Kyle Harrington

about research software teaching Kyle I. S. Harrington, Ph.D.,
Group Leader,
Image Data Analysis,
Max Delbrueck Center for Molecular Medicine in the Helmholtz Association,
Berlin, Germany

1 Indices and Databases

2 Journal Articles

21.  Epstein, L., Dubois, Z., Smith, J., Lee, Y., & Harrington, K. (2021). Complex population dynamics in a spatial microbial ecosystem with Physarum polycephalum. BioSystems, 208, 104483.
20.  Bahry, E., Breimann, L., Epstein, L., Kolyvanov, K., Harrington, K. I.*, Lionnet, T.*, and Preibisch, S.* (2021). RS-FISH: Precise, interactive and scalable smFISH spot detection using Radial Symmetry. bioRxiv.
​* Co-corresponding authors
19.  Arshadi, C., Günther, U., Eddison, M., Harrington, K. I., and Ferreira, T. A. (2021). SNT: a unifying toolbox for quantification of neuronal anatomy. Nature Methods, 18, 374–377.
18.  Zakirov, B., Charalambous, G., Thuret, R., Aspalter, I. M., Van-Vuuren, K., Mead, T., Harrington, K., Regan, E., Herbert, S., and Bentley, K. (2021). Active perception during angiogenesis: filopodia speed up Notch selection of tip cells in silico and in vivo. Philosophical Transactions of the Royal Society B, 376(1821), 20190753.
17.  Prahst, C., Ashrafzadeh, P., Mead, T., Figueiredo, A., Chang, K., Richardson, D., Venkaraman, L., Richards, M., Russo, A., Harrington, K., Ouarne, M., Pena, A., Chen, D., Claesson-Welsh, L., Cho, K., Franco, C., and Bentley, K. (2020). Mouse retinal cell behaviour in space and time using light sheet fluorescence microscopy. Elife, 9, e49779..
16.  Sharir, A., Marangoni, P., Wan, M., Zilionis, R., Wald, T., Hu, J., Kawaguchi, K., Epstein, L., Harrington, K., Pagella, P., Mitsiadis, T., Siebel, C., Klein, A. M. and Klein, O, D., (2019) "A large pool of actively cycling progenitors orchestrates self-renewal and injury repair
of an ectodermal appendage." In Nature Cell Biology.
15.  Daetwyler, S., Günther, U., Modes, C.D., Harrington, K.* and Huisken, J.*, (2019). Multi-sample SPIM image acquisition, processing and analysis of vascular growth in zebrafish. In Development 146: dev173757. pdf
​* Co-corresponding authors
14.  Harrington, K., and Pollack, J., (2019) "Escalation of Memory Length in Finite Populations". In Artificial Life 25(1), pp. 22-32. (preprint bioRxiv 130583, pdf)
13.  Crawford-Young, S., Dittapongpitch, S., Gordon, R., Harrington, K., (2018) "Acquisition
and reconstruction of 4D surfaces of axolotl embryos with the flipping stage robotic microscope". In Biosystems, Vol. 173, pp. 214-220.
12.  Cussat-Blanc, S., Harrington, K., and Banzhaf, W., (2018) "Artificial Gene Regulatory Networks—A Review". In Artificial Life 24(4), pp. 296-328.
11.  Harrington, K., C. Rueden and K. Eliceiri, (2017) "FunImageJ: a Lisp framework for scientific image processing". In Bioinformatics, btx710.  pdf
10.  Harrington, K. I. S, (2016) "Wolfgang Banzhaf and Lidia Yamamoto: Artificial Chemistries". In Genetic Programming and Evolvable Machines, Vol. 17, pp. 317-319.  pdf
9.  Wang, A. L., J. M. Gold, N. Tompkins, M. Heymann, K. I. Harrington, and S. Fraden, (2016) "Configurable NOR Gate Arrays from Belousov-Zhabotinsky Micro-droplets". In European Physics Journal: Special Topics, Vol. 225, no. 1, pp. 211-227.  pdf
8.  Costa G.*, K. Harrington*, H. Lovegrove*, D. Page, S. Chakravartula, K. Bentley, S. Herbert, (2016) "Asymmetric division coordinates collective cell migration in angiogenesis". In Nature Cell Biology, Vol. 18, pp. 1292–1301.  
\* Joint primary authors
7.  Kur, E., Kim, J., Tata, A., Comin, C. H., Harrington, K. I., Costa, L, Bentley, K., Gu, C., (2016) "Temporal modulation of collective cell behavior controls vascular network topology". In eLife, Vol. 5, pp. e13212.  pdf
6.  Harrington, K. I. S., (2016) "A Circuit Basis for Morphogenesis". In Theoretical Computer Science, Vol. 633, pp. 28-36.  pdf
5.  Cussat-Blanc, S., K. Harrington, and J. Pollack, (2015) "Gene Regulatory Network Evolution Through Augmenting Topologies". In IEEE Transactions on Evolutionary Computation, pp. 823-837.  pdf
4.  Harrington, K., and Sanchez, A., (2014) "Eco-evolutionary dynamics of complex social strategies in microbial communities". In Communicative and Integrative Biology, Vol. 7,
pp. e28230.  pdf
3.  Shang, Y., P. Haynes, N. Pírez, K. Harrington, F. Guo, J. Pollack, P. Hong, L. Griffith, and M. Rosbash, (2011) "Imaging analysis of clock neurons: light buffers the wake-promoting effect of dopamine". In Nature Neuroscience, Vol. 14, no. 7, pp. 889-895.  pdf
2.  Olsen, M., K. Harrington, and H. Siegelmann, (2010) "Conspecific Emotional Cooperation Biases Population Dynamics: A Cellular Automata Approach". In International Journal of Natural Computing Research, Vol. 1, no. 3, pp. 51-65.  pdf
1.   Spector, L., J. Klein, and K. Harrington, (2005) "Selection Songs: Evolutionary Music Computation". In YLEM Journal, Vol. 25, no. 6 & 8, pp. 24-26.  pdf

3 Peer-reviewed conference and workshop papers

20.  Günther, U., Harrington, K. I., Dachselt, R., & Sbalzarini, I. F. (2020, August). Bionic Tracking: Using Eye Tracking to Track Biological Cells in Virtual Reality. In European Conference on Computer Vision (pp. 280-297). Springer, Cham.
19.  Günther, U., and Harrington, K.I., 2020. Tales from the Trenches: Developing a new 3D viewer for the ImageJ community. In VisGap/Eurographics and Eurovis.
18.  Günther, U., Pietzsch, T., Gupta, A., Harrington, K.I., Tomancak, P., Gumhold, S. and
Sbalzarini, I.F., 2019. scenery–Flexible Virtual Reality Visualisation on the Java VM. 2019 IEEE Visualization Conference (VIS), Vancouver, BC, Canada, 2019, pp. 1-5.
17.  Wilson, D. G., Harrington, K., Cussat-Blanc, S., and Luga, H. (2018). "Evolving Differentiable Gene Regulatory Networks". In Parallel Problem Solving from Nature: PPSN XV, Evolutionary Machine Learning workshop, arxiv.org/abs/1807.05948. pdf
16.  Harrington, K., and L. Magbunduku, (2017) "Competitive dynamics in eco-evolutionary genetically-regulated swarms". In Proceedings of the 14th European Conference on Artificial Life ECAL 2017, pp. 190-197.  pdf
15.  Cussat-Blanc, S. and K. Harrington, (2015) "Genetically-regulated Neuromodulation Facilitates Multi-Task Reinforcement Learning". In Proceedings of the Genetic and Evolutionary Computation Conference, pp. 551-558.  
14.  Lowell, J., K. Harrington, and J. Pollack, (2014) "The Resilience of a Swarm Ecosystem Under Environmental Variation". In Proceedings of Artificial Life XIV, pp. 827-834.  pdf 13.  Gold, J., A. Wang, and K. Harrington, (2014) "Feedback Control of Evolving Swarms". In Proceedings of Artificial Life XIV, pp. 884-891.  pdf
12.  Bentley, K., K. Harrington, and E. R. Regan, (2014) "Can active perception generate bistability? Heterogeneous collective dynamics and vascular patterning". In Proceedings of Artificial Life XIV, pp. 328-335.  pdf
11.  Harrington, K., J. Freeman, and J. Pollack, (2014) "Coevolution in Hide and Seek: Camouflage and Vision". In Proceedings of Artificial Life XIV, pp. 25-32.  pdf
10.  Harrington, K., E. Awa, S. Cussat-Blanc, and J. Pollack, (2013) "Robot Coverage Control by Evolved Neuromodulation". In Proceedings of the International Joint Conference on Neural Networks, pp. 543-550.  pdf
9.  Ozisik, A. P., Harrington, K. I., (2012) "The Effect of Tags on the Evolution of Honest Signaling". In Proceedings of the Genetic and Evolutionary Computation Conference Companion,
pp. 345-352.  pdf
8.  Harrington, K. I., L. Spector, J. B. Pollack, and U.M. O'Reilly, (2012) "Autoconstructive Evolution for Structural Problems". In Proceedings of the fourteenth international conference on
Genetic and evolutionary computation conference companion, pp. 75-82.  pdf
7.  Spector, L., K. Harrington, and T. Helmuth, (2012) "Tag-based Modularity in Tree-based Genetic Programming". In Proceedings of the Genetic and Evolutionary Computation Conference,
pp. 815-822.  pdf
6.  Harrington, K. I., A. P. Ozisik, and J. Pollack, (2012) "The Effects of Finite Populations and Selection on the Emergence of Signaling". In Proceedings of Artificial Life XIII, pp. 194-201.  pdf
5.  Harrington, K., E. Tosch, L. Spector, and J. Pollack, (2011) "Compositional Autoconstructive Dynamics". In Unifying Themes in Complex Systems Volume VIII: Proceedings of the Eighth International Conference on Complex Systems, pp. 856-870.  pdf
4.  Spector, L., B. Martin, K. Harrington, and T. Helmuth, (2011) "Tag-Based Modules in Genetic
Programming". In Proceedings of the Genetic and Evolutionary Computation Conference, pp. 1419-1426.  pdf
3.  Harrington, K., M. Olsen, and H. Siegelmann, (2011) "Communicated Somatic Markers Benefit the Individual and the Species". In Proceedings of the International Joint Conference on Neural Networks, pp. 3272-3278.  pdf
2.  Olsen, M., K. Harrington. and H. Siegelmann, (2011) "Computational Emotions in a Population
Dynamics Cellular Automata Encourage Collective Behavior". In Unifying Themes in Complex Systems Volume VIII: Proceedings of the Eighth International Conference on Complex Systems, pp. 196-210.  pdf
1.  Olsen, M., K. Harrington, and H. Siegelmann, (2008) "Emotions for Strategic Real-Time Systems". In AAAI Spring Symposium on Emotion, Personality, and Social Behavior, pp. 104-110.  pdf

4 Preprints

1.  Wilson, D.G., Cussat-Blanc, S., Luga, H. and Harrington, K.,
"Neuromodulated Learning in Deep Neural Networks." arXiv preprint
arXiv:1812.03365. pdf

5 Book chapters

3.  Spector, L., K. Harrington, B. Martin, and T. Helmuth, (2011) "What's in an Evolved Name? The Evolution of Modularity via Tag-Based Reference". In Genetic Programming Theory and Practice IX, edited by Riolo, R., E. Vladislavleva, and J.H. Moore, pp. 1-16.  pdf
2.  Harrington, K., and H. Siegelmann, (2007) "Adaptive Multi-modal Sensors". In 50 Years of Artificial Intelligence, edited by Lungarella, M., F. Iida, J. Bongard, and R. Pfeifer, pp. 164-173.  pdf
1.  Harrington, K., and G. Trajkovski, (2006) "On an Evolutionary Approach to Language". In An Imitation-Based Approach to Modeling Homogenous Agents Societies, edited by Trajkovski, G., pp. 212-229.  

6 Short papers and abstracts

15.   Cahill, L. C., Rosen, M., Yoshitake, T., Harrington, K., Law, P. T., Fujimoto, J. G., Rosen, S., (2019) "Maximizing Data Retrieval From Renal Biopsy Tissue Using Nonlinear Microscopy: Examining the Paraffin Block After Processing". In Annual Meeting of United States and Canadian Academy of Pathology.
14.  Magbunduku, L., Harrington, K., (2017) "Dynamic Habitat Construction Through Evolving 3D Swarms". In Living Architectures Workshop at the European Conference on Artificial
Life,  doi
13.  Faulkner-Jones, B. E., Rosen, D., Rosen, S., Harrington, K., Law, C., (2016) "Maximizing Information from the Renal Biopsy: Computer-Generated Three-Dimensional Constructs". In Laboratory Investigation, pp. 405a.  
12.  Cussat-Blanc, S., K. Harrington, and J. Pollack, (2015) "Gene Regulatory Network Evolution Through Augmenting Topologies". In Proceedings of GECCO 2015, Hot-off-the-press., in
press.  
11.  Harrington, K I S, T. Stiles, L. Venkatraman, C. Prahst, K. Bentley, (2015) "Functional Image Processing in ImageJ/FIJI". In Proceedings of Bioimage Informatics, in press.  pdf 10.  Harrington, K I S, B. Faulkner-Jones, K. Bentley, S. Rosen, (2015) "Automated Quantification of Renal Microvascular Abnormalities: A Novel Computational Mapping Approach". In Proceedings of the American Society of Nephrology, in press.  
9.  Harrington, K I S, C. Prahst, C. Yoon, B. Lavina Siemsen, K. Bentley, (2015) "Quantitative Image Analysis Reveals Multiscale Patterns in Vascular Networks". In Gordon Research Conference
on Angiogenesis, pp. .  
8.  Gold, J., A. Wang, C. Girabawe, K. Harrington, and S. Fraden, (2014) "Modelling Nonlinear Chemical Oscillators with Inhibitory Coupling". In Proceedings of the Northeast Bioengineering Conference, pp. 1-2.  pdf
7.  Harrington, K. I., M. Olsen, and H. Siegelmann, (2012) "Computational Neuroecology of Communicated Somatic Markers". In Proceedings of Artificial Life XIII, pp. 555-556.  pdf
6.  Spector, L., T. Helmuth, and K. Harrington, (2011) "Fecundity and Selectivity in Evolutionary Computation". In Proceedings of the 13th annual conference companion on Genetic and evolutionary computation, pp. 129-130.  pdf
5.  Harrington, K. I., and J. B. Pollack, (2010) "Robot Phylogenetics". In Proceedings of the 12th annual conference companion on Genetic and evolutionary computation, pp. 2077-2078.  pdf
4.  Heymann, M., K. I. Harrington, J. Pollack, and S. Fraden, (2010) "En route to signal inversion in chemical computing". In Proceedings of Artificial Life XII, pp. 166-167.  pdf
3.  Harrington, K. I., (2007) "Predicting Reactions from Amino Acid Sequences in S. cerevisiae: an Evolutionary Computation Approach". In Proceedings of the 2007 GECCO conference companion on Genetic and evolutionary computation, pp. 2725-2728.  
2.  Harrington, K., and H. Siegelmann, (2006) "Adaptive Multi-modal Sensors". In Proceedings of the 50th Anniversary Summit of Artificial Intelligence, pp. 163-164.  
1.  Spector, L., J. Klein, K. Harrington, and R. Coppinger, (2005) "Teaching the Evolution of Behavior with SuperDuperWalker". In Proceedings of the 12th International Conference on Artificial Intelligence in Education, pp. 923-925.  pdf

7 Other publications

2.  Harrington, K. I. S, (2014) "Escalation of Coevolutionary Arms Races". In Department of Computer Science, Brandeis University.  pdf
1.  Harrington, K., and J. Pollack, (2011) "Zipper-based Meta-Genetic Programming". In Technical Report Brandeis University CS-11-275.  pdf

8 Talks

41.  Harrington, K I S, (2021) "Algorithms and computational tools for image data analysis across scales". iNAMES Graduate Program, Max Delbrueck Center for Molecular Medicine, Berlin, Germany  
40.  Harrington, K I S, (2021) "Algorithms and computational tools for image data analysis across scales (keynote)". Ultrahigh Field Magnetic Resonance Symposium, Berlin, Germany  
39.  Harrington, K I S, (2021) "Image data solutions across biological scales". Max Delbrueck Center for Molecular Medicine, Berlin, Germany  
38.  Harrington, K I S, (2021) "Image Data Solutions for Systems Biology and Beyond (invited)". Center for Advanced Systems Understanding (CASUS), Goerliz, Germany  
37.  Harrington, K I S, (2020) "Emergence of animal conflict from neurodevelopmental wiring: an artificial life model". J-theory, Janelia Research Campus, Howard Hughes Medical Institute   36.  Harrington, K I S, (2019) "Multiscale modeling and visualization with biological images". Center for Cell Analysis and Modeling Seminar, UConn, Farmington, CT
35.  Harrington, K I S, (2019) "Modeling from Morphology to Molecules: Blood Vessels to Synaptic Plasticity". J-theory, Janelia Research Campus, Howard Hughes Medical Institute  
34.  Harrington, K I S, (2019) "The Artificial Life of Image-based Modeling for Morphogenesis". Image-based Modeling and Simulation 2019  
33.  Harrington, K I S, (2018) "Bringing biological images to life: modeling and visualization". Wisconsin Institute for Discovery  
32.  Harrington, K I S, (2018) "Evolution of genetically-regulated swarming strategies". HHMI Collective Computation Conference  
31.  Harrington, K I S, (2017) "Image-based Modeling". Data Science Day, Washington State University, Pullman, WA  
30.  Harrington, K I S, (2017) "Functional Scientific Programming: Bringing Images to Life". BosLab, Somerville, MA  
29.  Harrington, K I S, (2017) "Image-based Computational Biology". IBEST, UIdaho, Moscow, ID  
28.  Harrington, K I S, (2017) "Fishing is in the Blood: Modeling, Quantification and Visualization of Zebrafish Vascular Development". Max Planck Institute for Molecular Cell Biology and Genetics  
27.  Harrington, K I S, (2017) "Computational Modeling of Physical Systems: from Chemistries to
Organisms (invited)". IRIT Symposium, University of Toulouse  
26.  Harrington, K I S, (2017) "Machine Learning (invited)". 2IS Innovative Information Systems, University of Toulouse  
25.  Harrington, K I S, (2017) "Escalation of Complexity through Competition". BEACON Institute, Michigan State University, East Lansing, MI & UIdaho, Moscow, ID  
24.  Harrington, K I S, (2017) "Image-based Modeling for Biological Systems (invited)". 2017 NIH IDeA Western Regional Conference  
23.  Harrington, K I S, (2017) "Biological Image Analysis using the ImageJ/Fiji Software Ecosystem". ImageXD, University of Washington, Seattle, WA
22.  Harrington, K I S, (2017) "Developing Computational Models with Biological Images". Mathematical Biology Seminar, Washington State University, Pullman, WA  
21.  Harrington, K I S, (2016) "Escalation in the Complexity of Cooperative Strategies".
University of Idaho, Institute for Bioinformatics and Evolutionary Studies, Moscow, ID  
20.  Harrington, K I S, (2016) "Virtual Morphogenesis: Toward Growing Models with Images". University of Wisconsin, Laboratory for Optical and Computational Instrumentation, Madison, WI  
19.  Harrington, K I S, (2016) "Virtual Morphogenesis: Directing Pattern Formation". University of Idaho, Center for Modeling Complex Interactions, Moscow, ID  
18.  Harrington, K I S, (2016) "Virtualization and Simulation for Biology and Evolution". Idaho EPSCoR Annual Meeting, Coeur d'Alene, ID  
17.  Harrington, K I S, (2015) "Scientific Computing in Clojure". Clojure/Conj 2015, Philadelphia, PA  
16.  Harrington, K I S, T. Stiles, L. Venkatraman, C. Prahst, K. Bentley, (2015) "Functional Image Processing in ImageJ/FIJI". Bioimage Informatics 2015, National Institute of Standards and Technology, Gaithersburg, MD  
15.  Harrington, K., (2014) "Evolution, the First Programmer". HHMI Interfaces Award Lecture Series, Waltham, MA  
14.  Harrington, K., A. Brilot, (2014) "Bridging Structure and Evolution". HHMI Interfaces Award Lecture Series, Waltham, MA  
13.  Harrington, K., J. Freeman, J. Pollack, (2014) "Coevolution in Hide and Seek: Camouflage and Vision". ALife 14, New York, NY  
12.  Harrington, K., E. Awa, S. Cussat-Blanc, J. Pollack, (2013) "Robot Coverage Control by Evolved Neuromodulation". IJCNN, Dallas, TX  
11.  Harrington, K., J. Chin, (2013) "Embracing the Inner Cyborg: the Computational Immunology of Organ Transplantation". Quantitative Biology Graduate Talks, Waltham, MA  
10.  Ozisik, A. P., Harrington, K. I., (2012) "The Effect of Tags on the Evolution of Honest Signaling". GECCO-2012, Philadelphia, PA  
9.  Harrington, K. I., L. Spector, J. B. Pollack, U.M. O'Reilly, (2012) "Autoconstructive Evolution for Structural Problems". GECCO-2012, Philadelphia, PA  
8.  Harrington, K., M. Olsen, H. Siegelmann, (2011) "Communicated Somatic Markers Benefit the Individual and the Species". IJCNN, San Jose, CA  
7.  Harrington, K., (2011) "Evolving Evolution". Quantitative Biology Graduate Talks, Waltham, MA  
6.  Harrington, K., (2011) "Evolving Evolution: part 1, Variation". ALFA Group, MIT, Cambridge, MA  
5.  Harrington, K., E. Tosch, L. Spector, J. Pollack, (2011) "Compositional Autoconstructive
Dynamics". ICCS, Quincy, MA  
4.  Harrington, K. I., J. B. Pollack, (2010) "Robot Phylogenetics". GECCO-2010, Portland, OR   3.  Harrington, K., (2010) "Attention to Details: from a Single-Cell to a Multi-cellular
Observer". Boston College, Boston, MA  
2.  Harrington, K., (2008) "Artificial Embryogenesis". Greythumb Artificial Life Group, Cambridge, MA  
1.  Harrington, K., (2007) "Predicting Reactions from Amino Acid
Sequences in S. cerevisiae: an Evolutionary Computation Approach".
GECCO-2007, London, UK  

9 Posters

12.  Harrington, K I S, B. E. Faulkner-Jones, K. Bentley, S. Rosen, (2015) "Automated quantification of renal microvascular abnormalities: A novel computational mapping approach". American Society of Nephrology 2015, San Diego, CA  
11.  Harrington, K I S, C. Prahst, C. Yoon, B. Lavina Siemsen, K. Bentley, (2015) "Quantitative Image Analysis Reveals Multiscale Patterns in Vascular Networks". Gordon Research Conference on
Angiogenesis  
10.  Lowell, J., K. Harrington, J. Pollack, (2014) "The Resilience of a Swarm Ecosystem Under Environmental Variation". ALife 14, New York, NY  
9.  Gold, J., A. Wang, C. Girabawe, K. Harrington, S. Fraden, (2014) "Modelling Nonlinear Chemical Oscillators with Inhibitory Coupling". Northeast Bioengineering Conference, Boston, MA  
8.  Gold, J., A. Wang, K. Harrington, (2014) "Feedback Control of Evolving Swarms". ALife 14, New York, NY   7.  Chin, J., K. Harrington, (2013) "Evolutionary Pressures of Dynamic Peptide Fragments on Immunological Selectivity". Brandeis Scifest, Waltham, MA  
6.  Harrington, K., (2013) "Brevis, a Functional Artificial Life Simulator". Volen Complex Systems Retreat, Provincetown, MA  
5.  Gold, J., A. Wang, K. Harrington, S. Fraden, J. Pollack, (2013) "Computing with Nonlinear Chemical Oscillators at the Microfluidic Scale". Brandeis Scifest, Waltham, MA  
4.  Bardasu, A., K. Harrington, (2013) "Coevolving Fitness Predictors for Pairwise Games". Brandeis Scifest, Waltham, MA  
3.  Harrington, K., M. Olsen, H. Siegelmann, (2012) "Computational Neuroecology of Communicated Somatic Markers". ALife 13, E. Lansing, MI  
2.  Harrington, K., A. P. Ozisik, J. Pollack, (2012) "The Effects of Finite Populations and Selection on the Emergence of Signaling". ALife 13, E. Lansing, MI  
1.  Harrington, K., H. Siegelmann, (2006) "Adaptive Multi-modal Sensors". Monte Verita, Switzerland  

1

Footnotes:

Author: Harrington

Created: 2021-11-28 Sun 14:45

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