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The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease

Mary Shimoyama, Jeff De Pons, G. Thomas Hayman, Stanley J.F. Laulederkind, Weisong Liu, Rajni Nigam, Victoria Petri, Jennifer R. Smith, Marek Tutaj, Shur-Jen Wang, Elizabeth Worthey, Melinda Dwinell (+1 others)
2014 Nucleic Acids Research  
The Rat Genome Database (RGD, http://rgd.mcw.edu) provides the most comprehensive data repository and informatics platform related to the laboratory rat, one of the most important model organisms for disease  ...  This update highlights recent developments that reflect an increasing focus on: (i) genomic variation, (ii) phenotypes and diseases, (iii) data related to the environment and experimental conditions and  ...  INTRODUCTION The Rat Genome Database (RGD) has been the premier resource for rat genetic, genomic and phenotypic data since its creation in 1999.  ... 
doi:10.1093/nar/gku1026 pmid:25355511 pmcid:PMC4383884 fatcat:2wlnpqd725hazik7iphaxaifk4

Exploring human disease using the Rat Genome Database

Mary Shimoyama, Stanley J. F. Laulederkind, Jeff De Pons, Rajni Nigam, Jennifer R. Smith, Marek Tutaj, Victoria Petri, G. Thomas Hayman, Shur-Jen Wang, Omid Ghiasvand, Jyothi Thota, Melinda R. Dwinell
2016 Disease Models & Mechanisms  
Since 1999, the Rat Genome Database (RGD; http://rgd.mcw.edu) has been the premier resource for genomic, genetic, phenotype and strain data for the laboratory rat.  ...  Rattus norvegicus, the laboratory rat, has been a crucial model for studies of the environmental and genetic factors associated with human diseases for over 150 years.  ...  Since the completion of the rat genome sequence in 2004 (Gibbs et al., 2004) , more than 40 inbred rat strains commonly used as disease models have been sequenced and genomic variations among these strains  ... 
doi:10.1242/dmm.026021 pmid:27736745 pmcid:PMC5087824 fatcat:vdsgvhtmfne7vp5ddubf3bp3hy

The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform

2019 Nucleic Acids Research  
Formed in late 1999, the Rat Genome Database (RGD, https://rgd.mcw.edu) will be 20 in 2020, the Year of the Rat.  ...  Since that time, RGD has expanded to include a wealth of structured and standardized genetic, genomic, phenotypic, and disease-related data for eight species, and a suite of innovative tools for querying  ...  INTRODUCTION The Rat Genome Database (RGD, https://rgd.mcw.edu) was created in late 1999, and rapidly became the premier online location for genetic, genomic, phenotypic and diseaserelated data for the  ... 
doi:10.1093/nar/gkz1041 pmid:31713623 pmcid:PMC7145519 fatcat:4a6ja3vobncmtbp7m2hivrebr4

Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database

Shur-Jen Wang, Stanley J. F. Laulederkind, G. Thomas Hayman, Victoria Petri, Jennifer R. Smith, Marek Tutaj, Rajni Nigam, Melinda R. Dwinell, Mary Shimoyama
2016 Physiological Genomics  
To facilitate progress in complex disease research, the Rat Genome Database (RGD) provides the community with a disease portal where genome objects and biological data related to cardiovascular diseases  ...  diovascular diseases are complex diseases caused by a combination of genetic and environmental factors.  ...  In the future, the phenotype database PhenoMiner (http:// www.rgd.mcw.edu/phenotypes/) will be integrated to the disease portals to provide links between genetic variation and quantitative phenotypes.  ... 
doi:10.1152/physiolgenomics.00046.2016 pmid:27287925 pmcid:PMC5005459 fatcat:rcxcvzeumva6rfhzhm6uvc5k7i

Environmentally induced epigenetic transgenerational inheritance of sperm epimutations promote genetic mutations

Michael K Skinner, Carlos Guerrero-Bosagna, M Muksitul Haque
2015 Epigenetics  
A variety of environmental factors have been shown to induce the epigenetic transgenerational inheritance of disease and phenotypic variation.  ...  A combination of epigenetics and genetics is suggested to be involved in the transgenerational phenotypes.  ...  Ethics Statement All experimental protocols for the procedures with rats were pre-approved by the Washington State University Animal Care and Use Committee (IACUC approval # 02568-032).  ... 
doi:10.1080/15592294.2015.1062207 pmid:26237076 pmcid:PMC4622673 fatcat:xtxwlihkwfdnfgwcaoobrbtorq

Programme Booklet Of The 11Th Iscb Student Council Symposium, Dublin, 2015 [article]

Mehedi Hassan, R Gonzalo Parra
2015 Zenodo  
This is a booklet containing programme of the day of the 11th ISCB Student Council Symposium, Dublin, 10 July 2015. This also contains all the abstracts of works presented on the day.  ...  Institute DNA methylation is one of the most widely used markers for the study of epigenetic contributions to phenotypic variation and disease.  ...  environmental effects and variations of genetic effects across environments.  ... 
doi:10.5281/zenodo.1253018 fatcat:b75h2xdwmralzfqdhs6jd6k4vm

DGHM Lecture 2015

2015 International Journal of Medical Microbiology  
Omnilog® Phenotypic Microarray assays, whole-genome sequence and RNA sequence analysis.  ...  to the database.  ...  disease, inappetence, and diarrhoea.  ... 
doi:10.1016/j.ijmm.2015.09.002 fatcat:yuxjcmjr4ffapmmbe54v2jofxy

Third Report on Chicken Genes and Chromosomes 2015

Michael Schmid, Jacqueline Smith, David W. Burt, Bronwen L. Aken, Parker B. Antin, Alan L. Archibald, Chris Ashwell, Perry J. Blackshear, Clarissa Boschiero, C. Titus Brown, Shane C. Burgess, Hans H. Cheng (+92 others)
2015 Cytogenetic and Genome Research  
This has also heralded an explosion in avian genomics, with the current availability of more than 48 bird genomes [Zhang G et al., 2014b; Eöry et al., 2015] , with many more planned.  ...  The First Report highlighted the availability of genetic and physical maps, while the Second Report was published as the chicken genome sequence was released.  ...  species, for example the Ensembl Data available from the Ensembl genome database (www.ensembl.org). gene annotation system [Cunningham et al., 2015] .  ... 
doi:10.1159/000430927 pmid:26282327 pmcid:PMC5120589 fatcat:66epxqpbhrdxpno7n5or4gnbzq

Abstracts from the 3rd International Genomic Medicine Conference (3rd IGMC 2015)

Jerry W. Shay, Noriko Homma, Ruyun Zhou, Muhammad Imran Naseer, Adeel G. Chaudhary, Mohammed Al-Qahtani, Nobutaka Hirokawa, Maryam Goudarzi, Albert J. Fornace, Saleh Baeesa, Deema Hussain, Mohammed Bangash (+992 others)
2016 BMC Genomics  
The authors, therefore, acknowledge with thanks DSR technical and financial support.  ...  Acknowledgements This project was funded by the National Science, Technology and Innovation Plan (MARRIFAH) -King Abdul Aziz City for Science and Technology (KACST), the Kingdom of Saudi Arabia, Award  ...  The Genome-Wide Repository of association between SNPs and phenotype (GRASP v2.0) database has most of the publically available data for diverse phenotypes including total cholesterol [1] .  ... 
doi:10.1186/s12864-016-2858-0 pmid:27454254 pmcid:PMC4959372 fatcat:tukrmp73jbgnncl7ryif4pds6y

Comparative Genome of GK and Wistar Rats Reveals Genetic Basis of Type 2 Diabetes

Tiancheng Liu, Hong Li, Guohui Ding, Zhen Wang, Yunqin Chen, Lei Liu, Yuanyuan Li, Yixue Li, Obul Reddy Bandapalli
2015 PLoS ONE  
Comparing these variations with known rat genome variations and known human T2D-associated genes, we obtained 192 candidate genes including 15 with high confidence that may be associated with the T2D phenotype  ...  Our result reveals that the T2D phenotype may be caused by the accumulation of multiple variations in GK rat, and that the mutated genes may affect biological functions including adipocytokine signaling  ...  ., Ltd for sequencing and technical support. We also appreciate critical reading and valuable comments from Dr. Alton Etheridge.  ... 
doi:10.1371/journal.pone.0141859 pmid:26529237 pmcid:PMC4631338 fatcat:ifojodf2bza4zhwacf6vctah2q

GeneWeaver: finding consilience in heterogeneous cross-species functional genomics data

Jason A. Bubier, Charles A. Phillips, Michael A. Langston, Erich J. Baker, Elissa J. Chesler
2015 Mammalian Genome  
Harmonizing and analyzing this data will enable investigators to discover relations of many genes to many diseases, and from many phenotypes and experimental paradigms to many diseases through their genomic  ...  curated repositories, including the Mouse Genome Database and other model organism databases, along with derived data from highly specialized resources, publications, and user submissions.  ...  , and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.  ... 
doi:10.1007/s00335-015-9575-x pmid:26092690 pmcid:PMC4602068 fatcat:ig3gxodwzjezzevoyqy2dwsrvu

2015 Annual Meeting Program

The Ohio Academy of Science
2015 The Ohio journal of science  
Abstracts from the 2015 OAS Annual Meeting  ...  Colleagues and/or sources of financial support to whom thanks are due for assistance rendered in completion of the research or preparation of the manuscript should be recognized in this section rather  ...  than in the body of the text.  ... 
doi:10.18061/ojs.v115i1.4844 fatcat:rtzvu5ltcjcsloj2syy3lqa7d4

Human Health Biotechnologies to 2015

Anthony Arundel, Ioana Valeanu, David Sawaya
2009 OECD Journal General Papers  
, and/or prescribing of nearly all new drugs by 2015.  ...  by 2015.  ...  Correlation of genomic markers with clinical phenotypes Identify drug targets Toxicogenomics In vitro pharmacogenetic studies Study relationship between genetic variation and drug response  ... 
doi:10.1787/gen_papers-2009-5kmjkjtfxdg7 fatcat:jnk726fhgvefxehyww4gldsemi

Epigenetics and the burden of noncommunicable disease: a paucity of research in Africa

Angela Hobbs, Michèle Ramsay
2015 Epigenomics  
This emphasizes the need to build capacity in Africa for research that leads to an understanding of the association between genetic, epigenetic and environmental risk factors for noncommunicable diseases  ...  , only a small percentage of genomic and epigenetic studies have focused on populations from this continent.  ...  The effect of fixed genetic variation on DNA methylation When interpreting the role of epigenetic variation in a complex disease, it is important to consider both fixed genetic variation and environmental  ... 
doi:10.2217/epi.15.17 pmid:26111033 fatcat:q4acfm2hdfaxrptbvzltbf4lvy

Abstracts: 3rd Annual Congress of the European Society for Translational Medicine (EUSTM-2015) 1-4 September, 2015, Vienna, Austria

Aamir Shahzad, Randall J Cohrs
2015 European Journal of Molecular and Clinical Medicine  
Health promotion interventions should start at the community level, in primary and secondary schools, encouraging local and national active involvement.  ...  at enhancing and establishing a healthier dietary pattern.  ...  from those in paired normal tissue of the same organs and correlating with the clinical phenotype of the disease and, in some cases, with responsiveness to therapy.  ... 
doi:10.1016/j.nhtm.2015.12.001 fatcat:eolsgmzrlzas3gml6f2dox6vty
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