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http://www.niehs.nih.gov/

National institute that reduces the burden of human illness and dysfunction from environmental causes by, defining how environmental exposures, genetic susceptibility, and age interact to affect an individual''s health. Its mission is to discover how the environment affects people in order to promote healthier lives. Achieving this mission depends on a set of core values that apply to all activities of the Institute: * Research excellence (innovation; discovery of new scientific knowledge and technology); * Management excellence; and * Community outreach, education, and involvement. At NIEHS and the National Toxicology Program, they engage in a special form of public service - producing scientific knowledge that promotes individual and public health. The Institute is uniquely positioned to help prevent disease and transform new scientific knowledge into improvements in human health. There are many opportunities before us to build and expand the contributions of the NIEHS: * Foster research on environmental triggers of disease; * Communicate advances in environmental health sciences to the public; * Foster training and development of emerging young environmental health scientists and practitioners; * Enhance translation of knowledge from research to disease prevention; and * Foster safety assessment research on chemicals and other environmental factors. The fulfillment of this mission requires the partnership and effort of everyone in the environmental health sciences communities.

Proper citation: National Institute of Environmental Health Sciences (RRID:SCR_011430) Copy   

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http://neuroscienceblueprint.nih.gov/

Collaborative framework that includes the NIH Office of the Director and the 14 NIH Institutes and Centers that support research on the nervous system. By pooling resources and expertise, the Blueprint identifies cross-cutting areas of research, and confronts challenges too large for any single Institute or Center. The Blueprint makes collaboration a day-to-day part of how the NIH does business in neuroscience, complementing the basic missions of Blueprint partners. During each fiscal year, the partners contribute a small percentage of their funds to a common pool. Since the Blueprint's inception in 2004, this pool has comprised less than 1 percent of the total neuroscience research budget of the partners. In 2009, the Blueprint Grand Challenges were launched to catalyze research with the potential to transform our basic understanding of the brain and our approaches to treating brain disorders. * The Human Connectome Project is an effort to map the connections within the healthy brain. It is expected to help answer questions about how genes influence brain connectivity, and how this in turn relates to mood, personality and behavior. The investigators will collect brain imaging data, plus genetic and behavioral data from 1,200 adults. They are working to optimize brain imaging techniques to see the brain's wiring in unprecedented detail. * The Grand Challenge on Pain supports research to understand the changes in the nervous system that cause acute, temporary pain to become chronic. The initiative is supporting multi-investigator projects to partner researchers in the pain field with researchers in the neuroplasticity field. * The Blueprint Neurotherapeutics Network is helping small labs develop new drugs for nervous system disorders. The Network provides research funding, plus access to millions of dollars worth of services and expertise to assist in every step of the drug development process, from laboratory studies to preparation for clinical trials. Project teams across the U.S. have received funding to pursue drugs for conditions from vision loss to neurodegenerative disease to depression. Since its inception in 2004, the Blueprint has supported the development of new resources, tools and opportunities for neuroscientists. For example, the Blueprint supports several training programs to help students pursue interdisciplinary areas of neuroscience, and to bring students from underrepresented groups into the neurosciences. The Blueprint also funds efforts to develop new approaches to teaching neuroscience through K-12 instruction, museum exhibits and web-based platforms. From fiscal years 2007 to 2009, the Blueprint focused on three major themes of neuroscience - neurodegeneration, neurodevelopment, and neuroplasticity. These efforts enabled unique funding opportunities and training programs, and helped establish new resources including the Blueprint Non-Human Primate Brain Atlas.

Proper citation: NIH Blueprint for Neuroscience Research (RRID:SCR_003670) Copy   

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http://cebs.niehs.nih.gov

Repository for toxicogenomics data, including study design and timeline, clinical chemistry and histopathology findings and microarray and proteomics data. Data derived from studies of chemicals and of genetic alterations, and is compatible with clinical and environmental studies. Data relating to environmental health, pharmacology, and toxicology. It is not necessary to have microarray data, but study design and phenotypic anchoring data are required.CEBS contains raw microarray data collected in accordance with MIAME guidelines and provides tools for data selection, pre-processing and analysis resulting in annotated lists of genes of interest. Biomedical Investigation Database is another component of CEBS system. used to load and curate study data prior to export to CEBS, in addition to capturing and displaying novel data types such as PCR data, or additional fields of interest, including those defined by the HESI Toxicogenomics Committee. BID has been shared with Health Canada and the US Environmental Protection Agency.

Proper citation: Chemical Effects in Biological Systems (CEBS) (RRID:SCR_006778) Copy   

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http://www.nih.gov/

NIH is the nations medical research agency - making important medical discoveries that improve health and save lives. The National Institutes of Health (NIH), a part of the U.S. Department of Health and Human Services, is the primary Federal agency for conducting and supporting medical research. Helping to lead the way toward important medical discoveries that improve peoples health and save lives, NIH scientists investigate ways to prevent disease as well as the causes, treatments, and even cures for common and rare diseases. NIH research impacts: * child and teen health, * men's health, * minority health, * seniors' health, * women's health, and * wellness and lifestyle issues. Composed of 27 Institutes and Centers, the NIH provides leadership and financial support to researchers in every state and throughout the world.

Proper citation: National Institutes of Health (RRID:SCR_011417) Copy   

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http://www.niehs.nih.gov/news/newsletter/2006/march/science-genetic.cfm

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. The NIEHS Genetic Alterations in Cancer (GAC) knowledgebase is a comprehensive collection of data compiled from studies reported in the published literature on genetic alterations in tumors associated with exposure to specific chemical, physical, or biological agents that can be linked to genes implicated in the development of cancers. GAC provides access to data from peer reviewed journals for hundreds of studies of gene mutations, loss of heterozygosity, and/or chromosome changes in tumors from humans, mice, or rats. Results are summarized in tables and graphic profiles that show the incidence (percent) of tumors with alterations in each gene that has been studied. Detailed data tables display results for each subject studied in the cited reference and the reference ID is hyperlinked to its PubMed abstract for more information. A mutation spectrum for individual genes and links to gene information from The Cancer Genome Anatomy Project and the Rat Genome Database are also provided.

Proper citation: Genetic Alterations in Cancer (RRID:SCR_010533) Copy   

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http://www.niehs.nih.gov/research/resources/software/biostatistics/art/

A set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms: Illumina''''s Solexa, Roche''''s 454 and Applied Biosystems'''' SOLiD. ART can be used to test or benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART outputs reads in the FASTQ format, and alignments in the ALN format. ART can also generate alignments in the SAM alignment or UCSC BED file format.

Proper citation: ART (RRID:SCR_006538) Copy   

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http://www.niehs.nih.gov/research/resources/software/biostatistics/eagleview/

An information-rich viewer for next-generation genome assembles with data integration capability. EagleView can display a dozen different types of information including base qualities, machine specific trace signals, and genome feature annotations. It provides an easy way for inspecting visually the quality of a genome assembly and validating polymorphism candidate sites (e.g., SNPs) reported by polymorphism discovery tools. It can also facilitate data interpretation and hypothesis generation. EagleView is a multi-platform application developed with C++ and is available for all three major platforms: Windows, Linux, and Mac OS.

Proper citation: EagleView (RRID:SCR_006859) Copy   

•   Source: SciCrunch Registry

http://snpinfo.niehs.nih.gov/

SNPinfo Web Server is a set of freely available web-based SNP selection tools where investigators can specify genes or linkage regions and select SNPs based on GWAS results, linkage disequilibrium (LD), and predicted functional characteristics of both coding and non-coding SNPs. The algorithm uses GWAS SNP P-value data and finds all SNPs in high LD with GWAS SNPs, so that selection is from a much larger set of SNPs than the GWAS itself. The program can also identify and choose tag SNPs for SNPs not in high LD with any GWAS SNP. We incorporate functional predictions of protein structure, gene regulation, splicing and miRNA binding, and consider whether the alternative alleles of a SNP are likely to have differential effects on function. Users can assign weights for different functional categories of SNPs to further tailor SNP selection. The program accounts for LD structure of different populations so that a GWAS study from one ethnic group can be used to choose SNPs for one or more other ethnic groups. SNP Selection and Functional Information *Candidate Gene SNP Selection (GenePipe):SNP selection for candidate genes based on Genome Wide Association Study (GWAS) results, functional SNP prediction and Linkage Disequilibrium (LD) information. *GWAS Functional SNP Selection (GenomePipe):Functional SNP selection from SNPs that are in high LD with GWAS SNPs *GWAS SNP Selection in Linkage Loci (LinkagePipe):GWAS SNP selection in candidate genomic regions (such as linkage loci) *LD TAG SNP Selection (TagSNP):LD tag SNP selection and visualization for single or multiple populations. Finalization of SNP list from various queries. *SNP Function Prediction (FuncPred): Querying SNP function predictions and ethnic-specific allele frequencies. *SNP Information in DNA Sequence (SNPseq):Visualization of SNP related information in the context of DNA sequence. Preparing DNA Sequence for PCR Primer Design considering SNP information. Detailed information of CpG region.

Proper citation: SNPinfo Web Server (RRID:SCR_010589) Copy   

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http://tools.niehs.nih.gov/polg/

Database that lists all known mutations in the coding region of the POLG gene and describes the associated disease. Human DNA polymerase is composed of two subunits, a 140 kDa catalytic subunit encoded by the POLG on chromosome 15q25, and a 55kDa accessory subunit encoded by the POLG2 gene on chromosome 17q23-24. A number of mutations have been mapped to the gene for the catalytic subunit of DNA polymerase, POLG, and found to be associated with mitochondrial diseases. The nucleotide changes are numbered from the initiation Methionine codon and are based on the cDNA (accession U60325.1) and gene sequence (accession AF497906.1).

Proper citation: Human DNA Polymerase Gamma Mutation Database (RRID:SCR_004722) Copy   

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http://www.niehs.nih.gov/research/resources/databases/alu/index.cfm

On line database of alu pairs. This map file is a subfile of repbase (Genetic Information Research Institute(GIRI)), derived by comparing genomic sequences in the GenBank database (release 112.0, National center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD) with the Alu consensus sequence, was made in April 1999 and is maintained at the GIRI), Sunnyvale, CA). The Alu map includes the following information in columnar form: locus, beginning sequence position, ending sequence position, fragment start relative to repeat consensus, type of Alu sequence, the fragment start relative to repeat consensus, the fragment end relative to repeat consensus, the orientation of the sequence (D, denoting direct, versus C, denoting complementary), the percent similarity to the Alu consensus sequence, the ratio of mismatches to matches, and the alignment score. The database is available for download. An Alu element is a short stretch of DNA originally characterized by the action of the Alu (Arthrobacter luteus) restriction endonuclease. Alu elements of different kinds occur in large numbers in primate genomes. In fact, Alu elements are the most abundant Transposable elements in the human genome. They are derived from the small cytoplasmic 7SL RNA, a component of the signal recognition particle. The event, when a copy of the 7SL RNA became a precursor of the Alu elements, took place in the genome of an ancestor of Supraprimates. (from Wikipedia).

Proper citation: Alu Pairs Database (RRID:SCR_013353) Copy   

•   Source: SciCrunch Registry