The Experts below are selected from a list of 156 Experts worldwide ranked by ideXlab platform

Molly A Bogue - One of the best experts on this subject based on the ideXlab platform.

  • Mouse Phenome Database an integrative Database and analysis suite for curated empirical phenotype data from laboratory mice
    Nucleic Acids Research, 2018
    Co-Authors: Molly A Bogue, Stephen C Grubb, David O Walton, Vivek M Philip, Georgi Kolishovski, Tim Stearns, Matthew H Dunn, Daniel A Skelly, Beena M Kadakkuzha, Gregg Tehennepe
    Abstract:

    The Mouse Phenome Database (MPD; https://Phenome.jax.org) is a widely used resource that provides access to primary experimental trait data, genotypic variation, protocols and analysis tools for Mouse genetic studies. Data are contributed by investigators worldwide and represent a broad scope of phenotyping endpoints and disease-related traits in naive mice and those exposed to drugs, environmental agents or other treatments. MPD houses individual animal data with detailed, searchable protocols, and makes these data available to other resources via API. MPD provides rigorous curation of experimental data and supporting documentation using relevant ontologies and controlled vocabularies. Most data in MPD are from inbreds and other reproducible strains such that the data are cumulative over time and across laboratories. The resource has been expanded to include the QTL Archive and other primary phenotype data from mapping crosses as well as advanced high-diversity Mouse populations including the Collaborative Cross and Diversity Outbred mice. Furthermore, MPD provides a means of assessing replicability and reproducibility across experimental conditions and protocols, benchmarking assays in users' own laboratories, identifying sensitized backgrounds for making new Mouse models with genome editing technologies, analyzing trait co-inheritance, finding the common genetic basis for multiple traits and assessing sex differences and sex-by-genotype interactions.

  • accessing data resources in the Mouse Phenome Database for genetic analysis of murine life span and health span
    Journals of Gerontology Series A-biological Sciences and Medical Sciences, 2016
    Co-Authors: Molly A Bogue, Rong Yuan, Luanne L. Peters, Beverly Paigen, Stephen C Grubb, Gary A Churchill, Ron Korstanje, Cheryl L Ackertbicknell, Elissa J Chesler
    Abstract:

    Understanding the source of genetic variation in aging and using this variation to define the molecular mechanisms of healthy aging require deep and broad quantification of a host of physiological, morphological, and behavioral endpoints. The murine model is a powerful system in which to understand the relations across age-related phenotypes and to identify research models with variation in life span and health span. The Jackson Laboratory Nathan Shock Center of Excellence in the Basic Biology of Aging has performed broad characterization of aging in genetically diverse laboratory mice and has placed these data, along with data from several other major aging initiatives, into the interactive Mouse Phenome Database. The data may be accessed and analyzed by researchers interested in finding Mouse models for specific aging processes, age-related health and disease states, and for genetic analysis of aging variation and trait covariation. We expect that by placing these data in the hands of the aging community that there will be (a) accelerated genetic analyses of aging processes, (b) discovery of genetic loci regulating life span, (c) identification of compelling correlations between life span and susceptibility for age-related disorders, and (d) discovery of concordant genomic loci influencing life span and aging phenotypes between Mouse and humans.

  • doi:10.1093/nar/gkr1061 Mouse Phenome Database (MPD)
    2011
    Co-Authors: Terry P Maddatu, Stephen C Grubb, Carol J Bult, Molly A Bogue
    Abstract:

    The Mouse Phenome Project was launched a decade ago to complement Mouse genome sequencing efforts by promoting new phenotyping initiatives under standardized conditions and collecting the data in a central public Database, the Mouse Phenome Database (MPD

  • Mouse Phenome Database
    Nucleic Acids Research, 2009
    Co-Authors: Stephen C Grubb, Carol J Bult, Molly A Bogue
    Abstract:

    The Mouse Phenome Database (MPD; Phenome.jax.org) was launched in 2001 as the data coordination center for the international Mouse Phenome Project. MPD integrates quantitative phenotype, gene expression and genotype data into a common annotated framework to facilitate query and analysis. MPD contains >3500 phenotype measurements or traits relevant to human health, including cancer, aging, cardiovascular disorders, obesity, infectious disease susceptibility, blood disorders, neurosensory disorders, drug addiction and toxicity. Since our 2012 NAR report, we have added >70 new data sets, including data from Collaborative Cross lines and Diversity Outbred mice. During this time we have completely revamped our homepage, improved search and navigational aspects of the MPD application, developed several web-enabled data analysis and visualization tools, annotated phenotype data to public ontologies, developed an ontology browser and released new single nucleotide polymorphism query functionality with much higher density coverage than before. Here, we summarize recent data acquisitions and describe our latest improvements.

  • doi:10.1093/nar/gkn778 Mouse Phenome Database
    2008
    Co-Authors: Stephen C Grubb, Carol J Bult, Terry P Maddatu, Molly A Bogue
    Abstract:

    The Mouse Phenome Database (MPD

Stephen C Grubb - One of the best experts on this subject based on the ideXlab platform.

  • Mouse Phenome Database an integrative Database and analysis suite for curated empirical phenotype data from laboratory mice
    Nucleic Acids Research, 2018
    Co-Authors: Molly A Bogue, Stephen C Grubb, David O Walton, Vivek M Philip, Georgi Kolishovski, Tim Stearns, Matthew H Dunn, Daniel A Skelly, Beena M Kadakkuzha, Gregg Tehennepe
    Abstract:

    The Mouse Phenome Database (MPD; https://Phenome.jax.org) is a widely used resource that provides access to primary experimental trait data, genotypic variation, protocols and analysis tools for Mouse genetic studies. Data are contributed by investigators worldwide and represent a broad scope of phenotyping endpoints and disease-related traits in naive mice and those exposed to drugs, environmental agents or other treatments. MPD houses individual animal data with detailed, searchable protocols, and makes these data available to other resources via API. MPD provides rigorous curation of experimental data and supporting documentation using relevant ontologies and controlled vocabularies. Most data in MPD are from inbreds and other reproducible strains such that the data are cumulative over time and across laboratories. The resource has been expanded to include the QTL Archive and other primary phenotype data from mapping crosses as well as advanced high-diversity Mouse populations including the Collaborative Cross and Diversity Outbred mice. Furthermore, MPD provides a means of assessing replicability and reproducibility across experimental conditions and protocols, benchmarking assays in users' own laboratories, identifying sensitized backgrounds for making new Mouse models with genome editing technologies, analyzing trait co-inheritance, finding the common genetic basis for multiple traits and assessing sex differences and sex-by-genotype interactions.

  • accessing data resources in the Mouse Phenome Database for genetic analysis of murine life span and health span
    Journals of Gerontology Series A-biological Sciences and Medical Sciences, 2016
    Co-Authors: Molly A Bogue, Rong Yuan, Luanne L. Peters, Beverly Paigen, Stephen C Grubb, Gary A Churchill, Ron Korstanje, Cheryl L Ackertbicknell, Elissa J Chesler
    Abstract:

    Understanding the source of genetic variation in aging and using this variation to define the molecular mechanisms of healthy aging require deep and broad quantification of a host of physiological, morphological, and behavioral endpoints. The murine model is a powerful system in which to understand the relations across age-related phenotypes and to identify research models with variation in life span and health span. The Jackson Laboratory Nathan Shock Center of Excellence in the Basic Biology of Aging has performed broad characterization of aging in genetically diverse laboratory mice and has placed these data, along with data from several other major aging initiatives, into the interactive Mouse Phenome Database. The data may be accessed and analyzed by researchers interested in finding Mouse models for specific aging processes, age-related health and disease states, and for genetic analysis of aging variation and trait covariation. We expect that by placing these data in the hands of the aging community that there will be (a) accelerated genetic analyses of aging processes, (b) discovery of genetic loci regulating life span, (c) identification of compelling correlations between life span and susceptibility for age-related disorders, and (d) discovery of concordant genomic loci influencing life span and aging phenotypes between Mouse and humans.

  • doi:10.1093/nar/gkr1061 Mouse Phenome Database (MPD)
    2011
    Co-Authors: Terry P Maddatu, Stephen C Grubb, Carol J Bult, Molly A Bogue
    Abstract:

    The Mouse Phenome Project was launched a decade ago to complement Mouse genome sequencing efforts by promoting new phenotyping initiatives under standardized conditions and collecting the data in a central public Database, the Mouse Phenome Database (MPD

  • Mouse Phenome Database
    Nucleic Acids Research, 2009
    Co-Authors: Stephen C Grubb, Carol J Bult, Molly A Bogue
    Abstract:

    The Mouse Phenome Database (MPD; Phenome.jax.org) was launched in 2001 as the data coordination center for the international Mouse Phenome Project. MPD integrates quantitative phenotype, gene expression and genotype data into a common annotated framework to facilitate query and analysis. MPD contains >3500 phenotype measurements or traits relevant to human health, including cancer, aging, cardiovascular disorders, obesity, infectious disease susceptibility, blood disorders, neurosensory disorders, drug addiction and toxicity. Since our 2012 NAR report, we have added >70 new data sets, including data from Collaborative Cross lines and Diversity Outbred mice. During this time we have completely revamped our homepage, improved search and navigational aspects of the MPD application, developed several web-enabled data analysis and visualization tools, annotated phenotype data to public ontologies, developed an ontology browser and released new single nucleotide polymorphism query functionality with much higher density coverage than before. Here, we summarize recent data acquisitions and describe our latest improvements.

  • doi:10.1093/nar/gkn778 Mouse Phenome Database
    2008
    Co-Authors: Stephen C Grubb, Carol J Bult, Terry P Maddatu, Molly A Bogue
    Abstract:

    The Mouse Phenome Database (MPD

Carol J Bult - One of the best experts on this subject based on the ideXlab platform.

  • doi:10.1093/nar/gkr1061 Mouse Phenome Database (MPD)
    2011
    Co-Authors: Terry P Maddatu, Stephen C Grubb, Carol J Bult, Molly A Bogue
    Abstract:

    The Mouse Phenome Project was launched a decade ago to complement Mouse genome sequencing efforts by promoting new phenotyping initiatives under standardized conditions and collecting the data in a central public Database, the Mouse Phenome Database (MPD

  • Mouse Phenome Database
    Nucleic Acids Research, 2009
    Co-Authors: Stephen C Grubb, Carol J Bult, Molly A Bogue
    Abstract:

    The Mouse Phenome Database (MPD; Phenome.jax.org) was launched in 2001 as the data coordination center for the international Mouse Phenome Project. MPD integrates quantitative phenotype, gene expression and genotype data into a common annotated framework to facilitate query and analysis. MPD contains >3500 phenotype measurements or traits relevant to human health, including cancer, aging, cardiovascular disorders, obesity, infectious disease susceptibility, blood disorders, neurosensory disorders, drug addiction and toxicity. Since our 2012 NAR report, we have added >70 new data sets, including data from Collaborative Cross lines and Diversity Outbred mice. During this time we have completely revamped our homepage, improved search and navigational aspects of the MPD application, developed several web-enabled data analysis and visualization tools, annotated phenotype data to public ontologies, developed an ontology browser and released new single nucleotide polymorphism query functionality with much higher density coverage than before. Here, we summarize recent data acquisitions and describe our latest improvements.

  • Cancer Biology Data Curation at the Mouse Tumor Biology Database (MTB)
    2009
    Co-Authors: Debra M. Krupke, Carol J Bult, Dale A. Begley, Steven B. Neuhauser, Joel E. Richardson, John P. Sundberg, Janan T. Eppig
    Abstract:

    Many advances in the field of cancer biology have been made using Mouse models of human cancer. The Mouse Tumor Biology (MTB, "http://tumor.informatics.jax.org":http://tumor.informatics.jax.org) Database provides web-based access to data on spontaneous and induced tumors from genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice). These data include standardized tumor names and classifications, pathology reports and images, Mouse genetics, genomic and cytogenetic changes occurring in the tumor, strain names, tumor frequency and latency, and literature citations. Although primary source for the data represented in MTB is peer-reviewed scientific literature an increasing amount of data is derived from disparate sources. MTB includes annotated histopathology images and cytogenetic assay images for Mouse tumors where these data are available from The Jackson Laboratory’s Mouse colonies and from outside contributors. MTB encourages direct submission of Mouse tumor data and images from the cancer research community and provides investigators with a web-accessible tool for image submission and annotation. Integrated searches of the data in MTB are facilitated by the use of several controlled vocabularies and by adherence to standard nomenclature. MTB also provides links to other related online resources such as the Mouse Genome Database, Mouse Phenome Database, the Biology of the Mammary Gland Web Site, Festing's Listing of Inbred Strains of Mice, the JAX® Mice Web Site, and the Mouse Models of Human Cancers Consortium's Mouse Repository. MTB provides access to data on Mouse models of cancer via the internet and has been designed to facilitate the selection of experimental models for cancer research, the evaluation of Mouse genetic models of human cancer, the review of patterns of mutations in specific cancers, and the identification of genes that are commonly mutated across a spectrum of cancers. MTB is supported by NCI grant CA089713

  • doi:10.1093/nar/gkn778 Mouse Phenome Database
    2008
    Co-Authors: Stephen C Grubb, Carol J Bult, Terry P Maddatu, Molly A Bogue
    Abstract:

    The Mouse Phenome Database (MPD

  • Mouse Phenome Database mpd
    Nucleic Acids Research, 2007
    Co-Authors: Terry P Maddatu, Stephen C Grubb, Carol J Bult, Molly A Bogue
    Abstract:

    The Mouse Phenome Project was launched a decade ago to complement Mouse genome sequencing efforts by promoting new phenotyping initiatives under standardized conditions and collecting the data in a central public Database, the Mouse Phenome Database (MPD; http://Phenome.jax.org). MPD houses a wealth of strain characteristics data to facilitate the use of the laboratory Mouse in translational research for human health and disease, helping alleviate problems involving experimentation in humans that cannot be done practically or ethically. Data sets are voluntarily contributed by researchers from a variety of institutions and settings, or in some cases, retrieved by MPD staff from public sources. MPD maintains a growing collection of standardized reference data that assists investigators in selecting Mouse strains for research applications; houses treatment/control data for drug studies and other interventions; offers a standardized platform for discovering genotype-phenotype relationships; and provides tools for hypothesis testing. MPD improvements and updates since our last NAR report are presented, including the addition of new tools and features to facilitate navigation and data mining as well as the acquisition of new data (phenotypic, genotypic and gene expression).

Elissa J Chesler - One of the best experts on this subject based on the ideXlab platform.

  • accessing data resources in the Mouse Phenome Database for genetic analysis of murine life span and health span
    Journals of Gerontology Series A-biological Sciences and Medical Sciences, 2016
    Co-Authors: Molly A Bogue, Rong Yuan, Luanne L. Peters, Beverly Paigen, Stephen C Grubb, Gary A Churchill, Ron Korstanje, Cheryl L Ackertbicknell, Elissa J Chesler
    Abstract:

    Understanding the source of genetic variation in aging and using this variation to define the molecular mechanisms of healthy aging require deep and broad quantification of a host of physiological, morphological, and behavioral endpoints. The murine model is a powerful system in which to understand the relations across age-related phenotypes and to identify research models with variation in life span and health span. The Jackson Laboratory Nathan Shock Center of Excellence in the Basic Biology of Aging has performed broad characterization of aging in genetically diverse laboratory mice and has placed these data, along with data from several other major aging initiatives, into the interactive Mouse Phenome Database. The data may be accessed and analyzed by researchers interested in finding Mouse models for specific aging processes, age-related health and disease states, and for genetic analysis of aging variation and trait covariation. We expect that by placing these data in the hands of the aging community that there will be (a) accelerated genetic analyses of aging processes, (b) discovery of genetic loci regulating life span, (c) identification of compelling correlations between life span and susceptibility for age-related disorders, and (d) discovery of concordant genomic loci influencing life span and aging phenotypes between Mouse and humans.

Beverly Paigen - One of the best experts on this subject based on the ideXlab platform.

  • accessing data resources in the Mouse Phenome Database for genetic analysis of murine life span and health span
    Journals of Gerontology Series A-biological Sciences and Medical Sciences, 2016
    Co-Authors: Molly A Bogue, Rong Yuan, Luanne L. Peters, Beverly Paigen, Stephen C Grubb, Gary A Churchill, Ron Korstanje, Cheryl L Ackertbicknell, Elissa J Chesler
    Abstract:

    Understanding the source of genetic variation in aging and using this variation to define the molecular mechanisms of healthy aging require deep and broad quantification of a host of physiological, morphological, and behavioral endpoints. The murine model is a powerful system in which to understand the relations across age-related phenotypes and to identify research models with variation in life span and health span. The Jackson Laboratory Nathan Shock Center of Excellence in the Basic Biology of Aging has performed broad characterization of aging in genetically diverse laboratory mice and has placed these data, along with data from several other major aging initiatives, into the interactive Mouse Phenome Database. The data may be accessed and analyzed by researchers interested in finding Mouse models for specific aging processes, age-related health and disease states, and for genetic analysis of aging variation and trait covariation. We expect that by placing these data in the hands of the aging community that there will be (a) accelerated genetic analyses of aging processes, (b) discovery of genetic loci regulating life span, (c) identification of compelling correlations between life span and susceptibility for age-related disorders, and (d) discovery of concordant genomic loci influencing life span and aging phenotypes between Mouse and humans.

  • Mice as a Mammalian Model for Research on the Genetics of Aging
    ILAR journal, 2011
    Co-Authors: Rong Yuan, Luanne L. Peters, Beverly Paigen
    Abstract:

    Mice are an ideal mammalian model for studying the genetics of aging: considerable resources are available, the generation time is short, and the environment can be easily controlled, an important consideration when performing mapping studies to identify genes that influence lifespan and age-related diseases. In this review we highlight some salient contributions of the Mouse in aging research: lifespan intervention studies in the Interventions Testing Program of the National Institute on Aging; identification of the genetic underpinnings of the effects of calorie restriction on lifespan; the Aging Phenome Project at the Jackson Laboratory, which has submitted multiple large, freely available phenotyping datasets to the Mouse Phenome Database; insights from spontaneous and engineered Mouse mutants; and complex traits analyses identifying quantitative trait loci that affect lifespan. We also show that genomewide association peaks for lifespan in humans and lifespan quantitative loci for mice map to homologous locations in the genome. Thus, the vast bioinformatic and genetic resources of the Mouse can be used to screen candidate genes identified in both Mouse and human mapping studies, followed by functional testing, often not possible in humans, to determine their influence on aging.