Research Areas

  • Bioinformatics

  • Pipelines for large-scale data analysis

  • Scientific informatics

  • Open data

  • Data commons and clouds

  • Complex systems

  • Large-scale data management

  • High performance analytics


Publications


Grossman, RL. (2019). Data Lakes, Clouds, and Commons: A Review of Platforms for Analyzing and Sharing Genomic Data. Trends in Genetics. 35(3), 223-234, doi:10.1016/j.tig.2018.12.006.


Khan SI, Flamig Z, Hong Y. (2019). Flood Monitoring System Using Distributed Hydrologic Modeling for Indus River Basin. Khan(Ed). Indus River Basin. 335-355. Elsevier. doi:10.1016/B978-0-12-812782-7.09990-2.


Terti G, Ruin I, Gourley JJ, Kirstetter P, Flamig Z, Blanchet J, Arthur A, Anquetin S. (2019). Toward Probabilistic Prediction of Flash Flood Human Impacts. (2019). Risk Analysis, 39(1), 140-161, doi:10.1111/risa.12921.


Lee JS, Kibbe WA, Grossman RL. (2018). Data Harmonization for a Molecularly Driven Health System. Cell. 174(5), 1045-1048, doi:10.1016/j.cell.2018.08.012.


Geeleher P, Nath A, Wang F, Zhang Z, Barbeira AN, Fessler J, Grossman RL, Seoighe C, Huang RS. (2018) Cancer expression quantitative trait loci (eQTLs) can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity. Genome Biology. 19(130). doi:10.1186/s13059-018-1507-0.


Alfieria L, Cohen S, Galantowicz J, Schumannde G, Trigg MA, Zsoterg E, Prudhommegh C, Kruczkiewicz A, de Perez EC, Flamig Z, Rudarin R, Wu H, Adler RF, Brakenridger RG, Kettnerr A, Weerts A, Matgen P, A.K.M Islam S, de Groevea T, Salamona P. (2018). A global network for operational flood risk reduction. Environmental Science and Policy. 84, 149–158, doi:10.1016/j.envsci.2018.03.014.


Clark RA, Flamig ZL, Vergara H, Hong Y, Gourley JJ, Mandl DJ, Frye S, Handy M, Patterson M. (2017). Hydrological Modeling and Capacity Building in the Republic of Namibia. Bull. Amer. Meteor. Soc., 98, 1697–1715, doi:10.1175/BAMS-D-15-00130.1.


Geeleher P, Zhang Z, Wang F, Gruener RF, Nath A, Morrison G, Bhutra S, Grossman RL, Huang RS. (2017). Discovering novel pharmacogenomic biomarkers by imputing drug response in cancer patients from large genomics studies. Genome Research. doi:10.1101/gr.221077.117


Patterson MT, Anderson N, Bennett C, Bruggemann J, Grossman RL, Handy M, Ly V, Mandl DJ, Pederson S, Pivarski J, Powell R, Spring J, Wells W, Xia J. (2017). The Matsu Wheel: a reanalysis framework for Earth satellite imagery in data commons. Int J Data Sci Anal 2017. 1-14. doi:10.1007/s41060-017-0052-3.


Hungate EA, Applebaum MA, Skol AD, Vaksman Z, Diamond M, McDaniel L, Volchenboum SL, Stranger BE, Maris JM, Diskin SJ, Onel K, Cohn SL. (2017). Evaluation of Genetic Predisposition for MYCN-Amplified Neuroblastoma. J Natl Cancer Inst 2017. 109 (10): djx093. doi:10.1093/jnci/djx093.


Jensen MA, Ferretti V, Grossman RL, Staudt LM. (2017). The NCI Genomic Data Commons as an engine for precision medicine. Blood. 130(4), 453-459. doi:10.1182/blood-2017-03-735654.


Stricker TP, Brown CD, Bandlamudi C, McNerney M, Kittler R, et al. (2017). Robust stratification of breast cancer subtypes using differential patterns of transcript isoform expression. PLOS Genetics 13(3): e1006589. doi:10.1371/journal.pgen.1006589.


Nguyen TD, Chiesa M, Canini M. (2017). Decentralized Consistent Updates in SDN. In Proceedings of the Symposium on SDN Research (SOSR '17). ACM, New York, NY, USA, 21-33. doi:10.1145/3050220.3050224.


Grossman R, Abel B, Angiuoli S, Barrett J, Bassett D, Bramlett K, Blumenthal G, Carlsson A, Cortese R, DiGiovanna J, Davis-Dusenbery B, Dittamore R, Eberhard D, Febbo P, Fitzsimons M, Flamig Z, Godsey J, Goswami J, Gruen A, Ortuño F, Han J, Hayes D, Hicks J, Holloway D, Hovelson D, Johnson J, Juhl H, Kalamegham R, Kamal R, Kang Q, Kelloff G, Klozenbuecher M, Kolatkar A, Kuhn P, Langone K, Leary R, Loverso P, Manmathan H, Martin A.-M, Martini J, Miller D, Mitchell M, Morgan T, Mulpuri R, Nguyen T, Otto G, Pathak A, Peters E, Philip R, Posadas E, Reese D, Reese M, Robinson D, Dei Rossi A, Sakul H, Schageman J, Singh S, Scher H, Schmitt K, Silvestro A, Simmons J, Simmons T, Sislow J, Talasaz A, Tang P, Tewari M, Tomlins S, Toukhy H, Tseng H, Tuck M, Tzou A, Vinson J, Wang Y, Wells W, Welsh A, Wilbanks J, Wolf J, Young L, Lee J, and Leiman L. (2017). Collaborating to Compete: Blood Profiling Atlas in Cancer (BloodPAC) Consortium. Clin. Pharmacol. Ther. doi:10.1002/cpt.666.


Wheeler HE, Shah KP, Brenner J, Garcia T, Aquino-Michaels K; GTEx Consortium., Cox NJ, Nicolae DL, Im HK. (2016). Survey of the Heritability and Sparse Architecture of Gene Expression Traits across Human Tissues. PLoS Genet. 12(11):e1006423. doi: 10.1371/journal.pgen.1006423.

 

 

Grossman RL, Heath AP, Ferretti V, Varmus HE, Lowy DR, Kibbe WA, Staudt LM. (2016). Toward a Shared Vision for Cancer Genomic Data. N Engl J Med, 375(12), 1109-1112. doi:10.1056/NEJMp1607591.

 

Grossman RL, Heath A, Murphy M, Patterson M, Wells W. (2016). A case for data commons: Toward data science as a service. Computing in Science & Engineering, 18(5), 10-20. doi:10.1109/MCSE.2016.92.

 

Patterson MT, Anderson N, Bennett C, Bruggemann J, Grossman RL, Handy M, Ly V, Mandl DJ, Pederson S, Pivarski J, Powell R. (2016). The Matsu Wheel: A Cloud-Based Framework for Efficient Analysis and Reanalysis of Earth Satellite Imagery. Big Data Computing Service and Applications (BigDataService), 2016 IEEE Second International Conference. IEEE. 156-165. doi: 10.1109/BigDataService.2016.39.

 

Gamazon ER, Wheeler HE, Shah KP, Mozaffari SV, Aquino-Michaels K, Carroll RJ, Eyler AE, Denny JC; GTEx Consortium., Nicolae DL, Cox NJ, Im HK. (2015). A gene-based association method for mapping traits using reference transcriptome data. Nat Genet. 47(9):1091-8. doi:10.1038/ng.3367.

 

Heath AP, Greenway M, Powell R, Spring J, Suarez R, Hanley D, Bandlamudi C, McNerney M, White KP, Grossman RL. (2014). Bionimbus: a cloud for managing, analyzing and sharing large genomics datasets. J Am Med Inform Assoc, 21(6), 969-975. doi:10.1136/amiajnl-2013-002155.

 

Wheeler HE, Aquino-Michaels K, Gamazon ER, Trubetskoy VV, Dolan ME, Huang RS, Cox NJ, Im HK. (2014). Poly-omic prediction of complex traits: OmicKriging. Genet Epidemiol. 38(5):402-15. doi:10.1002/gepi.21808.

 

Kolker E, Özdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, Choiniere J, Dearth SP, Feng WC, Ferguson L, Fox G, Frishman D, Grossman R, Heath A, Higdon R, Hutz MH, Janko I, Jiang L, Joshi S, Kel A, Kemnitz JW, Kohane IS, Kolker N, Lancet D, Lee E, Li W, Lisitsa A, Llerena A, MacNealy-Koch C, Marshall JC, Masuzzo P, May A, Mias G, Monroe M, Montague E, Mooney S, Nesvizhskii A, Noronha S, Omenn G, Rajasimha H, Ramamoorthy P, Sheehan J, Smarr L, Smith CV, Smith T, Snyder M, Rapole S Srivastava S, Stanberry L, Stewart E, Toppo S, Uetz P, Verheggen K, Voy BH, Warnich L, Wilhelm SW, Yandl G. (2014). Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications. OMICS: A Journal of Integrative Biology. 18(1): 10-14. doi:10.1089/omi.2013.0149.