Ryan M - Search Results

1

LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures.

Ryan M, Diekhans M, Lien S, Liu Y, Karchin R. Ryan M, et al. Bioinformatics. 2009 Jun 1;25(11):1431-2. doi: 10.1093/bioinformatics/btp242. Epub 2009 Apr 15. Bioinformatics. 2009. PMID: 19369493 Free PMC article.

2

CRAVAT: cancer-related analysis of variants toolkit.

Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R. Douville C, et al. Among authors: ryan m. Bioinformatics. 2013 Mar 1;29(5):647-8. doi: 10.1093/bioinformatics/btt017. Epub 2013 Jan 16. Bioinformatics. 2013. PMID: 23325621 Free PMC article.

3

MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures.

Niknafs N, Kim D, Kim R, Diekhans M, Ryan M, Stenson PD, Cooper DN, Karchin R. Niknafs N, et al. Among authors: ryan m. Hum Genet. 2013 Nov;132(11):1235-43. doi: 10.1007/s00439-013-1325-0. Epub 2013 Jun 23. Hum Genet. 2013. PMID: 23793516 Free PMC article.

4

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer.

Wong WC, Kim D, Carter H, Diekhans M, Ryan MC, Karchin R. Wong WC, et al. Among authors: ryan mc. Bioinformatics. 2011 Aug 1;27(15):2147-8. doi: 10.1093/bioinformatics/btr357. Epub 2011 Jun 17. Bioinformatics. 2011. PMID: 21685053 Free PMC article.

5

Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure.

Tokheim C, Bhattacharya R, Niknafs N, Gygax DM, Kim R, Ryan M, Masica DL, Karchin R. Tokheim C, et al. Among authors: ryan m. Cancer Res. 2016 Jul 1;76(13):3719-31. doi: 10.1158/0008-5472.CAN-15-3190. Epub 2016 Apr 28. Cancer Res. 2016. PMID: 27197156 Free PMC article.

6

Integrated Informatics Analysis of Cancer-Related Variants.

Pagel KA, Kim R, Moad K, Busby B, Zheng L, Tokheim C, Ryan M, Karchin R. Pagel KA, et al. Among authors: ryan m. JCO Clin Cancer Inform. 2020 Mar;4:310-317. doi: 10.1200/CCI.19.00132. JCO Clin Cancer Inform. 2020. PMID: 32228266 Free PMC article.

7

Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel).

Douville C, Masica DL, Stenson PD, Cooper DN, Gygax DM, Kim R, Ryan M, Karchin R. Douville C, et al. Among authors: ryan m. Hum Mutat. 2016 Jan;37(1):28-35. doi: 10.1002/humu.22911. Epub 2015 Oct 26. Hum Mutat. 2016. PMID: 26442818 Free PMC article.

8

Ontogenomic study of the relationship between number of gene splice variants and GO categorization.

Kahn AB, Zeeberg BR, Ryan MC, Jamison DC, Rockoff DM, Pommier Y, Weinstein JN. Kahn AB, et al. Among authors: ryan mc. Bioinformatics. 2010 Aug 15;26(16):1945-9. doi: 10.1093/bioinformatics/btq335. Epub 2010 Jul 8. Bioinformatics. 2010. PMID: 20616384 Free PMC article.

9

SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts.

Ryan MC, Cleland J, Kim R, Wong WC, Weinstein JN. Ryan MC, et al. Bioinformatics. 2012 Sep 15;28(18):2385-7. doi: 10.1093/bioinformatics/bts452. Epub 2012 Jul 20. Bioinformatics. 2012. PMID: 22820202 Free PMC article.

10

Bridging the Chromosome-centric and Biology/Disease-driven Human Proteome Projects: Accessible and Automated Tools for Interpreting the Biological and Pathological Impact of Protein Sequence Variants Detected via Proteogenomics.

Sajulga R, Mehta S, Kumar P, Johnson JE, Guerrero CR, Ryan MC, Karchin R, Jagtap PD, Griffin TJ. Sajulga R, et al. J Proteome Res. 2018 Dec 7;17(12):4329-4336. doi: 10.1021/acs.jproteome.8b00404. Epub 2018 Sep 5. J Proteome Res. 2018. PMID: 30130115

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