Publications

My publications are divided into the following categories:
   Journals and proceedings (peer reviewed)
   Book chapters (invited)
   Technical reports, preprints, etc.
   Theses
   Other contributions (popular science, travel, etc.)
Click on the title of an article to view the official publication on the publisher's website, or on the PDF icon next to the title to download a free preprint.


Journals and proceedings (peer reviewed)


74. On the emergence of ecological and economic niches
Roberto Cazzolla Gatti, Roger Koppl, Brian D. Fath, Stuart Kauffman, Wim Hordijk and Robert E. Ulanowicz
Journal of Bioeconomics 22:99-127, 2020


73. Autocatalytic chemical networks at the origin of metabolism
Joana C. Xavier, Wim Hordijk, Stuart A. Kauffman, Mike Steel and William F. Martin
Proceedings of the Royal Society B 287:20192377, 2020


72. Dynamics of a birth-death process based on combinatorial innovation
Mike Steel, Wim Hordijk and Stuart A. Kauffman
Journal of Theoretical Biology 491:110187, 2020


71. Developmental structuring of phenotypic variation: A case study with a cellular automaton model of ontogeny
Wim Hordijk and Lee Altenberg
Evolution & Development 22(1-2):20-34, 2020


70. Average fitness differences on NK landscapes
Wim Hordijk, Stuart A. Kauffman and Peter F. Stadler
Theory in Biosciences 139(1):1-7, 2020


69. A history of autocatalytic sets
Wim Hordijk
Biological Theory 14(4):224-246, 2019


68. Molecular diversity required for the formation of autocatalytic sets
Wim Hordijk, Mike Steel and Stuart A. Kauffman
Life 9:23, 2019


67. Autocatalytic networks in biology: structural theorems and algorithms
Mike Steel, Wim Hordijk and Joana C. Xavier
Journal of the Royal Society Interface 16:20180808, 2019


66. Autocatalytic networks at the basis of life's origin and organization
Wim Hordijk and Mike Steel
Life 8:62, 2018


65. Population dynamics of autocatalytic sets in a compartmentalized spatial world
Wim Hordijk, Jonathan Naylor, Natalio Krasnogor and Harold Fellermann
Life 8:33, 2018


64. Niche emergence as an autocatalytic process in the evolution of ecosystems
Roberto Cazzolla Gatti, Brian Fath, Wim Hordijk, Stuart Kauffman and Robert Ulanowicz
Journal of Theoretical Biology 454:110-117, 2018


63. The influence of modularity, seeding, and product inhibition on peptide autocatalytic network dynamics
Wim Hordijk, Shira Shichor and Gonen Ashkenasy
ChemPhysChem 19:2437-2444, 2018


62. Autocatalytic sets and chemical organizations: Modeling self-sustaining reaction networks at the origin of life
Wim Hordijk, Mike Steel and Peter Dittrich
New Journal of Physics 20:015011, 2018


61. Autocatalytic confusion clarified
Wim Hordijk
Journal of Theoretical Biology 435:22-28, 2017


60. Autocatalytic sets and RNA secondary structure
Wim Hordijk
Journal of Molecular Evolution 84(4):153-158, 2017


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


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


57. 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 40(6):774-787, 2017


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


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


54. 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


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


52. 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


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


50. 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


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


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


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


46. 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


45. 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


44. 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


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


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


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


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


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


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


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


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


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


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


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


32. 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


31. 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


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


29. 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


28. The ideal storage cellular automaton model
Wim Hordijk, Lin Wei, Peter Serocka and Andreas Dress
In A. Apostolico, A. Dress and L. Parida (eds.), Structure discovery in biology: Motifs, networks & phylogenies, pp. 1-8, 2010


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 Rekh, Subha Rani, Wim Hordijk, Princy Gift, 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 (invited)


3. Collective decision making
Wim Hordijk
In F. Matthäus, S. Matthäus, S. Harris and T. Hillen (eds.), The Art of Theoretical Biology, Springer, pp. 44-45, 2020


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


Technical reports, preprints, etc.


3. Emergence of autocatalytic sets in a simple model of technological evolution
Wim Hordijk and Stuart Kauffman
Preprint posted on arXiv, April 2022


2. Autocatalytic sets: Complexity at the interface of chemistry and biology
Wim Hordijk
Research review commissioned by the John Templeton Foundation, March 2022


1. Snooker statistics and Zipf's law
Wim Hordijk
Preprint posted on arXiv, January 2022


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
Undergraduate thesis, Erasumus University Rotterdam, 1994.


Other contributions (popular science, travel, etc.)


Dozens of contributions to various online popular science and travel magazines, most notably:

   Plus Magazine

   ORBITER Magazine

   The Naked Scientists

   NPR 13.7