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Items: 28


Caspase-1 from Human Myeloid-Derived Suppressor Cells Can Promote T Cell-Independent Tumor Proliferation.

Zeng Q, Fu J, Korrer M, Gorbounov M, Murray PJ, Pardoll D, Masica DL, Kim YJ.

Cancer Immunol Res. 2018 May;6(5):566-577. doi: 10.1158/2326-6066.CIR-17-0543. Epub 2018 Apr 13.


Network Analysis of Protein Adaptation: modeling the functional impact of multiple mutations.

Beleva Guthrie V, Masica DL, Fraser A, Federico J, Fan Y, Camps M, Karchin R.

Mol Biol Evol. 2018 Mar 7. doi: 10.1093/molbev/msy036. [Epub ahead of print]


IPMNs with co-occurring invasive cancers: neighbours but not always relatives.

Felsenstein M, Noë M, Masica DL, Hosoda W, Chianchiano P, Fischer CG, Lionheart G, Brosens LAA, Pea A, Yu J, Gemenetzis G, Groot VP, Makary MA, He J, Weiss MJ, Cameron JL, Wolfgang CL, Hruban RH, Roberts NJ, Karchin R, Goggins MG, Wood LD.

Gut. 2018 Mar 2. pii: gutjnl-2017-315062. doi: 10.1136/gutjnl-2017-315062. [Epub ahead of print]


Assessment of the Clinical Relevance of BRCA2 Missense Variants by Functional and Computational Approaches.

Guidugli L, Shimelis H, Masica DL, Pankratz VS, Lipton GB, Singh N, Hu C, Monteiro ANA, Lindor NM, Goldgar DE, Karchin R, Iversen ES, Couch FJ.

Am J Hum Genet. 2018 Jan 17. pii: S0002-9297(17)30502-5. doi: 10.1016/j.ajhg.2017.12.013. [Epub ahead of print]


Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework.

Glusman G, Rose PW, Prlić A, Dougherty J, Duarte JM, Hoffman AS, Barton GJ, Bendixen E, Bergquist T, Bock C, Brunk E, Buljan M, Burley SK, Cai B, Carter H, Gao J, Godzik A, Heuer M, Hicks M, Hrabe T, Karchin R, Leman JK, Lane L, Masica DL, Mooney SD, Moult J, Omenn GS, Pearl F, Pejaver V, Reynolds SM, Rokem A, Schwede T, Song S, Tilgner H, Valasatava Y, Zhang Y, Deutsch EW.

Genome Med. 2017 Dec 18;9(1):113. doi: 10.1186/s13073-017-0509-y.


CRAVAT 4: Cancer-Related Analysis of Variants Toolkit.

Masica DL, Douville C, Tokheim C, Bhattacharya R, Kim R, Moad K, Ryan MC, Karchin R.

Cancer Res. 2017 Nov 1;77(21):e35-e38. doi: 10.1158/0008-5472.CAN-17-0338.


Autologous reconstitution of human cancer and immune system in vivo.

Fu J, Sen R, Masica DL, Karchin R, Pardoll D, Walter V, Hayes DN, Chung CH, Kim YJ.

Oncotarget. 2017 Jan 10;8(2):2053-2068. doi: 10.18632/oncotarget.14026.


A novel approach for selecting combination clinical markers of pathology applied to a large retrospective cohort of surgically resected pancreatic cysts.

Masica DL, Dal Molin M, Wolfgang CL, Tomita T, Ostovaneh MR, Blackford A, Moran RA, Law JK, Barkley T, Goggins M, Irene Canto M, Pittman M, Eshleman JR, Ali SZ, Fishman EK, Kamel IR, Raman SP, Zaheer A, Ahuja N, Makary MA, Weiss MJ, Hirose K, Cameron JL, Rezaee N, He J, Joon Ahn Y, Wu W, Wang Y, Springer S, Diaz LL Jr, Papadopoulos N, Hruban RH, Kinzler KW, Vogelstein B, Karchin R, Lennon AM.

J Am Med Inform Assoc. 2017 Jan;24(1):145-152. doi: 10.1093/jamia/ocw069. Epub 2016 Jun 21.


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.

Cancer Res. 2016 Jul 1;76(13):3719-31. doi: 10.1158/0008-5472.CAN-15-3190. Epub 2016 Apr 28.


Towards Increasing the Clinical Relevance of In Silico Methods to Predict Pathogenic Missense Variants.

Masica DL, Karchin R.

PLoS Comput Biol. 2016 May 12;12(5):e1004725. doi: 10.1371/journal.pcbi.1004725. eCollection 2016 May. Review. No abstract available.


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.

Hum Mutat. 2016 Jan;37(1):28-35. doi: 10.1002/humu.22911. Epub 2015 Oct 26.


A combination of molecular markers and clinical features improve the classification of pancreatic cysts.

Springer S, Wang Y, Dal Molin M, Masica DL, Jiao Y, Kinde I, Blackford A, Raman SP, Wolfgang CL, Tomita T, Niknafs N, Douville C, Ptak J, Dobbyn L, Allen PJ, Klimstra DS, Schattner MA, Schmidt CM, Yip-Schneider M, Cummings OW, Brand RE, Zeh HJ, Singhi AD, Scarpa A, Salvia R, Malleo G, Zamboni G, Falconi M, Jang JY, Kim SW, Kwon W, Hong SM, Song KB, Kim SC, Swan N, Murphy J, Geoghegan J, Brugge W, Fernandez-Del Castillo C, Mino-Kenudson M, Schulick R, Edil BH, Adsay V, Paulino J, van Hooft J, Yachida S, Nara S, Hiraoka N, Yamao K, Hijioka S, van der Merwe S, Goggins M, Canto MI, Ahuja N, Hirose K, Makary M, Weiss MJ, Cameron J, Pittman M, Eshleman JR, Diaz LA Jr, Papadopoulos N, Kinzler KW, Karchin R, Hruban RH, Vogelstein B, Lennon AM.

Gastroenterology. 2015 Nov;149(6):1501-10. doi: 10.1053/j.gastro.2015.07.041. Epub 2015 Aug 4.


Genomic alterations in head and neck squamous cell carcinoma determined by cancer gene-targeted sequencing.

Chung CH, Guthrie VB, Masica DL, Tokheim C, Kang H, Richmon J, Agrawal N, Fakhry C, Quon H, Subramaniam RM, Zuo Z, Seiwert T, Chalmers ZR, Frampton GM, Ali SM, Yelensky R, Stephens PJ, Miller VA, Karchin R, Bishop JA.

Ann Oncol. 2015 Jun;26(6):1216-23. doi: 10.1093/annonc/mdv109. Epub 2015 Feb 23.


Missense variants in CFTR nucleotide-binding domains predict quantitative phenotypes associated with cystic fibrosis disease severity.

Masica DL, Sosnay PR, Raraigh KS, Cutting GR, Karchin R.

Hum Mol Genet. 2015 Apr 1;24(7):1908-17. doi: 10.1093/hmg/ddu607. Epub 2014 Dec 8.


Predicting survival in head and neck squamous cell carcinoma from TP53 mutation.

Masica DL, Li S, Douville C, Manola J, Ferris RL, Burtness B, Forastiere AA, Koch WM, Chung CH, Karchin R.

Hum Genet. 2015 May;134(5):497-507. doi: 10.1007/s00439-014-1470-0. Epub 2014 Aug 10.


Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene.

Sosnay PR, Siklosi KR, Van Goor F, Kaniecki K, Yu H, Sharma N, Ramalho AS, Amaral MD, Dorfman R, Zielenski J, Masica DL, Karchin R, Millen L, Thomas PJ, Patrinos GP, Corey M, Lewis MH, Rommens JM, Castellani C, Penland CM, Cutting GR.

Nat Genet. 2013 Oct;45(10):1160-7. doi: 10.1038/ng.2745. Epub 2013 Aug 25.


Neutron reflectometry studies of the adsorbed structure of the amelogenin, LRAP.

Tarasevich BJ, Perez-Salas U, Masica DL, Philo J, Kienzle P, Krueger S, Majkrzak CF, Gray JL, Shaw WJ.

J Phys Chem B. 2013 Mar 21;117(11):3098-109. doi: 10.1021/jp311936j. Epub 2013 Mar 12.


Collections of simultaneously altered genes as biomarkers of cancer cell drug response.

Masica DL, Karchin R.

Cancer Res. 2013 Mar 15;73(6):1699-708. doi: 10.1158/0008-5472.CAN-12-3122. Epub 2013 Jan 21.


Phenotype-optimized sequence ensembles substantially improve prediction of disease-causing mutation in cystic fibrosis.

Masica DL, Sosnay PR, Cutting GR, Karchin R.

Hum Mutat. 2012 Aug;33(8):1267-74. doi: 10.1002/humu.22110. Epub 2012 May 22.


Partial high-resolution structure of phosphorylated and non-phosphorylated leucine-rich amelogenin protein adsorbed to hydroxyapatite.

Masica DL, Gray JJ, Shaw WJ.

J Phys Chem C Nanomater Interfaces. 2011 Jul 21;115(28):13775-13785.


Correlation of somatic mutation and expression identifies genes important in human glioblastoma progression and survival.

Masica DL, Karchin R.

Cancer Res. 2011 Jul 1;71(13):4550-61. doi: 10.1158/0008-5472.CAN-11-0180. Epub 2011 May 9.


Enzyme replacement therapy prevents dental defects in a model of hypophosphatasia.

McKee MD, Nakano Y, Masica DL, Gray JJ, Lemire I, Heft R, Whyte MP, Crine P, Millán JL.

J Dent Res. 2011 Apr;90(4):470-6. doi: 10.1177/0022034510393517. Epub 2011 Jan 6.


Toward a structure determination method for biomineral-associated protein using combined solid- state NMR and computational structure prediction.

Masica DL, Ash JT, Ndao M, Drobny GP, Gray JJ.

Structure. 2010 Dec 8;18(12):1678-87. doi: 10.1016/j.str.2010.09.013.


De novo design of peptide-calcite biomineralization systems.

Masica DL, Schrier SB, Specht EA, Gray JJ.

J Am Chem Soc. 2010 Sep 8;132(35):12252-62. doi: 10.1021/ja1001086.


Phosphorylation-dependent inhibition of mineralization by osteopontin ASARM peptides is regulated by PHEX cleavage.

Addison WN, Masica DL, Gray JJ, McKee MD.

J Bone Miner Res. 2010 Apr;25(4):695-705. doi: 10.1359/jbmr.090832.


Modulation of calcium oxalate dihydrate growth by selective crystal-face binding of phosphorylated osteopontin and polyaspartate peptide showing occlusion by sectoral (compositional) zoning.

Chien YC, Masica DL, Gray JJ, Nguyen S, Vali H, McKee MD.

J Biol Chem. 2009 Aug 28;284(35):23491-501. doi: 10.1074/jbc.M109.021899. Epub 2009 Jul 6.


Solution- and adsorbed-state structural ensembles predicted for the statherin-hydroxyapatite system.

Masica DL, Gray JJ.

Biophys J. 2009 Apr 22;96(8):3082-91. doi: 10.1016/j.bpj.2009.01.033.


Structure prediction of protein-solid surface interactions reveals a molecular recognition motif of statherin for hydroxyapatite.

Makrodimitris K, Masica DL, Kim ET, Gray JJ.

J Am Chem Soc. 2007 Nov 7;129(44):13713-22. Epub 2007 Oct 12.


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