David van Dijk, PhD
Assistant Professor
Research & Publications
Biography
News
Research Summary
The mission of our lab is to provide machine learning tools that extract meaningful insight from high-throughput, high-dimensional biomedical data.
Coauthors
Research Interests
Neurosciences; Computational Biology; Single-Cell Analysis; Machine Learning; Deep Learning
Selected Publications
- A phenomapping-derived tool to personalize the selection of anatomical vs. functional testing in evaluating chest pain (ASSIST).Oikonomou EK, Van Dijk D, Parise H, Suchard MA, de Lemos J, Antoniades C, Velazquez EJ, Miller EJ, Khera R. A phenomapping-derived tool to personalize the selection of anatomical vs. functional testing in evaluating chest pain (ASSIST). European Heart Journal 2021, 42:2536-2548.
- Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes.Ravindra NG, Alfajaro MM, Gasque V, Huston NC, Wan H, Szigeti-Buck K, Yasumoto Y, Greaney AM, Habet V, Chow RD, Chen JS, Wei J, Filler RB, Wang B, Wang G, Niklason LE, Montgomery RR, Eisenbarth SC, Chen S, Williams A, Iwasaki A, Horvath TL, Foxman EF, Pierce RW, Pyle AM, van Dijk D, Wilen CB. Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes. PLoS Biology 2021, 19:e3001143.
- Quantifying the effect of experimental perturbations at single-cell resolution.Burkhardt DB, Stanley JS, Tong A, Perdigoto AL, Gigante SA, Herold KC, Wolf G, Giraldez AJ, van Dijk D, Krishnaswamy S. Quantifying the effect of experimental perturbations at single-cell resolution. Nature Biotechnology 2021, 39:619-629.
- TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics.Tong A, Huang J, Wolf G, van Dijk D, Krishnaswamy S. TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics. Proceedings Of Machine Learning Research 2020, 119:9526-9536.
- Transcriptomic and clonal characterization of T cells in the human central nervous system.Pappalardo JL, Zhang L, Pecsok MK, Perlman K, Zografou C, Raddassi K, Abulaban A, Krishnaswamy S, Antel J, van Dijk D, Hafler DA. Transcriptomic and clonal characterization of T cells in the human central nervous system. Science Immunology 2020, 5.
- Visualizing structure and transitions in high-dimensional biological data.Moon KR, van Dijk D, Wang Z, Gigante S, Burkhardt DB, Chen WS, Yim K, Elzen AVD, Hirn MJ, Coifman RR, Ivanova NB, Wolf G, Krishnaswamy S. Visualizing structure and transitions in high-dimensional biological data. Nature Biotechnology 2019, 37:1482-1492.