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https://software.broadinstitute.org/software/discovar/blog/

Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes.

Proper citation: Discovar assembler (RRID:SCR_016755) Copy   

•   Source: SciCrunch Registry

https://www.iigm.it/site/index.php?l=ENG

Private research institute in Turin, Italy. Research programs in immunogenetics, functional genomics, genomic epidemiology, tumour diagnostic and prognostic biomarker research, epigenetic modifications in disease, quantitative biology and computational neuroscience.

Proper citation: Italian Institute for Genomic Medicine; Turin; Italy (RRID:SCR_017062) Copy   

•   Source: SciCrunch Registry

http://ihec-epigenomes.org/

Consortium to coordinate epigenome mapping and characterization worldwide to avoid redundant research effort, to implement high data quality standards, to coordinate data storage, management and analysis and to provide free access to the high resolution reference human epigenome maps for normal and disease cell types to the research community. Promotes data sharing. You may view, search and download the data already released by the different IHEC associated projects via the IHEC Data Portal.

Proper citation: International Human Epigenome Consortium (RRID:SCR_016937) Copy   

•   Source: SciCrunch Registry

https://www.sciencescott.com/pyminer

Software tool to automate cell type identification, cell type-specific pathway analyses, graph theory-based analysis of gene regulation, and detection of autocrine-paracrine signaling networks. Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq.

Proper citation: PyMINEr (RRID:SCR_016990) Copy   

•   Source: SciCrunch Registry

http://www.bx.psu.edu/~giardine/vision/

International project to analyze mouse and human hematopoiesis, and provide a tractable system with clear clinical significance and importance to NIDDK. Collection of information from the flood of epigenomic data on hematopoietic cells as catalogs of validated regulatory modules, quantitative models for gene regulation, and a guide for translation of research insights from mouse to human.

Proper citation: ValIdated Systematic IntegratiON of epigenomic data (RRID:SCR_016921) Copy   

•   Source: SciCrunch Registry

http://dabi.loni.usc.edu/

Organize, Store, Disseminate, Analyze and Visualize Invasive Neurophysiology Data. Shared archive and resource for human invasive neurophysiology data that have been established by Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative along with software tools for data uploading, visualization and analysis. Users can view and query datasets through online interface but cannot access raw data. Platform utilizes centralized and federated model. Investigators may upload data to central archive or house it themselves.

Proper citation: Data Archive BRAIN Initiative (RRID:SCR_017114) Copy   

•   Source: SciCrunch Registry

http://coot.embl.de/g2d/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of candidate genes for mapped inherited human diseases. Candidate priorities are automatically established by a data mining algorithm that extracts putative genes in the chromosomal region where the disease is mapped, and evaluates their possible relation to the disease based on the phenotype of the disorder. Data analysis uses a scoring system developed for the possible functional relations of human genes to genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene. Methodology can be divided in two parts: the association of genes to phenotypic features, and the identification of candidate genes on a chromosonal region by homology. This is an analysis of relations between phenotypic features and chemical objects, and from chemical objects to protein function terms, based on the whole MEDLINE and RefSeq databases.

Proper citation: Candidate Genes to Inherited Diseases (RRID:SCR_008190) Copy   

•   Source: SciCrunch Registry

http://neibank.nei.nih.gov

An integrated resource for genomics and bioinformatics in vision research including expressed sequence tag (EST) data and sequence-verified cDNA clones for multiple eye tissues of several species, web-based access to human eye-specific SAGE data through EyeSAGE, and comprehensive, annotated databases of known human eye disease genes and candidate disease gene loci. All expression- and disease-related data are integrated in EyeBrowse, an eye-centric genome browser. NEIBank provides a comprehensive overview of current knowledge of the transcriptional repertoires of eye tissues and their relation to pathology. The data can be interrogated in several ways. Specific gene names can be entered into the search window. Alternatively, regions of the genome can be displayed. For example, entering two STS markers separated by a semicolon (e.g. RH18061;RH80175) allows the display of the entire chromosomal region associated with the mapping of a specific disease locus. ESTs for each tissue can then be displayed to help in the selection of candidate genes. In addition, sequences can be entered into a BLAST search and rapidly aligned on the genome, again showing eye derived ESTs for the same region. To see the same region at the full UCSC site, cut and paste the location from the position window of the genome browser. EyeBrowse includes a custom track display SAGE data for human eye tissues derived from the EyeSAGE project. The track shows the normalized sum of SAGE tag counts from all published eye-related SAGE datasets centered on the position of each identifiable Unigene cluster. This indicates relative activity of each gene locus in eye. Clicking on the vertical count bar for a particular location will bring up a display listing gene details and linking to specific SAGE counts for each eye SAGE library and comparisons with normalized sums for neural and non-neural tissues. To view or alter settings for the EyeSAGE track on EyeBrowse, click on the vertical gray bar at the left of the display. Other custom tracks display known eye disease genes and mapped intervals for candidate loci for retinal disease, cataract, myopia and cornea disease. These link back to further information at NEIBank.

Proper citation: NEIBank (RRID:SCR_007294) Copy   

•   Source: SciCrunch Registry

https://hirnetwork.org

Network helps to organize and support collaborative research related to loss of functional beta cell mass in Type 1 Diabetes (T1D). Project consists of four independent research initiatives: Consortium on Beta Cell Death and Survival (CBDS), Consortium on Human Islet Biomimetics (CHIB), Consortium on Modeling Autoimmune Interactions (CMAI), Consortium on Targeting and Regeneration (CTAR), and Human Pancreas Analysis Program (HPAP).

Proper citation: Human Islet Research Network (HIRN) (RRID:SCR_014393) Copy   

•   Source: SciCrunch Registry

http://www.seattle.eric.research.va.gov/VETR/Home.asp

The Vietnam Era Twin (VET) Registry is a closed cohort composed of approximately 7,000 middle-aged male-male twin pairs both of whom served in the military during the time of the Vietnam conflict (1964-1975). The Registry is a United States Department of Veterans Affairs (VA) resource that was originally constructed from military records; the Registry has been in existence for almost 20 years. It is one of the largest national twin registries in the US and currently has members living in all 50 states. Initially formed to address questions about the long-term health effects of service in Vietnam, the Registry has evolved into a resource for genetic epidemiological studies of mental and physical health conditions. Several waves of mail and telephone surveys have collected a wealth of health-related information on Registry twins, referred to as members. In addition to twins, selected adult offspring of twins and the mothers of those offspring are also VET Registry members. More recent data collection efforts have focused on specific sets of twin pairs and have conducted detailed clinical or laboratory testing. Selected Vietnam Era Registry Research Studies: * Veteran Health Study * VETSA 2: A Longitudinal Study of Cognitive Aging * Alcoholism Course thought Midlife: A Twin Family Study and Offspring of Twins: G, E and GxE Risk for Alcoholism * GE: Offspring of Twins with Substance Use Disorder * Mechanisms Linking Depression to Cardiovascular Risk (Twins Heart Study 2) * Post-traumatic Stress Disorder and Cardiovascular Disease * Biological Markers for Post-traumatic Stress Disorder (T3) * Memory and the Hippocampus in Vietnam-era Twins with PTSD (Time 3)

Proper citation: Vietnam Era Twin Registry (RRID:SCR_008807) Copy   

•   Source: SciCrunch Registry

http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases

THIS RESOURCE IS NO LONGER IS SERVICE. Documented on July,29,2022. Surface-based atlases of human, macaque, rat and mouse cerebral and cerebellar cortices derived from structural MRI volumes developed in the Van Essen laboratory can be downloaded by direct links on the SumsDB database and can be viewed using freely available Caret (offline) and WebCaret (online) software. The human and macaque atlases include a large and growing compendium of experimental data pertaining to the structural and functional organization of primate cerebral cortex.

Proper citation: Surface-Based Atlases (RRID:SCR_002099) Copy   

•   Source: SciCrunch Registry

http://www.eideneurolearningblog.blogspot.com/

Weekly articles related to brain-based learning and learning styles, problem-solving and creativity, kids, families, and parenting, gifted and visual learners, dyslexia, attention deficit disorders, autism, and more.

Proper citation: Eide Neurolearning Blog (RRID:SCR_000680) Copy   

•   Source: SciCrunch Registry

http://www.biobanque-picardie.com/index_En.php

A secure repository of biological samples and data dedicated for medical and research purposes. These biological samples are linked to consenting patient relative data. Biobanque de Picardie provides quality and traceability services for establishment, conservation and use of biological samples collections. It houses collections of human tissue in a variety of areas of disease. Samples are used in basic research and translational studies, physiopathology of diseases and identification of new diagnostic, and as prognostic or therapeutic biomarkers. Biobanque de Picardie also develops healthy or pathological human primary stem cell banks, such as: mesenchymal stem cells in umbilical cord (HUC-MSC), primary hepatocytes (HPH), peripheral blood mononuclear cells (PBMC), and fibroblasts. Biological samples are stored at - 80 degrees C in electric freezers, at - 196 degrees C in liquid nitrogen or -130 degrees C in nitrogen vapor.

Proper citation: Biobanque de Picardie (RRID:SCR_004731) Copy   

•   Source: SciCrunch Registry

http://www.brainimmune.com/

BrainImmune is a free web-based reference that provides comprehensive and up-to-date information on the broad spectrum of medical research related to brain-immune interactions and their impact on health and disease. BrainImmune is written collaboratively by experts in the field from all around the world. Here, concise summaries of basic and clinical research describe how the brain and the immune system ''talk'' to each other in order to maintain homeostasis. BrainImmune is continually updated, with articles and opinions on history, the present state of the art, and new ideas and conceptual frameworks for the neurohormonal- and stress-immune interactions and their implications for common human diseases. Our goal in developing BrainImmune is to facilitate and advance neuroendocrine-immunology research, and the communication and collaborations in this vast interdisciplinary area.

Proper citation: BrainImmune (RRID:SCR_005418) Copy   

•   Source: SciCrunch Registry

http://psydoctor8.tumblr.com/

Called The Marquis de fMRI by Dr. Anon, NeuroPsyDoctor8 is about neurolaw and related moral cognition research, by someone who has a forensic psych type biz in NYC & then decided to pursue a neuropsych PhD. Now she uses fMRI and a side of bourbon to figure it all out.

Proper citation: NeuroPsyDoctor8 (RRID:SCR_005471) Copy   

•   Source: SciCrunch Registry

http://blog.aids.gov/

The AIDS.gov blog serves as a forum to foster public discussion on using new media effectively in response to HIV/AIDS, as well as HIV/AIDS research and policies. Along with weekly new media posts, the blog features other AIDS.gov-authored posts, guest posts, cross-posts from the White House Office of National AIDS Policy blog and the CDC Health Protection Perspectives blog, PEPFAR blog, and posts from the National Institute of Allergies and Infectious Diseases'' (NIAID) Division of AIDS. A large number of Federal agencies and programs are engaged in HIV/AIDS prevention, testing, treatment, policy, and research efforts in the United States. AIDS.gov serves as a gateway for information about these Federal efforts, with a focus on domestic programs. Since the launch of AIDS.gov on December 1, 2006 (World AIDS Day), there has been a growing interest in using new media tools to disseminate information about HIV/AIDS and improve prevention, testing, treatment, and research outcomes. AIDS.gov created this blog to address that interest, and has since expanded content areas to include key US Government HIV/AIDS-related research and policy posts, among other topics.

Proper citation: AIDS.gov Blog (RRID:SCR_007156) Copy   

•   Source: SciCrunch Registry

https://him.uchicago.edu/

Facility serves as specialized laboratory performing correlative assays for cancer-based clinical trials. Participates in project development to assist in assay selection and optimization prior to study initiation. Offers pick-up service for specimens from patients at U of C Hospital or outpatient clinics, and process samples as indicated for assays being performed. For some studies, isolation and freezing of peripheral blood lymphocytes for analysis at later date is performed, while for others immediate staining of whole blood for specific cell surface markers of interest is carried out. Prepares clinical grade products, such as peptide vaccines, for administration into patients.Assays performed include ELISA, ELISPOT, tetramer binding assays, detection of cell surface markers by flow cytometry, and biochemical assays such as Western Blots, RNA extraction from tumor biopsies and either real time RT-PCR for specific transcripts or preparation of samples for gene expression profiling. Facility is equipped with MACSQuant Flow Cytometer, ELISA microplate reader, ELISPOT reader, PCR thermocyclers, CO2 incubators, biosafety cabinets, centrifuges, and equipment for Western blot analysis. Performs assays on human samples but consideration will be given to expanding these services to mouse-model systems.

Proper citation: University of Chicago Human Immunologic Monitoring Core Facility (RRID:SCR_017916) Copy   

•   Source: SciCrunch Registry

https://med.nyu.edu/research/scientific-cores-shared-resources/center-biospecimen-research-development

Core mission is to drive scientific discovery through use of human specimens.Helps facilitate translational research, match human specimen resources to scientific needs, foster multi-investigator collaborative projects, and catalyze scientific innovation,improving researcher access to existing biospecimen resources, and enhancing institution-wide tissue-banking efforts and capacity. Another priority is to implement campus-wide policy for human biospecimen collection and storage to ensure regulatory compliance.

Proper citation: New York University School of Medicine Langone Health Center for Biospecimen Research and Development Core Facility (RRID:SCR_017930) Copy   

•   Source: SciCrunch Registry

http://hormone.facilities.northwestern.edu

Core provides hormone analyses for both human and animal studies for scientific community at Northwestern, small rodent metabolic phenotyping resources for diabetes, obesity and other metabolic research.Maintains quality control and standardize internal references for hormone assays.Maintains reference database information on mouse metabolic phenotyping models from Northwestern University community.Services include:Immunoassays for endocrine hormones, assays using technology from Luminex,Lipid and glucose chemical analyeses,Roche Cobas e 411 analyzer employing sophisticated electrochemiluminescence (ECL) technology to deliver excellent low-end sensitivity and broad dynamic range of assays including metabolic and reproductive hormones, thyroid function test, cardiac markers, maternal care, tumor markers and bone turnover markers.,TSE LabMaster Automated Phenotyping system is a state-of-the-art system for studying energy metabolism at whole animal level.

Proper citation: Northwestern University Comprehensive Metabolic Core Facility (RRID:SCR_017871) Copy   

•   Source: SciCrunch Registry

http://www.mskcc.org/research/molecular-cytogenetics

Core supports cytogenetic analysis of cells from human and research animal sources. Range of chromosome analysis techniques are ranging from basic G-banded karyotyping, to 24-color Spectral Karyotyping (SKY), as well as Fluorescence in situ Hybridization (FISH) mapping of cloned DNAs.Services include:Karyotype characterization of new cell lines,Confirmation of cell line identity or stability,Karyotype screening of ES cells prior to transgenesis,Mapping of transgene integration sites,Chromosome or locus copy number enumeration,Publication-quality illustrations.Cytogenetic techniques available:Short-term cell culture,Metaphase chromosome preparation,G-banded karyotyping.FISH techniques available:DNA labeling for custom probe generation (for FISH projects),DNA amplification by DOP-PCR,Chromosome painting,FISH mapping (on chromosomes, interphase nuclei or DNA fibers),Tissue FISH (paraffin or frozen sections),Immuno-FISH (DNA FISH combined with fluorescent immunostaining) , Spectral karyotyping (SKY),Q-FISH (measurement of telomere lengths).

Proper citation: Memorial Sloan Kettering Cancer Center Molecular Cytogenetics Core Facility (RRID:SCR_017850) Copy   

•   Source: SciCrunch Registry