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:

- Journals and proceedings (peer reviewed scientific articles)
- Book chapters (invited)
- Other contributions (mostly popular science articles)
- Theses

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

**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.

**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.

**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...)

**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.