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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 Nov 12. pii: gkz1041. doi: 10.1093/nar/gkz1041. [Epub ahead of print]


FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources.

Clarke DJB, Wang L, Jones A, Wojciechowicz ML, Torre D, Jagodnik KM, Jenkins SL, McQuilton P, Flamholz Z, Silverstein MC, Schilder BM, Robasky K, Castillo C, Idaszak R, Ahalt SC, Williams J, Schurer S, Cooper DJ, de Miranda Azevedo R, Klenk JA, Haendel MA, Nedzel J, Avillach P, Shimoyama ME, Harris RM, Gamble M, Poten R, Charbonneau AL, Larkin J, Brown CT, Bonazzi VR, Dumontier MJ, Sansone SA, Ma'ayan A.

Cell Syst. 2019 Oct 10. pii: S2405-4712(19)30345-X. doi: 10.1016/j.cels.2019.09.011. [Epub ahead of print]


Immune correlates of the differing pathological and therapeutic effects of neoadjuvant chemotherapy in breast cancer.

Kim R, Kawai A, Wakisaka M, Sawada S, Shimoyama M, Yasuda N, Hidaka M, Morita Y, Ohtani S, Arihiro K.

Eur J Surg Oncol. 2019 Sep 18. pii: S0748-7983(19)30812-1. doi: 10.1016/j.ejso.2019.09.146. [Epub ahead of print]


Homozygous familial hypercholesterolemia with stenosis of the left anterior descending coronary artery successfully treated with weekly low-density lipoprotein apheresis for 16 years without percutaneous coronary intervention.

Yasu T, Shimoyama M, Wada H, Iwakura T, Toyoda S, Kawabe A, Sugiyama T.

Clin Case Rep. 2019 Jul 16;7(8):1608-1611. doi: 10.1002/ccr3.2299. eCollection 2019 Aug.


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.


Predicting instances of pathway ontology classes for pathway integration.

Wang LL, Thomas Hayman G, Smith JR, Tutaj M, Shimoyama ME, Gennari JH.

J Biomed Semantics. 2019 Jun 13;10(1):11. doi: 10.1186/s13326-019-0202-8.


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.


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.


Approach to Half-Nose and Proboscis Lateralis.

Horoz U, Kuroki T, Shimoyama M, Yoshimoto S.

J Craniofac Surg. 2018 Nov;29(8):2234-2236. doi: 10.1097/SCS.0000000000004803.


The prevalence of mental health problems in adults with intellectual disabilities in Japan, associated factors and mental health service use.

Shimoyama M, Iwasa K, Sonoyama S.

J Intellect Disabil Res. 2018 Nov;62(11):931-940. doi: 10.1111/jir.12515. Epub 2018 Jul 2.


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.


Protective Effect of a Mitochondria-Targeted Peptide against the Development of Chemotherapy-Induced Peripheral Neuropathy in Mice.

Toyama S, Shimoyama N, Szeto HH, Schiller PW, Shimoyama M.

ACS Chem Neurosci. 2018 Jul 18;9(7):1566-1571. doi: 10.1021/acschemneuro.8b00013. Epub 2018 Apr 18.


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.


Nonpeptide Orexin-2 Receptor Agonist Attenuates Morphine-induced Sedative Effects in Rats.

Toyama S, Shimoyama N, Tagaito Y, Nagase H, Saitoh T, Yanagisawa M, Shimoyama M.

Anesthesiology. 2018 May;128(5):992-1003. doi: 10.1097/ALN.0000000000002161.


Genetics and Genomics in Clinical Practice: The Views of Wisconsin Physicians.

McCauley MP, Marcus RK, Strong KA, Visotcky AM, Shimoyama ME, Derse AR.

WMJ. 2017 Jun;116(2):69-74.


Rat Genome and Model Resources.

Shimoyama M, Smith JR, Bryda E, Kuramoto T, Saba L, Dwinell M.

ILAR J. 2017 Jul 1;58(1):42-58. doi: 10.1093/ilar/ilw041. Review.


Out-of-hospital cardiac arrest related to coronary arterial spasm in three elderly patients with no obstructive coronary artery disease.

Ueno A, Kawabe A, Sugiyama T, Ishikawa M, Uema A, Shimoyama M, Horie Y, Hoshi T, Sugimura H, Yasu T.

J Cardiol Cases. 2017 Aug 24;16(5):154-157. doi: 10.1016/j.jccase.2017.07.003. eCollection 2017 Nov.


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. doi: 10.1055/s-0036-1593968. Epub 2016 Nov 28.


The analgesic effect of orexin-A in a murine model of chemotherapy-induced neuropathic pain.

Toyama S, Shimoyama N, Shimoyama M.

Neuropeptides. 2017 Feb;61:95-100. doi: 10.1016/j.npep.2016.12.007. Epub 2016 Dec 24.


[Perioperative Management of Patients Receiving Chronic Opioid Therapy].

Shimoyama M, Shimoyama N.

Masui. 2016 Nov;65(11):1112-1118. Japanese.


Patient-controlled epidural analgesia for labour in a patient after Ross procedure for congenital bicuspid aortic valve.

Toyama S, Tagaito Y, Shimoyama M.

J Obstet Gynaecol. 2016 Nov;36(8):1010-1011. Epub 2016 Oct 18. No abstract available.


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.


Disease, Models, Variants and Altered Pathways-Journeying RGD Through the Magnifying Glass.

Petri V, Hayman GT, Tutaj M, Smith JR, Laulederkind S, Wang SJ, Nigam R, De Pons J, Shimoyama M, Dwinell MR.

Comput Struct Biotechnol J. 2015 Nov 26;14:35-48. doi: 10.1016/j.csbj.2015.11.006. eCollection 2016.


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.


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 12;2016. pii: baw073. doi: 10.1093/database/baw073. Print 2016.


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.


[Understanding Oral and Nasal Mucosal Absorption of Fentanyl, and Rectal Absorption of Buprenorphine].

Shimoyama N, Shimoyama M, Kubota Y, Kato Y.

Masui. 2015 Nov;64(11):1160-5. Japanese.


STX11 functions as a novel tumor suppressor gene in peripheral T-cell lymphomas.

Yoshida N, Tsuzuki S, Karube K, Takahara T, Suguro M, Miyoshi H, Nishikori M, Shimoyama M, Tsukasaki K, Ohshima K, Seto M.

Cancer Sci. 2015 Oct;106(10):1455-62. doi: 10.1111/cas.12742. Epub 2015 Aug 13.


Glaucomatous visual field defect severity and the prevalence of motor vehicle collisions in Japanese: a hospital/clinic-based cross-sectional study.

Ono T, Yuki K, Asaoka R, Kouyama K, Abe T, Tanabe S, Fukagawa K, Uchino M, Shimoyama M, Ozawa Y, Ozeki N, Shiba D, Tsubota K.

J Ophthalmol. 2015;2015:497067. doi: 10.1155/2015/497067. Epub 2015 Apr 1.


2015 Guidelines for Establishing Genetically Modified Rat Models for Cardiovascular Research.

Flister MJ, Prokop JW, Lazar J, Shimoyama M, Dwinell M, Geurts A; International Committee on Standardized Genetic Nomenclature for Mice; Rat Genome and Nomenclature Committee.

J Cardiovasc Transl Res. 2015 Jun;8(4):269-77. doi: 10.1007/s12265-015-9626-4. Epub 2015 Apr 29. Review.


Accumulation of squalene in a microalga Chlamydomonas reinhardtii by genetic modification of squalene synthase and squalene epoxidase genes.

Kajikawa M, Kinohira S, Ando A, Shimoyama M, Kato M, Fukuzawa H.

PLoS One. 2015 Mar 12;10(3):e0120446. doi: 10.1371/journal.pone.0120446. eCollection 2015.


EHR-based phenome wide association study in pancreatic cancer.

Adamusiak T, Shimoyama M.

AMIA Jt Summits Transl Sci Proc. 2014 Apr 7;2014:9-15. eCollection 2014.


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.


Multicenter cooperative case survey of hepatitis B virus reactivation by chemotherapeutic agents.

Takahashi H, Ikeda M, Kumada T, Osaki Y, Kondo S, Kusumoto S, Ohkawa K, Nadano S, Furuse J, Kudo M, Ito K, Yokoyama M, Okusaka T, Shimoyama M, Mizokami M.

Hepatol Res. 2015 Dec;45(12):1220-7. doi: 10.1111/hepr.12496. Epub 2015 Mar 2.


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.


Next generation phenotyping using the unified medical language system.

Adamusiak T, Shimoyama N, Shimoyama M.

JMIR Med Inform. 2014 Mar 18;2(1):e5. doi: 10.2196/medinform.3172.


Driving self-restriction and motor vehicle collision occurrence in glaucoma.

Ono T, Yuki K, Awano-Tanabe S, Fukagawa K, Shimoyama M, Ozawa Y, Ozeki N, Shiba D, Tsubota K.

Optom Vis Sci. 2015 Mar;92(3):357-64. doi: 10.1097/OPX.0000000000000493.


Efficacy and safety of sublingual fentanyl orally disintegrating tablet at doses determined from oral morphine rescue doses in the treatment of breakthrough cancer pain.

Shimoyama N, Gomyo I, Teramoto O, Kojima K, Higuchi H, Yukitoshi N, Ohta E, Shimoyama M.

Jpn J Clin Oncol. 2015 Feb;45(2):189-96. doi: 10.1093/jjco/hyu182. Epub 2014 Nov 6.


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.


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.


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. 2015 May 1;215:106-16. doi: 10.1016/j.ygcen.2014.09.010. Epub 2014 Sep 26.


Multivariable logistic regression model: a novel mathematical model that predicts visual field sensitivity from macular ganglion cell complex thickness in glaucoma.

Shiba D, Hatou S, Ono T, Hosoda S, Tanabe S, Ozeki N, Yuki K, Shimoyama M, Fukagawa K, Shimmura S, Tsubota K.

PLoS One. 2014 Aug 18;9(8):e104126. doi: 10.1371/journal.pone.0104126. eCollection 2014.


Japan Clinical Oncology Group (JCOG) prognostic index and characterization of long-term survivors of aggressive adult T-cell leukaemia-lymphoma (JCOG0902A).

Fukushima T, Nomura S, Shimoyama M, Shibata T, Imaizumi Y, Moriuchi Y, Tomoyose T, Uozumi K, Kobayashi Y, Fukushima N, Utsunomiya A, Tara M, Nosaka K, Hidaka M, Uike N, Yoshida S, Tamura K, Ishitsuka K, Kurosawa M, Nakata M, Fukuda H, Hotta T, Tobinai K, Tsukasaki K.

Br J Haematol. 2014 Sep;166(5):739-48. doi: 10.1111/bjh.12962. Epub 2014 Jun 14.


Efficacy and safety of sublingual fentanyl orally disintegrating tablet at doses determined by titration for the treatment of breakthrough pain in Japanese cancer patients: a multicenter, randomized, placebo-controlled, double-blind phase III trial.

Shimoyama N, Gomyo I, Katakami N, Okada M, Yukitoshi N, Ohta E, Shimoyama M.

Int J Clin Oncol. 2015 Feb;20(1):198-206. doi: 10.1007/s10147-014-0697-z. Epub 2014 May 20.


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. doi: 10.1111/josh.12160. No abstract available.


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.


Meeting report on the possible proposal of an extranodal primary cutaneous variant in the lymphoma type of adult T-cell leukemia-lymphoma.

Tsukasaki K, Imaizumi Y, Tokura Y, Ohshima K, Kawai K, Utsunomiya A, Amano M, Watanabe T, Nakamura S, Iwatsuki K, Kamihira S, Yamaguchi K, Shimoyama M.

J Dermatol. 2014 Jan;41(1):26-8. doi: 10.1111/1346-8138.12374.


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 22;4(1):36. doi: 10.1186/2041-1480-4-36.


The association between visual field defect severity and fear of falling in primary open-angle glaucoma.

Yuki K, Tanabe S, Kouyama K, Fukagawa K, Uchino M, Shimoyama M, Ozeki N, Shiba D, Ozawa Y, Abe T, Tsubota K.

Invest Ophthalmol Vis Sci. 2013 Nov 21;54(12):7739-45. doi: 10.1167/iovs.13-12079.


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