Browse by Research Team

AAAI Spring Symposium

Emotions for Strategic Real-Time Systems.
Olsen, M.M., Harrington, K. and Siegelmann, H.T.
In: 2008 AAAI Spring Symposium, 26-28 Mar 2008, Stanford, CA, USA. 2008

Artificial Life

Escalation of memory length in finite populations.
Harrington, K. and Pollack, J.
Artificial Life 25 (1): 22-32. 2 April 2019

Artificial gene regulatory networks-a review.
Cussat-Blanc, S., Harrington, K. and Banzhaf, W.
Artificial Life 24 (4): 296-328. 2018

Artificial Life Conference Proceedings

Can active perception generate bistability? Heterogeneous collective dynamics and vascular patterning.
Bentley, K., Harrington, K.I. and Regan, E.
In: 14th International Conference on the Synthesis and Simulation of Living Systems (ALIFE 2014), 30 Jul - 02 Aug 2014, Manhattan, New York, USA. July 2014

Coevolution in hide and seek: camouflage and vision.
Harrington, K.I., Freeman, J. and Pollack, J.
In: 14th International Conference on the Synthesis and Simulation of Living Systems (ALIFE 2014), 30 Jul - 02 Aug 2014, Manhattan, New York, USA. July 2014

Feedback control of evolving swarms.
Gold, J., Wang, A. and Harrington, K.I.
In: 14th International Conference on the Synthesis and Simulation of Living Systems (ALIFE 2014), 30 Jul - 02 Aug 2014, Manhattan, New York, USA. July 2014

The resistance of swarm ecosystem under environmental variation.
Lowell, J., Harrington, K. and Pollack, J.
In: 14th International Conference on the Synthesis and Simulation of Living Systems (ALIFE 2014), 30 Jul - 02 Aug 2014, Manhattan, New York, USA. July 2014

The effects of finite populations and selection on the emergence of signaling.
Harrington, K.I., Ozisik, A.P. and Pollack, J.B.
In: 13th International Conference on the Synthesis and Simulation of Living Systems (ALIFE 2012), 19-22 Jul 2012, East Lansing, Michigan, USA. July 2012

Bioinformatics

FunImageJ: a lisp framework for scientific image processing.
Harrington, K.I.S., Rueden, C.T. and Eliceiri, K.W.
Bioinformatics 34 (5): 899-900. 1 March 2018

Biosystems

Complex population dynamics in a spatial microbial ecosystem with Physarum polycephalum.
Epstein, L., Dubois, Z., Smith, J., Lee, Y. and Harrington, K.
Biosystems 208 : 104483. October 2021

Acquisition and reconstruction of 4D surfaces of axolotl embryos with the flipping stage robotic microscope.
Crawford-Young, S.J., Dittapongpitch, S., Gordon, R. and Harrington, K.I.S.
Biosystems 173 : 214-220. November 2018

Communicative & Integrative Biology

Eco-evolutionary dynamics of complex social strategies in microbial communities.
Harrington, K.I. and Sanchez, A.
Communicative & Integrative Biology 7 (1): e28230. 25 February 2014

Development

Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish.
Daetwyler, S., Günther, U., Modes, C.D., Harrington, K. and Huisken, J.
Development 146 (6): dev173757. 15 March 2019

EMBO Molecular Medicine

Single-cell profiling and zebrafish avatars reveal LGALS1 as immunomodulating target in glioblastoma.
Finotto, L., Cole, B., Giese, W., Baumann, E., Claeys, A., Vanmechelen, M., Decraene, B., Derweduwe, M., Dubroja Lakic, N., Shankar, G., Nagathihalli Kantharaju, M., Albrecht, J.P., Geudens, I., Stanchi, F., Ligon, K.L., Boeckx, B., Lambrechts, D., Harrington, K., Van Den Bosch, L., De Vleeschouwer, S., De Smet, F. and Gerhardt, H.
EMBO Molecular Medicine 15 (11): e18144. 8 November 2023

Ecology and Evolution

Can fractal dimensions objectivize gastropod shell morphometrics? A case study from Lake Lugu (SW China).
Wiese, R., Harrington, K., Hartmann, K., Hethke, M., Rintelen, T., Zhang, H., Zhang, L.J. and Riedel, F.
Ecology and Evolution 12 (3): e8622. February 2022

European Physical Journal Special Topics

Configurable NOR gate arrays from Belousov-Zhabotinsky micro-droplets.
Wang, A.L., Gold, J.M., Tompkins, N., Heymann, M., Harrington, K.I. and Fraden, S.
European Physical Journal Special Topics 225 (1): 211-227. February 2016

Frontiers in Big Data

Machine learning-based ozone and PM2.5 forecasting: application to multiple AQS sites in the Pacific Northwest.
Fan, K., Dhammapala, R., Harrington, K., Lamb, B. and Lee, Y.
Frontiers in Big Data 6 : 1124148. 24 February 2023

Development of a machine learning approach for local-scale ozone forecasting: application to Kennewick, WA.
Fan, K., Dhammapala, R., Harrington, K., Lamastro, R., Lamb, B. and Lee, Y.
Frontiers in Big Data 5 : 781309. 10 February 2022

Frontiers in Cell and Developmental Biology

PyZebraScope: an open-source platform for brain-wide neural activity imaging in zebrafish.
Barbara, R., Nagathihalli Kantharaju, M., Haruvi, R., Harrington, K. and Kawashima, T.
Frontiers in Cell and Developmental Biology 10 : 875044. 19 May 2022

Frontiers in Computer Science

LABKIT: labeling and segmentation toolkit for big image data.
Arzt, M., Deschamps, J., Schmied, C., Pietzsch, T., Schmidt, D., Tomancak, P., Haase, R. and Jug, F.
Frontiers in Computer Science 4 : 777728. 10 February 2022

IEEE Transactions on Evolutionary Computation

Gene regulatory network evolution through augmenting topologies.
Cussat-Blanc, S., Harrington, K. and Pollack, J.
IEEE Transactions on Evolutionary Computation 19 (6): 823-837. December 2015

International Journal of Natural Computing Research

Conspecific emotional cooperation biases population dynamics:a cellular automata approach.
Olsen, M.M., Harrington, K.I. and Siegelmann, H.T.
International Journal of Natural Computing Research 1 (3): 51-65. July 2010

Lecture Notes in Computer Science

Bionic tracking: using eye tracking to track biological cells in virtual reality.
Günther, U., Harrington, K.I.S., Dachselt, R. and Sbalzarini, I.F.
Lecture Notes in Computer Science 12535 : 280-297. 2021

Adaptive multi-modal sensors.
Harrington, K.I. and Siegelmann, H.T.
In: 50 years of artificial intelligence. Lecture Notes in Computer Science, 4850 (4850). Springer, Berlin, Heidelberg, 164-173. ISBN 978-3-540-77295-8 2007

Nature Cell Biology

A large pool of actively cycling progenitors orchestrates self-renewal and injury repair of an ectodermal appendage.
Sharir, A., Marangoni, P., Zilionis, R., Wan, M., Wald, T., Hu, J.K., Kawaguchi, K., Castillo-Azofeifa, D., Epstein, L., Harrington, K., Pagella, P., Mitsiadis, T., Siebel, C.W., Klein, A.M. and Klein, O.D.
Nature Cell Biology 21 (9): 1102-1112. September 2019

Asymmetric division coordinates collective cell migration in angiogenesis.
Costa, G., Harrington, K.I., Lovegrove, H.E., Page, D.J., Chakravartula, S., Bentley, K. and Herbert, S.P.
Nature Cell Biology 18 (12): 1292-1301. December 2016

Nature Communications

Polarity-JaM: an image analysis toolbox for cell polarity, junction and morphology quantification.
Giese, W., Albrecht, J.P., Oppenheim, O., Akmeriç, E.B., Kraxner, J., Schmidt, D., Harrington, K.I. and Gerhardt, H.
Nature Communications 16 (1): 1474. 8 February 2025

Nature Methods

RS-FISH: precise, interactive, fast, and scalable FISH spot detection.
Bahry, E., Breimann, L., Zouinkhi, M., Epstein, L., Kolyvanov, K., Mamrak, N., King, B., Long, Xi, Harrington, K.I.S., Lionnet, T. and Preibisch, S.
Nature Methods 19 (12): 1563-1567. December 2022

SNT: a unifying toolbox for quantification of neuronal anatomy.
Arshadi, C., Günther, U., Eddison, M., Harrington, K.I.S. and Ferreira, T.A.
Nature Methods 18 : 374-377. April 2021

Nature Neuroscience

Imaging analysis of clock neurons reveals light buffers the wake-promoting effect of dopamine.
Shang, Y., Haynes, P., Pírez, N., Harrington, K.I., Guo, F., Pollack, J., Hong, P., Griffith, L.C. and Rosbash, M.
Nature Neuroscience 14 (7): 889-895. July 2011

Philosophical Transactions of the Royal Society of London Series B Biological Sciences

Active perception during angiogenesis: filopodia speed up Notch selection of tip cells in silico and in vivo.
Zakirov, B., Charalambous, G., Thuret, R., Aspalter, I.M., Van-Vuuren, K., Mead, T., Harrington, K., Regan, E.R., Herbert, S.P. and Bentley, K.
Philosophical Transactions of the Royal Society of London Series B Biological Sciences 376 (1821): 20190753. 29 March 2021

Proceedings of the Conference on Genetic and Evolutionary Computation

Genetically-regulated neuromodulation facilitates multi-task reinforcement learning.
Cussat-Blanc, S. and Harrington, K.I.S.
In: GECCO '15: Genetic and Evolutionary Computation Conference, Jul 2015, Madrid, Spain. July 2015

Autoconstructive evolution for structural problems.
Harrington, K.I., Spector, L., Pollack, J.B. and O'Reilly, U.M.
In: GECCO '12: Genetic and Evolutionary Computation Conference, 7-11 Jul 2012, Philadelphia, PA, USA. July 2012

Tag-based modularity in tree-based genetic programming.
Spector, L., Harrington, K. and Helmuth, T.
In: GECCO '12: Genetic and Evolutionary Computation Conference, 7-11 Jul 2012, Philadelphia, PA, USA. July 2012

The effects of tags on the evolution of honest signaling.
Ozisik, A.P. and Harrington, K.I.
In: GECCO '12: Genetic and Evolutionary Computation Conference, 7-11 Jul 2012, Philadelphia, PA, USA. July 2012

Fecundity and selectivity in evolutionary computation.
Spector, L., Helmuth, T. and Harrington, K.
In: GECCO '11: Genetic and Evolutionary Computation Conference, 12-16 Jul 2011, Dublin, Ireland. July 2011

Tag-based modules in genetic programming.
Spector, L., Martin, B., Harrington, K. and Helmuth, T.
In: GECCO '11: Genetic and Evolutionary Computation Conference, 12-16 Jul 2011, Dublin, Ireland. July 2011

Predicting reactions from amino acid sequences in S. cerevisiae: an evolutionary computation approach.
Harrington, K.
In: GECCO '07: Genetic and Evolutionary Computation Conference, 7-11 Jul 2007, London, UK. July 2007

Proceedings of the IEEE Annual Northeast Bioengineering Conference, NEBEC

Modelling nonlinear chemical oscillators with inhibitory coupling.
Gold, J., Wang, A., Girabawe, C., Harrington, K. and Fraden, S.
In: 2014 40th Annual Northeast Bioengineering Conference (NEBEC), 25-27 Apr 2014, Boston, MA, USA. 4 December 2014

Proceedings of the International Joint Conference on Neural Networks

Robot coverage control by evolved neuromodulation.
Harrington, K.I., Awa, E., Cussat-Blanc, S. and Pollack, J.
In: 2013 International Joint Conference on Neural Networks (IJCNN 2013), 4-9 Aug 2013, Dallas, TX, USA. 9 January 2014

Communicated somatic markers benefit both the individual and the species.
Harrington, K.I., Olsen, M.M. and Siegelmann, H. T.
In: 2011 International Joint Conference on Neural Networks (IJCNN 2011), 31 Jul - 5 Aug 2011, San Jose, CA, USA. 3 October 2011

Quarterly Review of Biology

The digital cell: cell biology as a data science by Stephen J. Royle.
Harrington, K.I.S.
University of Chicago Press / Stony Brook University. March 2021

Theoretical Computer Science

A circuit basis for morphogenesis.
Harrington, K.I.S.
Theoretical Computer Science 633 : 28-36. 20 June 2016

bioRxiv

A connectome of the male Drosophila ventral nerve cord.
Takemura, S.Y., Hayworth, K.J., Huang, G.B., Januszewski, M., Lu, Z., Marin, E.C., Preibisch, S., Xu, C.S., Bogovic, J., Champion, A.S., Cheong, H.S.J., Costa, M., Eichler, K., Katz, W., Knecht, C., Li, F., Morris, B.J., Ordish, C., Rivlin, P.K., Schlegel, P., Shinomiya, K., Sturner, T., Zhao, T., Badalamente, G., Bailey, D., Brooks, P., Canino, B.S., Clements, J., Cook, M., Duclos, O., Dunne, C.R., Fairbanks, K., Fang, S., Finley-May, S., Francis, A., George, R., Gkantia, M., Harrington, K., Hopkins, G.P., Hsu, J., Hubbard, P.M., Javier, A., Kainmueller, D., Korff, W., Kovalyak, J., Krzeminski, D., Lauchie, S.A., Lohff, A., Maldonado, C., Manley, E.A., Mooney, C., Neace, E., Nichols, M., Ogundeyi, O., Okeoma, N., Paterson, T., Phillips, E., Phillips, E.M., Ribeiro, C., Ryan, S.M., Rymer, J.T., Scott, A.K., Scott, A.L., Shepherd, D., Shinomiya, A., Smith, C., Smith, N., Suleiman, A., Takemura, S., Talebi, I., Tamimi, I.F.M., Trautman, E.T., Umayam, L., Walsh, J.J., Yang, T., Rubin, G.M., Scheffer, L.K., Funke, J., Saalfeld, S., Hess, H.F., Plaza, S.M., Card, G.M., Jefferis, G.S.X.E. and Berg, S.
bioRxiv : 2023.06.05.543757. 6 June 2023

eLife

Mouse retinal cell behaviour in space and time using light sheet fluorescence microscopy.
Prahst, C., Ashrafzadeh, P., Mead, T., Figueiredo, A., Chang, K., Richardson, D., Venkaraman, L., Richards, M., Russo, A.M., Harrington, K., Ouarné, M., Pena, A., Chen, J.X., Claesson-Welsh, L., Cho, K.S., Franco, C.A. and Bentley, K.
eLife 9 : e49779. 19 February 2020

Temporal modulation of collective cell behavior controls vascular network topology.
Kur, E., Kim, J., Tata, A., Comin, C.H., Harrington, K.I., Costa, L.d.F., Bentley, K. and Gu, C.
eLife 5 : e13212. 24 February 2016