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Items: 41

1.

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
2.

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.

3.

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.

Köhler S, Carmody L, Vasilevsky N, Jacobsen JOB, Danis D, Gourdine JP, Gargano M, Harris NL, Matentzoglu N, McMurry JA, Osumi-Sutherland D, Cipriani V, Balhoff JP, Conlin T, Blau H, Baynam G, Palmer R, Gratian D, Dawkins H, Segal M, Jansen AC, Muaz A, Chang WH, Bergerson J, Laulederkind SJF, Yüksel Z, Beltran S, Freeman AF, Sergouniotis PI, Durkin D, Storm AL, Hanauer M, Brudno M, Bello SM, Sincan M, Rageth K, Wheeler MT, Oegema R, Lourghi H, Della Rocca MG, Thompson R, Castellanos F, Priest J, Cunningham-Rundles C, Hegde A, Lovering RC, Hajek C, Olry A, Notarangelo L, Similuk M, Zhang XA, Gómez-Andrés D, Lochmüller H, Dollfus H, Rosenzweig S, Marwaha S, Rath A, Sullivan K, Smith C, Milner JD, Leroux D, Boerkoel CF, Klion A, Carter MC, Groza T, Smedley D, Haendel MA, Mungall C, Robinson PN.

Nucleic Acids Res. 2019 Jan 8;47(D1):D1018-D1027. doi: 10.1093/nar/gky1105.

4.

Model organism data evolving in support of translational medicine.

Howe DG, Blake JA, Bradford YM, Bult CJ, Calvi BR, Engel SR, Kadin JA, Kaufman TC, Kishore R, Laulederkind SJF, Lewis SE, Moxon SAT, Richardson JE, Smith C.

Lab Anim (NY). 2018 Oct;47(10):277-289. doi: 10.1038/s41684-018-0150-4. Epub 2018 Sep 17. Review.

5.

A Primer for the Rat Genome Database (RGD).

Laulederkind SJF, Hayman GT, Wang SJ, Smith JR, Petri V, Hoffman MJ, De Pons J, Tutaj MA, Ghiasvand O, Tutaj M, Thota J, Dwinell MR, Shimoyama M.

Methods Mol Biol. 2018;1757:163-209. doi: 10.1007/978-1-4939-7737-6_8.

6.

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 12;11(3). pii: dmm032839. doi: 10.1242/dmm.032839.

7.

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;11(2):e001813. doi: 10.1161/CIRCGEN.117.001813.

8.

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 1;9(10):1089-1095. Review.

9.

Overview of the interactive task in BioCreative V.

Wang Q, S Abdul S, Almeida L, Ananiadou S, Balderas-Martínez YI, Batista-Navarro R, Campos D, Chilton L, Chou HJ, Contreras G, Cooper L, Dai HJ, Ferrell B, Fluck J, Gama-Castro S, George N, Gkoutos G, Irin AK, Jensen LJ, Jimenez S, Jue TR, Keseler I, Madan S, Matos S, McQuilton P, Milacic M, Mort M, Natarajan J, Pafilis E, Pereira E, Rao S, Rinaldi F, Rothfels K, Salgado D, Silva RM, Singh O, Stefancsik R, Su CH, Subramani S, Tadepally HD, Tsaprouni L, Vasilevsky N, Wang X, Chatr-Aryamontri A, Laulederkind SJ, Matis-Mitchell S, McEntyre J, Orchard S, Pundir S, Rodriguez-Esteban R, Van Auken K, Lu Z, Schaeffer M, Wu CH, Hirschman L, Arighi CN.

Database (Oxford). 2016 Sep 1;2016. pii: baw119. doi: 10.1093/database/baw119. Print 2016.

10.

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 Aug 1;48(8):589-600. doi: 10.1152/physiolgenomics.00046.2016. Epub 2016 Jun 10.

11.

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 23;2016. pii: baw034. doi: 10.1093/database/baw034. Print 2016.

12.

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, Liu W, Smith JR, Nigam R, Dwinell MR, Shimoyama M.

Database (Oxford). 2015 Jan 28;2015. pii: bau128. doi: 10.1093/database/bau128. Print 2015.

13.

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 25;2015. pii: bau129. doi: 10.1093/database/bau129. Print 2015.

14.

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;43(Database issue):D743-50. doi: 10.1093/nar/gku1026. Epub 2014 Oct 29.

15.

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 SJ, Wang SJ, Nigam R, De Pons J, Shimoyama M, Dwinell MR, Worthey EA, Jacob HJ.

Hum Genomics. 2014 Sep 30;8:17. doi: 10.1186/s40246-014-0017-8.

16.

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 25;2014. pii: bau086. doi: 10.1093/database/bau086. Print 2014.

17.

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 28;2014. pii: bau074. doi: 10.1093/database/bau074. Print 2014.

18.

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;5(1):7. doi: 10.1186/2041-1480-5-7.

19.

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, Pons JD, Tutaj M, Liu W, Worthey EA, Shimoyama M, Dwinell MR.

J Biomed Semantics. 2013 Oct 8;4(1):26. doi: 10.1186/2041-1480-4-26.

20.

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 16;45(18):809-16. doi: 10.1152/physiolgenomics.00065.2013. Epub 2013 Jul 23.

21.

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 21;2013:bat046. doi: 10.1093/database/bat046. Print 2013.

22.

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 19;2013:bat015. doi: 10.1093/database/bat015. Print 2013.

23.

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, Munzenmaier DH, Worthey EA, Jacob HJ.

Brief Bioinform. 2013 Jul;14(4):520-6. doi: 10.1093/bib/bbt007. Epub 2013 Feb 22.

24.

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:Unit1.14. doi: 10.1002/0471250953.bi0114s40.

25.

In the beginning there was babble...

Klionsky DJ, Bruford EA, Cherry JM, Hodgkin J, Laulederkind SJ, Singer AG.

Autophagy. 2012 Aug;8(8):1165-7. doi: 10.4161/auto.20665. Epub 2012 Jul 27. No abstract available.

26.

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 20;2012:bas016. doi: 10.1093/database/bas016. Print 2012.

27.

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. doi: 10.1093/database/bar002. Print 2011.

28.

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. doi: 10.1007/s00335-010-9284-4. Epub 2010 Oct 8.

29.

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. doi: 10.1371/journal.pcbi.1000582. Epub 2009 Nov 26. No abstract available.

30.

Defective expression of Tamm-Horsfall protein/uromodulin in COX-2-deficient mice increases their susceptibility to urinary tract infections.

Dou W, Thompson-Jaeger S, Laulederkind SJ, Becker JW, Montgomery J, Ruiz-Bustos E, Hasty DL, Ballou LR, Eastman PS, Srichai B, Breyer MD, Raghow R.

Am J Physiol Renal Physiol. 2005 Jul;289(1):F49-60. Epub 2005 Mar 1.

31.

Congenital lack of COX-2 affects mechanical and geometric properties of bone in mice.

Chen Q, Rho JY, Fan Z, Laulederkind SJ, Raghow R.

Calcif Tissue Int. 2003 Oct;73(4):387-92. Epub 2003 Jul 24.

PMID:
12874706
32.

Renal pathology resulting from PGHS-2 gene ablation in DBA/B6 mice.

Laulederkind SJ, Wall BM, Ballou LR, Raghow R.

Prostaglandins Other Lipid Mediat. 2002 Sep;70(1-2):161-8.

PMID:
12428686
33.

Both constitutive and inducible prostaglandin H synthase affect dermal wound healing in mice.

Laulederkind SJ, Thompson-Jaeger S, Goorha S, Chen Q, Fu A, Rho JY, Ballou LR, Raghow R.

Lab Invest. 2002 Jul;82(7):919-27.

PMID:
12118094
34.

The regulation of PGE(2) biosynthesis in MG-63 osteosarcoma cells by IL-1 and FGF is cell density-dependent.

Laulederkind SJ, Kirtikara K, Raghow R, Ballou LR.

Exp Cell Res. 2000 Aug 1;258(2):409-16.

PMID:
10896792
35.

Transcriptional regulation of cyclooxygenase-2 in the human microvascular endothelial cell line, HMEC-1: control by the combinatorial actions of AP2, NF-IL-6 and CRE elements.

Kirtikara K, Raghow R, Laulederkind SJ, Goorha S, Kanekura T, Ballou LR.

Mol Cell Biochem. 2000 Jan;203(1-2):41-51.

PMID:
10724331
36.

Cholecalciferol induces prostaglandin E2 biosynthesis and transglutaminase activity in human keratinocytes.

Kanekura T, Laulederkind SJ, Kirtikara K, Goorha S, Ballou LR.

J Invest Dermatol. 1998 Oct;111(4):634-9.

37.

An accessory role for ceramide in interleukin-1beta induced prostaglandin synthesis.

Kirtikara K, Laulederkind SJ, Raghow R, Kanekura T, Ballou LR.

Mol Cell Biochem. 1998 Apr;181(1-2):41-8.

PMID:
9562240
38.

Compensatory prostaglandin E2 biosynthesis in cyclooxygenase 1 or 2 null cells.

Kirtikara K, Morham SG, Raghow R, Laulederkind SJ, Kanekura T, Goorha S, Ballou LR.

J Exp Med. 1998 Feb 16;187(4):517-23.

39.

Ceramide signalling and the immune response.

Ballou LR, Laulederkind SJ, Rosloniec EF, Raghow R.

Biochim Biophys Acta. 1996 Jun 11;1301(3):273-87. Review.

PMID:
8664339
40.

Ceramide induces interleukin 6 gene expression in human fibroblasts.

Laulederkind SJ, Bielawska A, Raghow R, Hannun YA, Ballou LR.

J Exp Med. 1995 Aug 1;182(2):599-604.

41.

Sphingosine-mediated phosphatidylinositol metabolism and calcium mobilization.

Chao CP, Laulederkind SJ, Ballou LR.

J Biol Chem. 1994 Feb 25;269(8):5849-56.

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