Publication Spotlight

This month, we highlight a multi-national collaborative publication titled, "Establishment and Comprehensive Characterization of a Novel Preclinical Platform of Metastatic Retinoblastoma for Therapeutic Developments". The highlighted study aimed to address the challenges in managing metastatic retinoblastoma, a highly aggressive tumor with poor survival rates and treatment-related toxicities. The researchers in this study developed a preclinical platform using primary cell cultures and xenograft models obtained from metastatic retinoblastoma patients, in part, by examining somatic copy number alterations. These alterations were analyzed using resources on the Cancer Genomics Cloud including computing space, and an existing tool (FACETS: fraction and allele-specific copy number estimates from tumor sequencing). By analyzing genomic, immunohistochemical, and pharmacological aspects, they successfully established five primary cell lines and corresponding xenograft models that accurately mirrored the histological and genomic features of the original tumors. The platform serves as an innovative tool for understanding the tumor biology and conducting drug screening to identify potential treatment candidates for patients with limited therapeutic options.

Publications

The following published manuscripts report work completed using the Cancer Genomics Cloud. Additionally, many manuscripts listed below have directly cited our CGC flagship paper:

Lau, Jessica W., et al. "The Cancer Genomics Cloud: collaborative, reproducible, and democratized—a new paradigm in large-scale computational research." Cancer Res. 77.21 (2017): e3-e6.

The list below is presented in reverse-chronological order and will be updated on a monthly basis with the latest publications.

  1. Zugbi S., Aschero R., Ganiewich D., Cancela M. B., Winter U., Ottaviani D., Sampor C., Dinardi M., Torbidoni A. V., Mena M., Balaguer-Lluna L., Lamas G., Sgroi M., Lagomarsino E., Lubieniecki F., Fandiño A., Radvanyi F., Abramson D. H., Podhajcer O., Llera A. S., Cafferata E. G., Chantada G., Carcaboso A. M., Schaiquevich P.. “Establishment and Comprehensive Characterization of a Novel Preclinical Platform of Metastatic Retinoblastoma for Therapeutic Developments.” Invest Ophthalmol Vis Sci. 2023 Dec 1;64(15):27.

  2. Forsdick, Natalie J., Jana Wold, Anton Angelo, François Bissey, Jamie Hart, Mitchell Head, Libby Liggins, Dinindu Senanayake, and Tammy E. Steeves. 2023. “Journeying towards Best Practice Data Management in Biodiversity Genomics.” Molecular Ecology Resources, October.

  3. London, Cheryl A., Heather Gardner, Shaying Zhao, Deborah W. Knapp, Sagar M. Utturkar, Dawn L. Duval, Melissa R. Chambers, Elaine Ostrander, Jeffrey M. Trent, and Gina Kuffel. 2023. “Leading the Pack: Best Practices in Comparative Canine Cancer Genomics to Inform Human Oncology.” Veterinary and Comparative Oncology, October.

  4. Post, Andrew R., Nancy Ho, Erik Rasmussen, Ivan Post, Aika Cho, John Hofer, Arthur T. Maness, Timothy Parnell, and David A. Nix. 2023. “Hypermedia-Based Software Architecture Enables Test-Driven Development.” JAMIA Open 6 (4): ooad089.

  5. Sridhar, Aksheetha, Ankita S. More, Amruta R. Jadhav, Komal Patil, Anuj Mavlankar, Vaishnavi M. Dixit, and Sharmila A. Bapat. 2023. “Pattern Recognition in the Landscape of Seemingly Random Chimeric Transcripts.” Computational and Structural Biotechnology Journal 21 (October): 5153–64.

  6. Dong, Xinran, Liang Ding, Andrew Thrasher, Xinge Wang, Jingjing Liu, Qingfei Pan, Jordan Rash, et al. 2023. “NetBID2 Provides Comprehensive Hidden Driver Analysis.” Nature Communications 14 (1): 2581.

  7. Rubinacci, Simone, Robin J. Hofmeister, Bárbara Sousa da Mota, and Olivier Delaneau. 2023. “Imputation of Low-Coverage Sequencing Data from 150,119 UK Biobank Genomes.” Nature Genetics 55 (7): 1088–90.

  8. Schilling, Vincent, Peter Beyerlein, and Jeremy Chien. 2023. “A Bioinformatics Analysis of Ovarian Cancer Data Using Machine Learning.” Algorithms 16 (7): 330.

  9. Sousa da Mota, Bárbara, Simone Rubinacci, Diana Ivette Cruz Dávalos, Carlos Eduardo G. Amorim, Martin Sikora, Niels N. Johannsen, Marzena H. Szmyt, et al. 2023. “Imputation of Ancient Human Genomes.” Nature Communications 14 (1): 3660.

  10. Thomas, Kristen T., Anaïs Vermare, Suzannah O. Egleston, Yong-Dong Wang, Ashutosh Mishra, Tong Lin, Junmin Peng, and Stanislav S. Zakharenko. 2023. “MicroRNA 3′ Ends Shorten during Adolescent Brain Maturation.” Frontiers in Molecular Neuroscience 16: 1168695.

  11. Zou, Trudy, Rahil Sethi, Jiefei Wang, Gungor Budak, Uma Chandran, Ivy John, Rebecca Watters, and Kurt Weiss. 2023. “Whole Genome Sequencing for Metastatic Mutational Burden in Extraskeletal Myxoid Chondrosarcoma.” Frontiers in Molecular Medicine 3: 1152550.

  12. Nguyen, T., Bian, X., Roberson, D., Khanna, R., Chen, Q., Yan, C., Beck, R., Worman, Z., & Meerzaman, D. (2023). Multi-omics Pathways Workflow (MOPAW): An Automated Multi-omics Workflow on the Cancer Genomics Cloud. Cancer Informatics, 22, 11769351231180992.

  13. Koc, S., Varjacic, V., Rankovic, M., Slavkovic-Ilic, M., Danicic, A., Black, S., Ohashi, N., Sarkar, T., Worman, Z., DiGiovanna, J., Davis-Dusenbery, B., & Dean, D. A. (2023). Abstract 5356: Collaborating to ensure data-driven drug discovery on the Cancer Genomics Cloud: Realizing the possibilities for MoDaC and ATOM. Cancer Research, 83(7_Supplement), 5356–5356.

  14. Vukojicic, N., Danicic, A., Worman, Z., Beck, R., Veljkovic, D., Matic, M., DiGiovanna, J., & Davis-Dusenbery, B. (2023). Abstract 2075: Highly customizable multi-sample single cell RNA-Seq pipeline on the CGC. Cancer Research, 83(7_Supplement), 2075–2075.

  15. McKerrow, W., Kagermazova, L., Doudican, N., Frazzette, N., Kaparos, E. I., Evans, S. A., Rocha, A., Sedivy, J. M., Neretti, N., Carucci, J., Boeke, J. D., & Fenyö, D. (2023). LINE-1 retrotransposon expression in cancerous, epithelial and neuronal cells revealed by 5′ single-cell RNA-Seq. Nucleic Acids Res, 51(5), 2033–2045.

  16. Dixit, V. M., & Bapat, S. (2023). Antigenicity prediction of peptides generated by chimeric transcripts provides proof-of-concept of tumor-specific cryptic neoepitopes. Preprint in Research Square.

  17. Rahman, G., Morton, J. T., Martino, C., Sepich-Poore, G. D., Allaband, C., Guccione, C., Chen, Y., Hakim, D., Estaki, M., & Knight, R. (2023). BIRDMAn: A Bayesian differential abundance framework that enables robust inference of host-microbe associations. Preprint in bioRxiv (p. 2023.01.30.526328).

  18. Erwin GS, Gürsoy G, Al-Abri R, Suriyaprakash A, Dolzhenko E, Zhu K, et al. Recurrent repeat expansions in human cancer genomes. Nature. 2023 Jan 5;613(7942):96–102.

  19. Petrosyan, V., Dobrolecki, L. E., Thistlethwaite, L., Lewis, A. N., Sallas, C., Srinivasan, R. R., Lei, J. T., Kovacevic, V., Obradovic, P., Ellis, M. J., Osborne, C. K., Rimawi, M. F., Pavlick, A., Shafaee, M. N., Dowst, H., Jain, A., Saltzman, A. B., Malovannaya, A., Marangoni, E., … Lewis, M. T. (2023). Identifying biomarkers of differential chemotherapy response in TNBC patient-derived xenografts with a CTD/WGCNA approach. iScience, 26(1), 105799.

  20. Yu, J., Dong, X., Ding, L., Thrasher, A., Wang, X., Liu, J., Pan, Q., Rash, J., Dhungana, Y., Yang, X., Risch, I., Li, Y., Peng, J., Rusch, M., McLeod, C., Chi, H., & Zhang, J. NetBID2 provides comprehensive hidden driver analysis. Preprint in Research Square. 2022.

  21. Narunsky-Haziza L, Sepich-Poore GD, Livyatan I, Asraf O, Martino C, Nejman D, et al. Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions. Cell. 2022 Sep;185(20):3789-3806.e17.

  22. Worman, Z., Ray, M., Miletic, N., Kovačević, M., Stankovic, A., Raicevic, N. I., Ventre, D., Subramanian, S., Randjelovic, J., DiGiovanna, J., & Davis-Dusenbery, B. (2022). 132. Variant analysis for exploration of cancer datasets on the Cancer Genomics Cloud, powered by Seven Bridges. Cancer Genetics, 268-269, 42.

  23. White, B. S., Woo, X. Y., Koc, S., Sheridan, T., Neuhauser, S. B., Wang, S., Evrard, Y. A., Landua, J. D., Jay Mashl, R., Davies, S. R., Fang, B., Raso, M. G., Evans, K. W., Bailey, M. H., Chen, Y., Xiao, M., Rubinstein, J., Pour, A. F., Dobrolecki, L. E., … Chuang, J. H. (2022). A pan-cancer PDX histology image repository with genomic and pathological annotations for deep learning analysis. Preprint in bioRxiv (p. 2022.10.26.512745).

  24. Jeong, J. C., Hands, I., Kolesar, J. M., Rao, M., Davis, B., Dobyns, Y., Hurt-Mueller, J., Levens, J., Gregory, J., Williams, J., Witt, L., Kim, E. M., Burton, C., Elbiheary, A. A., Chang, M., & Durbin, E. B. (2022). Local data commons: the sleeping beauty in the community of data commons. BMC Bioinformatics, 23(Suppl 12), 386.

  25. Hung, L.-H., Fukuda, B., Schmitz, R., Hoang, V., Lloyd, W., & Yeung, K. Y. (2022). Accessible, interactive and cloud-enabled genomic workflows integrated with the NCI Genomic Data Commons. Preprint in bioRxiv (p. 2022.08.11.503660).

  26. Koc, S., Babic, J., Nikolic, N., Stankovic, A., Ventre, D., Ray, M., Worman, Z. F., Subramanian, S. L., Dean, D. A., DiGiovanna, J., & Dusenbery, B. D. (2022). Abstract 6394: The SB Image Processing Toolkit: Machine learning for cancer research on the CGC. Cancer Research, 82(12_Supplement), 6394–6394.

  27. White, B. S., Woo, X., Koc, S., Sheridan, T., Neuhauser, S. B., Savaliya, A. M., Dobrolecki, L. E., Landua, J. D., Bailey, M. H., Fujita, M., Evans, K. W., Fang, B., Fujimoto, J., Raso, M. G., Wang, S., Xiao, G., Xie, Y., Davies, S. R., Fields, R. C., … Chuang, J. H. (2022). Abstract 1202: A repository of PDX histology images for exploring spatial heterogeneity and cancer dynamics. Cancer Research, 82(12_Supplement), 1202–1202.

  28. Zhao, L., Cho, W. C. S., & Luo, J.-L. (2022). Exploring the patient-microbiome interaction patterns for pan-cancer. Computational and Structural Biotechnology Journal, 20, 3068–3079.

  29. Koc, S., Lloyd, M. W., Grover, J. W., Xiao, N., Seepo, S., Subramanian, S. L., Ray, M., Frech, C., DiGiovanna, J., Webster, P., Neuhauser, S., Srivastava, A., Woo, X. Y., Sanderson, B. J., White, B., Lott, P., Dobrolecki, L. E., Dowst, H., PDXNet Consortium, … Chuang, J. H. (2022). PDXNet portal: patient-derived Xenograft model, data, workflow and tool discovery. NAR Cancer, 4(2).

  30. Lim, H. G.-M., Hsiao, S.-H., Fann, Y. C., & Lee, Y.-C. G. (2022). Robust Mutation Profiling of SARS-CoV-2 Variants from Multiple Raw Illumina Sequencing Data with Cloud Workflow. Genes, 13(4).

  31. Alser, M., Waymost, S., Ayyala, R., Lawlor, B., Abdill, R. J., Rajkumar, N., LaPierre, N., Brito, J., Ribeiro-dos-Santos, A. M., Firtina, C., Almadhoun, N., Sarwal, V., Eskin, E., Hu, Q., Strong, D., Byoung-Do, Kim, Abedalthagafi, M. S., Mutlu, O., & Mangul, S. (2022). Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities. In arXiv [q-bio.GN].

  32. Liu, Z., Roberts, R., Mercer, T. R., Xu, J., Sedlazeck, F. J., & Tong, W. (2022). Towards accurate and reliable resolution of structural variants for clinical diagnosis. Genome Biology, 23(1), 68.

  33. Yang, A., Ros, X. B.-D., Stanton, R., Shao, T.-J., Villanueva, P., & Gu, S. (2022). TENT2, TUT4, and TUT7 selectively regulate miRNA sequence and abundance. In bioRxiv (p. 2022.03.03.482894).

  34. Erady, C., Amin, K., Onilogbo, T. O. A. E., Tomasik, J., Jukes-Jones, R., Umrania, Y., Bahn, S., & Prabakaran, S. (2022). Novel open reading frames in human accelerated regions and transposable elements reveal new leads to understand schizophrenia and bipolar disorder. Molecular Psychiatry, 27(3), 1455–1468.

  35. McKerrow W, Wang X, Mendez-Dorantes C, et al. LINE-1 expression in cancer correlates with p53 mutation, copy number alteration, and S phase checkpoint. Proc Natl Acad Sci U S A. 2022;119(8):e2115999119.

  36. Bofill-De Ros X, Hong Z, Birkenfeld B, et al. Flexible pri-miRNA structures enable tunable production of 5' isomiRs. RNA Biol. 2022;19(1):279-289.

  1. Sahraeian, S. M. E., Fang, L. T., Karagiannis, K., Moos, M., Smith, S., Santana-Quintero, L., Xiao, C., Colgan, M., Hong, H., Mohiyuddin, M., & Xiao, W. (2022). Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample. Genome Biology, 23(1), 12.

  2. Erdem, M., Ozgul, İ., Dioken, D.N. et al. Identification of an mRNA isoform switch for HNRNPA1 in breast cancers. Sci Rep 11, 24444 (2021).

  3. Kalita, C. A., & Gusev, A. (2021). A novel method to identify cell-type specific regulatory variants and their role in cancer risk. Preprint in bioRxiv (p. 2021.11.11.468278).

  4. Ahmed, A. E., Allen, J. M., Bhat, T., Burra, P., Fliege, C. E., Hart, S. N., Heldenbrand, J. R., Hudson, M. E., Istanto, D. D., Kalmbach, M. T., Kapraun, G. D., Kendig, K. I., Kendzior, M. C., Klee, E. W., Mattson, N., Ross, C. A., Sharif, S. M., Venkatakrishnan, R., Fadlelmola, F. M., & Mainzer, L. S. (2021). Design considerations for workflow management systems use in production genomics research and the clinic. Sci Rep, 11(1), 21680.

  5. Zhao, Y., Fang, L. T., Shen, T.-W., Choudhari, S., Talsania, K., Chen, X., Shetty, J., Kriga, Y., Tran, B., Zhu, B., Chen, Z., Chen, W., Wang, C., Jaeger, E., Meerzaman, D., Lu, C., Idler, K., Zheng, Y., Shi, L., … Xiao, W. (2021). Whole Genome and Exome Sequencing Reference Datasets from A Multi-center and Cross-platform Benchmark Study. Scientific Data, 8(1), 296.

  6. Rossi, N. M., Dai, J., Xie, Y., Lou, H., Boland, J. F., Yeager, M., Orozco, R., Alvirez, E., Mirabello, L., Gharzouzi, E., & Dean, M. (2021). Extrachromosomal Amplification of Human Papillomavirus Episomes as a Mechanism of Cervical Carcinogenesis. Preprint in bioRxiv (p. 2021.10.22.465367).

  7. Lim, H. G.-M., Hsiao, S.-H., & Lee, Y.-C. G. (2021). Orchestrating an Optimized Next-Generation Sequencing-Based Cloud Workflow for Robust Viral Identification during Pandemics. Biology, 10(10).

  8. Keskus, A. G., Tombaz, M., Arici, B. I., Dincaslan, F. B., Nabi, A., Shehwana, H., & Konu, O. (2021). Functional analysis of co-expression networks of zebrafish ace2 reveals enrichment of pathways associated with development and disease. Genome / National Research Council Canada = Genome / Conseil National de Recherches Canada, 1–18.

  9. Ayaz, G., Turan, G., Olgun, Ç. E., Kars, G., Karakaya, B., Yavuz, K., Demiralay, Ö. D., Can, T., Muyan, M., & Yaşar, P. (2021). A prelude to the proximity interaction mapping of CXXC5. Scientific Reports, 11(1), 17587.

  10. Fang, L. T., Zhu, B., Zhao, Y., Chen, W., Yang, Z., Kerrigan, L., Langenbach, K., de Mars, M., Lu, C., Idler, K., Jacob, H., Zheng, Y., Ren, L., Yu, Y., Jaeger, E., Schroth, G. P., Abaan, O. D., Talsania, K., Lack, J., … Somatic Mutation Working Group of Sequencing Quality Control Phase II Consortium. (2021). Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing. Nature Biotechnology, 39(9), 1151–1160.

  11. Xiao, W., Ren, L., Chen, Z., Fang, L. T., Zhao, Y., Lack, J., Guan, M., Zhu, B., Jaeger, E., Kerrigan, L., Blomquist, T. M., Hung, T., Sultan, M., Idler, K., Lu, C., Scherer, A., Kusko, R., Moos, M., Xiao, C., … Shi, L. (2021). Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing. Nature Biotechnology, 39(9), 1141–1150.

  12. Sun, H., Cao, S., Mashl, R. J., Mo, C.-K., Zaccaria, S., Wendl, M. C., Davies, S. R., Bailey, M. H., Primeau, T. M., Hoog, J., Mudd, J. L., Dean, D. A., 2nd, Patidar, R., Chen, L., Wyczalkowski, M. A., Jayasinghe, R. G., Rodrigues, F. M., Terekhanova, N. V., Li, Y., … Ding, L. (2021). Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment. Nature Communications, 12(1), 5086.

  13. Dehghannasiri, R., Olivieri, J. E., Damljanovic, A., & Salzman, J. (2021). Specific splice junction detection in single cells with SICILIAN. Genome Biology, 22(1), 219.

  14. Drljaca, T., Zukic, B., Kovacevic, V., Gemovic, B., Klaassen-Ljubicic, K., Perovic, V., Lazarevic, M., Pavlovic, S., & Veljkovic, N. (2021). The first insight into the genetic structure of the population of modern Serbia. Scientific Reports, 11(1).

  15. Subramanian, S. L., Ray, M., DiGiovanna, J., Radenkovic, J., Tosic, M., Mirkovic, N., Stanojevic, M., Trboljevac, M., Andjus, V., Stelkic, A., & Davis-Dusenbery, B. (2021). Abstract 253: The Cancer Genomics Cloud: A secure and scalable cloud-based platform to access, share and analyze multi-omics datasets. Cancer Research, 81(13 Supplement), 253–253.

  16. Bardadym, T. O., Gorbachuk, V. М., & Novoselova, N. А. (n.d.). Intelligent Analytical System as a Tool to Ensure the Reproducibility of Biomedical Calculations. Retrieved February 22, 2021.

  17. Bartha, Á., & Gyorffy, B. (n.d.). Whole Exome Sequencing Data Analysis Algorithms in Cancer Diagnostics. Videleaf.com.

  18. Bhattacharya, S., Hu, Z., & Butte, A. J. (2021). Opportunities and Challenges in Democratizing Immunology Datasets. Frontiers in Immunology, 12, 647536.

  19. Ahmed, A. E., Allen, J., Bhat, T., Burra, P., Fliege, C. E., Hart, S. N., Heldenbrand, J. R., Istanto, D. D., Hudson, M. E., Kalmbach, M. T., Kapraun, et al (2021). Design considerations for workflow management systems use in production genomics research and the clinic. Preprint in bioRxiv (p. 2021.04.03.437906).

  20. Patel, J. A., Dean, D. A., King, C. H., Xiao, N., Koc, S., Minina, E., Golikov, A., Brooks, P., Kahsay, R., Navelkar, R., Ray, M., Roberson, D., Armstrong, C., Mazumder, R., & Keeney, J. (2021) Bioinformatics tools developed to support BioCompute Objects. Database: The Journal of Biological Databases and Curation, 2021.

  21. Guillen, K. P., Fujita, M., Butterfield, A. J., Scherer, S. D., Bailey, M. H., Chu, Z., DeRose, Y. S., Zhao, L., Cortes-Sanchez, E., Yang, C.-H., Toner, J., Wang, G., Qiao, Y., Huang, X., Greenland, J. A., Vahrenkamp, J. M., Lum, D. H., Factor, R. E., Nelson, E. W., … Welm, A. L. (2021). A breast cancer patient-derived xenograft and organoid platform for drug discovery and precision oncology. In Cold Spring Harbor Laboratory (p. 2021.02.28.433268).

  22. Canbezdi, C., Tarin, M., Houy, A., Bellanger, D., Popova, T., Stern, M.-H., Roman-Roman, S., & Alsafadi, S. (2021). Functional and conformational impact of cancer-associated SF3B1 mutations depends on the position and the charge of amino acid substitution. Computational and Structural Biotechnology Journal.

  23. Zhao, Y., Fang, L. T., Shen, T.-W., Choudhari, S., Talsania, K., Chen, X., Shetty, J., Kriga, Y., Tran, B., Zhu, B., Chen, Z., Chen, W., Wang, C., Jaeger, E., Meerzaman, D., Lu, C., Idler, K., Zheng, Y., Shi, L., … Xiao, W. (2021). Whole Genome and Exome Sequencing Reference Datasets from A Multi-center and Cross-platform Benchmark Study. In Cold Spring Harbor Laboratory (p. 2021.02.27.433136).

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  25. Böck, J., Krogsaeter, E., Passon, M., Chao, Y.-K., Sharma, S., Grallert, H., Peters, A., & Grimm, C. (2021). Human genome diversity data reveal that L564P is the predominant TPC2 variant and a prerequisite for the blond hair associated M484L gain-of-function effect. PLoS Genetics, 17(1), e1009236. https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009236

  26. Keskus, A. G., Tombaz, M., Arici, B. I., Dincaslan, F. B., Nabi, A., Shehwana, H., & Konu, O. (2020). ace2 expression is higher in intestines and liver while being tightly regulated in development and disease in zebrafish. In Cold Spring Harbor Laboratory (p. 2020.12.24.424209).

  27. Drljaca, T., Zukic, B., Kovacevic, V., Gemovic, B., Klaassen-Ljubicic, K., Perovic, V., Lazarevic, M., Pavlovic, S., & Veljkovic, N. (2020). The first insight into the genetic structure of the population of modern Serbia. In Cold Spring Harbor Laboratory (p. 2020.12.18.423408).

  28. Zayas, R., Sisson, A., Kuhnsman, A., Nagalo, B. M., Roberts, L. R., & Buetow, K. (2020). Transcriptional Landscape of Hepatocellular Carcinoma Reveals that Patient Ethnic-Origin Influences Patterns of Expression. In Cold Spring Harbor Laboratory (p. 2020.12.01.404285).

  29. Stephens, S. H., King, C. H., Watford, S., Patel, J., Dean, D. A., Koc, S., Xiao, N., Donaldson, E. F., Thompson, E. E., Purkayastha, A., Mazumder, R., Johanson, E., & Keeney, J. (2020). Strengthening the BioCompute Standard by Crowdsourcing on PrecisionFDA. In Cold Spring Harbor Laboratory (p. 2020.11.02.365528).

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  33. Cappelli, E., Cumbo, F., Bernasconi, A., Canakoglu, A., Ceri, S., Masseroli, M., & Weitschek, E. (2020). OpenGDC: Unifying, Modeling, Integrating Cancer Genomic Data and Clinical Metadata. NATO Advanced Science Institutes Series E: Applied Sciences, 10(18), 6367. https://doi.org/10.3390/app10186367

  34. Vucic, N., Ray, M., Veljkovic, D., Cidilko, S., & Davis-Dusenbery, B. (2020). Abstract 4414: Single-cell analysis on the Cancer Genomics Cloud reveals changes in the transcriptome profiles of endothelial tumor cells over time - novel insights from a public dataset of a mouse model of melanoma. Cancer Research, 80(16 Supplement), 4414–4414. https://doi.org/10.1158/1538-7445.AM2020-4414

  35. Krissaane, I., De Niz, C., Gutiérrez-Sacristán, A., Korodi, G., Ede, N., Kumar, R., Lyons, J., Manrai, A., Patel, C., Kohane, I., & Avillach, P. (2020). Scalability and cost-effectiveness analysis of whole genome-wide association studies on Google Cloud Platform and Amazon Web Services. Journal of the American Medical Informatics Association: JAMIA.

  36. Kang, J., Loh, K., Belyayev, L., Cha, P., Sadat, M., Khan, K., Gusev, Y., Bhuvaneshwar, K., Ressom, H., Moturi, S., Kaiser, J., Hawksworth, J., Robson, S. C., Matsumoto, C. S., Zasloff, M., Fishbein, T. M., & Kroemer, A. (2020). Type 3 innate lymphoid cells are associated with a successful intestinal transplant. American Journal of Transplantation: Official Journal of the American Society of Transplantation and the American Society of Transplant Surgeons.

  37. McKerrow, W., Wang, X., Mita, P., Cao, S., Grivainis, M., Ding, L., LaCava, J., Boeke, J., & Fenyö, D. (2020). LINE-1 expression in cancer correlates with DNA damage response, copy number variation, and cell cycle progression. In Cold Spring Harbor Laboratory (p. 2020.06.26.174052).

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