Browse by Research Team

AAAI Spring Symposium

Emotions for Strategic Real-Time Systems.
Olsen, M.M. and 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. and 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. and 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. and 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. and 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. and 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. and 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. and 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. and Dubois, Z. and Smith, J. and 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. and Dittapongpitch, S. and 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. and Günther, U. and Modes, C.D. and 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. and Cole, B. and Giese, W. and Baumann, E. and Claeys, A. and Vanmechelen, M. and Decraene, B. and Derweduwe, M. and Dubroja Lakic, N. and Shankar, G. and Nagathihalli Kantharaju, M. and Albrecht, J.P. and Geudens, I. and Stanchi, F. and Ligon, K.L. and Boeckx, B. and Lambrechts, D. and Harrington, K. and Van Den Bosch, L. and De Vleeschouwer, S. and 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. and Harrington, K. and Hartmann, K. and Hethke, M. and Rintelen, T. and Zhang, H. and 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. and Gold, J.M. and Tompkins, N. and Heymann, M. and 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. and Dhammapala, R. and Harrington, K. and 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. and Dhammapala, R. and Harrington, K. and Lamastro, R. and 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. and Nagathihalli Kantharaju, M. and Haruvi, R. and 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. and Deschamps, J. and Schmied, C. and Pietzsch, T. and Schmidt, D. and Tomancak, P. and 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. and 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. and 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. and Harrington, K.I.S. and 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. and Marangoni, P. and Zilionis, R. and Wan, M. and Wald, T. and Hu, J.K. and Kawaguchi, K. and Castillo-Azofeifa, D. and Epstein, L. and Harrington, K. and Pagella, P. and Mitsiadis, T. and Siebel, C.W. and 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. and Harrington, K.I. and Lovegrove, H.E. and Page, D.J. and Chakravartula, S. and Bentley, K. and Herbert, S.P.
Nature Cell Biology 18 (12): 1292-1301. December 2016

Nature Methods

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

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

Nature Microbiology

Modelling viral encephalitis caused by herpes simplex virus 1 infection in cerebral organoids.
Rybak-Wolf, A. and Wyler, E. and Pentimalli, T.M. and Legnini, I. and Oliveras Martinez, A. and Glažar, P. and Loewa, A. and Kim, S.J. and Kaufer, B.B. and Woehler, A. and Landthaler, M. and Rajewsky, N.
Nature Microbiology 8 (7): 1252-1266. July 2023

Nature Neuroscience

Imaging analysis of clock neurons reveals light buffers the wake-promoting effect of dopamine.
Shang, Y. and Haynes, P. and Pírez, N. and Harrington, K.I. and Guo, F. and Pollack, J. and Hong, P. and 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. and Charalambous, G. and Thuret, R. and Aspalter, I.M. and Van-Vuuren, K. and Mead, T. and Harrington, K. and Regan, E.R. and 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. and Spector, L. and 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. and 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. and 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. and Martin, B. and 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. and Wang, A. and Girabawe, C. and 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. and Awa, E. and 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. and 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

Theoretical Computer Science

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

bioRxiv

PyZebraScope: an open-source platform for brain-wide neural activity imaging in zebrafish.
Barbara, R. and Nagathihalli Kantharaju, M. and Haruvi, R. and Harrington, K. and Kawashima, T.
bioRxiv : bioRxiv. 15 February 2022

RS-FISH: Precise, interactive, fast, and scalable FISH spot detection.
Bahry, E. and Breimann, L. and Zouinkhi, M. and Epstein, L. and Kolyvanov, K. and Long, X. and Harrington, K.I.S. and Lionnet, T. and Preibisch, S.
bioRxiv : 2021.03.09.434205v2. 18 October 2021

Complex population dynamics in a spatial microbial ecosystem with Physarum polycephalum.
Epstein, L. and Dubois, Z. and Smith, J. and Lee, Y. and Harrington, K.
bioRxiv : 2021.03.14.435300. 15 March 2021

eLife

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

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