All Publications

A complete list, newest first. My earlier work was in evolutionary computation and artificial life; the more recent work is in machine learning for microscopy.

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.
PDF Code Dataset Poster Video Source Document DOI Protein Science
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.
PDF Code Dataset Poster Video Source Document DOI 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.
Code Dataset Poster Video Source Document DOI Nature 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.
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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.
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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.
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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.
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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).
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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.
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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.
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Ella Bahry, Laura Breimann, Marwan Zouinkhi, Leo Epstein, Klim Kolyvanov, Nicholas Mamrak, Benjamin King, Xi Long, Kyle I. S. Harrington, Timothée Lionnet, Stephan Preibisch (2022). RS-FISH: precise, interactive, fast, and scalable FISH spot detection. Nature Methods, 19(12).
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Rani Barbara, Madhu Nagathihalli Kantharaju, Ravid Haruvi, Kyle Harrington, Takashi Kawashima (2022). PyZebrascope: An Open-Source Platform for Brain-Wide Neural Activity Imaging in Zebrafish. Frontiers in Cell and Developmental Biology, 10.
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Robert Wiese, Kyle Harrington, Kai Hartmann, Manja Hethke, Thomas Von Rintelen, Hucai Zhang, Le-Jia Zhang, Frank Riedel (2022). Can fractal dimensions objectivize gastropod shell morphometrics? A case study from Lake Lugu (SW China). Ecology and Evolution, 12(e8622).
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Kai Fan, Ranil Dhammapala, Kyle Harrington, Ryan Lamastro, Brian Lamb, Yunha Lee (2022). Development of a Machine Learning Approach for Local-Scale Ozone Forecasting: Application to Kennewick, WA. Front. Big Data.
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Leo Epstein, Zeth Dubois, Jessica Smith, Yunha Lee, Kyle Harrington (2021). Complex population dynamics in a spatial microbial ecosystem with Physarum polycephalum. Biosystems, 208(104334).
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Cameron Arshadi, Ulrik Günther, Mark Eddison, Kyle I. S. Harrington, Tiago A. Ferreira (2021). SNT: a unifying toolbox for quantification of neuronal anatomy. Nature Methods, 18(4).
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Bahti Zakirov, Georgios Charalambous, Raphael Thuret, Irene M. Aspalter, Kelvin Van-Vuuren, Thomas Mead, Kyle Harrington, Erzsébet Ravasz Regan, Shane Paul Herbert, Katie Bentley (2021). Active perception during angiogenesis: filopodia speed up Notch selection of tip cells in silico and in vivo. Phil. Trans. R. Soc. B.
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Ulrik Günther, Kyle I. S. Harrington, Raimund Dachselt, Ivo F. Sbalzarini (2020). Bionic Tracking: Using Eye Tracking to Track Biological Cells in Virtual Reality. In ICAROB-2020.
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Ulrik Günther, Kyle I.S. Harrington (2020). Tales from the Trenches: Developing sciview, a new 3D viewer for the ImageJ community. In VisGap 2020.
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Ulrik Günther, Tobias Pietzsch, Aryaman Gupta, Kyle Harrington, Pavel Tomancak, Stefan Gumhold, Ivo F. Sbalzarini (2020). scenery: Flexible Virtual Reality Visualization on the Java VM. In VIS 2019.
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Claudia Prahst, Parham Ashrafzadeh, Thomas Mead, Ana Figueiredo, Karen Chang, Douglas Richardson, Lakshmi Venkaraman, Mark Richards, Ana Martins Russo, Kyle Harrington, Marie Ouarné, Andreia Pena, Dong Feng Chen, Lena Claesson-Welsh, Kin-Sang Cho, Claudio a Franco, Katie Bentley (2020). Mouse retinal cell behaviour in space and time using light sheet fluorescence microscopy. eLife, 9.
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Amnon Sharir, Pauline Marangoni, Rapolas Zilionis, Mian Wan, Tomas Wald, Jimmy K. Hu, Kyogo Kawaguchi, David Castillo-Azofeifa, Leo Epstein, Kyle Harrington, Pierfrancesco Pagella, Thimios Mitsiadis, Christian W. Siebel, Allon M. Klein, Ophir D. Klein (2019). A large pool of actively cycling progenitors orchestrates self-renewal and injury repair of an ectodermal appendage. Nature Cell Biology, 21(9).
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Stephan Daetwyler, Ulrik Günther, Carl D. Modes, Kyle I. S. Harrington, Jan Huisken (2019). Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish. Development, 146(dev173757).
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Dennis G. Wilson, Sylvain Cussat-Blanc, Herve Luga, Kyle Harrington (2018). Neuromodulated Learning in Deep Neural Networks. arXiv.
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Sylvain Cussat-Blanc, Kyle Harrington, Wolfgang Banzhaf (2018). Artificial Gene Regulatory Networks—A Review. Artificial Life.
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Dennis G. Wilson, Kyle Harrington, Sylvain Cussat-Blanc, Hervé Luga (2018). Evolving Differentiable Gene Regulatory Networks. arXiv.
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Kyle I. S. Harrington, Curtis T. Rueden, Kevin W. Eliceiri (2018). FunImageJ: a Lisp framework for scientific image processing. Bioinformatics, 34(5), 899-900.
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Kyle Harrington, Louise Magbunduku (2017). Competitive Dynamics in Eco-evolutionary Genetically-regulated Swarms. In ECAL 2017.
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Kyle I. Harrington, Jordan Pollack (2017). Escalation of Memory Length in Finite Populations. bioRxiv.
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Guilherme Costa, Kyle I. S. Harrington, Holly E. Lovegrove, Donna J. Page, Shilpa Chakravartula, Katie Bentley, Shane P. Herbert (2016). Asymmetric division coordinates collective cell migration in angiogenesis. Nature Cell Biology, 18(12).
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Kyle I.S. Harrington (2016). A circuit basis for morphogenesis. Theoretical Computer Science, 633.
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A.L. Wang, J.M. Gold, N. Tompkins, M. Heymann, Kyle I. Harrington, S. Fraden (2016). Configurable NOR gate arrays from Belousov-Zhabotinsky micro-droplets. European Physical Journal Special Topics, 225(1).
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Esther Kur, Jiha Kim, Aleksandra Tata, Cesar H Comin, Kyle I Harrington, Luciano Da F Costa, Katie Bentley, Chenghua Gu (2016). Temporal modulation of collective cell behavior controls vascular network topology. eLife.
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Sylvain Cussat-Blanc, Kyle Harrington (2015). Genetically-regulated Neuromodulation Facilitates Multi-Task Reinforcement Learning. In GECCO-2015.
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Sylvain Cussat-Blanc, Kyle I. Harrington, Jordan Pollack (2015). Gene Regulatory Network Evolution Through Augmenting Topologies. IEEE Transactions on Evolutionary Computation, 19(6).
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Katie Bentley, Kyle I. Harrington, Erzsébet Ravasz Regan (2014). Can active perception generate bistability? Heterogeneous collective dynamics and vascular patterning. In ALIFE 14.
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Jacob Gold, Adam Wang, Kyle I. Harrington (2014). Feedback Control of Evolving Swarms. In ALIFE 14.
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Jessica Lowell, Kyle Harrington, Jordan Pollack (2014). The Resilience of a Swarm Ecosystem Under Environmental Variation. In ALIFE 14.
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Kyle I. Harrington, Jesse Freeman, Jordan Pollack (2014). Coevolution in Hide and Seek: Camouflage and Vision. In ALIFE 14.
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Kyle I. Harrington, Alvaro Sanchez (2014). Eco-evolutionary dynamics of complex social strategies in microbial communities. Communicative & Integrative Biology, 7(1).
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Kyle I. Harrington, Emmanuel Awa, Sylvain Cussat-Blanc, Jordan Pollack (2013). Robot Coverage Control by Neuromodulation. In IJCNN-2013.
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Kyle I. Harrington, Megan M. Olsen, Hava T. Siegelmann (2012). Computational Neuroecology of Communicated Somatic Markers. In Alife 2012.
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Kyle I. Harrington, Lee Spector, Jordan B. Pollack, Una-May O’Reilly (2012). Autoconstructive Evolution for Structural Problems. In GECCO-2012.
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Lee Spector, Kyle Harrington, Thomas Helmuth (2012). Tag-Based Modularity in Tree-Based Genetic Programming. In GECCO-2012.
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Kyle I. Harrington, A. Pinar Ozisik, Jordan B. Pollack (2012). The Effects of Finite Populations and Selection on the Emergence of Signaling. In ALIFE 13.
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A. Pinar Ozisik, Kyle I. Harrington (2012). The Effects of Tags on the Evolution of Honest Signaling. In GECCO-2012 Companion.
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Yuhua Shang, Paula Haynes, Nicolás Pírez, Kyle I. S. Harrington, Fang Guo, Jordan Pollack, Pengyu Hong, Leslie C. Griffith, Michael Rosbash (2011). Imaging analysis of clock neurons: light buffers the wake-promoting effect of dopamine. Nature Neuroscience, 14(7).
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Kyle I. Harrington, Megan M. Olsen, Hava T. Siegelmann (2011). Communicated Somatic Markers Benefit Both the Individual and the Species. In IJCNN-2011.
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Lee Spector, Brian Martin, Kyle Harrington, Thomas Helmuth (2011). Tag-Based Modules in Genetic Programming. In GECCO-2011.
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Lee Spector, Kyle Harrington, Brian Martin, Thomas Helmuth (2011). What’s in an Evolved Name? The Evolution of Modularity via Tag-Based Reference. In GPTP IX.
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Michael Heymann, Kyle I. Harrington, Jordan Pollack, Seth Fraden (2010). En Route to Signal Inversion in Chemical Computing. In ALIFE XII.
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Megan M. Olsen, Kyle Harrington, Hava T. Siegelmann (2008). Emotions for Strategic Real-Time Systems. In AAAI Spring Symposium.
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Kyle I. Harrington, Hava T. Siegelmann (2007). Adaptive Multi-modal Sensors. In 50 Years of AI.
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Lee Spector, Jon Klein, Kyle Harrington, Raymond Coppinger (2005). Teaching the Evolution of Behavior with SuperDuperWalker. In AIED 2005.
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Lee Spector, Jon Klein, Kyle Harrington (2005). Selection Songs: Evolutionary Music Computation. In YLEM Journal.
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