Other Recent RGD Publications:

Rare Disease Research Resources at the Rat Genome Database.
Kaldunski ML, Smith JR, Brodie KC, De Pons JL, Demos WM, Gibson AC, Hayman GT, Lamers L, Laulederkind SJF, Thorat K, Thota J, Tutaj MA, Tutaj M, Vedi M, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. Rare Disease Research Resources at the Rat Genome Database. Genetics. 2023 Apr 29:iyad078. doi: 10.1093/genetics/iyad078. Epub ahead of print. PMID: 37119810.

2022 updates to the Rat Genome Database: a Findable, Accessible, Interoperable, and Reusable (FAIR) resource.
Vedi M, Smith JR, Hayman GT, Tutaj M, Brodie KC, De Pons JL, Demos WM, Gibson AC, Kaldunski ML, Lamers L, Laulederkind SJF, Thota J, Thorat K, Tutaj MA, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. Genetics, 2023:iyad042. doi: 10.3390/genes13122304.
PMID: 36930729

Ontological analysis of Coronavirus associated human genes at the COVID-19 Disease Portal.
Wang SJ, Brodie KC, De Pons JL, Demos WM, Gibson AC, Hayman GT, Hill ML, Kaldunski ML, Lamers L, Laulederkind SJF, Nalabolu HS, Thota J, Thorat K, Tutaj MA, Tutaj M, Vedi M, Zacher S, Smith JR, Dwinell MR, Kwitek AE. Genes (Basel). 2022 Dec 7;13(12):2304. doi: 10.3390/genes13122304.
PMID: 36553571

MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses.
Vedi M, Nalabolu HS, Lin CW, Hoffman MJ, Smith JR, Brodie K, De Pons JL, Demos WM, Gibson AC, Hayman GT, Hill ML, Kaldunski ML, Lamers L, Laulederkind SJF, Thorat K, Thota J, Tutaj M, Tutaj MA, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. Genetics. 2022. 220(4):iyac005. doi: 10.1093/genetics/iyac005.
PMID: 35380657

The Rat Genome Database (RGD) facilitates genomic and phenotypic data integration across multiple species for biomedical research.
Kaldunski ML, Smith JR, Hayman GT, Brodie K, De Pons JL, Demos WM, Gibson AC, Hill ML, Hoffman MJ, Lamers L, Laulederkind SJF, Nalabolu HS, Thorat K, Thota J, Tutaj M, Tutaj MA, Vedi M, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. Mamm Genome. 2021. 48(D1):D731-D742. https://doi.org/10.1007/s00335-021-09932-x.
PMID: 34741192

The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform.
Smith JR, Hayman GT, Wang SJ, Laulederkind SJF, Hoffman MJ, Kaldunski ML, Tutaj M, Thota J, Nalabolu HS, Ellanki SLR, Tutaj MA, De Pons JL, Kwitek AE, Dwinell MR, Shimoyama ME.
Nucleic Acids Res. 2019. pii: gkz1041. doi: 10.1093/nar/gkz1041.
PMID:31713623

Rat Genomics
Editors: G. Thomas Hayman, Jennifer R. Smith, Melinda R. Dwinell, Mary Shimoyama
Methods in Molecular Biology book series (MIMB, volume 2018)

The Rat: A Model Used in Biomedical Research.
Smith JR, Bolton ER, Dwinell MR.
Methods Mol Biol. 2019;2018:1-41. doi: 10.1007/978-1-4939-9581-3_1.
PMID:31228150

Rat Genome Assemblies, Annotation, and Variant Repository.
Tutaj M, Smith JR, Bolton ER.
Methods Mol Biol. 2019;2018:43-70. doi: 10.1007/978-1-4939-9581-3_2.
PMID: 31228151

Rat Genome Databases, Repositories, and Tools.
Laulederkind SJF, Hayman GT, Wang SJ, Hoffman MJ, Smith JR, Bolton ER, De Pons J, Tutaj MA, Tutaj M, Thota J, Dwinell MR, Shimoyama M.
Methods Mol Biol. 2019;2018:71-96. doi: 10.1007/978-1-4939-9581-3_3.
PMID: 31228152

Quantitative phenotype analysis to identify, validate and compare rat disease models.
Zhao Y, Smith JR, Wang SJ, Dwinell MR, Shimoyama M.
Database (Oxford). 2019 Jan 1;2019. pii: baz037. doi: 10.1093/database/baz037.
PMID: 30938777

Integrated curation and data mining for disease and phenotype models at the Rat Genome Database.
Wang SJ, Laulederkind SJF, Zhao Y, Hayman GT, Smith JR, Tutaj M, Thota J, Tutaj MA, Hoffman MJ, Bolton ER, De Pons J, Dwinell MR, Shimoyama M.
Database (Oxford). 2019 Jan 1;2019. doi: 10.1093/database/baz014.
PMID: 30753478

A Primer for the Rat Genome Database (RGD).
Laulederkind SJF, Hayman GT, Smith JR, Wang SJ, Petri V, De Pons J, Tutaj MA, Ghiasvand O, Thota J, Dwinell MR, Shimoyama M. Methods Mol Biol. 2018; 1757:163-209.
PMID:29761460

Rat Genome and Model Resources.
Shimoyama M, Smith JR, Bryda E, Kuramoto T, Saba L, Dwinell M. ILAR J. 2017 Jul; 58:42-58.
PMID:28838068

Exploring human disease using the Rat Genome Database.
Shimoyama M, Laulederkind SJ, De Pons J, Nigam R, Smith JR, Tutaj M, Petri V, Hayman GT, Wang SJ, Ghiasvand O, Thota J, Dwinell MR. Dis Model Mech. 2016 Oct; 9:1089-1095.
PMID:27736745

Disease, models, variants and altered pathways – journeying RGD through the magnifying glass.
Petri V, Hayman GT, Tutaj M, Smith JR, Laulederkind SJ, Wang SJ, Nigam R, De Pons J, Shimoyama M, Dwinell MR. Comput Struct Biotechnol J. 2015 Nov; 14:35-48.
PMID:27602200

Comprehensive coverage of cardiovascular disease data in the Disease Portals at the Rat Genome Database.
Wang SJ, Laulederkind SJ, Hayman GT, Petri V, Smith JR, Tutaj M, Nigam R, Dwinell MR, Shimoyama M. Physiol Genomics. 2016 Jun; doi: 10.1152/physiolgenomics.00046.2016.
PMID:27287925

The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database.
Hayman GT, Laulederkind SJ, Smith JR, Wang SJ, Petri V, Nigam R, Tutaj M, De Pons J, Dwinell MR, Shimoyama M. Database (Oxford). 2016 Mar; doi: 10.1093/database/baw034.
PMID:27009807

The Chinchilla Research Resource Database: resource for an otolaryngology disease model.
Shimoyama M, Smith JR, De Pons J, Tutaj M, Khampang P, Hong W, Erbe CB, Ehrlich GD, Bakaletz LO, Kerschner JE. Database (Oxford). 2016 May; doi: 10.1093/database/baw073.
PMID:27173523

PhenoMiner: a quantitative phenotype database for the laboratory rat, Rattus norvegicus. Application in hypertension and renal disease.
Wang SJ, Laulederkind SJ, Hayman GT, Petri V, Smith JR, Nigam R, Dwinell MR, Shimoyama M. Database (Oxford). 2015 Jan; doi: 10.1093/database/bau128.
PMID:25632109

OntoMate: a text-mining tool aiding curation at the Rat Genome Database.
Liu W, Laulederkind SJ, Hayman GT, Wang SJ, Nigam R, Smith JR, De Pons J, Dwinell MR, Shimoyama M. Database (Oxford). 2015 Jan; doi: 10.1093/database/bau129.
PMID:25619558

The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease.
Shimoyama M, De Pons J, Hayman GT, Laulederkind SJ, Liu W, Nigam R, Petri V, Smith JR, Tutaj M, Wang SJ, Worthey E, Dwinell M, Jacob H. Nucleic Acids Res. 2015 Jan 28;43(Database issue):D743-50.
PMID:25355511

Gene Ontology Consortium: going forward.
Blake JA, Christie KR, Dolan M, Drabkin H, Hill DP, Li N, Sitnikov D, Burgess S, Buza T, Gresham C, McCarthy F, Pillai L, Wang H, Carbon S, Dietze H, Lewis SE, Mungall CJ, Munoz-Torres MC, Feuermann M, Gaudet P, Basu S, Chrisholm RL, Dodson RJ, Fey P, Mi H, Thomas PD, Muruganujan A, Poudel S, Hu JC, Aleksander SA, McIntosh BK, Renfro DP, Siegele DA, Atrill H, Brown NH, Tweedie S, Lomax J, Osumi-Sutherland D, Parkinson H, Roncaglia P, Lovering RC, Talmud PJ, Humphries SE, Denny P, Campbell NH, Foulger RE, Chibucos M, Gwinn Giglio M, Chang HY, Finn R, Fraser M, Mitchell A, Nuka G, Pesseat S, Sangrador A, Scheremetjew M, Young SY, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J, Lock A, Kersey PJ, McDowall DM, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman GT, Wang SJ, Petri V, D’Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Costanzo MC, Demeter J, Dwight SS, Engel SR, Hitz BC, Inglis DO, Lloyd P, Miyasato SR, Paskov K, Roe G, Simison RS, Nash RS, Skrzypek MS, Weng S, Wong ED, Berardini TZ, Li D, Huala E, Argasinska J, Arighi C, Auchinchloss A, Axelsen K, Argoud-Puy G, Bateman A, Bely B, Blatter MC, Bonilla C, Bouguerleret L, Boutet E, Breuza L, Bridge A, Britto R, Casals C, Cibrian-Uhalte E, Coudert E, Cusin I, Duek-Roggli P, Estreicher A, Famiglietti L, Gane P, Garmiri P, Gos A, Gruaz-Gumowski N, Hatton-Ellis E, Hinz U, Hulo C, Huntley R, Jungo F, Keller G, Laiho K, Lemercier P, Lieberherr D, MacDougall A, Magrane M, Martin M, Masson P, Mutowo P, O’Donovan C, Pedruzzi I, Pichler K, Poggioli D, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Shypitsyna A, Stutz A, Sundaram S, Tognolli M, Wu C, Xenarios I, Chan J, Kishore R, Sternberg P, Van Auken K, Muller HM, Done J, Li Y, Howe D, Westerfield M. Nucleic Acids Res. 2015 Jan; 43(Database issue):D1049-D1056.
PMID:25428369

Disease pathways at the Rat Genome Database Pathway Portal: genes in context – a network approach to understanding the molecular mechanisms of disease.
Petri V, Hayman GT, Tutaj M, Smith JR, Laulederkind SJF, Wang S-J, Nigam R, De Pons J,  Shimoyama M, Dwinell MR, Worthey EA, Jacob HJ. Hum Genomics. 2014 Sep; 8(1):17.
PMID:25265995

The pathway ontology – updates and applications.
Petri V, Jayaraman P, Tutaj M, Hayman GT, Smith JR, De Pons J, Laulederkind SJ, Lowry TF, Nigam R, Wang SJ, Shimoyama M, Dwinell MR, Munzenmaier DH, Worthey EA, Jacob HJ. J Biomed Semantics. 2014 Feb; 5(1):7.
PMID:24499703

Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD.
Nigam R, Munzenmaier DH, Worthey EA, Dwinell MR,  Shimoyama M, Jacob HJ. J Biomed Semantics. 2013 Nov; 4(1):36.
PMID:24267899

The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.
Smith JR, Park CA, Nigam R, Laulederkind SJ, Hayman GT, Wang SJ, Lowry TF, Petri V, De Pons J, Tutaj M, Liu W, Worthey EA, Shimoyama M, Dwinell MR. J Biomed Semantics. 2013 Oct; 4(1):26.
PMID:24103152

Rat Genome Database: A unique resource for rat, human and mouse quantitative trait locus data.
Nigam R, Laulederkind SJ, Hayman GT, Smith JR, Wang SJ, Lowry TF, Petri V, De Pons J, Tutaj M, Liu W, Jayaraman P, Munzenmaier DH, Worthey EA, Dwinell MR, Shimoyama M, Jacob HJ.
Physiol Genomics. 2013 Sep; 45(18):809-16.
PMID:23881287

The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species.
Park CA, Bello SM, Smith CL, Hu ZL, Munzenmaier DH, Nigam R, Smith JR, Shimoyama M, Eppig JT, Reecy JM.
J Biomed Semantics. 2013 Aug; 4(1):13.
PMID:23937709

Analysis of disease-associated objects at the Rat Genome Database.
Wang SJ, Laulederkind SJ, Hayman GT, Smith JR, Petri V, Lowry TF, Nigam R, Dwinell MR, Worthey EA, Munzenmaier DH, Shimoyama M, Jacob HJ.
Database (Oxford). 2013 Jun; doi:10.1093/database/bat046.
PMID:23794737

PhenoMiner: quantitative phenotype curation at the rat genome database.
Laulederkind SJ, Liu W, Smith JR, Hayman GT, Wang SJ, Nigam R, Petri V, Lowry TF, De Pons J, Dwinell MR, Shimoyama M.
Database (Oxford). 2013 Apr; doi:10.1093/database/bat015.
PMID:23603846

The Rat Genome Database 2013–data, tools and users.
Laulederkind SJ, Hayman GT, Wang SJ, Smith JR, Lowry TF, Nigam R, Petri V, De Pons J, Dwinell MR, Shimoyama M.
Brief Bioinform. 2013 Feb; doi:10.1093/bib/bbt007.
PMID:23434633

The updated RGD Pathway Portal utilizes increased curation efficiency and provides expanded pathway information.
Hayman GT, Jayaraman P, Petri V, Tutaj M, Liu W, De Pons J, Dwinell MR, Shimoyama M, Worthey E, Munzenmaier DH, Jacob HJ.
Hum Genomics. 2013 Feb; 7(1):4.
PMID:23379628

Gene Ontology annotation and resources.
Blake JA, Dolan M, Drabkin H, Hill DP, Ni L, Sitnikov D, Bridges S, Burgess S, Buza T, McCarthy F, Peddinti D, Pillai L, Carbon S, Dietze H, Lewis SE, Mungall CJ, Gaudet P, Chisholm RL, Fey P, Kibbe WA, Basu S, Siegele DA, McIntosh BK, Renfro DP, Zweifel AE, Hu JC, Brown NH, Tweedie S, Alam-Faruque Y, Apweiler R, Auchinchloss A, Axelsen K, Bely B, Blatter MC, Bonilla C, Bougueleret L, Boutet E, Breuza L, Bridge A, Chan WM, Chavali G, Coudert E, Dimmer E, Estreicher A, Famiglietti L, Feuermann M, Gos A, Gruaz-Gumowski N, Hieta R, Hinz U, Hulo C, Huntley R, James J, Jungo F, Keller G, Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, Martin MJ, Masson P, Mutowo-Muellenet P, O’Donovan C, Pedruzzi I, Pichler K, Poggioli D, Millán P, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Stutz A, Sundaram S, Tognolli M, Xenarios I, Foulger R, Lomax J, Roncaglia P, Khodiyar VK, Lovering RC, Talmud PJ, Chibucos M, Giglio M, Chang HY, Hunter S, McAnulla C, Mitchell A, Sangrador A, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J, Lock A, Kersey PJ, McDowall MD, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman T, Wang S-, Petri V, Lowry T, D’Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hitz BC, Hong EL, Karra K, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED, Berardini TZ, Li D, Huala E, Mi H, Thomas P, Chan J, Kishore R, Sternberg P, Van Auken K, Howe D, Westerfield M. Nucleic Acids Res. 2013 Jan; 41(Database issue):D530-D535.
PMID:23161678

Exploring genetic, genomic, and phenotypic data at the rat genome database.
Laulederkind SJ, Hayman GT, Wang SJ, Lowry TF, Nigam R, Petri V, Smith JR, Dwinell MR, Jacob HJ, Shimoyama M.
Curr Protoc Bioinformatics. 2012 Dec; Chapter 1:Unit 1.
PMID:23255149

Three ontologies to define phenotype measurement data.
Shimoyama M, Nigam R, McIntosh LS, Nagarajan R, Rice T, Rao DC, Dwinell MR.
Front Genet. 2012 May; 3:87.
PMID:22654893

Model organism databases in behavioral neuroscience.
Shimoyama M, Smith JR, Hayman GT, Petri V, Nigam R.
Int Rev Neurobiol. 2012;104:25-46.
PMID:23195310

Ontology searching and browsing at the Rat Genome Database.
Laulederkind SJ, Tutaj M, Shimoyama M, Hayman GT, Lowry TF, Nigam R, Petri V, Smith JR, Wang SJ, de Pons J, Dwinell MR, Jacob HJ.
Database (Oxford). 2012 Mar; doi:10.1093/database/bas016.
PMID:22434847

The Gene Ontology: enhancements for 2011.
Blake JA, Dolan M, Drabkin H, Hill DP, Ni L, Sitnikov D, Burgess S, Buza T, Gresham C, McCarthy F, Pillai L, Wang H, Carbon S, Lewis SE, Mungall CJ, Gaudet P, Chisholm RL, Fey P, Kibbe WA, Basu S, Siegele DA, McIntosh BK, Renfro DP, Zweifel AE, Hu JC, Brown NH, Tweedie S, Alam-Faruque Y, Apweiler R, Auchinchloss A, Axelsen K, Argoud-Puy G, Bely B, Blatter M-, Bougueleret L, Boutet E, Branconi S, Breuza L, Bridge A, Browne P, Chan WM, Coudert E, Cusin I, Dimmer E, Duek-Roggli P, Eberhardt R, Estreicher A, Famiglietti L, Ferro-Rojas S, Feuermann M, Gardner M, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, Huntley R, James J, Jimenez S, Jungo F, Keller G, Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, Martin MJ, Masson P, Moinat M, O’Donovan C, Pedruzzi I, Pichler K, Poggioli D, Porras Millán P, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Sehra H, Stanley E, Stutz A, Sundaram S, Tognolli M, Xenarios I, Foulger R, Lomax J, Roncaglia P, Camon E, Khodiyar VK, Lovering RC, Talmud PJ, Chibucos M, Gwinn Giglio M, Dolinski K, Heinicke S, Livstone MS, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J, Lock A, Kersey PJ, McDowall MD, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman T, Wang S-, Petri V, Lowry T, D’Eustachio P, Matthews L, Amundsen CD, Balakrishnan R, Binkley G, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED, Berardini TZ, Li D, Huala E, Slonim D, Wick H, Thomas P, Chan J, Kishore R, Sternberg P, Van Auken K, Howe D, Westerfield M. Nucleic Acids Res. 2012 Jan; 40(Database issue):D559-D564.
PMID:22102568

Recent RGD Member Publications:

Disease Ontology: improving and unifying disease annotations across species.
Bello SM, Shimoyama M, Mitraka E, Laulederkind SJF, Smith CL, Eppig JT, Schriml LM. Dis Model Mech. 2018 Mar; doi: 10.1242/dmm.032839.
PMID:29590633

Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology.
Lovering RC, Roncaglia P, Howe DG, Laulederkind SJF, Khodiyar VK, Berardini TZ, Tweedie S, Foulger RE, Osumi-Sutherland D, Campbell NH, Huntley RP, Talmud PJ, Blake JA, Breckenridge R, Riley PR, Lambiase PD, Elliott PM, Clapp L, Tinker A, Hill DP. Circ Genom Precis Med. 2018 Feb; doi: 10.1161/CIRCGEN.117.001813.
PMID:29440116

Successful Application of Whole Genome Sequencing in a Medical Genetics Clinic.
Bick D, Fraser PC, Gutzeit MF, Harris JM, Hambuch TM, Helbling DC, Jacob HJ, Kersten JN, Leuthner SR, May T, North PE, Prisco SZ, Schuler BA, Shimoyama M, Strong KA, Van Why SK, Veith R, Verbsky J, Weborg AM Jr, Wilk BM, Willoughby RE Jr, Worthey EA, Dimmock DP. J Pediatr Genet. 2017 Jun; 6(2):61-76.
PMID:28496993

The Human Phenotype Ontology in 2017.
Köhler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Aymé S, Baynam G, Bello SM, Boerkoel CF, Boycott KM, Brudno M, Buske OJ, Chinnery PF, Cipriani V, Connell LE, Dawkins HJ, DeMare LE, Devereau AD, de Vries BB, Firth HV, Freson K, Greene D, Hamosh A, Helbig I, Hum C, Jähn JA, James R, Krause R, Laulederkind SJ, Lochmüller H, Lyon GJ, Ogishima S, Olry A, Ouwehand WH, Pontikos N, Rath A, Schaefer F, Scott RH, Segal M, Sergouniotis PI, Sever R, Smith CL, Straub V, Thompson R, Turner C, Turro E, Veltman MW, Vulliamy T, Yu J, von Ziegenweidt J, Zankl A, Züchner S, Zemojtel T, Jacobsen JO, Groza T, Smedley D, Mungall CJ, Haendel M, Robinson PN. Nucleic Acids Res. 2016 Nov; doi:10.1093/nar/gkw1039.
PMID:27899602

Ndufc2 Gene Inhibition Is Associated With Mitochondrial Dysfunction and Increased Stroke Susceptibility in an Animal Model of Complex Human Disease.
Rubattu S, Di Castro S, Schulz H, Geurts AM, Cotugno M, Bianchi F, Maatz H, Hummel O, Falak S, Stanzione R, Marchitti S, Scarpino S, Giusti B, Kura A, Gensini GF, Peyvandi F, Mannucci PM, Rasura M, Sciarretta S, Dwinell MR, Hubner N, Volpe M. J Am Heart Assoc. 2016 Feb; 5(2):e002701.
PMID:26888427

Guidelines for the functional annotation of microRNAs using the Gene Ontology.
Huntley RP, Sitnikov D, Orlic-Milacic M, Balakrishnan R, D’Eustachio P, Gillespie ME, Howe D, Kalea AZ, Maegdefessel L, Osumi-Sutherland D, Petri V, Smith JR, Van Auken K, Wood V, Zampetaki A, Mayr M, Lovering RC. RNA. 2016 Feb; 22(5):667-676.
PMID:26917558

2015 guidelines for establishing genetically modified rat models for cardiovascular research.
Flister MJ, Prokop JW, Lazar J, Shimoyama M, Dwinell M, Geurts A. J Cardiovasc Transl Res. 2015 Apr; 8(4):269-77.
PMID:25920443

Plasma genetic and genomic abnormalities predict treatment response and clinical outcome in advanced prostate cancer.
Xia S, Kohli M, Du M, Dittmar RL, Lee A, Nandy D, Yuan T, Guo Y, Wang Y, Tschannen MR, Worthey E, Jacob H, See W, Kilari D, Wang X, Hovey RL, Huang CC, Wang L. Oncotarget. 2015 Apr; 6(18):16411-21.
PMID:25915538

Prostate cancer risk locus at 8q24 as a regulatory hub by physical interactions with multiple genomic loci across the genome.
Du M, Yuan T, Schilter KF, Dittmar RL, Mackinnon A, Huang X, Tschannen M, Worthey E, Jacob H, Xia S, Gao J, Tillmans L, Lu Y, Liu P, Thibodeau SN, Wang L. Hum Mol Genet. 2015 Jan; 24(1):154-160.
PMID:25149474

Structural libraries of protein models for multiple species to understand evolution of the renin-angiotensin system.
Prokop JW, Petri V, Shimoyama ME, Watanabe IK, Casarini DE, Leeper TC, Bilinovich SM, Jacob HJ, Santos RA, Martins AS, Araujo FC, Reis FM, Milsted A. Gen Comp Endocrinol. 2014 Sep; doi:10.1016/j.ygcen.2014.09.010.
PMID:25260253

Overview of the gene ontology task at BioCreative IV.
Mao Y, Van Auken K, Li D, Arighi CN, McQuilton P, Hayman GT, Tweedie S, Schaeffer ML, Laulederkind SJ, Wang SJ, Gobeill J, Ruch P, Luu AT, Kim JJ, Chiang JH, Chen YD, Yang CJ, Liu H, Zhu D, Li Y, Yu H, Emadzadeh E, Gonzalez G, Chen JM, Dai HJ, Lu Z. Database (Oxford). 2014 Aug; doi:10.1093/database/bau086.
PMID:25157073

BC4GO: a full-text corpus for the BioCreative IV GO task.
Van Auken K, Schaeffer ML, McQuilton P, Laulederkind SJ, Li D, Wang SJ, Hayman GT, Tweedie S, Arighi CN, Done J, Müller HM, Sternberg PW, Mao Y, Wei CH, Lu Z. Database (Oxford). 2014 Jul; doi:10.1093/database/bau074.
PMID:25070993

Matching the pace of genomic advances through the integration of genomic education into high school health education.
Zusevics KL, Strong KA, Farrell MH, Shimoyama ME. J Sch Health. 2014 Jun; 84(6):351-4.
PMID:24749916

EHR-based phenome wide association study in pancreatic cancer. Adamusiak T, Shimoyama M. AMIA Jt Summits Transl Sci Proc. 2014 Apr; 2014:9-15.
PMID:25717392

Characterization of biological pathways associated with a 1.37 Mbp genomic region protective of hypertension in Dahl S rats. Cowley AW Jr, Moreno C, Jacob HJ, Peterson CB, Stingo FC, Ahn KW, Liu P, Vannucci M, Laud PW, Reddy P, Lazar J, Evans L, Yang C, Kurth T, Liang M. Physiol Genomics. 2014 Apr; doi:10.1152/physiolgenomics.00179.2013
PMID:24714719

Next generation phenotyping using the unified medical language system.
Adamusiak T, Shimoyama N, Shimoyama M. JMIR Med Inform. 2014 Mar; 2(1):e5.
PMID:25601137

A172: Metaphyseal chondrodysplasia, ectodermal dysplasia, short stature, hypergammaglobulinemia, and spontaneous inflammation Without Infections in an extended family due to mutation in NFKB1A.
Oberle EJ, Verbsky JW, Routes J, Hintermeyer M, Worthey E, Dasu T, Bengtson C, Buzzell A. Arthritis Rheumatol. 2014 Mar; 66 Suppl 11:S224-5.

In the absence of evidentiary harm, existing societal norms regarding parental authority should prevail.
Strong KA, Derse AR, Dimmock DP, Zusevics KL, Jeruzal J, Worthey E, Bick D, Scharer G, La Pean Kirschner A, Spellecy R, Farrell MH, Geurts J, Veith R, May T. Am J Bioeth. 2014 Mar; 14(3):24-6.
PMID:24592835

Amelioration of salt-induced vascular dysfunction in mesenteric arteries of Dahl salt-sensitive rats by missense mutation of extracellular superoxide dismutase.
Beyer AM, Raffai G, Weinberg BD, Fredrich K, Rodgers MS, Geurts AM, Jacob HJ, Dwinell MR, Lombard JH. Am J Physiol Heart Circ Physiol. 2014 Feb; 306(3):H339-47.
PMID:24322611

IreB, a Ser/Thr Kinase Substrate, Influences Antimicrobial Resistance in Enterococcus faecalis.
Hall CL, Tschannen M, Worthey EA, Kristich CJ. Antimicrob Agents Chemother. 2013 Dec; 57(12):6179-86.
PMID:24080657

Identifying multiple causative genes at a single GWAS locus.
Flister MJ, Tsaih SW, O’Meara CC, Endres B, Hoffman MJ, Geurts AM, Dwinell MR, Lazar J, Jacob HJ, Moreno C. Genome res. 2013 Dec; 23(12):1996-2002.
PMID:24006081

Targeting the endothelial progenitor cell surface proteome to identify novel mechanisms that mediate angiogenic efficacy in a rodent model of vascular disease.
Kaczorowski CC, Stodola TJ, Hoffmann BR, Prisco AR, Liu PY, Didier DN, Karcher JR, Liang M, Jacob HJ, Greene AS. Physiol Genomics. 2013 Nov; 45(21):999-1011.
PMID:24022221

Analysis and annotation of whole-genome or whole-exome sequencing-derived variants for clinical diagnosis.
Worthey EA. Curr Protoc Hum Genet. 2013 Oct; 79:Unit9.24.
PMID:24510652

Next-generation sequencing for clinical diagnostics.
Jacob HJ. N Engl J Med. 2013 Oct; 369(16):1557-8.
PMID:24088040

Whole-exome sequencing supports genetic heterogeneity in childhood apraxia of speech.
Worthey EA, Raca G, Laffin JJ, Wilk BM, Harris JM, Jakielski KJ, Dimmock DP, Strand EA, Shriberg LD. J Neurodev Disord. 2013 Oct; 5(1):29.
PMID:24083349

FMRI and fcMRI phenotypes map the genomic effect of chromosome 13 in Brown Norway and Dahl salt-sensitive rats. Li Z, Ward BD, Dwinell MR, Lombard JH, Pawela CP. Neuroimage. 2013 Sep; doi:10.1016/j.neuroimage.2013.09.049.
PMID:24084065

Genomics in clinical practice:lessons from the front lines.
Jacob HJ, Abrams K, Bick DP, Brodie K, Dimmock DP, Farrell M, Geurts J, Harris J, Helbling D, Joers BJ, Kliegman R, Kowalski G, Lazar J, Margolis DA, North P, Northup J, Roquemore-Goins A, Sharer G, Shimoyama M, Strong K, Taylor B, Tsaih SW, Tschannen MR, Veith RL, Wendt-Andrae J, Wilk B, Worthey EA. Sci Transl Med. 2013 Jul; 5(194):194cm5.
PMID:23863829

InterMOD: integrated data and tools for the unification of model organism research.
Sullivan J, Karra K, Moxon SA, Vallejos A, Motenko H, Wong JD, Aleksic J, Balakrishnan R, Binkley G, Harris T, Hitz B, Jayaraman P, Lyne R, Neuhauser S, Pich C, Smith RN, Trinh Q, Cherry JM, Richardson J, Stein L, Twigger S, Westerfield M, Worthey E, Micklem G. Sci Rep. 2013 May; 3:1802.
PMID:23652793

Derivation and genetic modification of embryonic stem cells from disease-model inbred rat strains.
Yang S, Takizawa A, Foeckler J, Zappa A, Gjoka M, Schilling R, Hansen C, Xu H, Kalloway S, Grzybowski M, Davis GD, Jacob HJ, Geurts AM. Stem Cells Dev. 2013 May; doi:10.1089/scd.2012.0416.
PMID:23635087

Copy number variation analysis in 98 individuals with PHACE syndrome.
Siegel DH, Shieh JT, Kwon EK, Baselga E, Blei F, Cordisco M, Dobyns WB, Duffy KJ, Garzon MC, Gibbs DL, Grimmer JF, Hayflick SJ, Krol AL, Kwok PY, Lorier R, Matter A, McWeeney S, Metry D, Mitchell S, Pope E, Santoro JL, Stevenson DA, Bayrak-Toydemir P, Wilmot B, Worthey EA, Frieden IJ, Drolet BA, Broeckel U. J Invest Dermatol. 2013 Mar; 133(3):677-84.
PMID:23096700

Chromosome substitution modulates resistance to ischemia reperfusion injury in Brown Norway rats.
Basile DP, Dwinell MR, Wang SJ, Shames BD, Donohoe DL, Chen S, Sreedharan R, Van Why SK. Kidney Int. 2013 Feb; 83(2):242-250.
PMID:23235564

Genome interpretation and assembly-recent progress and next steps.
Baker S, Joecker A, Church G, Snyder M, West J, Salzberg S, Worthey E, Smith T, Wang J, Reid JG. Nat Biotechnol. 2012 Nov; 30(11):1081-3.
PMID:23138307

Multiscale modeling and data integration in the virtual physiological rat project.
Beard DA, Neal ML, Tabesh-Saleki N, Thompson CT, Bassingthwaighte JB, Shimoyama M, Carlson BE. Ann Biomed Eng. 2012 Nov;  40(11):2365-78.
PMID:22805979
Erratum: Ann Biomed Eng. 2012 Nov; 40(11):2501.

Clinical diagnostic whole genome sequencing in a paediatric population: experience from our WGS genetics clinic.
Worthey E, Bick D, Dimmock D, Shimoyama M, Veith R, Kowalski G, Taylor B, Wilk B, Tsaih S, Harris J, Tschannen M, Wendt-Andrae J, Brodie K, Jacob H. BMC Proceedings. 2012 Oct; 6(Suppl 6):011.
PMID:23046958

In the beginning there was babble…
Klionsky DJ, Bruford EA, Cherry JM, Hodgkin J, Laulederkind SJ, Singer AG. Autophagy. 2012 Aug; 8(8):1165-1167.
PMID:22836666

A prioritization analysis of disease association by data-mining of functional annotation of human genes.
Taniya T, Tanaka S, Yamaguchi-Kabata Y, Hanaoka H, Yamasaki C, Maekawa H, Barrero RA, Lenhard B, Datta MW, Shimoyama M, Bumgarner R, Chakraborty R, Hopkinson I, Jia L, Hide W, Auffray C, Minoshima S, Imanishi T, Gojobori T. Genomics. 2012 Jan; 99(1):1-9.
PMID:22019378

Previous RGD Publications:

Pathway Resources at the Rat Genome Database: A Dynamic Platform for Integrating Gene, Pathway and Disease Information.
Petri, V
Chapter 14 in Handbook of Research on Computational and Systems Biology: Interdisciplinary Applications, IGI Global Publishers, 2011.

The rat genome database pathway portal.
Petri V, Shimoyama M, Hayman GT, Smith JR, Tutaj M, de Pons J, Dwinell MR, Munzenmaier DH, Twigger SN, Jacob HJ; RGD Team.
Database (Oxford). 2011 Apr; doi:10.1093/database/bar010.
PMID:21478484

The Rat Genome Database curation tool suite: a set of optimized software tools enabling efficient acquisition, organization, and presentation of biological data.
Laulederkind SJ, Shimoyama M, Hayman GT, Lowry TF, Nigam R, Petri V, Smith JR, Wang SJ, de Pons J, Kowalski G, Liu W, Rood W, Munzenmaier DH, Dwinell MR, Twigger SN, Jacob HJ; RGD Team.
Database (Oxford). 2011 Feb; doi:10.1093/database/bar002.
PMID:21321022

RGD: a comparative genomics platform.
Shimoyama M, Smith JR, Hayman T, Laulederkind S, Lowry T, Nigam R, Petri V, Wang SJ, Dwinell M, Jacob H; RGD Team. Human Genomics. 2011 Jan; 5(2):124-9.
PMID:21296746

Recommended nomenclature for five mammalian carboxylesterase gene families: human, mouse, and rat genes and proteins.
Holmes RS, Wright MW, Laulederkind SJ, Cox LA, Hosokawa M, Imai T, Ishibashi S, Lehner R, Miyazaki M, Perkins EJ, Potter PM, Redinbo MR, Robert J, Satoh T, Yamashita T, Yan B, Yokoi T, Zechner R, Maltais LJ. Mamm Genome. 2010 Oct; 21(9-10): 427-41.
PMID:20931200

The rat genome database curators: who, what, where, why.
Shimoyama M, Hayman GT, Laulederkind SJ, Nigam R, Lowry TF, Petri V, Smith JR, Wang SJ, Munzenmaier DH, Dwinell MR, Twigger SN, Jacob HJ; RGD Team. PLoS Comput Biol. 2009 Nov; 5(11):e1000582.
PMID:19956751

The Rat Genome Database 2009: variation, ontologies and pathways.
Dwinell MR, Worthey EA, Shimoyama M, Bakir-Gungor B, DePons J, Laulederkind S, Lowry T, Nigam R, Petri V, Smith J, Stoddard A, Twigger SN, Jacob HJ; RGD Team. Nucleic Acids Res. 2009 Jan; 37(Database issue): D744-9.
PMID:18996890

What everybody should know about the rat genome and its online resources.
Twigger SN, Pruitt KD, Fernández-Suárez XM, Karolchik D, Worley KC, Maglott DR, Brown G, Weinstock G, Gibbs RA, Kent J, Birney E, Jacob HJ. Nat Genet. 2008 May; 40(5): 523-7.
PMID:18443589

A revised nomenclature for the human and rodent alpha-tubulin gene family.
Khodiyar VK, Maltais LJ, Ruef BJ, Sneddon KM, Smith JR, Shimoyama M, Cabral F, Dumontet C, Dutcher SK, Harvey RJ, Lafanechère L, Murray JM, Nogales E, Piquemal D, Stanchi F, Povey S, Lovering RC. Genomics. 2007 Aug; 90(2):285-9.
PMID:17543498

A standardized nomenclature for the mouse and rat prolactin superfamilies.
Soares MJ, Alam SM, Duckworth ML, Horseman ND, Konno T, Linzer DI, Maltais LJ, Nilsen-Hamilton M, Shiota K, Smith JR, Wallis M. Mamm Genome. 2007 Mar; 18(3): 154-6.
PMID:17476555

The Rat Genome Database, update 2007- easing the path from disease to data and back again.
Twigger SN, Shimoyama M, Bromberg S, Kwitek AE, Jacob HJ; RGD Team. Nucleic Acids Res. 2007 Jan; 35(Database issue): D658-62.
PMID:17151068

Exploring phenotypic data at the rat genome database.
Twigger SN, S Smith J, Zuniga-Meyer A, Bromberg SK. Curr Protoc Bioinformatics. 2006 Jul; Chapter 1:Unit 1.14.
PMID:18428755

Using multiple ontologies to integrate complex biological data.
Shimoyama M, Petri V, Pasko D, Bromberg S, Wu W, Chen J, Nenasheva N, Kwitek A, Twigger S, Jacob H. Comp Funct Genomics. 2005; 6(7-8): 373-8.
PMID:18629202

Tools and strategies for physiological genomics: the Rat Genome Database.
Twigger SN, Pasko D, Nie J, Shimoyama M, Bromberg S, Campbell D, Chen J, dela Cruz N, Fan C, Foote C, Harris G, Hickmann B, Ji Y, Jin W, Li D, Mathis J, Nenasheva N, Nigam R, Petri V, Reilly D, Ruotti V, Schauberger E, Seiler K, Slyper R, Smith J, Wang W, Wu W, Zhao L, Zuniga-Meyer A, Tonellato PJ, Kwitek AE, Jacob HJ. Physiol Genomics. 2005 Oct; 23(2): 246-56.
PMID:16106031

The Rat Genome Database (RGD): developments towards a phenome database.
de la Cruz N, Bromberg S, Pasko D, Shimoyama M, Twigger S, Chen J, Chen CF, Fan C, Foote C, Gopinath GR, Harris G, Hughes A, Ji Y, Jin W, Li D, Mathis J, Nenasheva N, Nie J, Nigam R, Petri V, Reilly D, Wang W, Wu W, Zuniga-Meyer A, Zhao L, Kwitek A, Tonellato P, Jacob H. Nucleic Acids Res. 2005 Jan; 33(Database issue): D485-91.
PMID:15608243

Rat Genome Database (RGD): mapping disease onto the genome.
Twigger S, Lu J, Shimoyama M, Chen D, Pasko D, Long H, Ginster J, Chen CF, Nigam R, Kwitek A, Eppig J, Maltais L, Maglott D, Schuler G, Jacob H, Tonellato PJ. Nucleic Acids Res. 2002 Jan; 30(1): 125-8.
PMID:11752273

Previous RGD Member Publications:

The emerging role for rat models in gene discovery.  Dwinell MR, Lazar J, Geurts AM. Mamm Genome. 2011 Aug; 22(7-8):466-75.
PMID: 21732192

Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease.
Worthey EA, Mayer AN, Syverson GD, Helbling D, Bonacci BB, Decker B, Serpe JM, Dasu T, Tschannen MR, Veith RL, Basehore MJ, Broeckel U, Tomita-Mitchell A, Arca MJ, Casper JT, Margolis DA, Bick DP, Hessner MJ, Routes JM, Verbsky JW, Jacob HJ, Dimmock DP. Genet Med. 2011 Mar; 13(3):255-62.
PMID:21173700

A timely arrival for genomic medicine.
Mayer AN, Dimmock DP, Arca MJ, Bick DP, Verbsky JW, Worthey EA, Jacob HJ, Margolis DA. Genet Med. 2011 Mar; 13(3):195-6.
PMID:21169843

The BioPAX community standard for pathway data sharing.
Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D’Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Reubenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD. Nat Biotechnol. 2010 Sep; 28(9): 935-42.
PMID:20829833
Corrigendum: Nat Biotechnol. 2012 Apr;30(4):365. Reubenacker O [corrected to Ruebenacker O].

The rat: a model used in biomedical research.
Jacob HJ. Methods Mol Biol. 2010; 597:1-11.
PMID:20013222

Sequencing of the rat genome and databases.
Worthey EA, Stoddard AJ, Jacob HJ. Methods Mol Biol. 2010; 597:33-53.
PMID:20013224

Knockout rats via embryo microinjection of zinc-finger nucleases.
Geurts AM, Cost GJ, Freyvert Y, Zeitler B, Miller JC, Choi VM, Jenkins SS, Wood A, Cui X, Meng X, Vincent A, Lam S, Michalkiewicz M, Schilling R, Foeckler J, Kalloway S, Weiler H, Ménoret S, Anegon I, Davis GD, Zhang L, Rebar EJ, Gregory PD, Urnov FD, Jacob HJ, Buelow R. Science. 2009 Jul; 325(5939):433.
PMID:19628861

The Gene Ontology’s Reference Genome Project: a unified framework for functional annotation across species.
Gaudet P, Chisholm R, Berardini T, Dimmer E, Engel SR, Fey P, Hill DP, Howe D, Hu JC, Huntley R, Khodiyar VK, Kishore R, Li D, Lovering RC, McCarthy F, Ni L, Petri V, Siegele DA, Tweedie S, Van Auken K, Wood V, Basu S, Carbon S, Dolan M, Mungall CJ, Dolinski K, Thomas P, Ashburner M, Blake JA, Cherry JM, Lewis SE, Balakrishnan R, Christie KR, Costanzo MC, Deegan J, Diehl AD, Drabkin H, Fisk DG, Harris M, Hirschman JE, Hong EL, Ireland A, Lomax J, Nash RS, Park J, Sitnikov D, Skrzypek MS, Apweiler R, Bult C, Eppig J, Jacob H, Parkhill J, Rhee S, Ringwald M, Sternberg P, Talmud P, Twigger S, Westerfield M. PLoS Comput Biol. 2009 Jul; 5(7):e1000431.
PMID:19578431

Low cost, scalable proteomics data analysis using Amazon’s cloud computing services and open source search algorithms.
Halligan BD, Geiger JF, Vallejos AK, Greene AS, Twigger SN. J Proteome Res. 2009 Jun; 8(6):3148-53.
PMID:19358578

Rats!
Iannaccone PM, Jacob HJ. Dis Model Mech. 2009 May-Jun; 2(5-6):206-10.
PMID:19407324

Why do professional service anyway? Do it for you!
Munzenmaier D. Physiologist. 2008 Oct; 51(5):180-1.
PMID:18988518

Big data: The future of biocuration.
Howe D, Costanzo M, Fey P, Gojobori T, Hannick L, Hide W, Hill DP, Kania R, Schaeffer M, St Pierre S, Twigger S, White O, Rhee SY. Nature. 2008 Sep; 455(7209):47-50.
PMID:18769432

Progress and prospects in rat genetics: a community view.
Aitman TJ, Critser JK, Cuppen E, Dominiczak A, Fernandez-Suarez XM, Flint J, Gauguier D, Geurts AM, Gould M, Harris PC, Holmdahl R, Hubner N, Izsvák Z, Jacob HJ, Kuramoto T, Kwitek AE, Marrone A, Mashimo T, Moreno C, Mullins J, Mullins L, Olsson T, Pravenec M, Riley L, Saar K, Serikawa T, Shull JD, Szpirer C, Twigger SN, Voigt B, Worley K. Nat Genet. 2008 May; 40(5):516-22.
PMID:18443588

Comparative genomics for detecting human disease genes.
Moreno C, Lazar J, Jacob HJ, Kwitek AE. Adv Genet. 2008; 60:655-97.
PMID:18358336

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.
Genome Information Integration Project And H-Invitational 2, Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O’Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo Mde F, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares MB, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, Gojobori T. Nucleic Acids Res. 2008 Jan; 36(Database Issue):D793-9.
PMID:18089548

Structures of proteins of biomedical interest from the Center for Eukaryotic Structural Genomics.
Phillips GN Jr, Fox BG, Markley JL, Volkman BF, Bae E, Bitto E, Bingman CA, Frederick RO, McCoy JG, Lytle BL, Pierce BS, Song J, Twigger SN. J Struct Funct Genomics. 2007 Sep; 8(2-3):73-84.
PMID:17786587

Sequence analysis of the complete mitochondrial DNA in 10 commonly used inbred rat strains.
Schlick NE, Jensen-Seaman MI, Orlebeke K, Kwitek AE, Jacob HJ, Lazar J. Am J Physiol Cell Physiol. 2006 Dec; 291(6):1183-92.
PMID:16855218

Nomenclature of the rat Cyp genes and the problems of gene nomenclature in general [Nelson, D.R. (2005), ‘Gene nomenclature by default, or BLASTing to Babel’, Hum Genomics Vol. 2, pp. 196-201].
Levan G, Jacob HJ. Hum Genomics. 2006 Jun; 2(6):343.
PMID:16848971

BN phenome: detailed characterization of the cardiovascular, renal, and pulmonary systems of the sequenced rat.
Kwitek AE, Jacob HJ, Baker JE, Dwinell MR, Forster HV, Greene AS, Kunert MP, Lombard JH, Mattson DL, Pritchard KA Jr, Roman RJ, Tonellato PJ, Cowley AW Jr. Physiol Genomics. 2006 Apr; 25(2):303-13.
PMID:16478827

Physiogenomic resources for rat models of heart, lung and blood disordser.
Malek RL, Wang HY, Kwitek AE, Greene AS, Bhagabati N, Borchardt G, Cahill L, Currier T, Frank B, Fu X, Hasinoff M, Howe E, Letwin N, Luu TV, Saeed A, Sajadi H, Salzberg SL, Sultana R, Thiagarajan M, Tsai J, Veratti K, White J, Quackenbush J, Jacob HJ, Lee NH. Nat Genet. 2006 Feb; 38(2):234-9.
PMID:16415889

Impact of genomics on research in the rat.
Lazar J, Moreno C, Jacob HJ, Kwitek AE. Genome Res. 2005 Dec; 15(12):1717-28.
PMID:16339370

A new method for identifying informative genetic markers in selectively bred rats.
Weinshenker D, Wilson MM, Williams KM, Weiss JM, Lamb NE, Twigger SN. Mamm Genome. 2005 Oct; 16(10):784-91.
PMID:16261420

Genome-wide scanning with SSLPs in the rat.
Moreno C, Kennedy K, Andrae JW, Jacob HJ. Methods Mol Med. 2005; 108:131-8.
PMID:16028680

DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy.
Halligan BD, Ruotti V, Twigger SN, Greene AS. Nucleic Acids Res. 2005 Jul; 33(Web Server Issue):W376-81.
PMID:15980493

Simultaneous quantification and identification using 18O labeling with an ion trap mass spectrometer and the analysis software application “ZoomQuant”.
Hicks WA, Halligan BD, Slyper RY, Twigger SN, Greene AS, Olivier M. J Am Soc Mass Spectrom. 2005 Jun; 16(6):916-25.
PMID:15907706

ZoomQuant: an application for the quantitation of stable isotope labeled peptides.
Halligan BD, Slyper RY, Twigger SN, Hicks W, Olivier M, Greene AS. J Am Soc Mass Spectrom. 2005 Mar; 16(3):302-6.
PMID:15734322

Peptide identification using peptide amino acid attribute vectors.
Halligan BD, Dratz EA, Feng X, Twigger SN, Tonellato PJ, Greene AS. J Proteome Res. 2004 Jul-Aug; 3(4):813-20.
PMID:15359736

ProMoST (Protein Modification Screening Tool): a web-based tool for mapping protein modifications on two-dimensional gels.
Halligan BD, Ruotti V, Jin W, Laffoon S, Twigger SN, Dratz EA. Nucleic Acids Res. 2004 Jul; 32(Web Server Issue):W638-44.
PMID:15215467

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
Imanishi T, Itoh T, Suzuki Y, O’Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S. PLoS Biol. 2004 Jun; 2(6):e162.
PMID:15103394
Erratum in PLoS Biol. 2004 Jul; 2(7):e256.

High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence.
Kwitek AE, Gullings-Handley J, Yu J, Carlos DC, Orlebeke K, Nie J, Eckert J, Lemke A, Andrae JW, Bromberg S, Pasko D, Chen D, Scheetz TE, Casavant TL, Soares MB, Sheffield VC, Tonellato PJ, Jacob HJ. Genome Res. 2004 Apr; 14(4):750-7.
PMID:15060019

Integrative genomics: in silico coupling of rat physiology and complex traits with mouse and human data.
Twigger SN, Nie J, Ruotti V, Yu J, Chen D, Li D, Mathis J, Narayanasamy V, Gopinath GR, Pasko D, Shimoyama M, De La Cruz N, Bromberg S, Kwitek AE, Jacob HJ, Tonellato PJ. Genome Res. 2004 Apr; 14(4): 651-60.
PMID:15060006

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
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Of rats and men.
Twigger SN. Genome Biol. 2004; 5(3):314.
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Phylogenetics of rat inbred strains.
Thomas MA, Chen CF, Jensen-Seaman MI, Tonellato PJ, Twigger SN. Mamm Genome. 2003 Jan; 14(1):61-4.
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Rat genetics: attaching physiology and pharmacology to the genome.
Jacob HJ, Kwitek AE. Nat Rev Genet. 2002 Jan; 3(1):33-42.
PMID:11823789

Automated construction of high-density comparative maps between rat, human, and mouse.
Kwitek AE, Tonellato PJ, Chen D, Gullings-Handley J, Cheng YS, Twigger S, Scheetz TE, Casavant TL, Stoll M, Nobrega MA, Shiozawa M, Soares MB, Sheffield VC, Jacob HJ. Genome Res. 2001 Nov; 11(11):1935-43.
PMID:11691858

Sequence interpretation. Functional annotation of mouse genome sequences.
Nadeau JH, Balling R, Barsh G, Beier D, Brown SD, Bucan M, Camper S, Carlson G, Copeland N, Eppig J, Fletcher C, Frankel WN, Ganten D, Goldowitz D, Goodnow C, Guenet JL, Hicks G, Hrabe de Angelis M, Jackson I, Jacob HJ, Jenkins N, Johnson D, Justice M, Kay S, Kingsley D, Lehrach H, Magnuson T, Meisler M, Poustka A, Rinchik EM, Rossant J, Russell LB, Schimenti J, Shiroishi T, Skarnes WC, Soriano P, Stanford W, Takahashi JS, Wurst W, Zimmer A; International Mouse Mutagenesis Consortium. Science. 2001 Feb; 291(5507):1251-5.
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New target regions for human hypertension via comparative genomics.
Stoll M, Kwitek-Black AE, Cowley AW Jr, Harris EL, Harrap SB, Krieger JE, Printz MP, Provoost AP, Sassard J, Jacob HJ. Genome Res. 2000 Apr; 10(4):473-82.
PMID:10779487

High-throughput scanning of the rat genome using interspersed repetitive sequence-PCR markers.
Gösele C, Hong L, Kreitler T, Rossmann M, Hieke B, Gross U, Kramer M, Himmelbauer H, Bihoreau MT, Kwitek-Black AE, Twigger S, Tonellato PJ, Jacob HJ, Schalkwyk LC, Lindpaintner K, Ganten D, Lehrach H, Knoblauch M. Genomics. 2000 Nov; 69(3):287-94.
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Functional genomics and rat models.
Jacob HJ. Genome Res. 1999 Nov; 9(11):1013-6.
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A rat genetic linkage map including 67 new microsatellite markers.
Fakhrai-Rad H, Jiao H, Li LS, Glaser A, Koike G, Jacob HJ, Luthman H, Galli J. Mamm Genome. 1999 Nov; 10(11): 1102-5.
PMID:10556432

Physiological genetics: application to hypertension research.
Jacob HJ. Clin Exp Pharmacol Physiol. 1999 Jul; 26(7):530-5.
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Zebrafish genetic map with 2000 microsatellite markers.
Shimoda N, Knapik EW, Ziniti J, Sim C, Yamada E, Kaplan S, Jackson D, de Sauvage F, Jacob H, Fishman MC. Genomics. 1999 Jun; 58(3):219-32.
PMID:10373319

A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat.
Steen RG, Kwitek-Black AE, Glenn C, Gullings-Handley J, Van Etten W, Atkinson OS, Appel D, Twigger S, Muir M, Mull T, Granados M, Kissebah M, Russo K, Crane R, Popp M, Peden M, Matise T, Brown DM, Lu J, Kingsmore S, Tonellato PJ, Rozen S, Slonim D, Young P, Jacob HJ. Genome Res. 1999 Jun; 9(6): AP1-8, insert. Erratum in: Genome Res 1999 Aug; 9(8):793.
PMID:10400928

Gene-based anchoring of the rat genetic linkage and cytogenetic maps.
Szpirer C, Szpirer J, Van Vooren P, Tissir F, Simon JS, Koike G, Jacob HJ, Lander ES, Helou K, Klinga-Levan K, Levan G. Transplant Proc. 1999 May; 31(3):1541-3.
PMID:10330994

EbEST: an automated tool using expressed sequence tags to delineate gene structure.
Jiang J, Jacob HJ. Genome Res. 1998 Mar; 8(3):268-75.
PMID:9521930