| A genome sequencing system for universal newborn screening, diagnosis, and precision medicine for severe genetic diseases SF Kingsmore, LD Smith, CM Kunard, M Bainbridge, S Batalov, W Benson, ... The American Journal of Human Genetics 109 (9), 1605-1619, 2022 | 123 | 2022 |
| Inhibition of dual-specificity tyrosine phosphorylation-regulated kinase 2 perturbs 26S proteasome-addicted neoplastic progression S Banerjee, T Wei, J Wang, JJ Lee, HL Gutierrez, O Chapman, SE Wiley, ... Proceedings of the National Academy of Sciences 116 (49), 24881-24891, 2019 | 56 | 2019 |
| Functional precision medicine identifies new therapeutic candidates for medulloblastoma JM Rusert, EF Juarez, S Brabetz, J Jensen, A Garancher, LQ Chau, ... Cancer Research 80 (23), 5393-5407, 2020 | 53 | 2020 |
| Progress towards computational 3-d multicellular systems biology P Macklin, HB Frieboes, JL Sparks, A Ghaffarizadeh, SH Friedman, ... Systems Biology of Tumor Microenvironment: Quantitative Modeling and …, 2016 | 44 | 2016 |
| Quantifying differences in cell line population dynamics using CellPD EF Juarez, R Lau, SH Friedman, A Ghaffarizadeh, E Jonckheere, ... BMC systems biology 10, 1-12, 2016 | 29 | 2016 |
| A FZD7-specific Antibody-Drug Conjugate Induces Ovarian Tumor Regression in Preclinical Models. M Do, CCN Wu, PR Sonavane, EF Juarez, SR Adams, J Ross, RY Baena, ... Molecular cancer therapeutics 21 (1), 113-124, 2022 | 28 | 2022 |
| Imaging-Based Machine Learning Analysis of Patient-Derived Tumor Organoid Drug Response ER Spiller, N Ung, S Kim, K Patsch, R Lau, C Strelez, C Doshi, S Choung, ... Frontiers in Oncology 11, 771173, 2021 | 27 | 2021 |
| Model-based assessment of mammalian cell metabolic functionalities using omics data A Richelle, BP Kellman, AT Wenzel, AWT Chiang, T Reagan, ... Cell Reports Methods 1 (3), 100040, 2021 | 27 | 2021 |
| Automated prioritization of sick newborns for whole genome sequencing using clinical natural language processing and machine learning B Peterson, EJ Hernandez, C Hobbs, S Malone Jenkins, B Moore, ... Genome Medicine 15 (1), 1-9, 2023 | 15 | 2023 |
| Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma OS Chapman, J Luebeck, S Sridhar, ITL Wong, D Dixit, S Wang, G Prasad, ... Nature genetics 55 (12), 2189-2199, 2023 | 14 | 2023 |
| The landscape of extrachromosomal circular DNA in medulloblastoma OS Chapman, J Luebeck, S Wani, A Tiwari, M Pagadala, S Wang, ... bioRxiv, 2021.10. 18.464907, 2021 | 13 | 2021 |
| MultiCellDS: a standard and a community for sharing multicellular data SH Friedman, ARA Anderson, DM Bortz, AG Fletcher, HB Frieboes, ... bioRxiv, 090696, 2016 | 13 | 2016 |
| MultiCellDS: a community-developed standard for curating microenvironment-dependent multicellular data SH Friedman, ARA Anderson, DM Bortz, AG Fletcher, HB Frieboes, ... bioRxiv, 090456, 2016 | 11 | 2016 |
| 3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma K Okonechnikov, A Camgöz, O Chapman, S Wani, DE Park, JM Hübner, ... Nature Communications 14 (1), 2300, 2023 | 10 | 2023 |
| High-throughput microscopy reveals the impact of multifactorial environmental perturbations on colorectal cancer cell growth CT Chiang, R Lau, A Ghaffarizadeh, M Brovold, D Vyas, EF Juarez, ... GigaScience 10 (4), giab026, 2021 | 10 | 2021 |
| What does your cell really do? Model-based assessment of mammalian cells metabolic functionalities using omics data A Richelle, BP Kellman, AT Wenzel, AWT Chiang, T Reagan, ... bioRxiv, 2020.04. 26.057943, 2020 | 10 | 2020 |
| An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data CK Mah, AT Wenzel, EF Juarez, T Tabor, MM Reich, JP Mesirov F1000Research 7, 2018 | 10 | 2018 |
| Systems Biology of Tumor Microenvironment P Macklin, HB Frieboes, JL Sparks, A Ghaffarizadeh, SH Friedman, ... Cham: Springer, 2016 | 9 | 2016 |
| Estimating cell cycle model parameters using systems identification E Juarez, A Ghaffarizadeh, SH Friedman, E Jonckheere, P Macklin bioRxiv, 035766, 2015 | 3 | 2015 |
| Quantification of Cancer Cell Migration with an Integrated Experimental-Computational Pipeline EF Juarez, C Garri, A Ghaffarizadeh, P Macklin, K Kani bioRxiv, 130526, 2017 | 2 | 2017 |