Other Recent Publications:

Corrigendum: 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.
Nature Biotechnology. 2012 Apr 10;30(4):365. doi: 10.1038/nbt0412-365c.
PMID:22491292

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 8;2011:bar010. Print 2011.
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 14;2011:bar002. Print 2011.
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

Previous RGD Publications:

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. Epub 2010 Oct 8.  PMID: 20931200

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. Epub 2010 Sep 9.  PMID: 20829833


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. Epub 2009 Nov 26.  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, Nigram R, Petri V, Smith J, Stoddard A, Twigger SN, Jacob HJ; RGD Team.
Nucleic Acids Res. 2009 Jan; 37(Database issue): D744-9. Epub 2008 Nov 7.  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 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. Epub 2007 May 3.  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. Epub 2006 Dec 6.  PMID: 17151068


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 17; 23(2): 246-56. Epub 2005 Aug 16.  PMID: 16106031


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


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 1; 33(Database issue): D485-91.  PMID: 15608243


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


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 1; 30(1): 125-8.  PMID: 11752273


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