Daniel B Burkhardt
Daniel B Burkhardt
Cellarity - Machine Learning Scientist
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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
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
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
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
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
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), 1-15, 2019
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
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
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
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
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
KR Moon, D van Dijk, Z Wang, S Gigante, DB Burkhardt, WS Chen, K Yim
A. vd, Hirn, MJ, Coifman, RR, Ivanova, NB, Wolf, G., and Krishnaswamy, S …, 2019
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), 1-15, 2022
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), 100288, 2021
The Human Accelerated Region HACNS1 modifies developmental gene expression in humanized mice
EV Dutrow, D Emera, K Yim, S Uebbing, AA Kocher, M Kren-zer, T Nottoli, ...
bioRxiv, 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
Multimodal single cell data integration challenge: results and lessons learned
C Lance, MD Luecken, DB Burkhardt, R Cannoodt, P Rautenstrauch, ...
bioRxiv, 2022
Vertex-Frequency Clustering
DB Burkhardt, JS Stanley III, G Wolf, S Krishnaswamy
2019 IEEE Data Science Workshop (DSW), 145-149, 2019
Immune cells and their inflammatory mediators modify beta cells and cause checkpoint inhibitor-induced diabetes
AL Perdigoto, S Deng, KC Du, M Kuchroo, DB Burkhardt, A Tong, G Israel, ...
JCI insight, 2022
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
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