| Visualizing structure and transitions in high-dimensional biological data KR Moon, D Van Dijk, Z Wang, S Gigante, DB Burkhardt, WS Chen, K Yim, ... Nature biotechnology 37 (12), 1482-1492, 2019 | 1050 | 2019 |
| Quantifying the effect of experimental perturbations in single-cell RNA-sequencing data using graph signal processing DB Burkhardt, JS Stanley, A Tong, AL Perdigoto, SA Gigante, KC Herold, ... Nature Biotechnology, 619-629, 2021 | 198 | 2021 |
| Manifold learning-based methods for analyzing single-cell RNA-sequencing data KR Moon, JS Stanley III, D Burkhardt, D van Dijk, G Wolf, S Krishnaswamy Current Opinion in Systems Biology 7, 36-46, 2018 | 177 | 2018 |
| Endocrine-exocrine signaling drives obesity-associated pancreatic ductal adenocarcinoma KM Chung, J Singh, L Lawres, KJ Dorans, C Garcia, DB Burkhardt, ... Cell 181 (4), 832-847. e18, 2020 | 117 | 2020 |
| A sandbox for prediction and integration of DNA, RNA, and proteins in single cells MD Luecken, DB Burkhardt, R Cannoodt, C Lance, A Agrawal, H Aliee, ... Thirty-fifth conference on neural information processing systems datasets …, 2021 | 111 | 2021 |
| Long-term warming alters carbohydrate degradation potential in temperate forest soils G Pold, AF Billings, JL Blanchard, DB Burkhardt, SD Frey, JM Melillo, ... Applied and environmental microbiology 82 (22), 6518-6530, 2016 | 90 | 2016 |
| Multimodal single cell data integration challenge: results and lessons learned C Lance, MD Luecken, DB Burkhardt, R Cannoodt, P Rautenstrauch, ... BioRxiv, 2022.04. 11.487796, 2022 | 71 | 2022 |
| Multiscale PHATE identifies multimodal signatures of COVID-19 M Kuchroo, J Huang, P Wong, JC Grenier, D Shung, A Tong, C Lucas, ... Nature Biotechnology 40 (5), 681-691, 2022 | 63 | 2022 |
| MLL-AF9 initiates transformation from fast-proliferating myeloid progenitors X Chen, DB Burkhardt, AA Hartman, X Hu, AE Eastman, C Sun, X Wang, ... Nature Communications 10 (1), 5767, 2019 | 57 | 2019 |
| Mapping phenotypic plasticity upon the cancer cell state landscape using manifold learning DB Burkhardt, BP San Juan, JG Lock, S Krishnaswamy, CL Chaffer Cancer discovery 12 (8), 1847-1859, 2022 | 44 | 2022 |
| Immune cells and their inflammatory mediators modify β cells and cause checkpoint inhibitor–induced diabetes AL Perdigoto, S Deng, KC Du, M Kuchroo, DB Burkhardt, A Tong, G Israel, ... JCI insight 7 (17), e156330, 2022 | 33 | 2022 |
| Modeling uniquely human gene regulatory function via targeted humanization of the mouse genome EV Dutrow, D Emera, K Yim, S Uebbing, AA Kocher, M Krenzer, T Nottoli, ... Nature Communications 13 (1), 304, 2022 | 30* | 2022 |
| Final results of a phase II prospective trial evaluating the combination of stereotactic body radiotherapy (SBRT) with concurrent pembrolizumab in patients with metastatic non … AM Campbell, WL Cai, D Burkhardt, SN Gettinger, SB Goldberg, ... International Journal of Radiation Oncology, Biology, Physics 105 (1), S36-S37, 2019 | 25 | 2019 |
| How to build the virtual cell with artificial intelligence: Priorities and opportunities C Bunne, Y Roohani, Y Rosen, A Gupta, X Zhang, M Roed, T Alexandrov, ... Cell 187 (25), 7045-7063, 2024 | 21 | 2024 |
| Finding archetypal spaces using neural networks D van Dijk, DB Burkhardt, M Amodio, A Tong, G Wolf, S Krishnaswamy 2019 IEEE International Conference on Big Data (Big Data), 2634-2643, 2019 | 21* | 2019 |
| 1-deoxysphingolipids bind to COUP-TF to modulate lymphatic and cardiac cell development T Wang, Z Wang, L de Fabritus, J Tao, EM Saied, HJ Lee, BR Ramazanov, ... Developmental cell 56 (22), 3128-3145. e15, 2021 | 19 | 2021 |
| Multiscale PHATE exploration of SARS-CoV-2 data reveals multimodal signatures of disease M Kuchroo, J Huang, P Wong, JC Grenier, D Shung, A Tong, C Lucas, ... bioRxiv, 2020 | 17 | 2020 |
| Defining and benchmarking open problems in single-cell analysis MD Luecken, S Gigante, DB Burkhardt, R Cannoodt, DC Strobl, ... Research Square, rs. 3. rs-4181617, 2024 | 9 | 2024 |
| Generating hard-to-obtain information from easy-to-obtain information: applications in drug discovery and clinical inference M Amodio, D Shung, DB Burkhardt, P Wong, M Simonov, Y Yamamoto, ... Patterns 2 (7), 2021 | 9 | 2021 |
| AAnet resolves a continuum of spatially-localized cell states to unveil tumor complexity A Venkat, SE Youlten, BPS Juan, C Purcell, M Amodio, DB Burkhardt, ... bioRxiv, 2024.05. 11.593705, 2024 | 1 | 2024 |
