Publications

Below is a complete list of my publications. For most of them a pre-print is available for download (as PDF). Click on the icons provided with each title to:
    read the abstract;     download a PDF version;     follow the link to the online article.
You can also download my list of publications as a PDF file.

The publications are divided into the following categories:

There are also several press articles about my work, especially related to autocatalytic sets and origin of life.



Journals and proceedings

59. Autocatalytic sets and RNA secondary structure
Wim Hordijk
Journal of Molecular Evolution, in press, 2017.


58. Chasing the tail: The emergence of autocatalytic networks
Wim Hordijk and Mike Steel
BioSystems 152:1-10, 2017.


57. Biodiversity is autocatalytic
Roberto Cazzolla Gatti, Wim Hordijk and Stuart Kauffman
Ecological Modelling 346:70-76, 2017.


56. ecospat: an R package to support spatial analyses and modeling of species niches and distributions
V. Di Cola, O. Broennimann, B. Petitpierre, F. T. Breiner, M. D'Amen, C. Randin, R. Engler, J. Pottier, D. Pio, A. Dubuis, L. Pellissier, R. G. Mateo, W. Hordijk, N. Salamin and A. Guisan
Ecography (in press), 2017.


55. Evolution: Limited & predictable or unbounded & lawless?
Wim Hordijk
Biological Theory 11(4):187-191, 2016.


54. Autocatalytic sets in polymer networks with variable catalysis distributions
Wim Hordijk and Mike Steel
Journal of Mathematical Chemistry, 54(10):1997-2021, 2016.


53. Evolution of autocatalytic sets in computational models of chemical reaction networks
Wim Hordijk
Origins of Life and Evolution of Biospheres 46(2):233-245, 2016.


52. Comment on "Tibor Gánti and Robert Rosen" by Athel Cornish-Bowden
Wim Hordijk and Mike Steel
Journal of Theoretical Biology 392:122-123, 2016.


51. Prebiotic network evolution: six key parameters
Philippe Nghe, Wim Hordijk, Stuart A. Kauffman, Sara I. Walker, Francis J. Schmidt, Harry Kemble, Jessica A. M. Yeates and Niles Lehman
Molecular BioSystems 11:3206-3217, 2015.


50. Algorithms for detecting and analysing autocatalytic sets
Wim Hordijk, Joshua I. Smith and Mike Steel
Algorithms for Molecular Biology 10:15, 2015.


49. A genetic algorithm for finding good balanced sequences in a customer assignment problem with no state information
Wim Hordijk, Arie Hordijk and Bernd Heidergott
Asia-Pacific Journal of Operational Research 32(3):1550015, 2015.


48. Autocatalytic sets in E. coli metabolism
Filipa L. Sousa, Wim Hordijk, Mike Steel and William F. Martin
Journal of Systems Chemistry 6:4, 2015.


47. Autocatalytic sets and boundaries
Wim Hordijk and Mike Steel
Journal of Systems Chemistry 6:1, 2015.


46. The algorithmic mind and what it means to solve a problem
Wim Hordijk
Emergence: Complexity & Organization 16(4), 2014.


45. Conditions for evolvability of autocatalytic sets: A formal example and analysis
Wim Hordijk and Mike Steel
Origins of Life and Evolution of Biospheres 44(2):111-124, 2014.


44. On RAF sets and autocatalytic cycles in random reaction networks
Alessandro Filisetti, Marco Villani, Chiara Damiani, Alex Graudenzi, Andrea Roli, Wim Hordijk and Roberto Serra
Communications in Computer and Information Science, 445:113-126, 2014.


43. An investigation into irreducible autocatalytic sets and power law distributed catalysis
Wim Hordijk, Leonard Hasenclever, Jie Gao, Dilyana Mincheva and Jotun Hein
Natural Computing 13(3):287-296, 2014.


42. Serial transfer can aid the evolution of autocatalytic sets
Wim Hordijk, Nilesh Vaidya and Niles Lehman
Journal of Systems Chemistry 5:4, 2014.


41. Autocatalytic sets in a partitioned biochemical network
Joshua I. Smith, Mike Steel and Wim Hordijk
Journal of Systems Chemistry 5:2, 2014.


40. Autocatalytic sets and biological specificity
Wim Hordijk, Peter R. Wills and Mike Steel
Bulletin of Mathematical Biology 76(1):201-224, 2014.


39. Autocatalytic sets: From the origin of life to the economy
Wim Hordijk
BioScience 63(11):877-881, 2013.


38. Minimal autocatalytic networks
Mike Steel, Wim Hordijk and Joshua Smith
Journal of Theoretical Biology 332:96-107, 2013.


37. Complexity by subtraction
Daniel W. McShea and Wim Hordijk
Evolutionary Biology 40(4):504-520, 2013.


36. The EvCA project: A brief history
Wim Hordijk
Complexity 18(5):15-19, 2013.


35. A formal model of autocatalytic sets emerging in an RNA replicator system
Wim Hordijk and Mike Steel
Journal of Systems Chemistry 4:3, 2013.


34. The structure of autocatalytic sets: Evolvability, enablement, and emergence
Wim Hordijk, Mike Steel and Stuart Kauffman
Acta Biotheoretica 60(4):379-392, 2012.


33. Autocatalytic sets extended: Dynamics, inhibition, and a generalization
Wim Hordijk and Mike Steel
Journal of Systems Chemistry 3:5, 2012.


32. Dispersal routes reconstruction and the minimum cost arborescence problem
Wim Hordijk and Olivier Broennimann
Journal of Theoretical Biology 308:115-122, 2012.


31. The MigClim R package – seamless integration of dispersal constraints into projections of species distribution models
Robin Engler, Wim Hordijk and Antoine Guisan
Ecography 35:872-878, 2012.


30. Predicting present and future intra-specific genetic structure through niche hindcasting across 24 millennia
Anahí Espíndola, Loïc Pellissier, Luigi Maiorano, Wim Hordijk, Antoine Guisan and Nadir Alvarez
Ecology Letters 15(7):649-657, 2012.


29. Predicting template-based catalysis rates in a simple catalytic reaction model
Wim Hordijk and Mike Steel
Journal of Theoretical Biology 295:132-138, 2012.


28. Required levels of catalysis for emergence of autocatalytic sets in models of chemical reaction systems
Wim Hordijk, Stuart A. Kauffman and Mike Steel
International Journal of Molecular Sciences 12(5):3085-3101, 2011.


27. Autocatalytic sets and the origin of life
Wim Hordijk, Jotun Hein and Mike Steel
Entropy 12(7):1733-1742, 2010.


26. New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0
Stephane Guindon, Jean-Francois Dufayard, Vincent Lefort, Maria Anisimova, Wim Hordijk and Olivier Gascuel
Systematic Biology 59(3):307-321, 2010.


25. Cellular automata for image noise filtering
P. Jebaraj Selvapeter and Wim Hordijk
In A. Abraham, A. Carvalho, F. Herrera and V. Pai (eds.), Proceedings of the World Congress on Nature and Biologically Inspired Computing 2009, pp. 193-197, 2009.


24. Parameter control methods for selection operators in genetic algorithms
Peter Vajda, Agoston E. Eiben and Wim Hordijk
In G. Rudolph et al. (eds.), Parallel Problem Solving from Nature -- PPSN X, Springer, pp. 620-630, 2008.


23. Design of an interleaver for turbo codes using genetic algorithms
Shoba Paulson, Wim Hordijk, Princy Gift, Subarani and Shanmugam
International Journal of Artificial Intelligence and Machine Learning 6(2), pp. 1-5, 2006.


22. An overview of biologically inspired computing in information security
Wim Hordijk
In K. Anbumani (ed.), Proceedings of the National Conference on Information Security, pp. 1-14, 2005.


21. An introduction to evolutionary computation
Wim Hordijk
In K. Krithivasan and R. Rama (eds.), Formal Language Aspects of Natural Computing, pp. 77-84, 2005.


20. An overview of computation in cellular automata
Wim Hordijk
In K. Krithivasan and R. Rama (eds.), Formal Language Aspects of Natural Computing, pp. 7-16, 2005.


19. Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood
Wim Hordijk and Olivier Gascuel
Bioinformatics 21(24):4338-4347, 2005.


18. Correlation analysis of coupled fitness landscapes
Wim Hordijk and Stuart A. Kauffman
Complexity 10(6):41-49, 2005.


17. Material representations: From the genetic code to the evolution of cellular automata
Luis M. Rocha and Wim Hordijk
Artificial Life 11(1-2):189-214, 2005.


16. Supertree algorithms for ancestral divergence dates and nested taxa
Charles Semple, Philip Daniel, Wim Hordijk, Roderic M. Page and Mike Steel
Bioinformatics 20(15):2355-2360, 2004.


15. Detecting autocatalytic, self-sustaining sets in chemical reaction systems
Wim Hordijk and Mike Steel
Journal of Theoretical Biology 227(4):451-461, 2004.


14.The footprint sorting problem
Claudia Fried, Wim Hordijk, Sonja J. Prohaska, Claus R. Stadler and Peter F. Stadler
Journal of Chemical Information and Computer Sciences 44:332-338, 2004.


13. Graph laplacians, nodal domains, and hyperplane arrangements
Türker Biyikoglu, Wim Hordijk, Josef Leydold, Tomaz Pisanski and Peter F. Stadler
Linear Algebra and its Applications 390:155-174, 2004.


12. Catalytic reaction sets, decay, and the preservation of information
Wim Hordijk and José F. Fontanari
Proceedings of the IEEE International Conference on Integration of Knowledge Intensive Multi-Agent Systems, pp. 133-138, 2003.


11. Phase transition and landscape statistics of the number partitioning problem
Peter F. Stadler, Wim Hordijk and José F. Fontanari
Physical Review E 67:056701, 2003.


10 Shapes of tree representations of spin-glass landscapes
Wim Hordijk, Peter F. Stadler and José F. Fontanari
Journal of Physics A 36:3671-3681, 2003.


9. Fast fourier transform for fitness landscapes
Dan Rockmore, Peter Kostelec, Wim Hordijk and Peter F. Stadler
Applied and Computational Harmonic Analysis 12(1):57-76, 2002.


8. Upper bound on the products of particle interactions in cellular automata
Wim Hordijk, Cosma R. Shalizi and James P. Crutchfield
Physica D 154:240-258, 2001.


7. Mechanisms of emergent computation in cellular automata
Wim Hordijk, James P. Crutchfield and Melanie Mitchell
In A.E. Eiben, Th. Bäck, M. Schoenauer and H.-P. Schwefel (eds.), Parallel Problem Solving from Nature, pp. 613-622, 1998.


6. Amplitute spectra of fitness landscapes
Wim Hordijk and Peter F. Stadler
Advances in Complex Systems 1(1):39-66, 1998.


5. Correlation analysis of the synchronizing-CA landscape
Wim Hordijk
Physica D 107:225-264, 1997.


4. The structure of the synchronizing-CA landscape
Wim Hordijk
In M. Coombs and M. Sulcoski (eds.), Proceedings of the Workshop on Control Mechanisms for Complex Systems, pp. 93-107, 1996.


3. Embedded-particle computation in evolved cellular automata
Wim Hordijk, James P. Crutchfield and Melanie Mitchell
In T. Toffoli, M. Biafore and J. Leao (eds.), PhysComp96, New England Complex Systems Institute, pp. 153-158, 1996.


2. A measure of landscapes
Wim Hordijk
Evolutionary Computation 4(4):335-360, 1996.


1. The usefulness of recombination
Wim Hordijk and Bernard Manderick
In F. Moran, A. Moreno, J.J. Merelo and P. Chacon (eds.), Advances in Artificial Life: Proceedings of the Third European Conference on Artificial Life, pp. 908-919, 1995.



Book chapters

2. Correlation analysis of coupled fitness landscapes
Wim Hordijk
In H. Richter and A. Engelbrecht (eds.), Recent Advances in the Theory and Application of Fitness Landscapes, Springer, pp. 369-393, 2013.


1. Autocatalytic sets: The origin of life, evolution, and functional organization
Wim Hordijk, Mike Steel and Stuart Kauffman
In P. Pontarotti (ed.), Evolutionary Biology: Exobiology and Evolutionary Mechanisms, Springer, pp. 49-60, 2013.



Other contributions

17. Citizen science: Facts or fake news?
Wim Hordijk
Plus magazine, 20 March 2017.


16. Can computers help us conserve biodiversity?
Wim Hordijk
The Naked Scientists, 15 February 2017.


15. A perfect view from mount le Grammont
Wim Hordijk
Swiss Vistas, 23 January 2017.


14. Spontaneous spirals
Wim Hordijk
Plus magazine, 22 December 2016.


13. Grande Dixence: The tallest gravity dam in the world
Wim Hordijk
Swiss Vistas, 1 December 2016.


12. The mathematics of kindness
Wim Hordijk
Plus magazine, 1 November 2016.


11. Evolution: It's as real as gravity!
Wim Hordijk
Plus magazine, 13 July 2016.


10. Preserving species in the face of climate change
Wim Hordijk
Plus magazine, 25 April 2016.


9. How a game of billiards solved a queueing problem
Wim Hordijk
Plus magazine, 29 March 2016.


8. Life: It's chemistry!
Wim Hordijk
The Naked Scientists, 15 March 2016.


7. The living set
Wim Hordijk
The Scientist, 1 June 2015.


6. Is the mind algorithmic? Confusing science speak with layman language
Wim Hordijk
Sciworthy, 1 January 2015.


5. From salt to salary: Linguists take a page from science
Wim Hordijk
NPR 13.7, 8 November 2014.


4. Recognizing the illusion of 'Homo Economicus'
Wim Hordijk
NPR 13.7, 20 July 2014.


3. An eclectic mix of giants takes on the origin of life
Wim Hordijk
NPR 13.7, 10 March 2013.


2. Particles that compute
Wim Hordijk
SFI Bulletin 16(1):17-20, 2001.

Note: this will download the entire issue of the bulletin (1.7MB).


1. Optimization through evolution
Wim Hordijk
Medium Econometrische Toepassingen, 4(2), 1996.

(Sorry, no electronic version available...)



Theses

2. Dynamics, Emergent Computation, and Evolution in Cellular Automata
Wim Hordijk
Ph.D. dissertation, University of New Mexico, 1999.


1. Population Flow on Fitness Landscapes
Wim Hordijk
Unpublished undergraduate thesis, 1994.