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A research agenda to support the development and implementation of genomics-based clinical informatics tools and resources.
Wiley K, Findley L, Goldrich M, Rakhra-Burris TK, Stevens A, Williams P, Bult CJ, Chisholm R, Deverka P, Ginsburg GS, Green ED, Jarvik G, Mensah GA, Ramos E, Relling MV, Roden DM, Rowley R, Alterovitz G, Aronson S, Bastarache L, Cimino JJ, Crowgey EL, Del Fiol G, Freimuth RR, Hoffman MA, Jeff J, Johnson K, Kawamoto K, Madhavan S, Mendonca EA, Ohno-Machado L, Pratap S, Taylor CO, Ritchie MD, Walton N, Weng C, Zayas-Cabán T, Manolio TA, Williams MS. Wiley K, et al. Among authors: bult cj. J Am Med Inform Assoc. 2022 Jul 12;29(8):1342-1349. doi: 10.1093/jamia/ocac057. J Am Med Inform Assoc. 2022. PMID: 35485600 Free PMC article.
RESULTS: Outcomes from the meeting included identifying short-term research needs, such as designing and implementing standards-based interfaces between laboratory information systems and electronic health records, as well as long-term projects, such as identifying …
RESULTS: Outcomes from the meeting included identifying short-term research needs, such as designing and implementing standards-based …
PDXNet portal: patient-derived Xenograft model, data, workflow and tool discovery.
Koc S, Lloyd MW, Grover JW, Xiao N, Seepo S, Subramanian SL, Ray M, Frech C, DiGiovanna J, Webster P, Neuhauser S, Srivastava A, Woo XY, Sanderson BJ, White B, Lott P, Dobrolecki LE, Dowst H; PDXNet Consortium; Evrard YA, Wallace TA, Moscow JA, Doroshow JH, Mitsiades N, Kaochar S, Pan CX, Chen MS, Carvajal-Carmona L, Welm AL, Welm BE, Lewis MT, Govindan R, Ding L, Li S, Herlyn M, Davies MA, Roth J, Meric-Bernstam F, Robinson PN, Bult CJ, Davis-Dusenbery B, Dean DA 2nd, Chuang JH. Koc S, et al. Among authors: bult cj. NAR Cancer. 2022 Apr 22;4(2):zcac014. doi: 10.1093/narcan/zcac014. eCollection 2022 Jun. NAR Cancer. 2022. PMID: 35475145 Free PMC article.
These models have 2134 associated sequencing files from 873 samples across 308 patients, which are hosted on the Cancer Genomics Cloud powered by Seven Bridges and the NCI Cancer Data Service for long-term storage and access with dbGaP permissions. The portal includes resu …
These models have 2134 associated sequencing files from 873 samples across 308 patients, which are hosted on the Cancer Genomics Cloud power …
Alliance of Genome Resources Portal: unified model organism research platform.
Alliance of Genome Resources Consortium. Alliance of Genome Resources Consortium. Nucleic Acids Res. 2020 Jan 8;48(D1):D650-D658. doi: 10.1093/nar/gkz813. Nucleic Acids Res. 2020. PMID: 31552413 Free PMC article.
All data are open and freely available via a variety of mechanisms. Long-term plans for the Alliance project include a focus on coverage of additional model organisms including those without dedicated curation communities, and the inclusion of new data types with a particu …
All data are open and freely available via a variety of mechanisms. Long-term plans for the Alliance project include a focus on cover …
EphB4/EphrinB2 therapeutics in Rhabdomyosarcoma.
Randolph ME, Cleary MM, Bajwa Z, Svalina MN, Young MC, Mansoor A, Kaur P, Bult CJ, Goros MW, Michalek JE, Xiang S, Keck J, Krasnoperov V, Gill P, Keller C. Randolph ME, et al. Among authors: bult cj. PLoS One. 2017 Aug 17;12(8):e0183161. doi: 10.1371/journal.pone.0183161. eCollection 2017. PLoS One. 2017. PMID: 28817624 Free PMC article.
Unfortunately, few effective therapies have been discovered that improve the long-term survival rate for children with metastatic disease. Here we determined effectiveness of targeting the receptor tyrosine kinase, EphB4, in both alveolar and embryonal RMS either directly …
Unfortunately, few effective therapies have been discovered that improve the long-term survival rate for children with metastatic dis …
Visual annotation display (VLAD): a tool for finding functional themes in lists of genes.
Richardson JE, Bult CJ. Richardson JE, et al. Among authors: bult cj. Mamm Genome. 2015 Oct;26(9-10):567-73. doi: 10.1007/s00335-015-9570-2. Epub 2015 Jun 6. Mamm Genome. 2015. PMID: 26047590 Free PMC article.
The results for each analysis using VLAD includes a table of ontology terms, sorted in decreasing order of significance. Each row contains the term, statistics such as the number of annotated terms, the p value, etc., and the symbols of annotated genes. An accompanying gra …
The results for each analysis using VLAD includes a table of ontology terms, sorted in decreasing order of significance. Each row contains t …
From information to understanding: the role of model organism databases in comparative and functional genomics.
Bult CJ. Bult CJ. Anim Genet. 2006 Aug;37 Suppl 1:28-40. doi: 10.1111/j.1365-2052.2006.01475.x. Anim Genet. 2006. PMID: 16887000
Model organism databases have a critical role to play in ensuring that diverse kinds of data, especially genome-scale data sets and information, remain useful to the biological community in the long-term. The efforts of model organism database groups ensure not only that o …
Model organism databases have a critical role to play in ensuring that diverse kinds of data, especially genome-scale data sets and informat …