cancer research team will be able to request tissue from the Tissue Bank Network. Absolute priority will be afforded to projects whose principal researcher belongs to one of the Associated Centres of the TNB, to other institutions with special agreements concerning the exchange of samples, and to the CNIO's researchers.

Proper citation: Spanish National Tumour Bank Network (RRID:SCR_008707) Copy   

•   Source: SciCrunch Registry

http://www.vaccineinjury.info/vaccine-damage-reports-2010.html

Database of case reports of adverse reactions to vaccinations. There are 806 reports (May 2013). If you would like to report a case, please go to report your own vaccine reaction. The user may search by keywords or sort by vaccine, country, age, outcome, gender and hospital admission.

Proper citation: Vaccine damage reports database (RRID:SCR_010740) Copy   

•   Source: SciCrunch Registry

https://genome-cancer.ucsc.edu/

A suite of web-based tools to visualize, integrate and analyze cancer genomics and its associated clinical data. It is possible to display your own clinical data within one of their datasets.

Proper citation: UCSC Cancer Genomics Browser (RRID:SCR_011796) Copy   

•   Source: SciCrunch Registry

http://www.ninds.nih.gov/disorders/disorder_index.htm

Reference disease data set of neurological diseases along with their definitions, etiology, treatment, prognosis, ongoing research, clinical trials information and publications. The Disorder Index includes synonyms and research topics. Navigation is by letter of the alphabet., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: NINDS Disorder Index (RRID:SCR_000433) Copy   

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http://www.civm.duhs.duke.edu/

Biomedical technology research center dedicated to the development of novel imaging methods for the basic scientist and the application of the methods to important biomedical questions. The CIVM has played a major role in the development of magnetic resonance microscopy with specialized MR imaging systems capable of imaging at more than 500,000x higher resolution than is common in the clinical domain. The CIVM was the first to demonstrate MR images using hyperpolarized 3He which has been moved from mouse to man with recent clinical trials performed at Duke in collaboration with GE. More recently the CIVM has developed the molecular imaging workbench---a system dedicated to multimodality cardiopulmonary imaging in the rodent. Their collaborators are employing these unique imaging systems in an extraordinary range of mouse and rat models of neurologic disease, cardiopulmonary disease and cancer to illuminate the underlying biology and explore new therapies.

Proper citation: Center for In Vivo Microscopy (RRID:SCR_001426) Copy   

•   Source: SciCrunch Registry

http://www.ncigt.org/

Biomedical Technology Resource Center that serves as a national resource for all aspects of research into medical procedures that are enhanced by imaging. Its common goal is to provide more effective patient care. The center is focused on the multidisciplinary development of innovative image-guided intervention technologies to enable effective, less invasive clinical treatments that are not only more economical, but also produce better results for patients. The NCIGT is helping to implement this vision by serving as a proving ground for some of the next generation of medical therapies.

Proper citation: National Center for Image-Guided Therapy (RRID:SCR_001419) Copy   

•   Source: SciCrunch Registry

http://www.fmri.org

THIS RESOURCE IS NO LONGER IN SERVICE, documented on 7/28/13. Core facility of Columbia Neuroscience with the goal of establishing a collaborative and multi-investigator neuroimaging environment that is focused on the investigation of the neurocircuitry of the brain that underlies cognition, perception and action, and also the development of clinical applications that enhance the goals of personalized medicine. Within this environment the specific current research interests of the Hirsch group include several related directions of investigation. The first is conscious and subconscious neural processes that mediate emotion and cognition in healthy individuals and in patients with psychiatric disorders. This direction also includes neurocircuitry that is characteristic of disorders of consciousness such as minimally conscious or vegetative states, self and visual awareness, and attention. Neurocircuitry of other complex cognitive processes such as decisions, inductive and deductive reasoning, language, truthfulness and top-down influences of expectation, reward, and regulation on early visual and mid-level perceptual and emotional systems. On-going projects targeted for clinical applications include benefits for neurosurgery such as the development of task batteries to map the cortical locations of essential functions such as language, motor, sensation, memory, emotion and sensory functions including visions, audition and the chemical senses. Computational innovations for labeling correspondence between brain structure and specific functional regions are under development to achieve the highest interpretive precision. Current projects include integration of EEG and fMRI techniques to localize seizuregenic cortex in relation to eloquent and functioning cortex for neurosurgical planning; integration of TMS and fMRI to discriminate essential and associative language-sensitive cortical areas; and integration of VEP, EEG and fMRI to inform assessments of visual disease secondary to stroke or neural degeneration. Projects intended to refine and enhance diagnosis of psychiatric disorders such as anxiety, depression, and eating disorders include development of specialized paradigms to target dysfunctional neurocircuitry such as emotional systems (amygdala and basal ganglia) and control and regulatory systems (cingulate and pre-frontal cortex). Comparison of before-treatment images with after-treatment images to inform models of both treatment and disease and investigation of the hypothesis that individual genetic and functional differences have predictive value for treatment options and outcome are currently underway. The lab has pioneered techniques for functional mapping of single patients, and operates an active clinical service for mapping individuals for neurosurgical planning, assessments of the neurocircuitry that underlie acquired or inherited disabilities and the mechanisms of neuroplasticity that restore lost functions are actively investigated using both groups and single subject studies. :

Proper citation: fMRI Research Center at Columbia (RRID:SCR_002658) Copy   

•   Source: SciCrunch Registry

https://clinicaltrials.gov/study/NCT00342927?term=AREA%5BBasicSearch%5D(NIDDK%20endocrine%20and%20diabetes)%20AND%20AREA%5BSponsorSearch%5D(NIDDK)%20AND%20AREA%5BOverallStatus%5D(NOT_YET_RECRUITING%20OR%20RECRUITING%20OR%20ACTIVE_NOT_RECRUITING)&rank=1

Multicenter observational study designed to identify genetic determinants of diabetic nephropathy. It is conducted in eleven U.S. clinical centers and a coordinating center, and with four ethnic groups (European Americans, African Americans, Mexican Americans, and American Indians). Two strategies are used to localize susceptibility genes: a family-based linkage study and a case-control study using mapping by admixture linkage disequilibrium (MALD). In the family-based study, probands with diabetic nephropathy are recruited with their parents and selected siblings. Linkage analyses will be conducted to identify chromosomal regions containing genes that influence the development of diabetic nephropathy or related quantitative traits such as serum creatinine concentration, urinary albumin excretion, and plasma glucose concentrations. Regions showing evidence of linkage will be examined further with both genetic linkage and association studies to identify genes that influence diabetic nephropathy or related traits. Two types of MALD studies are being done. One is a case-control study of unrelated individuals of Mexican American heritage in which both cases and controls have diabetes, but only the case has nephropathy. The other is a case-control study of African American patients with nephropathy (cases) and their spouses (controls) unaffected by diabetes and nephropathy; offspring are genotyped when available to provide haplotype data. The specific goals of this program: * Delineate genomic regions associated with the development and progression of renal disease(s) * Evaluate whether there is a genetic link between diabetic nephropathy and diabetic retinopathy * Improve outcomes * Provide protection for people at risk and slow the progression of renal disease * Help establish a resource for genetic studies of kidney disease and diabetic complications by creating a repository of genetic samples and a database * Encourage studies of the genetics of progressive renal disease

Proper citation: Family Investigation of Nephropathy of Diabetes (RRID:SCR_001525) Copy   

•   Source: SciCrunch Registry

http://www.cmrr.umn.edu/

Biomedical technology research center that focuses on development of unique magnetic resonance (MR) imaging and spectroscopy methodologies and instrumentation for the acquisition of structural, functional, and biochemical information non-invasively in humans, and utilizing this capability to investigate organ function in health and disease. The distinctive feature of this resource is the emphasis on ultrahigh magnetic fields (7 Tesla and above), which was pioneered by this BTRC. This emphasis is based on the premise that there exists significant advantages to extracting biomedical information using ultrahigh magnetic fields, provided difficulties encountered by working at high frequencies corresponding to such high field strengths can be overcome by methodological and engineering solutions. This BTRC is home to some of the most advanced MR instrumentation in the world, complemented by human resources that provide unique expertise in imaging physics, engineering, and signal processing. No single group of scientists can successfully carry out all aspects of this type of interdisciplinary biomedical research; by bringing together these multi-disciplinary capabilities in a synergistic fashion, facilitating these interdisciplinary interactions, and providing adequate and centralized support for them under a central umbrella, this BTRC amplifies the contributions of each of these groups of scientists to basic and clinical biomedical research. Collectively, the approaches and instrumentation developed in this BTRC constitute some of the most important tools used today to study system level organ function and physiology in humans for basic and translational research, and are increasingly applied world-wide. CMRR Faculty conducts research in a variety of areas including: * High field functional brain mapping in humans; methodological developments, mechanistic studies, and neuroscience applications * Metabolism, bioenergetics, and perfusion studies of human pathological states (tumors, obesity, diabetes, hepatic encephalopathy, cystic fibrosis, and psychiatric disorders) * Cardiac bioenergetics under normal and pathological conditions * Automated magnetic field shimming methods that are critical for spectroscopy and ultrafast imaging at high magnetic fields * Development of high field magnetic resonance imaging and spectroscopy techniques for anatomic, physiologic, metabolic, and functional studies in humans and animal models * Radiofrequency (RF) pulse design based on adiabatic principles * Development of magnetic resonance hardware for high fields (e.g. RF coils, pre-amplifiers, digital receivers, phased arrays, etc.) * Development of software for data analysis and display for functional brain mapping.

Proper citation: Center for Magnetic Resonance Research (RRID:SCR_003148) Copy   

•   Source: SciCrunch Registry

http://genetherapy.unc.edu/jvl.htm

Core facility to access a comprehensive range of resources and services for gene transfer research including vector production services for research, preclinical and clinical materials. Services include: * Adeno-associated Virus (AAV) Custom Production; * AAV In-Stock Aliquots: Reporters, Deisseroth, Boyden, Roth, Uchida, Shah; * Lentivirus Custom Production

Proper citation: UNC Joint Vector Laboratories (RRID:SCR_002448) Copy   

•   Source: SciCrunch Registry

http://www.isletstudy.org/

Network of centers to conduct studies of islet transplantation in patients with type 1 diabetes to improve the safety and long-term success of methods for transplanting islets. It is the aim of this trial to improve methods of isolating islets, to improve techniques for the administering those transplanted islets; and to develop approaches to minimize the toxic effects of immunosuppressive drugs required for transplantation.

Proper citation: Clinical Islet Transplantation Study (RRID:SCR_001515) Copy   

•   Source: SciCrunch Registry