Article
Polarity-JaM: an image analysis toolbox for cell polarity, junction and morphology quantification.
Giese, W. 
ORCID: https://orcid.org/0000-0003-0872-0929, Albrecht, J.P. ORCID: https://orcid.org/0000-0002-3792-9695, Oppenheim, O. ORCID: https://orcid.org/0000-0002-5299-3193, Akmeriç, E.B. ORCID: https://orcid.org/0000-0003-4463-8017, Kraxner, J. ORCID: https://orcid.org/0000-0002-3515-7468, Schmidt, D. ORCID: https://orcid.org/0000-0002-8621-9438, Harrington, K.I. ORCID: https://orcid.org/0000-0002-7237-1973 and Gerhardt, H. ORCID: https://orcid.org/0000-0002-3030-0384
Nature Communications 16
(1): 1474.
8 February 2025
Single-cell profiling and zebrafish avatars reveal LGALS1 as immunomodulating target in glioblastoma.
Finotto, L. ORCID: https://orcid.org/0000-0002-4695-9343, Cole, B. ORCID: https://orcid.org/0000-0001-5899-5598, Giese, W. ORCID: https://orcid.org/0000-0003-0872-0929, Baumann, E. ORCID: https://orcid.org/0000-0002-7804-4885, Claeys, A., Vanmechelen, M. ORCID: https://orcid.org/0000-0002-8342-3150, Decraene, B. ORCID: https://orcid.org/0000-0002-2523-452X, Derweduwe, M. ORCID: https://orcid.org/0000-0002-4960-4847, Dubroja Lakic, N., Shankar, G., Nagathihalli Kantharaju, M., Albrecht, J.P. ORCID: https://orcid.org/0000-0002-3792-9695, Geudens, I. ORCID: https://orcid.org/0000-0003-3297-4208, Stanchi, F. ORCID: https://orcid.org/0000-0003-3393-2472, Ligon, K.L. ORCID: https://orcid.org/0000-0002-7733-600X, Boeckx, B. ORCID: https://orcid.org/0000-0002-0296-6680, Lambrechts, D. ORCID: https://orcid.org/0000-0002-3429-302X, Harrington, K. ORCID: https://orcid.org/0000-0002-7237-1973, Van Den Bosch, L. ORCID: https://orcid.org/0000-0003-0104-4067, De Vleeschouwer, S. ORCID: https://orcid.org/0000-0002-9576-9917, De Smet, F. ORCID: https://orcid.org/0000-0002-6669-3335 and Gerhardt, H. ORCID: https://orcid.org/0000-0002-3030-0384
EMBO Molecular Medicine 15
(11): e18144.
8 November 2023
Machine learning-based ozone and PM2.5 forecasting: application to multiple AQS sites in the Pacific Northwest.
Fan, K., Dhammapala, R., Harrington, K. ORCID: https://orcid.org/0000-0002-7237-1973, Lamb, B. and Lee, Y.
Frontiers in Big Data 6
: 1124148.
24 February 2023
RS-FISH: precise, interactive, fast, and scalable FISH spot detection.
Bahry, E. ORCID: https://orcid.org/0000-0002-6358-2576, Breimann, L. ORCID: https://orcid.org/0000-0001-7702-5749, Zouinkhi, M. ORCID: https://orcid.org/0000-0002-9441-2908, Epstein, L., Kolyvanov, K., Mamrak, N., King, B., Long, Xi, Harrington, K.I.S. ORCID: https://orcid.org/0000-0002-7237-1973, Lionnet, T. ORCID: https://orcid.org/0000-0003-1508-0202 and Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X
Nature Methods 19
(12): 1563-1567.
December 2022
PyZebraScope: an open-source platform for brain-wide neural activity imaging in zebrafish.
Barbara, R., Nagathihalli Kantharaju, M., Haruvi, R., Harrington, K. ORCID: https://orcid.org/0000-0002-7237-1973 and Kawashima, T.
Frontiers in Cell and Developmental Biology 10
: 875044.
19 May 2022
Development of a machine learning approach for local-scale ozone forecasting: application to Kennewick, WA.
Fan, K., Dhammapala, R., Harrington, K. ORCID: https://orcid.org/0000-0002-7237-1973, Lamastro, R., Lamb, B. and Lee, Y.
Frontiers in Big Data 5
: 781309.
10 February 2022
LABKIT: labeling and segmentation toolkit for big image data.
Arzt, M., Deschamps, J., Schmied, C., Pietzsch, T., Schmidt, D. ORCID: https://orcid.org/0000-0002-8621-9438, Tomancak, P., Haase, R. and Jug, F.
Frontiers in Computer Science 4
: 777728.
10 February 2022
Can fractal dimensions objectivize gastropod shell morphometrics? A case study from Lake Lugu (SW China).
Wiese, R. ORCID: https://orcid.org/0000-0003-4265-5454, Harrington, K. ORCID: https://orcid.org/0000-0002-7237-1973, Hartmann, K., Hethke, M., Rintelen, T., Zhang, H., Zhang, L.J. and Riedel, F.
Ecology and Evolution 12
(3): e8622.
February 2022
Complex population dynamics in a spatial microbial ecosystem with Physarum polycephalum.
Epstein, L., Dubois, Z., Smith, J., Lee, Y. ORCID: https://orcid.org/0000-0001-7478-2672 and Harrington, K. ORCID: https://orcid.org/0000-0002-7237-1973
Biosystems 208
: 104483.
October 2021
SNT: a unifying toolbox for quantification of neuronal anatomy.
Arshadi, C. ORCID: https://orcid.org/0000-0002-1885-080X, Günther, U. ORCID: https://orcid.org/0000-0002-1179-8228, Eddison, M., Harrington, K.I.S. ORCID: https://orcid.org/0000-0002-7237-1973 and Ferreira, T.A. ORCID: https://orcid.org/0000-0001-6866-1540
Nature Methods 18
: 374-377.
April 2021
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. ORCID: https://orcid.org/0000-0002-7237-1973, Regan, E.R., Herbert, S.P. and Bentley, K. ORCID: https://orcid.org/0000-0002-9391-659X
Philosophical Transactions of the Royal Society of London Series B Biological Sciences 376
(1821): 20190753.
29 March 2021
Bionic tracking: using eye tracking to track biological cells in virtual reality.
Günther, U. ORCID: https://orcid.org/0000-0002-1179-8228, Harrington, K.I.S. ORCID: https://orcid.org/0000-0002-7237-1973, Dachselt, R. ORCID: https://orcid.org/0000-0002-2176-876X and Sbalzarini, I.F. ORCID: https://orcid.org/0000-0003-4414-4340
Lecture Notes in Computer Science 12535
: 280-297.
2021
Mouse retinal cell behaviour in space and time using light sheet fluorescence microscopy.
Prahst, C., Ashrafzadeh, P., Mead, T. ORCID: https://orcid.org/0000-0003-2728-670X, Figueiredo, A., Chang, K., Richardson, D., Venkaraman, L., Richards, M., Russo, A.M., Harrington, K. ORCID: https://orcid.org/0000-0002-7237-1973, Ouarné, M., Pena, A., Chen, J.X. ORCID: https://orcid.org/0000-0001-6283-8843, Claesson-Welsh, L. ORCID: https://orcid.org/0000-0003-4275-2000, Cho, K.S. ORCID: https://orcid.org/0000-0003-4285-615X, Franco, C.A. ORCID: https://orcid.org/0000-0002-2861-3883 and Bentley, K. ORCID: https://orcid.org/0000-0002-9391-659X
eLife 9
: e49779.
19 February 2020
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. ORCID: https://orcid.org/0000-0002-7237-1973, Pagella, P. ORCID: https://orcid.org/0000-0001-6912-0957, Mitsiadis, T., Siebel, C.W., Klein, A.M. ORCID: https://orcid.org/0000-0001-8913-7879 and Klein, O.D. ORCID: https://orcid.org/0000-0002-6254-7082
Nature Cell Biology 21
(9): 1102-1112.
September 2019
Escalation of memory length in finite populations.
Harrington, K. ORCID: https://orcid.org/0000-0002-7237-1973 and Pollack, J.
Artificial Life 25
(1): 22-32.
2 April 2019
Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish.
Daetwyler, S. ORCID: https://orcid.org/0000-0002-7444-4734, Günther, U. ORCID: https://orcid.org/0000-0002-1179-8228, Modes, C.D. ORCID: https://orcid.org/0000-0001-9940-0730, Harrington, K. ORCID: https://orcid.org/0000-0002-7237-1973 and Huisken, J. ORCID: https://orcid.org/0000-0001-7250-3756
Development 146
(6): dev173757.
15 March 2019
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. ORCID: https://orcid.org/0000-0002-7237-1973
Biosystems 173
: 214-220.
November 2018
FunImageJ: a lisp framework for scientific image processing.
Harrington, K.I.S. ORCID: https://orcid.org/0000-0002-7237-1973, Rueden, C.T., Eliceiri, K.W. and
Bioinformatics 34
(5): 899-900.
1 March 2018
Asymmetric division coordinates collective cell migration in angiogenesis.
Costa, G., Harrington, K.I. ORCID: https://orcid.org/0000-0002-7237-1973, Lovegrove, H.E., Page, D.J., Chakravartula, S., Bentley, K. and Herbert, S.P.
Nature Cell Biology 18
(12): 1292-1301.
December 2016
A circuit basis for morphogenesis.
Harrington, K.I.S. ORCID: https://orcid.org/0000-0002-7237-1973
Theoretical Computer Science 633
: 28-36.
20 June 2016
Temporal modulation of collective cell behavior controls vascular network topology.
Kur, E., Kim, J., Tata, A., Comin, C.H., Harrington, K.I. ORCID: https://orcid.org/0000-0002-7237-1973, Costa, L.d.F., Bentley, K. and Gu, C. ORCID: https://orcid.org/0000-0002-4212-7232
eLife 5
: e13212.
24 February 2016
Configurable NOR gate arrays from Belousov-Zhabotinsky micro-droplets.
Wang, A.L., Gold, J.M., Tompkins, N., Heymann, M., Harrington, K.I. ORCID: https://orcid.org/0000-0002-7237-1973 and Fraden, S.
European Physical Journal Special Topics 225
(1): 211-227.
February 2016
Gene regulatory network evolution through augmenting topologies.
Cussat-Blanc, S., Harrington, K. ORCID: https://orcid.org/0000-0002-7237-1973 and Pollack, J.
IEEE Transactions on Evolutionary Computation 19
(6): 823-837.
December 2015
Eco-evolutionary dynamics of complex social strategies in microbial communities.
Harrington, K.I. ORCID: https://orcid.org/0000-0002-7237-1973 and Sanchez, A.
Communicative & Integrative Biology 7
(1): e28230.
25 February 2014
Imaging analysis of clock neurons reveals light buffers the wake-promoting effect of dopamine.
Shang, Y., Haynes, P., Pírez, N., Harrington, K.I. ORCID: https://orcid.org/0000-0002-7237-1973, Guo, F., Pollack, J., Hong, P., Griffith, L.C. and Rosbash, M.
Nature Neuroscience 14
(7): 889-895.
July 2011
Conspecific emotional cooperation biases population dynamics:a cellular automata approach.
Olsen, M.M., Harrington, K.I. ORCID: https://orcid.org/0000-0002-7237-1973 and Siegelmann, H.T.
International Journal of Natural Computing Research 1
(3): 51-65.
July 2010
Book Section
Mathematical and bioinformatic tools for cell tracking.
Hirsch, P. ORCID: https://orcid.org/0000-0002-2353-5310, Epstein, L. and Guignard, L. ORCID: https://orcid.org/0000-0002-3686-1385
In:
Cell Movement in Health and Disease.
Academic Press, London, 341-361.
ISBN 978-0-323-90195-6
2022
Adaptive multi-modal sensors.
Harrington, K.I. ORCID: https://orcid.org/0000-0002-7237-1973 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
Conference or Workshop Item
Genetically-regulated neuromodulation facilitates multi-task reinforcement learning.
Cussat-Blanc, S. and Harrington, K.I.S. ORCID: https://orcid.org/0000-0002-7237-1973
In: GECCO '15: Genetic and Evolutionary Computation Conference, Jul 2015, Madrid, Spain.
July 2015
Modelling nonlinear chemical oscillators with inhibitory coupling.
Gold, J., Wang, A., Girabawe, C., Harrington, K. ORCID: https://orcid.org/0000-0002-7237-1973 and Fraden, S.
In: 2014 40th Annual Northeast Bioengineering Conference (NEBEC), 25-27 Apr 2014, Boston, MA, USA.
4 December 2014
Can active perception generate bistability? Heterogeneous collective dynamics and vascular patterning.
Bentley, K., Harrington, K.I. ORCID: https://orcid.org/0000-0002-7237-1973 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. ORCID: https://orcid.org/0000-0002-7237-1973, 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. ORCID: https://orcid.org/0000-0002-7237-1973
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. ORCID: https://orcid.org/0000-0002-7237-1973 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
Robot coverage control by evolved neuromodulation.
Harrington, K.I. ORCID: https://orcid.org/0000-0002-7237-1973, 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
Autoconstructive evolution for structural problems.
Harrington, K.I. ORCID: https://orcid.org/0000-0002-7237-1973, 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. ORCID: https://orcid.org/0000-0002-7237-1973 and Helmuth, T.
In: GECCO '12: Genetic and Evolutionary Computation Conference, 7-11 Jul 2012, Philadelphia, PA, USA.
July 2012
The effects of finite populations and selection on the emergence of signaling.
Harrington, K.I. ORCID: https://orcid.org/0000-0002-7237-1973, 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
The effects of tags on the evolution of honest signaling.
Ozisik, A.P. and Harrington, K.I. ORCID: https://orcid.org/0000-0002-7237-1973
In: GECCO '12: Genetic and Evolutionary Computation Conference, 7-11 Jul 2012, Philadelphia, PA, USA.
July 2012
Communicated somatic markers benefit both the individual and the species.
Harrington, K.I. ORCID: https://orcid.org/0000-0002-7237-1973, 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
Fecundity and selectivity in evolutionary computation.
Spector, L., Helmuth, T. and Harrington, K. ORCID: https://orcid.org/0000-0002-7237-1973
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. ORCID: https://orcid.org/0000-0002-7237-1973 and Helmuth, T.
In: GECCO '11: Genetic and Evolutionary Computation Conference, 12-16 Jul 2011, Dublin, Ireland.
July 2011
Emotions for Strategic Real-Time Systems.
Olsen, M.M., Harrington, K. ORCID: https://orcid.org/0000-0002-7237-1973 and Siegelmann, H.T.
In: 2008 AAAI Spring Symposium, 26-28 Mar 2008, Stanford, CA, USA.
2008
Predicting reactions from amino acid sequences in S. cerevisiae: an evolutionary computation approach.
Harrington, K. ORCID: https://orcid.org/0000-0002-7237-1973
In: GECCO '07: Genetic and Evolutionary Computation Conference, 7-11 Jul 2007, London, UK.
July 2007
Review
Artificial gene regulatory networks-a review.
Cussat-Blanc, S., Harrington, K. ORCID: https://orcid.org/0000-0002-7237-1973 and Banzhaf, W.
Artificial Life 24
(4): 296-328.
2018
Other
The digital cell: cell biology as a data science by Stephen J. Royle.
Harrington, K.I.S. ORCID: https://orcid.org/0000-0002-7237-1973
University of Chicago Press / Stony Brook University.
March 2021
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