1. Hereditarily finitely based semigroup identities, M.Sc. thesis, University of Lisbon 1989 (Portuguese).
  2. Contributions to combinatorial semigroup theory, Ph.D. thesis, University of Glasgow 1991.
  3. A note on primeness of semigroup rings, Proc. Royal. Soc. Edinburgh 120A (1992), 191-197.
  4. Clifford monoid presentations, Math. Proc. Cambridge Phil. Soc. 111 (1992), 445-454.
  5. Rational languages and inverse monoid presentations, Int. J. Alg. Comp. 2.2 (1992), 187-207.
  6. One-relator presentations. In: Edição Comemorativa do Cinquentenário do Centro de Matemática do Porto, INIC (1992), 67-73 (Portuguese).
  7. Normal-convex embeddings of inverse semigroups, Glasgow Math. J. 35 (1993), 115-121.
  8. On the semilattice of idempotents of a free inverse monoid, Proc. Math. Soc. Edinburgh 36 (1993), 349-360.
  9. The divisibility problem for inverse monoid presentations. In: Semigroups, ed. C. Bonzini, A. Cherubini and C. Tibiletti, World Scientific 1993.
  10. The E-unitary problem for finite inverse monoid presentations. In: Actas do III Encontro Nacional de Algebristas, Universidade de Coimbra 1993, 169-174 (Portuguese).
  11. The word problem for nilpotent inverse monoids, Semigroup Forum 51 (1995), 285-293.
  12. On free inverse monoid languages, Theoretical Informatics and Applications 30.4 (1996), 349-378.
  13. Conjugacy and transposition for inverse monoid presentations, Int. J. Alg. Comp. 6.5 (1996), 607-622.
  14. (With J. Almeida and G. M. S. Gomes (Eds.)) Semigroups, Automata and Languages, World Scientific 1996.
  15. Introduction to inverse semigroup combinatorial theory, lecture notes, Centro Internacional de Matemática 1996 (Portuguese).
  16. (With M. Ito) Remarks on deletions, scattered deletions and related operations on languages. In: Proceedings of the First Symposium on Algebra, Languages and Computation, University of Aizu, Japan, 1997. Also in: Semigroups and applications, ed. J. M. Howie and N. Ruskuc, World Scientific 1998, 97-105.
  17. (With J. Almeida) On the hyperdecidability of semidirect products of pseudovarieties, Comm. in Algebra 26(12) (1998), 4065-4077.
  18. (With M. Petrich) On presentations of semigroup rings, Boll. Unione Matematica Italiana (8) 2-B (1999), 127-142.
  19. (With M. Petrich) On quasi directly infinite rings, Acta Scient. Matem. 65 (1999), 61-75.
  20. Word equations and inverse monoid presentations. In: Semigroups with Applications, Including Semigroup Rings, ed. S. Kublanovsky, A. Mikhalev, P. Higgins and J. Ponizovskii, TPO "Severny Ochag", Saint-Petersburg 1999.
  21. (With M. Petrich) On directly infinite rings, Acta Math. Hungarica 85 (1-2) (1999), 153-165.
  22. (With M. Petrich) A functor from semigroups to rings, J. Pure and Appl. Algebra 148 (2000), 285-307.
  23. (With M. Petrich) Relationship of certain rings of infinite matrices over integers, Boll. Unione Matematica Italiana (8) 3-B (2000), 347-365.
  24. (With M. Petrich) Relatively free bands, Comm. in Algebra 28(5) (2000), 2615-2631.
  25. (With M. Petrich) Relatively free *-bands, Beitrage zur Alg. und Geom. 41.2 (2000), 569-588.
  26. On unique factorization semilattices, Discussiones Mathematicae - General Alg. and Appl. 20 (2000), 97-120.
  27. (With A. Oliveira) Inverse automata and monoids and the undecidability of the Cayley subgraph problem for groups, Glasgow Math. J. 42 (2000), 421-437.
  28. (With J. Almeida) SC-Hyperdecidability of R, Theor. Comp. Science, 255 (2001), 569--591.
  29. (With M. Petrich) A canonical directly infinite ring, Czech. Math. J. 51(126) (2001), 545--560.
  30. Trees associated to inverse monoid presentations, J. Pure and Appl. Algebra 165 (2001), 307--335.
  31. (With M. Petrich) Structure of relatively free bands, Comm. in Algebra 30.9 (2002), 4165--4187.
  32. (With B. Steinberg) Extensions and submonoids of automatic monoids, Theor. Comp. Science 289 (2002), 727--754.
  33. (With A. Restivo) On the lattice of prefix codes, Theor. Comp. Science 289 (2002), 755-782.
  34. The homomorphism problem for the free monoid, Discrete Mathematics 259 (2002), 189--200.
  35. (With G. M. S. Gomes and J.-E. Pin (Eds.)) Semigroups, Algorithms, Automata and Languages, World Scientific 2002.
  36. Recognizable subsets of a group: finite extensions and the abelian case, Bulletin of the E.A.T.C.S. 77 (2002), 195-215.
  37. (With A. Restivo) Periodicity vectors for labelled trees, Discrete Appl. Math. 126 (2003), 241--260.
  38. (With F. Mignosi and A. Restivo) On Fine and Wilf's Theorem for bidimensional words, Theor. Comp. Science 292 (2003), 245--262.
  39. (With M. Petrich) On *-bands and their varieties, Rocky Mountain J. of Math. 33.1 (2003), 217--252.
  40. The homomorphism problem for trace monoids, Theor. Comp. Science 307 (2003), 199--215.
  41. A note on pure and p-pure languages, Acta Informatica 39 (2003), 579--595.
  42. Algebra, Mestrado M.F.A., notas de curso, Universidade do Porto, 2003 (Portuguese).
  43. Free group languages: rational versus recognizable, Theoretical Informatics and Applications 38 (2004), 49--67.
  44. (With B. Steinberg) A geometric characterization of automatic monoids, Quart. Oxford J. Math. 55.3 (2004), 333--356.
  45. An application of first order logic to the study of recognizable languages, Int. J. Alg. Comp. 14.5/6 (2004), 785--799.
  46. (With B. Steinberg) On a class of automata groups generalizing lamplighter groups, Int. J. Alg. Comp. 15.5/6 (2005), 1213--1234.
  47. (With A. Oliveira) Inverse subsemigroups of the monogenic free inverse semigroup, Comm. Algebra 33 (2005), 3887--3917.
  48. (With J.-E. Pin) A topological approach to transductions, Theor. Comp. Sci. 340 (2005), 443--456.
  49. (With J.-E. Pin) The algorithmic potential of continuous transductions, in Workshop on Semigroups and Automata, satellite workshop to ICALP'05, Lisbon, 16/7/2005, eds. V.H. Fernandes, G.M.S. Gomes, J.-E. Pin and M.V. Volkov, 86--103.
  50. (With I. Araujo and N. Ruskuc) Presentations for inverse subsemigroups with finite complement, preprint, CMUP 2005-9.
  51. (With M. Kambites and B. Steinberg) The spectra of lamplighter groups and Cayley machines, Geometriae Dedicata 120.1 (2006), 193--227.
  52. Problems of logic deduction: from sudoku to retrograde analysis, Boletin de Ciencias 62 (2006), 107--117. (Spanish)
  53. (With M. Kambites and B. Steinberg) On the rational subset problem for groups, J. Algebra 309 (2007), 622--639.
  54. (With P. Weil) On an algorithm to decide whether a free group is a free factor of another, RAIRO Theoretical Informatics and Applications 42 (2008), 395--414.
  55. (With J.-E. Pin) A Mahler's theorem for functions from words to integers, 25th International Symposium on Theoretical Aspects of Computer Science (STACS 2008), Susanne Albers and Pascal Weil, eds. Internationales Begegnungs- Und Forschungszentrum für Informatik (IBFI), Schloss Dagstuhl, Dagstuhl, Germany, 2008, 585--596.
  56. (With J. Rhodes) Turing machines and bimachines, Theoret. Comp. Sci. 400 (2008), 182--224.
  57. .
  58. (With S. Konstantinidis) Maximal error-detecting capabilities of formal languages, J. Alg., Lang. and Combinatorics 13.1 (2008), 55--71.
  59. Rational subsets of partially reversible monoids, Theoret. Comp. Sci. 409.3 (2008), 537--548.
  60. (With J. Cassaigne) Infinite periodic points of endomorphisms over special confluent rewriting systems, Ann. Inst. Fourier 59.2 (2009), 769--810.
  61. (With J. Cassaigne) Infinite words and confluent rewriting systems: endomorphism extensions, Internat. J. Algebra Comput. 19.4 (2009), 443--490.
  62. (With P. Weil) On finite-index extensions of subgroups of free groups, J. Group Theory 13.3 (2010), 365--381.
  63. (With P. Weil) Automorphic orbits in free groups: words versus subgroups, Internat. J. Algebra Comput. 20.4 (2010), 561--590.
  64. (With N. Pinto and A. Amorim), General derivation of the sets of pedigrees with the same kinship coefficients, Human Heredity 70 (2010), 194--204.
  65. (With S. Konstantinidis) Computing maximal error-detecting capabilities and distances of regular languages, Fundam. Inform. 101.4 (2010), 257--270.
  66. Fixed points of endomorphisms over special confluent rewriting systems, Monat. fur Math. 161.4 (2010), 417--447
  67. .
  68. (With J.-E. Pin) On profinite uniform structures defined by varieties of finite monoids, Internat. J. Algebra Comput. 21.1-2 (2011), 295--314.
  69. (With M. Ladra) The generalized conjugacy problem for virtually free groups, Forum Math. 23 (2011), 447--482.
  70. Finite idempotent inverse monoid presentations, Internat. J. Algebra Comput. 21.7 (2011), 1111--1133.
  71. (With E. Rodaro) Never minimal automata and the rainbow bipartite subgraph problem, LNCS proceedings volume of the 15th International Conference on Developments in Language Theory (DLT 2011), Milano, Springer, pp. 374--385, 2011.
  72. (With N. Pinto, L. Gusmao and A. Amorim) Estimating coancestry from genotypes using a linear regression method, Forensic Science International: Genetics Supplement Series 3 (2011), e373--e374.
  73. (With N. Pinto, L. Gusmao, T. Egeland and A. Amorim) Estimation of coancestry coefficient from genotypic data: a review of the autosomal case and extension to X-chromosome markers, preprint, IPATIMUP 2011.
  74. Fixed points of endomorphisms of certain free products, RAIRO Theoretical Informatics and Applications 46 (2012), 165--179.
  75. (With N. Pinto and A. Amorim) A general method to infer the usefulness of the X-chromosomal markers in kinship testing, Forensic Science International: Genetics 6 (2012), 198--207.
  76. (With J. Rhodes) Further results on monoids acting on trees, Internat. J. Algebra Comput. 22(4) 1250034 (2012) (69 pages).
  77. Groups and automata: a perfect match, In: M. Kutrib, N. Moreira and R. Reis (eds.), DCFS 2012, LNCS 7386, Springer, pp. 50--63, 2012; also J. Automata Lang. Combin. 17(2-4) (2012), 277-292.
  78. (With J. Rhodes) Matroids, hereditary collections and simplicial complexes having boolean representations, arXiv:1210.7064, preprint, 2012.
  79. (With E. Rodaro) Amalgams of inverse semigroups and reversible two-counter machines, J. Pure Appl. Algebra 217 (2013), 585--597.
  80. Fixed points of endomorphisms of virtually free groups, Pacific J. Math. 263(1) (2013), 207--240.
  81. (With E. Rodaro and M. Sykiotis) Fixed points of endomorphisms of graph groups, J. Group Theory 16(4) (2013), 573--583.
  82. (With E. Rodaro) On periodic points of free inverse monoid endomorphisms, Internat. J. Algebra Comput. 23(8) (2013), 1789--1804.
  83. Teoria geométrica de grupos, course notes, Universidade Federal da Bahia, 2013.
  84. (With J.-E. Pin) A noncommutative extension of Mahler's theorem on interpolation series, Europ. J. Combin. 36 (2014), 564--578.
  85. (With E. Rodaro) Fixed points of endomorphisms of trace monoids, Semigroup Forum 89(1) (2014), 266--279.
  86. (With J. Rhodes) A new notion of vertex independence and rank for finite graphs, Internat. J. Algebra Comput. 25(1/2) (2015), 123--167.
  87. (With V. Araújo and M. Sykiotis) Finiteness results for subgroups of finite extensions, J. Algebra 423 (2015), 592--614.
  88. (With J. Rhodes) Boolean Representations of Simplicial Complexes and Matroids, Springer Monographs in Mathematics, Springer, 2015.
  89. (With V. Diekert, F. Martin and G. Sénizergues) Equations over free inverse monoids with idempotent variables, in: Proc. 10th International Computer Science Symposium in Russia, CSR 2015, Listvyanka, Russia, July 13-17, 2015, L.~D.~Beklemishev and D.~V.~Musatov (Eds.), LNCS 9139, Springer, 2015, pp. 173--188.
  90. (With L. Bartholdi) Rational subsets of groups, Handbook of Automata Theory, Chapter 23, J.-E. Pin (ed.) (to appear).
  91. (With L. Bartholdi) Groups defined by automata, Handbook of Automata Theory, Chapter 24, J.-E. Pin (ed.) (to appear).
  92. (With X. Soler-Escrivà and E. Ventura) Finite automata for Schreier graphs of virtually free groups, J. Group Theory (to appear).
  93. (With M. Ladra and E. Ventura) Bounding the gap between a free group (outer) automorphism and its inverse, Collect. Math. (to appear).
  94. An automata-theoretic approach to the study of fixed points of endomorphisms, to appear in a volume of the series Advanced Courses in Mathematics CRM Barcelona, Birkhäuser.
  95. (With F. Soares) Howson's property for semidirect products of semilattices by groups, Comm. Algebra (to appear).
  96. (With V. Araújo) Hölder conditions for endomorphisms of hyperbolic groups, arxiv:1405.6310, preprint, CMUP 2014-13.
  97. (With V. Araújo) Geometric characterizations of virtually free groups, arxiv:1405.5400, preprint, CMUP 2014-14.
  98. (With M. J. J. Branco and G. M. S. Gomes) Takahasi semigroups, arxiv:1504.00219, preprint, CMUP 2015-9.
(last update: 3rd July 2015)