Publications

Utz Heinrich Ermel, Jonathan Schwartz, Zhuowen Zhao, Daniel Ji, Ariana Peck, Yue Yu, Mohammadreza Paraan, Bridget Carragher, Achilleas S. Frangakis, Kyle I. S. Harrington (2026). copick: An open dataset interface and toolkit for collaborative annotation and analysis of cryo-electron tomography data. Protein Sci.

Ella Bahry, Jeanine C. Pestoni, Kai Hirzel, Taras Savchyn, Diana Porras-Gonzalez, Vera Getmanchuk-Zaporoshchenko, Martin Gregor, Thomas M. Conlon, Ali Önder Yildirim, Kyle Harrington, Deborah Schmidt, Gerald Burgstaller, Michael Heymann (2026). A generative AI framework for disease-specific lung microtissue bioengineering. bioRxiv.

Ariana Peck, Yue Yu, Jonathan Schwartz, Anchi Cheng, Utz Heinrich Ermel, Joshua Hutchings, Saugat Kandel, Dari Kimanius, Elizabeth a Montabana, Daniel Serwas, Hannah Siems, Feng Wang, Zhuowen Zhao, Shawn Zheng, Matthias Haury, David Agard, Clinton Potter, Bridget Carragher, Kyle Harrington, * Co-Corresponding, Mohammadreza Paraan, * Co-Corresponding (2025). A realistic phantom dataset for benchmarking cryo-ET data annotation. Nat Methods.

Kyle I. Harrington, Zhuowen Zhao, Jonathan Schwartz, Saugat Kandel, Utz Ermel, Mohammadreza Paraan, Clinton Potter, Bridget Carragher (2024). Open-source Tools for CryoET Particle Picking Machine Learning Competitions. bioRxiv.

Kevin A. Yamauchi, Lorenz Lamm, Lorenzo Gaifas, Ricardo D. Righetto, Daniil Litvinov, Benjamin D. Engel, Kyle Harrington (2024). Surforama: interactive exploration of volumetric data by leveraging 3D surfaces. bioRxiv.

Wolfgang Giese, Jan Philipp Albrecht, Olya Oppenheim, Emir Bora Akmeriç, Julia Kraxner, Deborah Schmidt, Kyle Harrington, Holger Gerhardt (2024). Polarity-JaM: An image analysis toolbox for cell polarity, junction and morphology quantification. bioRxiv.

Gabriel J. Selzer, Curtis T. Rueden, Mark C. Hiner, Edward L. Evans, Kyle I. S. Harrington, Kevin W. Eliceiri (2023). napari-imagej: ImageJ Ecosystem Access from napari. Nature Methods, 20(10), 1443-1444.

Lise Finotto, Basiel Cole, Wolfgang Giese, Elisabeth Baumann, Annelies Claeys, Maxime Vanmechelen, Brecht Decraene, Marleen Derweduwe, Nikolina Dubroja Lakic, Gautam Shankar, Madhu Nagathihalli Kantharaju, Jan Philipp Albrecht, Ilse Geudens, Fabio Stanchi, Keith L. Ligon, Bram Boeckx, Diether Lambrechts, Kyle Harrington, Ludo Van Den Bosch, Steven De Vleeschouwer, Frederik De Smet, Holger Gerhardt (2023). Single‐cell profiling and zebrafish avatars reveal LGALS1 as immunomodulating target in glioblastoma. EMBO Molecular Medicine, 15(e18144).

Shin-Ya Takemura, Kenneth J Hayworth, Gary B Huang, Michal Januszewski, Zhiyuan Lu, Elizabeth C Marin, Stephan Preibisch, C Shan Xu, John Bogovic, Andrew S Champion, Han SJ Cheong, Marta Costa, Katharina Eichler, William Katz, Christopher Knecht, Feng Li, Billy J Morris, Christopher Ordish, Patricia K Rivlin, Philipp Schlegel, Kazunori Shinomiya, Tomke Stürner, Ting Zhao, Griffin Badalamente, Dennis Bailey, Paul Brooks, Brandon S Canino, Jody Clements, Michael Cook, Octave Duclos, Christopher R Dunne, Kelli Fairbanks, Siqi Fang, Samantha Finley-May, Audrey Francis, Reed George, Marina Gkantia, Kyle Harrington, Gary Patrick Hopkins, Joseph Hsu, Philip M Hubbard, Alexandre Javier, Dagmar Kainmueller, Wyatt Korff, Julie Kovalyak, Dominik Krzemiński, Shirley a Lauchie, Alanna Lohff, Charli Maldonado, Emily a Manley, Caroline Mooney, Erika Neace, Matthew Nichols, Omotara Ogundeyi, Nneoma Okeoma, Tyler Paterson, Elliott Phillips, Emily M Phillips, Caitlin Ribeiro, Sean M Ryan, Jon Thomson Rymer, Anne K Scott, Ashley L Scott, David Shepherd, Aya Shinomiya, Claire Smith, Natalie Smith, Alia Suleiman, Satoko Takemura, Iris Talebi, Imaan FM Tamimi, Eric T Trautman, Lowell Umayam, John J Walsh, Tansy Yang, Gerald M Rubin, Louis K Scheffer, Jan Funke, Stephan Saalfeld, Harald F Hess, Stephen M Plaza, Gwyneth M Card, Gregory SXE Jefferis, Stuart Berg (2023). A Connectome of the Male Drosophila Ventral Nerve Cord. bioRxiv.

Kai Fan, Ranil Dhammapala, Kyle Harrington, Brian Lamb, Yunha Lee (2023). Machine learning-based ozone and PM2.5 forecasting: Application to multiple AQS sites in the Pacific Northwest. Frontiers in Big Data, 6.