It seems there is no point in keeping lists like this one any more. Google, ResearchGate, Academia and the like are doing a better job. Email if you can't get a hold of a paper.

pdf Iterated Inverse Binary Transducers extended version
pdf Flipping Pebbles draft (and a warning rep)
pdf Iterated Inverse Binary Transducers DCFS 2012, LNCS 7386, 294--306.
pdf Inferring Automatic Sequences draft
pdf Universality, Turing Incompleteness and Observers A Computable Universe, ed. H. Zenil, 2012, chap 22.
pdf Computational Classification of Cellular Automata Int. Journal of General Systems, 41 (2012) 6, 1-13.
pdf Computational Processes, Observers and Turing Incompleteness TCS 412 (2011) 1-2, 183-190.
pdf Cellular Automata, Decidability and Phase Space Fundamentae Informaticae 140 (2010) 1-20.
pdf Model Checking One-Dimensional Cellular Automata J. Cellular Automata, 4 (2009) 3, 213-224.
pdf Classification of Cellular Automata Encyclopedia of Complexity and System Science, ed. R. A. Meyers, Springer 2009.
pdf Divisibility and State Complexity The Mathematica J., 11 (2009) 3, 430--445.
pdf CDM: Teaching Discrete Mathematics to Computer Science Majors J. Educ. Resour. Comput., 5 (2005) 2, 1-11.
pdf Universality and Cellular Automata LNCS 3354 (2005) 50-59.
pdf The Complexity of Reversible Cellular Automata TCS 325 (2004) 317-328.
pdf Almost Periodic Configurations on Linear Cellular Automata Fundamentae Informaticae 58/3-4 (2003), 223-240.
pdf The Ehrenfeucht-Mycielski Sequence CIAA'03, Santa Barbara.
pdf The Size of Power Automata Theoretical Computer Science, 295/1-3 (2003) 371--386.
pdf Cellular Automata and Intermediate Degrees Theoretical Computer Science, 296/2 (2003) 365-375
pdf Reduced Power Automata Proceedings CIAA 2002, J-M. Champarnaud, D. Maurel, eds., 2002, 191-200
pdf automata, a Hybrid System for Computational Automata Theory Proceedings CIAA 2002, J-M. Champarnaud, D. Maurel, eds., 2002, 217-222
pdf Cellular Automata and Intermediate Reachability Problems Fundamentae Informaticae 52 (2002) 1-3, 249-256
pdf Decomposition of Additive CA Complex Systems 13 (2001) 2, 245-270
pdf Sigma-Automata and Chebyshev Polynomials Theoretical Computer Science, 230 (2000) 49--73
pdf Linear Cellular Automata and De Bruijn Automata M. Delorme and J. Mazoyer, eds., Cellular Automata: A Parallel Model, Kluwer, 1999
pdf Linear Cellular Automata and Fischer Automata Parallel Computing, 23 (1997) 11, 1613--1634
pdf Optimal Link Assignments for All-Terminal Reliability Discrete Applied Mathematics, 75 (1997), 285--295
pdf The Lattice of beta-r.e. Sets Draft.