My publications are divided into the following categories:
   Journals and proceedings (peer reviewed scientific articles)
   Book chapters (invited)
   Other contributions (popular science pieces and travel stories)


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.

<-- Click on this icon to download my list of publications as PDF.

Don't hesitate to contact me if any of the article links are broken!

Journals and proceedings

73. 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

72. 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

71. 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

70. 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

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

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

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

66. 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

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

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

63. 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

62. 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

61. 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

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

59. Autocatalytic sets and RNA secondary structure
Wim Hordijk
Journal of Molecular Evolution 84(4):153-158, 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 40(6):774-787, 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

4. Autocatalytic sets: Complexity at the interface of chemistry and biology
Wim Hordijk
In J. Dunne (ed.), Progress in Complexity Science, Santa Fe Institute Press, in preparation, 2021

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

Other contributions

40. Why are sunsets red?
Wim Hordijk
Plus magazine, 5 February 2020

39. The evolution of robustness
Wim Hordijk and Lee Altenberg
Extended Evolutionary Synthesis Blog, 1 November 2019

38. The tooth of time
Wim Hordijk
ORBITER magazine, 25 September 2019

37. Kurt Gödel: A postcard from Vienna
Wim Hordijk
Plus magazine, 20 September 2019

36. StuFest - Celebrating Stuart Kauffman's 80th birthday
Wim Hordijk
Extended Evolutionary Synthesis Blog, 28 August 2019

35. How did life begin? (Part 3)
Wim Hordijk
ORBITER magazine, 14 August 2019

34. How did life begin? (Part 2)
Wim Hordijk
ORBITER magazine, 13 August 2019

33. How did life begin? (Part 1)
Wim Hordijk
ORBITER magazine, 12 August 2019

32. Beating the Avatar blues
Wim Hordijk
ORBITER magazine, 23 April 2019

31. The power of snooker
Wim Hordijk
Plus magazine, 16 April 2019

30. Workshop report: Developmental biases in evolution
Wim Hordijk
Extended Evolutionary Synthesis Blog, 20 November 2018

29. From an ecologist's nightmare to a mathematician's dream
Wim Hordijk
Plus magazine, 6 November 2018

28. The evolution of emergent computation
Wim Hordijk
TVOL, 10 September 2018

27. The evolutionary roots of irrationality
Wim Hordijk
TVOL, 16 July 2018

26. Citizen science: Schumann resonances
Wim Hordijk
Plus magazine, 7 June 2018

25. Evolution as a problem solver in computer science
Wim Hordijk
TVOL, 29 January 2018

24. What's your problem?
Wim Hordijk
Plus magazine, 24 January 2018

23. Geneva attractions: From high energy physics to high altitude views
Wim Hordijk
Swiss Vistas, 20 September 2017

22. The origin of life: A selfish act or a cooperative effort?
Wim Hordijk
TVOL, 18 September 2017

21. An unconventional place for unconventional science
Wim Hordijk
Extended Evolutionary Synthesis Blog, 11 September 2017

20. Citizen science: The statistics of language
Wim Hordijk
Plus magazine, 7 June 2017

19. Cause and process in evolution
Wim Hordijk
Extended Evolutionary Synthesis Blog, 17 May 2017

18. Grottes de Vallorbe
Wim Hordijk
Swiss Vistas, 2 May 2017

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

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


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.