| 2017 | CiE | Finite Language Forbidding-Enforcing Systems. | Daniela Genova, Hendrik Jan Hoogeboom |
| 2014 | CiE | Graph Polynomials Motivated by Gene Rearrangements in Ciliates. | Robert Brijder, Hendrik Jan Hoogeboom |
| 2010 | TAMC | Pivot and Loop Complementation on Graphs and Set Systems. | Robert Brijder, Hendrik Jan Hoogeboom |
| 2008 | LATA | Extending the Overlap Graph for Gene Assembly in Ciliates. | Robert Brijder, Hendrik Jan Hoogeboom |
| 2007 | DLT | Characterizing Reduction Graphs for Gene Assembly in Ciliates. | Robert Brijder, Hendrik Jan Hoogeboom |
| 2007 | FCT | From Micro to Macro: How the Overlap Graph Determines the Reduction Graph in Ciliates. | Robert Brijder, Hendrik Jan Hoogeboom, Grzegorz Rozenberg |
| 2007 | FUN | High Spies (or How to Win a Programming Contest). | Andr H. Deutz, Rudy van Vliet, Hendrik Jan Hoogeboom |
| 2007 | PODS | XML transformation by tree-walking transducers with invisible pebbles. | Joost Engelfriet, Hendrik Jan Hoogeboom, Bart Samwel |
| 2006 | DLT | Computing by Only Observing. | Matteo Cavaliere, Pierluigi Frisco, Hendrik Jan Hoogeboom |
| 2006 | STACS | Nested Pebbles and Transitive Closure. | Joost Engelfriet, Hendrik Jan Hoogeboom |
| 2004 | DNA | Combinatorial Aspects of Minimal DNA Expressions. | Rudy van Vliet, Hendrik Jan Hoogeboom, Grzegorz Rozenberg |
| 2003 | FCT | Languages Defined by Generalized Equality Sets. | Vesa Halava, Tero Harju, Hendrik Jan Hoogeboom, Michel Latteux |
| 2002 | DLT | Carriers and Counters: P Systems with Carriers vs. (Blind) Counter Automata. | Hendrik Jan Hoogeboom |
| 2001 | DLT | Context-Free Valence Grammars - Revisited. | Hendrik Jan Hoogeboom |
| 1999 | ICALP | Two-Way Finite State Transducers and Monadic Second-Order Logic. | Joost Engelfriet, Hendrik Jan Hoogeboom |
| 1994 | MFCS | MSO Definable Text Languages. | Hendrik Jan Hoogeboom, Paulien ten Pas |
| 1993 | DLT | An Introduction to Context-free Text Grammars. | Andrzej Ehrenfeucht, Hendrik Jan Hoogeboom, Paulien ten Pas, Grzegorz Rozenberg |
| 1989 | ICALP | Automata with Storage on Infinite Words. | Joost Engelfriet, Hendrik Jan Hoogeboom |
| 1987 | ICALP | Decision Problems for Regular Trace Languages. | IJsbrand Jan Aalbersberg, Hendrik Jan Hoogeboom |
| 1985 | FCT | On coordinated rewriting. | Andrzej Ehrenfeucht, Hendrik Jan Hoogeboom, Grzegorz Rozenberg |