Masica, David

Asst Research Prof.
Biomedical Engineering

Telecommuting
(443) 416-6693
dmasica2@jhu.edu

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About

Education
  • Ph.D. 2009, The Johns Hopkins University

Publications

Journal Articles
  • 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 (2018).  Assessment of the Clinical Relevance of BRCA2 Missense Variants by Functional and Computational Approaches.  American Journal of Human Genetics.  (2).
  • Glusman G, Rose PW, Prlic 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 JJ, 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 (2017).  Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: A proposed framework.  Genome Medicine.  9(1).
  • Masica DL, Douville C, Tokheim C, Bhattacharya R, Kim RG, Moad K, Ryan MC, Karchin R (2017).  CRAVAT 4: Cancer-related analysis of variants toolkit.  Cancer Research.  77(21).
  • Masica DL, Molin MD, Wolfgang CL, Tomita T, Ostovaneh MR, Blackford A, Moran RA, Law JK, Barkley T, Goggins M, Canto MI, 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, Ahn YJ, Wu W, Wang Y, Springer S, Diaz LL, Papadopoulos N, Hruban RH, Kinzler KW, Vogelstein B, Karchin R, Lennon AM (2017).  A novel approach for selecting combination clinical markers of pathology applied to a large retrospective cohort of surgically resected pancreatic cysts.  Journal of the American Medical Informatics Association.  24(1).
  • Fu J, Sen R, Masica DL, Karchin R, Pardoll D, Walter V, Hayes DN, Chung CH, Kim YJ (2017).  Autologous reconstitution of human cancer and immune system in vivo.  Oncotarget.  8(2).
  • Tokheim C, Bhattacharya R, Niknafs N, Gygax DM, Kim R, Ryan M, Masica DL, Karchin R (2016).  Exome-scale discovery of hotspot mutation regions in human cancer using 3D protein structure.  Cancer Research.  76(13).
  • Masica DL, Karchin R (2016).  Towards Increasing the Clinical Relevance of In Silico Methods to Predict Pathogenic Missense Variants.  PLoS Computational Biology.  12(5).
  • Scranton MA, Ostrand JT, Georgianna DR, Lofgren SM, Li D, Ellis RC, Carruthers DN, Dräger A, Masica DL, Mayfield SP (2016).  Synthetic promoters capable of driving robust nuclear gene expression in the green alga Chlamydomonas reinhardtii.  Algal Research.  15.
  • Douville C, Masica DL, Stenson PD, Cooper DN, Gygax DM, Kim R, Ryan M, Karchin R (2016).  Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel).  Human Mutation.  37(1).
  • Masica DL, Li S, Douville C, Manola J, Ferris RL, Burtness B, Forastiere AA, Koch WM, Chung CH, Karchin R (2015).  Predicting survival in head and neck squamous cell carcinoma from TP53 mutation.  Human Genetics.  134(5).
  • 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 (2015).  Genomic alterations in head and neck squamous cell carcinoma determined by cancer gene-targeted sequencing.  Annals of Oncology.  26(6).
  • 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 J-Y, Kim S-W, Kwon W, Hong S-M, Song K-B, 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, Papadopoulos N, Kinzler KW, Karchin R, Hruban RH, Vogelstein B, Lennon AM (2015).  A Combination of Molecular Markers and Clinical Features Improve the Classification of Pancreatic Cysts.  Gastroenterology.  149(6).
  • Li L, Masica D, Ishida M, Tomuleasa C, Umegaki S, Kalloo AN, Georgiades C, Singh VK, Khashab M, Amateau S, Li Z, Okolo P, Lennon AM, Saxena P, Geschwind JF, Schlachter T, Hong K, Pawlik TM, Canto M, Law J, Sharaiha R, Weiss CR, Thuluvath P, Goggins M, Shin EJ, Peng H, Kumbhari V, Hutfless S, Zhou L, Mezey E, Meltzer SJ, Karchin R, Selaru FM (2014).  Human bile contains MicroRNA-laden extracellular vesicles that can be used for cholangiocarcinoma diagnosis.  Hepatology.  60(3).
  • Masica DL, Sosnay PR, Raraigh KS, Cutting GR, Karchin R (2014).  Missense variants in CFTR nucleotide-binding domains predict quantitative phenotypes associated with cystic fibrosis disease severity.  Human Molecular Genetics.  24(7).
  • 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 (2013).  Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene.  Nature Genetics.  45(10).
  • Tarasevich BJ, Perez-Salas U, Masica DL, Philo J, Kienzle P, Krueger S, Majkrzak CF, Gray JL, Shaw WJ (2013).  Neutron reflectometry studies of the adsorbed structure of the amelogenin, LRAP.  Journal of Physical Chemistry B.  117(11).
  • Masica DL, Karchin R (2013).  Collections of simultaneously altered genes as biomarkers of cancer cell drug response.  Cancer Research.  73(6).
  • Roehrich A, Ash J, Zane A, Masica DL, Gray JJ, Goobes G, Drobny G (2012).  Solid-state NMR studies of biomineralization peptides and proteins.  ACS Symposium Series.  1120.
  • Masica DL, Sosnay PR, Cutting GR, Karchin R (2012).  Phenotype-optimized sequence ensembles substantially improve prediction of disease-causing mutation in cystic fibrosis.  Human Mutation.  33(8).
  • Masica DL, Gray JJ, Shaw WJ (2011).  Partial High-resolution structure of phosphorylated and non-phosphorylated leucine-rich amelogenin protein adsorbed to hydroxyapatite.  Journal of Physical Chemistry C.  115(28).
  • Masica DL, Karchin R (2011).  Correlation of somatic mutation and expression identifies genes important in human glioblastoma progression and survival.  Cancer Research.  71(13).
  • McKee MD, Nakano Y, Masica DL, Gray JJ, Lemire I, Heft R, Whyte MP, Crine P, Millán JL (2011).  Enzyme replacement therapy prevents dental defects in a model of hypophosphatasia.  Journal of Dental Research.  90(4).
  • Masica DL, Ash JT, Ndao M, Drobny GP, Gray JJ (2010).  Toward a structure determination method for biomineral-associated protein using combined solid- State NMR and computational structure prediction.  Structure.  18(12).
  • Masica DL, Schrier SB, Specht EA, Gray JJ (2010).  De novo design of peptide-calcite biomineralization systems.  Journal of the American Chemical Society.  132(35).
  • Addison WN, Masica DL, Gray JJ, McKee MD (2010).  Phosphorylation-dependent inhibition of mineralization by osteopontin ASARM peptides is regulated by PHEX cleavage.  Journal of Bone and Mineral Research.  25(4).
  • Chien YC, Masica DL, Gray JJ, Nguyen S, Vali H, McKee MD (2009).  Modulation of calcium oxalate dihydrate growth by selective crystal-face binding of phosphorylated osteopontin and polyaspartate peptide showing occlusion by sectoral (compositional) zoning.  Journal of Biological Chemistry.  284(35).
  • Masica DL, Gray JJ (2009).  Solution- and adsorbed-state structural ensembles predicted for the statherin-hydroxyapatite system.  Biophysical Journal.  96(8).
  • Masica D, Gray JJ (2008).  High-resolution adsorbed and solution-state ensembles of a naturally evolved biomineralization protein: Blind and nmr-guided predictions.  AIChE Annual Meeting, Conference Proceedings.
  • Makrodimitris K, Masica DL, Kim ET, Gray JJ (2007).  Structure prediction of protein-solid surface interactions reveals a molecular recognition motif of statherin for hydroxyapatite.  Journal of the American Chemical Society.  129(44).
  • Daily MD, Masica D, Sivasubramanian A, Somarouthu S, Gray JJ (2005).  CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock.  Proteins: Structure, Function and Genetics.  60(2).
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