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. Gabriel, Aurélie Anne-Gaëlle, Julien Racle, Maryline Falquet, Camilla Jandus, and David Gfeller. 2024. “Robust Estimation of Cancer and Immune Cell-Type Proportions from Bulk Tumor ATAC-Seq Data.” eLife 13 (October). https://doi.org/10.7554/eLife.94833. 

  2. Sahu, Divya, Jeffrey Shi, Isaac Andres Segura Rueda, Ajay Chatrath, and Anindya Dutta. 2024. “Development of a Polygenic Score Predicting Drug Resistance and Patient Outcome in Breast Cancer.” Npj Precision Oncology 8 (1): 219. https://doi.org/10.1038/s41698-024-00714-7. 

  3. Petralia, Francesca, Weiping Ma, Tomer M. Yaron, Francesca Pia Caruso, Nicole Tignor, Joshua M. Wang, Daniel Charytonowicz, et al. 2024. “Pan-Cancer Proteogenomics Characterization of Tumor Immunity.” Cell 187 (5): 1255–77.e27. https://doi.org/10.1016/j.cell.2024.01.027. 

  4. Liu, Qian, Qiang Hu, Song Liu, Alan Hutson, and Martin Morgan. 2024. “ReUseData: An R/Bioconductor Tool for Reusable and Reproducible Genomic Data Management.” BMC Bioinformatics 25 (1): 8. https://doi.org/10.1186/s12859-023-05626-0.  

  5. Rodriguez, Isabel, Nicole M. Rossi, Ayse G. Keskus, Yi Xie, Tanveer Ahmad, Asher Bryant, Hong Lou, et al. 2024. “Insights into the Mechanisms and Structure of Breakage-Fusion-Bridge Cycles in Cervical Cancer Using Long-Read Sequencing.” American Journal of Human Genetics, January. https://doi.org/10.1016/j.ajhg.2024.01.002. 

  6. Schary, Weronika, Florian Brockmann, Jonathan Simantzik, Filip Paskali, and Matthias Kohl. 2024. “Chapter 5 - Big Data and Health Analytics Explained.” In The New Era of Precision Medicine, edited by Mohamad Bydon, 115–29. Academic Press. https://doi.org/10.1016/B978-0-443-13963-5.00004-2. 

  7. Lott PC, Chiu K, Quino JE, Vang AP, Lloyd MW, Srivastava A, Chuang JH; PDXNet Consortium; Carvajal-Carmona LG. Development and Application of Genetic Ancestry Reconstruction Methods to Study Diversity of Patient-Derived Models in the NCI PDXNet Consortium. Cancer Res Commun. 2024 Aug 1;4(8):2147-2152. doi: 10.1158/2767-9764.CRC-23-0417. PMID: 39056190; PMCID: PMC11328913. 

  8. Thiriveedhi VK, Krishnaswamy D, Clunie D, Pieper S, Kikinis R, Fedorov A. Cloud-based large-scale curation of medical imaging data using AI segmentation. Res Sq [Preprint]. 2024 May 3:rs.3.rs-4351526. doi: 10.21203/rs.3.rs-4351526/v1. PMID: 38746269; PMCID: PMC11092813. 

  9. Pot D, Worman Z, Baumann A, Pathak S, Beck R, Beck E, Thayer K, Davidsen TM, Kim E, Davis-Dusenbery B, Otridge J, Pihl T; CRDC Program; Barnholtz-Sloan JS, Kerlavage AR. NCI Cancer Research Data Commons: Cloud-Based Analytic Resources. Cancer Res. 2024 May 2;84(9):1396-1403. doi: 10.1158/0008-5472.CAN-23-2657. PMID: 38488504; PMCID: PMC11063685. 

  10. Rossi, Nicole M., Jieqiong Dai, Yi Xie, Darawalee Wangsa, Kerstin Heselmeyer-Haddad, Hong Lou, Joseph F. Boland, et al. 2023. “Extrachromosomal Amplification of Human Papillomavirus Episomes Is a Mechanism of Cervical Carcinogenesis.” Cancer Research 83 (11): 1768–81. https://doi.org/10.1158/0008-5472.CAN-22-3030. 

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Lim HG, Fann YC, Lee YG. COWID: an efficient cloud-based genomics workflow for scalable identification of SARS-COV-2. Brief Bioinform. 2023 Sep 20;24(5):bbad280. doi: 10.1093/bib/bbad280. PMID: 37738400; PMCID: PMC10516370. 

  17. Banimfreg, Bayan H. 2023. “A Comprehensive Review and Conceptual Framework for Cloud Computing Adoption in Bioinformatics.” Healthcare Analytics 3: 100190. https://doi.org/10.1016/j.health.2023.100190. 

  18. Geffen, Yifat, Shankara Anand, Yo Akiyama, Tomer M. Yaron, Yizhe Song, Jared L. Johnson, Akshay Govindan, et al. 2023. “Pan-Cancer Analysis of Post-Translational Modifications Reveals Shared Patterns of Protein Regulation.” Cell. https://doi.org/10.1016/j.cell.2023.07.013. 

  19. Li, Yize, Yongchao Dou, Felipe Da Veiga Leprevost, Yifat Geffen, Anna P. Calinawan, François Aguet, Yo Akiyama, et al. 2023. “Proteogenomic Data and Resources for Pan-Cancer Analysis.” Cancer Cell 41 (8): 1397–1406. https://doi.org/10.1016/j.ccell.2023.06.009. 

  20. Li, Yize, Eduard Porta-Pardo, Collin Tokheim, Matthew H. Bailey, Tomer M. Yaron, Vasileios Stathias, Yifat Geffen, et al. 2023. “Pan-Cancer Proteogenomics Connects Oncogenic Drivers to Functional States.” Cell. https://doi.org/10.1016/j.cell.2023.07.014. 

  21. Liang, Wen-Wei, Rita Jui-Hsien Lu, Reyka G. Jayasinghe, Steven M. Foltz, Eduard Porta-Pardo, Yifat Geffen, Michael C. Wendl, et al. 2023. “Integrative Multi-Omic Cancer Profiling Reveals DNA Methylation Patterns Associated with Therapeutic Vulnerability and Cell-of-Origin.” Cancer Cell. https://doi.org/10.1016/j.ccell.2023.07.013. 

  22. Wang, Joshua M., Runyu Hong, Elizabeth G. Demicco, Jimin Tan, Rossana Lazcano, Andre L. Moreira, Yize Li, et al. 2023. “Deep Learning Integrates Histopathology and Proteogenomics at a Pan-Cancer Level.” Cell Reports Medicine, 101173. https://doi.org/10.1016/j.xcrm.2023.101173. 

  23. 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.

  24. 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.

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

  26. 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.

  27. 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.

  28. 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.

  29. 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.

  30. 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.

  31. 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.

  32. 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.

  33. 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.

  34. 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).

  35. 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.

  36. 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.

  37. 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.

  38. 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.

  39. 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.

  40. 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).

  41. 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.

  42. 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).

  43. 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.

  44. 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.

  45. 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.

  46. 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).

  47. 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).

  48. 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].

  49. 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.

  50. 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).

  51. 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.

  52. 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.

  53. 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.

  54. 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.

  55. 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).

  56. 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).

  57. 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.

  58. 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.

  59. 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).

  60. 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).

  61. 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.

  62. 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.

  63. 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.

  64. 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.

  65. 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.

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

  67. 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).

  68. 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.

  69. 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.

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

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

  72. 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).

  73. 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.

  74. 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).

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