Benitz, Simone, et al. "ROR2 regulates cellular plasticity in pancreatic neoplasia and adenocarcinoma." Cancer Discovery 14.11 (2024): 2162-2182.

Brady, Arthur, Amanda Charbonneau, Robert L. Grossman, Heather H. Creasy, Robinette Renner, Todd Pihl, John Otridge et al. "NCI Cancer Research Data Commons: core standards and services." Cancer Research 84, no. 9 (2024): 1384-1387.

Camera, Andrea, et al. "Aging and putative frailty biomarkers are altered by spaceflight." Scientific Reports 14.1 (2024): 13098.

Clark, M., Meyer, C., Ramos-Cejudo, J., Elbers, D. C., Pierce-Murray, K., Fricks, R., ... & Fillmore, N. R. (2024). Transfer Learning for Mortality Prediction in Non-Small Cell Lung Cancer with Low-Resolution Histopathology Slide Snapshots. Studies in Health Technology and Informatics, 310, 735-739.

Grossman, R. L. (2024). An Annotated Glossary for Data Commons, Data Meshes, and Other Data Platforms. arXiv preprint arXiv:2404.15475.

Grossman, R. L., Boyles, R. R., Davis-Dusenbery, B. N., Haddock, A., Heath, A. P., O’Connor, B. D., ... & Ahalt, S. (2024). A Framework for the Interoperability of Cloud Platforms: Towards FAIR Data in SAFE Environments. Scientific Data, 11(1), 241.

Grossman, R. L., Boyd, C., Do, N., Elbers, D. C., Fitzsimons, M. S., Giger, M. L., ... & Venkat, A. (2024). Ten Pillars for Data Meshes. arXiv preprint arXiv:2411.05248.

Lockwood, C. M., Merker, J. D., Bain, E., Compton, C., Grossman, R. L., Johann, D., ... & Leiman, L. C. Towards Preanalytical Best Practices for Liquid Biopsy Studies: A BLOODPAC Landscape Analysis. Clinical Pharmacology & Therapeutics.

Mathyk, Begum Aydogan, et al. "Spaceflight induces changes in gene expression profiles linked to insulin and estrogen." Communications Biology 7.1 (2024): 692.

McDonald, J. Tyson, et al. "Space radiation damage rescued by inhibition of key spaceflight associated miRNAs." Nature Communications 15.1 (2024): 4825.

Song, S., Subramanyam, A., Madejski, I., & Grossman, R. L. (2024). LaB-RAG: Label Boosted Retrieval Augmented Generation for Radiology Report Generation. arXiv preprint arXiv:2411.16523.

Trunnell, Matthew, et al. "The Pandemic Response Commons." JAMIA open 7.2 (2024): ooae025.

Venkat, A., Ribeyre, P., Qureshi, J., Narumanchi, S. S., Maxwell, J. M., Winslow, B., ... & Grossman, R. (2024). A workflow execution system in a data fabric for integrative cancer analyses. Cancer Research, 84(6_Supplement), 6242-6242.

Walsh, B., Beckman, L., Burchett, J. D., Peterkort, M., Lee, J., Fitzsimons, M., ... & Ellrott, K. (2024). An integrated data platform to support the international alliance for cancer early detection. Cancer Research, 84(6_Supplement), 3558-3558.

Wang, Zhining, Tanja M. Davidsen, Gina R. Kuffel, KanakaDurga Addepalli, Amanda Bell, Esmeralda Casas-Silva, Hayley Dingerdissen et al. "NCI Cancer Research Data Commons: resources to share key cancer data." Cancer Research 84, no. 9 (2024): 1388-1395.

Wyatt, K. D., Graglia, L., Furner, B., Kang, B., Fitzsimons, M., Grossman, R. L., & Volchenboum, S. L. (2024). An open-source platform for pediatric cancer data exploration: a report from Data for the Common Good. JAMIA open, 7(1), ooae004.

Adegunsoye, A., Baccile, R., Best, T. J., Zaksas, V., Zhang, H., Karnik, R., … Solway, J. (2023). Pharmacotherapy and pulmonary fibrosis risk after SARS-CoV-2 infection: a prospective nationwide cohort study in the United States. The Lancet Regional Health - Americas, 25, 100566. doi:10.1016/j.lana.2023.100566

Ahalt, S., Avillach, P., Boyles, R., Bradford, K., Cox, S., Davis-Dusenbery, B., Grossman, R. L., Krishnamurthy, A., Manning, A., Paten, B., Philippakis, A., Borecki, I., Chen, S. H., Kaltman, J., Ladwa, S., Schwartz, C., Thomson, A., Davis, S., Leaf, A., Lyons, J., … Asare, J. (2023). Building a collaborative cloud platform to accelerate heart, lung, blood, and sleep research. Journal of the American Medical Informatics Association : JAMIA, 30(7), 1293–1300. https://doi.org/10.1093/jamia/ocad048

Clarke, C. A., Lang, K., Putcha, G., Beer, J. P., Champagne, M., Ferris, A., Godsey, J. H., Grossman, R. L., Hoyos, J. M., Johann, D. J., Krunic, N., Kuhn, P., Lee, J. S. H., Maddala, T., Mata, M., McDole, J., Perez, O., Scher, H., Stewart, M. D., Bhan, S. S., … Leiman, L. C. (2023). BLOODPAC: Collaborating to chart a path towards blood-based screening for early cancer detection. Clinical and translational science, 16(1), 5–9. https://doi.org/10.1111/cts.13427

Dolezal, J. M., Wolk, R., Hieromnimon, H. M., Howard, F. M., Srisuwananukorn, A., Karpeyev, D., Ramesh, S., Kochanny, S., Kwon, J. W., Agni, M., Simon, R. C., Desai, C., Kherallah, R., Nguyen, T. D., Schulte, J. J., Cole, K., Khramtsova, G., Garassino, M. C., Husain, A. N., Li, H., … Pearson, A. T. (2023). Deep learning generates synthetic cancer histology for explainability and education. NPJ precision oncology, 7(1), 49. https://doi.org/10.1038/s41698-023-00399-4

Grossman, R. L., Giger, M. L., Johnson, J. A., Marks, J. D., Ridgway, J. P., Solway, J., & Stadler, W. M. (2023). Principles and Guidelines for Sharing Biomedical Data for Secondary Use: The University of Chicago Perspective. arXiv [q-Bio.OT]. Retrieved from http://arxiv.org/abs/2302.02425

Grossman, R. L. (2023). Ten lessons for data sharing with a data commons. Scientific Data, 10(1), 120. doi:10.1038/s41597-023-02029-x

Guarnieri, J. W., Dybas, J. M., Fazelinia, H., Kim, M. S., Frere, J., Zhang, Y., Soto Albrecht, Y., Murdock, D. G., Angelin, A., Singh, L. N., Weiss, S. L., Best, S. M., Lott, M. T., Zhang, S., Cope, H., Zaksas, V., Saravia-Butler, A., Meydan, C., Foox, J., Mozsary, C., … Wallace, D. C. (2023). Core mitochondrial genes are down-regulated during SARS-CoV-2 infection of rodent and human hosts. Science translational medicine, 15(708), eabq1533. https://doi.org/10.1126/scitranslmed.abq1533

Hernandez, K. M., Bramlett, K. S., Agius, P., Baden, J., Cao, R., Clement, O., Corner, A. S., Craft, J., Dean, D. A., 2nd, Dry, J. R., Grigaityte, K., Grossman, R. L., Hicks, J., Higa, N., Holzer, T. R., Jensen, J., Johann, D. J., Katz, S., Kolatkar, A., Keynton, J. L., … Leiman, L. C. (2023). Contrived Materials and a Data Set for the Evaluation of Liquid Biopsy Tests: A Blood Profiling Atlas in Cancer (BLOODPAC) Community Study. The Journal of molecular diagnostics : JMD, 25(3), 143–155. https://doi.org/10.1016/j.jmoldx.2022.12.003

Hernandez, K. M., Venkat, A., Elbers, D. C., Bihn, J. R., Brophy, M. T., Do, N. V., ... & Grossman, R. L. (2023). Prostate cancer patient stratification by molecular signatures in the Veterans Precision Oncology Data Commons. Molecular Case Studies, 9(4), a006298.

Hieromnimon, H. M., Dolezal, J., Doytcheva, K., Howard, F. M., Kochanny, S., Zhang, Z., … Riesenfeld, S. J. (2023). Latent transcriptional programs reveal histology-encoded tumor features spanning tissue origins. bioRxiv. doi:10.1101/2023.03.22.533810

Higgins, D., Thibert, J.-P., Mattioni, M., DiGiovanna, J., Grossman, R. L., Farrow, B. K., … Heath, A. P. (04 2023). Abstract 6576: Gabriella Miller Kids First Data Resource Center (KFDRC): Empowering discovery across germline and somatic variation in pediatric cancer. Cancer Research, 83(7_Supplement), 6576–6576. doi:10.1158/1538-7445.AM2023-6576

Lukowski, M., Prokhorenkov, A., & Grossman, R. L. (2023). Towards self-describing and FAIR bulk formats for biomedical data. PLoS computational biology, 19(3), e1010944. https://doi.org/10.1371/journal.pcbi.1010944

McConnell, S.C., Hernandez, K.M., Andrade, J. et al. Immune gene variation associated with chromosome-scale differences among individual zebrafish genomes. Sci Rep 13, 7777 (2023). https://doi.org/10.1038/s41598-023-34467-3

Putra, M. L., Kim, I. K., Gunawi, H. S., & Grossman, R. L. (2023, December). CNT: Semi-Automatic Translation from CWL to Nextflow for Genomic Workflows. In 2023 IEEE 23rd International Conference on Bioinformatics and Bioengineering (BIBE) (pp. 22-27). IEEE Computer Society.

Song, S., Mohsin, E., Kuznetsov, A., Weber, C., Grossman, R. L., & Khan, A. A. (2023, October). ATAT: Automated Tissue Alignment and Traversal. In NeurIPS 2023 AI for Science Workshop

Sweeney, S. M., Hamadeh, H. K., Abrams, N., Adam, S. J., Brenner, S., Connors, D. E., Davis, G. J., Fiore, L., Gawel, S. H., Grossman, R. L., Hanlon, S. E., Hsu, K., Kelloff, G. J., Kirsch, I. R., Louv, B., McGraw, D., Meng, F., Milgram, D., Miller, R. S., Morgan, E., … Srivastava, S. (2023). Challenges to Using Big Data in Cancer. Cancer research, 83(8), 1175–1182. https://doi.org/10.1158/0008-5472.CAN-22-1274

Zhang, R., Khan, A. A., Chen, Y., & Grossman, R. L. (2023). Enhancing Instance-Level Image Classification with Set-Level Labels. arXiv preprint arXiv:2311.05659.

Schumm, L. P., Giurcanu, M. C., Locey, K. J., Ortega, J. C., Zhang, Z., & Grossman, R. L. (2022). Racial and ethnic disparities in the observed COVID-19 case fatality rate among the U.S. population. Annals of epidemiology, 74, 118–124. https://doi.org/10.1016/j.annepidem.2022.07.010

Sheffield, N. C., Bonazzi, V. R., Bourne, P. E., Burdett, T., Clark, T., Grossman, R. L., Spjuth, O., & Yates, A. D. (2022). From biomedical cloud platforms to microservices: next steps in FAIR data and analysis. Scientific data, 9(1), 553. https://doi.org/10.1038/s41597-022-01619-5

Shi, C., Babiker, N., Urbanek, J. K., Grossman, R. L., Huisingh-Scheetz, M., & Rzhetsky, A. (2022). Free-living wrist and hip accelerometry forecast cognitive decline among older adults without dementia over 1- or 5-years in two distinct observational cohorts. npj aging, 8(1), 7. https://doi.org/10.1038/s41514-022-00087-w

O'Hara, T., Saldanha, A., Trunnell, M., Grossman, R. L., Hota, B., & Frankenberger, C. (2022). Economical Utilization of Health Information with Learning Healthcare System Data Commons. Perspectives in health information management, 19(Spring), 1d.

Schatz, M. C., Philippakis, A. A., Afgan, E., Banks, E., Carey, V. J., Carroll, R. J., Culotti, A., Ellrott, K., Goecks, J., Grossman, R. L., Hall, I. M., Hansen, K. D., Lawson, J., Leek, J. T., Luria, A. O., Mosher, S., Morgan, M., Nekrutenko, A., O'Connor, B. D., Osborn, K., … Wuichet, K. (2022). Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space. Cell genomics, 2(1), 100085. https://doi.org/10.1016/j.xgen.2021.100085

Jochum, M., Lee, M.D., Curry, K. et al. (2022) Analysis of bronchoalveolar lavage fluid metatranscriptomes among patients with COVID-19 disease. Sci Rep 12, 21125. https://doi.org/10.1038/s41598-022-25463-0

Barnes, C., Bajracharya, B., Cannalte, M., Gowani, Z., Haley, W., Kass-Hout, T., Hernandez, K., Ingram, M., Juvvala, H. P., Kuffel, G., Martinov, P., Maxwell, J. M., McCann, J., Malhotra, A., Metoki-Shlubsky, N., Meyer, C., Paredes, A., Qureshi, J., Ritter, X., Schumm, P., … Grossman, R. L. (2022). The Biomedical Research Hub: a federated platform for patient research data. Journal of the American Medical Informatics Association : JAMIA, 29(4), 619–625. https://doi.org/10.1093/jamia/ocab247

Kuang, X., Wang, F., Hernandez, K. M., Zhang, Z., & Grossman, R. L. (2022). Accurate and rapid prediction of tuberculosis drug resistance from genome sequence data using traditional machine learning algorithms and CNN. Scientific reports, 12(1), 2427. https://doi.org/10.1038/s41598-022-06449-4

Wcisel, D. J., Dornburg, A., McConnell, S. C., Hernandez, K. M., Andrade, J., de Jong, J. L. O., Litman, G. W., & Yoder, J. A. (2022). A highly diverse set of novel immunoglobulin-like transcript (NILT) genes in zebrafish indicates a wide range of functions with complex relationships to mammalian receptors. Immunogenetics, 10.1007/s00251-022-01270-9. Advance online publication. https://doi.org/10.1007/s00251-022-01270-9

Arnovitz, S., Mathur, P., Tracy, M., Mohsin, A., Mondal, S., Quandt, J., Hernandez, K. M., Khazaie, K., Dose, M., Emmanuel, A. O., & Gounari, F. (2022). Tcf-1 promotes genomic instability and T cell transformation in response to aberrant β-catenin activation. Proceedings of the National Academy of Sciences of the United States of America, 119(32), e2201493119. https://doi.org/10.1073/pnas.2201493119

Saravia-Butler A. M., Schisler J. C. , Taylor D., Beheshti A., Butler D., Meydan C., Foox J., Hernandez K., Mozsary C., Mason C. E. , Meller R. (2022) Host transcriptional responses in nasal swabs identify potential SARS-CoV-2 infection in PCR negative patients. iScience, 25(11):105310. https://doi.org/10.1016/j.isci.2022.105310

Rehm, H. L., Page, A. J. H., Smith, L., Adams, J. B., Alterovitz, G., Babb, L. J., Barkley, M. P., Baudis, M., Beauvais, M. J. S., Beck, T., Beckmann, J. S., Beltran, S., Bernick, D., Bernier, A., Bonfield, J. K., Boughtwood, T. F., Bourque, G., Bowers, S. R., Brookes, A. J., Brudno, M., … Birney, E. (2021). GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell genomics, 1(2), 100029. https://doi.org/10.1016/j.xgen.2021.100029

Howard, F. M., Dolezal, J., Kochanny, S., Schulte, J., Chen, H., Heij, L., Huo, D., Nanda, R., Olopade, O. I., Kather, J. N., Cipriani, N., Grossman, R. L., & Pearson, A. T. (2021). The impact of site-specific digital histology signatures on deep learning model accuracy and bias. Nature communications, 12(1), 4423. https://doi.org/10.1038/s41467-021-24698-1

Bao, R., Spranger, S., Hernandez, K., Zha, Y., Pytel, P., Luke, J. J., Gajewski, T. F., Volchenboum, S. L., Cohn, S. L., & Desai, A. V. (2021). Immunogenomic determinants of tumor microenvironment correlate with superior survival in high-risk neuroblastoma. Journal for immunotherapy of cancer, 9(7), e002417. https://doi.org/10.1136/jitc-2021-002417

Zhang, Z., Hernandez, K., Savage, J., Li, S., Miller, D., Agrawal, S., Ortuno, F., Staudt, L. M., Heath, A., & Grossman, R. L. (2021). Uniform genomic data analysis in the NCI Genomic Data Commons. Nature Communications, 12(1), 1226. https://doi.org/10.1038/s41467-021-21254-9

Sapoval, N., Mahmoud, M., Jochum, M. D., Liu, Y., Elworth, R. A. L., Wang, Q., Albin, D., Ogilvie, H. A., Lee, M. D., Villapol, S., Hernandez, K. M., Maljkovic Berry, I., Foox, J., Beheshti, A., Ternus, K., Aagaard, K. M., Posada, D., Mason, C. E., Sedlazeck, F. J., & Treangen, T. J. (2021). SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission. Genome Research, 31(4), 635–644. https://doi.org/10.1101/gr.268961.120

Grossman, R. L., Dry, J. R., Hanlon, S. E., Johann, D. J., Kolatkar, A., Lee, J. S. H., Meyer, C., Salvatore, L., Wells, W., & Leiman, L. (2021). BloodPAC Data Commons for Liquid Biopsy Data. JCO Clinical Cancer Informatics, 5, 479–486. https://doi.org/10.1200/CCI.20.00179

Bao, R., Spranger, S., Hernandez, K., Zha, Y., Pytel, P., Luke, J. J., Gajewski, T. F., Volchenboum, S. L., Cohn, S. L., & Desai, A. V. (2021). Immunogenomic determinants of tumor microenvironment correlate with superior survival in high-risk neuroblastoma. Journal for immunotherapy of cancer, 9(7), e002417. https://doi.org/10.1136/jitc-2021-002417

Heath, A. P., Ferretti, V., Agrawal, S., An, M., Angelakos, J. C., Arya, R., Bajari, R., Baqar, B., Barnowski, J. H. B., Burt, J., Catton, A., Chan, B. F., Chu, F., Cullion, K., Davidsen, T., Do, P.-M., Dompierre, C., Ferguson, M. L., Fitzsimons, M. S., … Grossman, R. L. (2021). The NCI Genomic Data Commons. Nature Genetics, 53(3), 257–262. https://doi.org/10.1038/s41588-021-00791-5

Singh, U., Hernandez, K., Aronow, B., & Wurtele, E. (2021). African Americans and European Americans exhibit distinct gene expression patterns across tissues and tumors that are associated with immunologic and infectious functions and environmental exposures. Nature Scientific Reports, 11, 9905. https://doi.org/10.1038/s41598-021-89224-1

Zhang, R., Khan, A. A., Grossman, R. L., & Chen, Y. (2021). Scalable Batch-Mode Deep Bayesian Active Learning via Equivalence Class Annealing. arXiv preprint arXiv:2112.13737.

Tong, M. H., Grossman, R. L., & Gunawi, H. S. (2021). Experiences in Managing the Performance and Reliability of a {Large-Scale} Genomics Cloud Platform. In 2021 USENIX Annual Technical Conference (USENIX ATC 21) (pp. 973-988).

Khomtchouk, B. B., Nelson, C. S., Vand, K. A., Palmisano, S., & Grossman, R. L. (2020). HeartBioPortal2.0: New developments and updates for genetic ancestry and cardiometabolic quantitative traits in diverse human populations. Database, 2020, baaa115. https://doi.org/10.1093/database/baaa115

Thomas, S., Lichtenberg, T., Dang, K., Fitzsimons, M., Grossman, R. L., Kundra, R., Lavery, J. A., Lenoue-Newton, M. L., Panageas, K. S., Sawyers, C., Schultz, N. D., Sirintrapun, S. J., Topaloglu, U., Welch, A., Yu, T., Zehir, A., & Gardos, S. (2020). Linked Entity Attribute Pair (LEAP): A Harmonization Framework for Data Pooling. JCO Clinical Cancer Informatics, 4, 691–699. https://doi.org/10.1200/CCI.20.00037

Elbers, D. C., Fillmore, N. R., Sung, F.-C., Ganas, S. S., Prokhorenkov, A., Meyer, C., Hall, R. B., Ajjarapu, S. J., Chen, D. C., Meng, F., Grossman, R. L., Brophy, M. T., & Do, N. V. (2020). The Veterans Affairs Precision Oncology Data Repository, a Clinical, Genomic, and Imaging Research Database. Patterns, 1(6), 100083. https://doi.org/10.1016/j.patter.2020.100083

Bao, R., Hernandez, K., Huang, L., & Luke, J. J. (2020). ACE2 and TMPRSS2 expression by clinical, HLA, immune, and microbial correlates across 34 human cancers and matched normal tissues: Implications for SARS-CoV-2 COVID-19. Journal for ImmunoTherapy of Cancer, 8(2), e001020. https://doi.org/10.1136/jitc-2020-001020

Febbo, P. G., Martin, A., Scher, H. I., Barrett, J. C., Beaver, J. A., Beresford, P. J., Blumenthal, G. M., Bramlett, K., Compton, C., Dittamore, R., Eberhard, D. A., Edelstein, D., Godsey, J., Gruen, A., Hanlon, S. E., Hicks, J., Hovelson, D., Hullings, M., Johann, D., … Leiman, L. C. (2020). Minimum Technical Data Elements for Liquid Biopsy Data Submitted to Public Databases. Clinical Pharmacology & Therapeutics, 107(4), 730–734. https://doi.org/10.1002/cpt.1747

PCAWG Technical Working Group, PCAWG Consortium, Yakneen, S., Waszak, S. M., Gertz, M., & Korbel, J. O. (2020). Butler enables rapid cloud-based analysis of thousands of human genomes. Nature Biotechnology, 38(3), 288–292. https://doi.org/10.1038/s41587-019-0360-3

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. (2020). Pan-cancer analysis of whole genomes. Nature, 578(7793), 82–93. https://doi.org/10.1038/s41586-020-1969-6

Zhang, R., Khan, A. A., & Grossman, R. L. (2020, October). Evaluation of hyperbolic attention in histopathology images. In 2020 IEEE 20th International Conference on Bioinformatics and Bioengineering (BIBE) (pp. 773-776). IEEE.

Friedman, P. N., Shaazuddin, M., Gong, L., Grossman, R. L., Harralson, A. F., Klein, T. E., Lee, N. H., Miller, D. C., Nutescu, E. A., O'Brien, T. J., O'Donnell, P. H., O'Leary, K. J., Tuck, M., Meltzer, D. O., & Perera, M. A. (2019). The ACCOuNT Consortium: A Model for the Discovery, Translation, and Implementation of Precision Medicine in African Americans. Clinical and translational science, 12(3), 209–217. https://doi.org/10.1111/cts.12608

Applebaum, M. A., Barr, E. K., Karpus, J., West-Szymanski, D. C., Oliva, M., Sokol, E. A., Zhang, S., Zhang, Z., Zhang, W., Chlenksi, A., Salwen, H. R., Wilkinson, E., Dobratic, M., Grossman, R. L., Godley, L. A., Stranger, B. E., He, C., & Cohn, S. L. (2019). 5-hydroxymethylcytosine profiles in circulating cell-free DNA associate with disease burden in children with neuroblastoma. Clinical Cancer Research, clincanres.2829.2019. https://doi.org/10.1158/1078-0432.CCR-19-2829

Gao, G. F., Parker, J. S., Reynolds, S. M., Silva, T. C., Wang, L. B., Zhou, W., Akbani, R., Bailey, M., Balu, S., Berman, B. P., Brooks, D., Chen, H., Cherniack, A. D., Demchok, J. A., Ding, L., Felau, I., Gaheen, S., Gerhard, D. S., Heiman, D. I., Hernandez, K. M., … Noble, M. S. (2019). Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data. Cell systems, 9(1), 24–34.e10. https://doi.org/10.1016/j.cels.2019.06.006

Do, N., Grossman, R., Feldman, T., Fillmore, N., Elbers, D., Tuck, D., Dhond, R., Selva, L., Meng, F., Fitzsimons, M., Ajjarapu, S., Ayandeh, S., Hall, R., Do, S., & Brophy, M. (2019). The Veterans Precision Oncology Data Commons: Transforming VA data into a national resource for research in precision oncology. Seminars in Oncology, 46(4–5), 314–320. https://doi.org/10.1053/j.seminoncol.2019.09.002

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.

Geeleher, P., Nath, A., Wang, F., Zhang, Z., Barbeira, A. N., Fessler, J., Grossman, R. L., Seoighe, C., & Stephanie Huang, R. (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(1), 130. https://doi.org/10.1186/s13059-018-1507-0

Grossman R. L. (2018). Progress Toward Cancer Data Ecosystems. Cancer journal (Sudbury, Mass.), 24(3), 126–130. https://doi.org/10.1097/PPO.0000000000000318

Peisert, S., Dart, E., Barnett, W., Balas, E., Cuff, J., Grossman, R. L., Berman, A., Shankar, A., & Tierney, B. (2018). The medical science DMZ: a network design pattern for data-intensive medical science. Journal of the American Medical Informatics Association : JAMIA, 25(3), 267–274. https://doi.org/10.1093/jamia/ocx104

Grossman RL. (2018). A framework for evaluating the analytic maturity of an organization. International Journal of Information Management. 38(1), 45-51. doi.org/10.1016/j.ijinfomgt.2017.08.005

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.

Wilson, S., Fitzsimons, M., Ferguson, M., Heath, A., Jensen, M., Miller, J., Murphy, M. W., Porter, J., Sahni, H., Staudt, L., Tang, Y., Wang, Z., Yu, C., Zhang, J., Ferretti, V., Grossman, R. L., & GDC Project (2017). Developing Cancer Informatics Applications and Tools Using the NCI Genomic Data Commons API. Cancer research, 77(21), e15–e18. https://doi.org/10.1158/0008-5472.CAN-17-0598

Patterson, M. T., & Grossman, R. L. (2017). Detecting Spatial Patterns of Disease in Large Collections of Electronic Medical Records Using Neighbor-Based Bootstrapping. Big data, 5(3), 213–224. https://doi.org/10.1089/big.2017.0028

Geeleher, P., Zhang, Z., Wang, F., Gruener, R. F., Nath, A., Morrison, G., Bhutra, S., Grossman, R. L., & Huang, R. S. (2017). Discovering novel pharmacogenomic biomarkers by imputing drug response in cancer patients from large genomics studies. Genome research, 27(10), 1743–1751. https://doi.org/10.1101/gr.221077.117

Jensen, M. A., Ferretti, V., Grossman, R. L., & Staudt, L. M. (2017). The NCI Genomic Data Commons as an engine for precision medicine. Blood, 130(4), 453–459. https://doi.org/10.1182/blood-2017-03-735654

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.

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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.

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Peisert, S., Barnett, W., Dart, E., Cuff, J., Grossman, R. L., Balas, E., Berman, A., Shankar, A., & Tierney, B. (2016). The Medical Science DMZ. Journal of the American Medical Informatics Association : JAMIA, 23(6), 1199–1201. https://doi.org/10.1093/jamia/ocw032

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.

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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.

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