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

Collaborators

 

UNIVERSITY OF CHICAGO FACULTY AFFILIATES

  • Andrew A. Chien
  • Anthony Kossiakoff
  • Barbara Stranger, PhD
  • Hae Kyung Im, PhD
  • Lixing Yang, PhD
  • Phil Schumm, MA
  • Robert Grossman, PhD
  • Sam Volchenboum, MD, PhD
  • Susan L. Cohn, MD, PhD

 

RESEARCH PARTNERS

  • AbbVie
  • Academia Sinica Taiwan
  • Johns Hopkins Applied Physics Laboratory
  • Northwestern University
  • The Ohio State University

Publications

 

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.