Featured Publications

  1. Lusha Cao, Yang Xu, Tina Glisovic-Aplenc, Han R Fisher, Saamia Farooki, Kelly D. Getz, Todd A. Alonzo, Alan S Gamis, Soheil Meshinchi, Yi Xing, Richard Aplenc; Molecular Characteristics Influencing Relapse Risk in Low-Risk Pediatric Acute Myeloid Leukemia. Blood 2024; 144 (Supplement 1): 2932. doi: https://doi.org/10.1182/blood-2024-200851

  2. Barnholtz-Sloan, Jill S., Dana E. Rollison, Amrita Basu, Alexander D. Borowsky, Alex Bui, Jack DiGiovanna, Montserrat Garcia-Closas, et al. 2020. “Cancer Informatics for Cancer Centers (CI4CC): Building a Community Focused on Sharing Ideas and Best Practices to Improve Cancer Care and Patient Outcomes.” JCO Clinical Cancer Informatics 4 (February): 108–16. https://doi.org/10.1200/CCI.19.00166.

  3. Bonner, Erin R., Adam Dawood, Heather Gordish-Dressman, Augustine Eze, Surajit Bhattacharya, Sridevi Yadavilli, Sabine Mueller, Sebastian M. Waszak, and Javad Nazarian. 2023. “Pan-Cancer Atlas of Somatic Core and Linker Histone Mutations.” NPJ Genomic Medicine 8 (1): 23. https://doi.org/10.1038/s41525-023-00367-8.

  4. Cao, Lusha, Yang Xu, Tina Glisovic-Aplenc, Han R. Fisher, Saamia Farooki, Kelly D. Getz, Todd A. Alonzo, et al. 2024. “Molecular Characteristics Influencing Relapse Risk in Low-Risk Pediatric Acute Myeloid Leukemia.” Blood 144 (Supplement 1): 2932–2932. https://doi.org/10.1182/blood-2024-200851.

  5. Cejovic, Jovan, Jelena Radenkovic, Vladimir Mladenovic, Adam Stanojevic, Milica Miletic, Stevan Radanovic, Dragan Bajcic, et al. 2018. “Using Semantic Web Technologies to Enable Cancer Genomics Discovery at Petabyte Scale.” Cancer Informatics 17 (September): 1176935118774787. https://doi.org/10.1177/1176935118774787.

  6. Chen, Fengju, Yiqun Zhang, Fritz J. Sedlazeck, and Chad J. Creighton. 2024. “Germline Structural Variation Globally Impacts the Cancer Transcriptome Including Disease-Relevant Genes.” Cell Reports. Medicine 5 (3): 101446. https://doi.org/10.1016/j.xcrm.2024.101446.

  7. Chen, Fengju, Yiqun Zhang, Lanlan Shen, and Chad J. Creighton. 2024. “The DNA Methylome of Pediatric Brain Tumors Appears Shaped by Structural Variation and Predicts Survival.” Nature Communications 15 (1): 6775. https://doi.org/10.1038/s41467-024-51276-y.

  8. Dahlquist, Jacklyn M., Sarah C. Nelson, and Stephanie M. Fullerton. 2023. “Cloud-Based Biomedical Data Storage and Analysis for Genomic Research: Landscape Analysis of Data Governance in Emerging NIH-Supported Platforms.” Human Genetics and Genomics Advances 4 (3): 100196. https://doi.org/10.1016/j.xhgg.2023.100196.

  9. Geng, Zhuangzhuang, Eric Wafula, Ryan J. Corbett, Yuanchao Zhang, Run Jin, Krutika S. Gaonkar, Sangeeta Shukla, et al. 2024. “The Open Pediatric Cancer Project.” bioRxiv.Org: The Preprint Server for Biology, July. https://doi.org/10.1101/2024.07.09.599086.

  10. Gozlan, Etienne C., Taha I. Huda, Jessica U. Quach, Mallika Varkhedi, John E. Desantis, and George Blanck. 2024. “High Level Immunoglobulin Gene Expression and Reduced Intra-Tumoral Bacteria Associated With the Transition from Initial to Progressive Diffuse Intrinsic Pontine Glioma.” Anticancer Research 44 (6): 2325–33. https://doi.org/10.21873/anticanres.17039.

  11. Grossman, Robert L. 2018. “Progress Toward Cancer Data Ecosystems.” The Cancer Journal from Scientific American 24 (3): 126–30. https://doi.org/10.1097/ppo.0000000000000318.

  12. Guo, Yiran, Jeremy Costanza, Christophe Botek, Miguel Brown, David Higgins, Yuankun Zhu, Bailey Farrow, Allison Heath, Adam Resnick, and Vincent Ferretti. 2022a. “Abstract LB501: Making Discoveries with Kids First Variant DataBase and WorkBench.” Cancer Research 82 (12_Supplement): lb501–lb501. https://doi.org/10.1158/1538-7445.am2022-lb501.

  13. ———. 2022b. “OTHR-45. Kids First Variant WorkBench: Application to Germline Genomic Discoveries in the Children’s Brain Tumor Network.” Neuro-Oncology 24 (Suppl 1): i157–i157. https://doi.org/10.1093/neuonc/noac079.583.

  14. Guo, Yiran, Qi Li, Jare Rozowsky, Jeremy Costanza, Michele Mattioni, Jean-Philippe Thibert, Miguel Brown, et al. 2024. “METB-09. VARIANT WORKBENCH IN THE KIDS FIRST PROGRAM FACILITATES GENOMIC DISCOVERIES IN PEDIATRIC NEURO-ONCOLOGY RESEARCH.” Neuro-Oncology 26 (Supplement_4): 0–0. https://doi.org/10.1093/neuonc/noae064.250.

  15. Heath, Allison P., Pichai Raman, Yuankun Zhu, Jena V. Lilly, Deanne Taylor, Phillip B. Storm, Angela J. Waanders, et al. 2018. “TBIO-27. GABRIELLA MILLER KIDS FIRST DATA RESOURCE CENTER ADVANCING GENETIC RESEARCH IN CHILDHOOD CANCER AND STRUCTURAL BIRTH DEFECTS THROUGH LARGE SCALE INTEGRATED DATA-DRIVEN DISCOVERY AND CLOUD-BASED PLATFORMS FOR COLLABORATIVE ANALYSIS.” Neuro-Oncology 20 (suppl_2): i186–i186. https://doi.org/10.1093/neuonc/noy059.715.

  16. Heath, Allison P., Yuankun Zhu, Michele Mattioni, Bailey Farrow, Jena Lilly, Yiran Guo, Jo Lynne Rokita, et al. 2020. “EPID-14. GABRIELLA MILLER KIDS FIRST DATA RESOURCE CENTER: COLLABORATIVE PLATFORMS FOR ACCELERATING RESEARCH IN PEDIATRIC CANCERS & STRUCTURAL BIRTH DEFECTS.” Neuro-Oncology 22 (Suppl 3): iii321–iii321. https://doi.org/10.1093/neuonc/noaa222.200.

  17. Higgins, David, Jean-Philippe Thibert, Michele Mattioni, Jack DiGiovanna, Robert L. Grossman, Bailey K. Farrow, Eric Wenger, et al. 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. https://doi.org/10.1158/1538-7445.am2023-6576.

  18. Hudson, Alexandra, Marcia Fournier, James Coulombe, and Danielle Daee. 2023. “Leveraging Existing Pediatric Cancer Data through the Gabriella Miller Kids First Data Resource.” JNCI Cancer Spectrum, October. https://doi.org/10.1093/jncics/pkad079.

  19. Ivanov, Nikolay A., Nadia Dahmane, Jeffrey P. Greenfield, and Christopher E. Mason. 2020. “4565 Sex-Specific Differences in the Genomic Landscape of Pediatric and Adult Glioblastoma.” Journal of Clinical and Translational Science 4 (s1): 112–13. https://doi.org/10.1017/cts.2020.343.

  20. Kerlavage, Anthony R., Anne C. Kirchhoff, Jaime M. Guidry Auvil, Norman E. Sharpless, Kara L. Davis, Karlyne Reilly, Gregory Reaman, et al. 2021. “Cancer Informatics for Cancer Centers: Scientific Drivers for Informatics, Data Science, and Care in Pediatric, Adolescent, and Young Adult Cancer.” JCO Clinical Cancer Informatics 5 (5): cci.21.00040. https://doi.org/10.1200/cci.21.00040.

  21. Kim, Jung, Ammar S. Naqvi, Ryan J. Corbett, Rebecca S. Kaufman, Zalman Vaksman, Miguel A. Brown, Daniel P. Miller, et al. 2023. “AutoGVP: A Dockerized Workflow Integrating ClinVar and InterVar Germline Sequence Variant Classification.” bioRxiv : The Preprint Server for Biology, December. https://doi.org/10.1101/2023.11.29.569103.

  22. Koptyra, Mateusz, Valerie Baubet, David Beale, Luke Patterson, Ian Biluck, Madison Hollawell, Christopher M. Beck, et al. 2022. “MODL-30. Children’s Brain Tumor Network Preclinical Tumor Models Development and Sharing Platform: Collaborative Model Empowering Pediatric Brain Tumor Discovery and Global Research.” Neuro-Oncology 24 (Suppl 1): i175–76. https://doi.org/10.1093/neuonc/noac079.653.

  23. Koptyra, Mateusz P., Komal Rahti, Yuankun Zhu, Bailey Farrow, Daniel Miller, Adam Kraya, Yiran Guo, et al. 2023. “Abstract 3566: Expansion of the Pediatric Brain Tumor Atlas: Children’s Brain Tumor Network, Kids First Data Resource and Childhood Cancer Data Initiative Open Science Effort.” Cancer Research 83 (7_Supplement): 3566–3566. https://doi.org/10.1158/1538-7445.am2023-3566.

  24. Levine, Adrian B., Liana Nobre, Anirban Das, Scott Milos, Vanessa Bianchi, Monique Johnson, Nicholas R. Fernandez, et al. 2024. “Immuno-Oncologic Profiling of Pediatric Brain Tumors Reveals Major Clinical Significance of the Tumor Immune Microenvironment.” Nature Communications 15 (1): 5790. https://doi.org/10.1038/s41467-024-49595-1.

  25. Lilly, Jena, Jennifer Mason, Elizabeth Appert, Allison Heath, Yuankun Zhu, Bo Zhang, Mateusz Koptyra, et al. 2020. “MODL-26. CHILDREN’S BRAIN TUMOR NETWORK: ACCELERATING RESEARCH THROUGH COLLABORATION AND OPEN-SCIENCE.” Neuro-Oncology 22 (Suppl 3): iii416–iii416. https://doi.org/10.1093/neuonc/noaa222.599.

  26. Mattioni, Michele, Surya Saha, Jared Rozowsky, Eric Tobin, Zelia Worman, Selena Vukadinovic, Milos Trboljevac, et al. 3 2024. “A Secure Data Lake for the CFDE Community on CAVATICA – Powered by Interoperability Standards.” https://doi.org/10.6084/m9.figshare.25421119.v1.

  27. Nabbi, Arash, Natalie Jäger, Sumedha Sudhaman, Pengbo Sun, S. Y. Cindy Yang, Kelsey Zhu, Marcel Kool, et al. 2019. “Abstract 2891: Landscape of Infiltrating Immune Repertoire in Pediatric Solid Tumors.” Cancer Research 79 (13_Supplement): 2891–2891. https://doi.org/10.1158/1538-7445.am2019-2891.

  28. Nabbi, Arash, Pengbo Sun, Sudhaman Sumedha, Kelsey Zhu, S. Y. Cindy Yang, Joseph N. Paulson, Marcel Kool, et al. 2020. “Abstract PR06: The Immunogenomic Landscape of Pediatric Primary Solid Tumors.” Cancer Research 80 (14_Supplement): r06-pr06. https://doi.org/10.1158/1538-7445.pedca19-pr06.

  29. Power, Phoebe C., Jacquelyn Jones, Susan N. Chi, Lissa Baird, Katie P. Fehnel, Nicole J. Ullrich, Keith L. Ligon, Sanda Alexandrescu*, Pratiti Bandopadhayay*, and Kee Kiat Yeo*. 2024. “METB-07. FREQUENCY AND OUTCOMES OF CDKN2A/B LOSS IN PEDIATRIC GLIOMA.” Neuro-Oncology 26 (Supplement_4): 0–0. https://doi.org/10.1093/neuonc/noae064.248.

  30. Raman, Pichai, Angela J. Waanders, Phillip B. Storm, Jena V. Lilly, Jennifer Mason, Allison P. Heath, Alex S. Felmeister, et al. 2017. “GENE-15. CAVATICA- A PEDIATRIC GENOMIC CLOUD EMPOWERING DATA DISCOVERY THROUGH THE PEDIATRIC BRAIN TUMOR ATLAS.” Neuro-Oncology 19 (suppl_4): iv21–iv21. https://doi.org/10.1093/neuonc/nox083.086.

  31. Resnick, Adam C., Phillip B. Storm, Angela J. Waanders, Jena V. Lilly, Rishi R. Lulla, Sabine Mueller, Michael Prados, et al. 2017. “Abstract LB-008: The Pediatric Brain Tumor Atlas: Building an Integrated, Multi-Platform Data-Rich Ecosystem for Collaborative Discovery in the Cloud.” Cancer Research 77 (13_Supplement): lb-008-lb-008. https://doi.org/10.1158/1538-7445.am2017-lb-008.

  32. Rozowsky, Jared M., Michele Mattioni, Surya Saha, Jack DiGiovanna, Jean-Philippe Thibert, Jeremy Costanza, Vincent Ferretti, et al. 9 2023. “Powering Kids First Variant Exploration on CAVATICA Using GA4GH Standards.” https://doi.org/10.6084/m9.figshare.24183495.v1.

  33. Sridhar, Sunita, Owen Chapman, Aditi Dutta, Shanqing Wang, Rishaan Kenkre, Jens Luebeck, Vineet Bafna, Jill P. Mesirov, and Lukas Chavez. 2024. “METB-08. CIRCULAR EXTRACHROMOSOMAL DNA IS ASSOCIATED WITH POOR SURVIVAL IN CHILDHOOD CANCER TYPES.” Neuro-Oncology 26 (Supplement_4): 0–0. https://doi.org/10.1093/neuonc/noae064.249.

  34. Tetikol, H. Serhat, Deniz Turgut, Kubra Narci, Gungor Budak, Ozem Kalay, Elif Arslan, Sinem Demirkaya-Budak, et al. 2022. “Pan-African Genome Demonstrates How Population-Specific Genome Graphs Improve High-Throughput Sequencing Data Analysis.” Nature Communications 13 (1): 4384. https://doi.org/10.1038/s41467-022-31724-3.

  35. Thirimanne, H. Nayanga, Damian Almiron-Bonnin, Nicholas Nuechterlein, Sonali Arora, Matt Jensen, Carolina A. Parada, Chengxiang Qiu, et al. 2024. “Meningioma Transcriptomic Landscape Demonstrates Novel Subtypes with Regional Associated Biology and Patient Outcome.” Cell Genomics, May, 100566. https://doi.org/10.1016/j.xgen.2024.100566.

  36. Vivelo, Christina, Karlyne M. Reilly, Brigitte C. Widemann, Mary Frances Wedekind, Corrie Painter, Allison F. O’Neill, Sabine Mueller, Olivier Elemento, Andrea M. Gross, and Abby B. Sandler. 2023. “The Landscape of US and Global Rare Tumor Research Programs: A Systematic Review.” The Oncologist, October. https://doi.org/10.1093/oncolo/oyad285.

  37. Xiao, Nan, Soner Koc, David Roberson, Phillip Brooks, Manisha Ray, and Dennis Dean. 2020. “BCO App: Tools for Generating BioCompute Objects from next-Generation Sequencing Workflows and Computations.” F1000Research 9 (1144): 1144. https://doi.org/10.12688/f1000research.25902.1.

  38. Yang, Yang, and Lixing Yang. 2023. “Somatic Structural Variation Signatures in Pediatric Brain Tumors.” Cell Reports 42 (10): 113276. https://doi.org/10.1016/j.celrep.2023.113276.

  39. Yuen, Denis, Louise Cabansay, Andrew Duncan, Gary Luu, Gregory Hogue, Charles Overbeck, Natalie Perez, et al. 2021. “The Dockstore: Enhancing a Community Platform for Sharing Reproducible and Accessible Computational Protocols.” Nucleic Acids Research 49 (W1): gkab346-. https://doi.org/10.1093/nar/gkab346.

  40. Zhu, Yuankun, Miguel Brown, Batsal Devkota, Bailey Farrow, Bogdan Gavrilovic, Allison Heath, Kyle Hernandez, et al. 2019. “Abstract 2465: Genomic Harmonization of the Data Resource Center for Gabriella Miller Kids First Pediatric Research Program.” Cancer Research 79 (13_Supplement): 2465–2465. https://doi.org/10.1158/1538-7445.am2019-2465.

  41. Zhu, Yuankun, Yiran Guo, Allison P. Heath, Pichai Raman, Elizabeth Appert, Jennifer Mason, Bo Zhang, et al. 2019. “Abstract 3667: The Pediatric Brain Tumor Atlas - Transforming the Landscape of Research.” Cancer Research 79 (13_Supplement): 3667–3667. https://doi.org/10.1158/1538-7445.am2019-3667.