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Faculty
Karsten Siller
Associate Professor of Data Science
School of Data Science
Email: khs3z@virginia.edu
Additional Contact Information
Karsten Siller is an Associate Professor at the School of Data Science at the University of Virginia. His academic interests span developmental and cell biology, image analysis, high-throughput data pipelines, and high-performance computing.
Siller joined UVA in 2013 as an Assistant Professor in the Department of Biology within the College of Arts & Sciences. Before his current appointment at the School of Data Science, he served as Associate Director for Research Computing User Services. In that role, he led a team of computational scientists and oversaw technical support operations, workshop portfolio, collaborative research initiatives, and community outreach.
He has deep expertise in image processing and image analysis and is a strong advocate for open-source software development and interactive, project-based teaching. His research focuses on building reproducible and resilient, scalable data analysis workflows that are portable across diverse computing environments. He is also interested in developing intuitive user interfaces for composing modular, multi-stage pipelines, with integrated visualization tools that are both user-friendly and extensible.
Siller earned his doctorate in Biology from the University of Tübingen, Germany. As part of his graduate studies, he conducted research at the University of Oregon. He also holds a Dipl. Biol. (M.S. equivalent) in Biology from the University of Tübingen.
Education
- Ph.D., Biology, University of Tübingen, Germany
- Dipl. Biol., Biology, University of Tübingen, Germany
Data Science Domains
Analytics; Systems; Design
Areas of Practice
Biomedical, Health, and Life Sciences; Human-Centered Design and Interaction
Selected Publications
Zhang J., Wallrabe H., Siller K., Mbogo B., Cassidy T., Alam S.R., Periasamy A. (2025) Measuring Metabolic Changes in Cancer Cells Using Two‐Photon Fluorescence Lifetime Imaging Microscopy and Machine‐Learning Analysis. Journal of Biophotonics 18(1), e202400426.
Sun R., Siller K. (2024) HPC Container Management at the University of Virginia. Practice and Experience in Advanced Research Computing 2024: Human Powered Computing, 2024/7/17.
Zimyanin V., Magaj M., Yu C.H., Gibney T., Mustafa B., Horton X., Siller K., Cueff L., Bouvrais H., Pécréaux J., Needleman D., Redemann S. (2024) Using 3D Large Scale Tomography to Study Force Generation in the Mitotic Spindle. Microscopy and Microanalysis (Suppl. 1), ozae044. 344.
Alam S.R., Wallrabe H., Christopher K.G., Siller K.H., Periasamy A. (2022). Characterization of mitochondrial dysfunction due to laser damage by 2-photon FLIM microscopy. Scientific Reports 12(1), 11938.
Rudenko L.K., Wallrabe H., Periasamy A., Siller K.H., Svindrych Z., Seward M.E., Best M.N., Bloom G.S. (2019) Intraneuronal tau misfolding induced by extracellular amyloid-β oligomers. J Alzheimers Dis. 71(4), 1125-1138.
Wallrabe H., Svindrych Z., Alam S.R., Siller K.H., Wang T., Kashatus D., Hu S., Periasamy A. (2018) Segmented cell analyses to measure redox states of autofluorescent NAD (P) H, FAD & Trp in cancer cells by FLIM. Scientific Reports 8(1), 79.
Doyle S.E., Pahl, M.C., Siller K.H., Ardiff, L., Siegrist S. E. (2017) Neuroblast niche position is controlled by Phosphoinositide 3-kinase-dependent DE-Cadherin adhesion. Development 144(5), 820-829.
Siller, K.H., Doe, C.Q. (2009). Spindle orientation during asymmetric cell division. Nature Cell Biol. 11(4), 365-74.
Siller, K.H., Doe, C.Q. (2008). Lis1/dynactin regulates metaphase spindle orientation in Drosophila neuroblasts. Dev Biol. 319(1), 1-9.
Siller, K.H., Cabernard, C., Doe, C.Q. (2006). The NuMA-related Mud protein binds Pins and regulates spindle orientation in Drosophila neuroblasts. Nature Cell Biol. 8 (6), 594-600.