| 2014 | ECCB | Observations on the Feasibility of Exact Pareto Optimization. | Cdric Saule, Robert Giegerich |
| 2011 | CPM | Forest Alignment with Affine Gaps and Anchors. | Stefanie Schirmer, Robert Giegerich |
| 2011 | PPDP | Bellman's GAP: a declarative language for dynamic programming. | Georg Sauthoff, Stefan Janssen, Robert Giegerich |
| 2010 | WABI | Prediction of RNA Secondary Structure Including Kissing Hairpin Motifs. | Corinna Theis, Stefan Janssen, Robert Giegerich |
| 2009 | PPAM | GPU Parallelization of Algebraic Dynamic Programming. | Peter Steffen, Robert Giegerich, Mathieu Giraud |
| 2008 | APBC | Alignment of Minisatellite Maps: A Minimum Spanning Tree-based Approach. | Mohamed Ibrahim Abouelhoda, Robert Giegerich, Behshad Behzadi, Jean-Marc Steyaert |
| 2007 | ISMB | Locomotif: from graphical motif description to RNA motif search. | Janina Reeder, Jens Reeder, Robert Giegerich |
| 2006 | GPCE | A graphical programming system for molecular motif search. | Janina Reeder, Robert Giegerich |
| 2006 | SAC | Challenges in the compilation of a domain specific language for dynamic programming. | Robert Giegerich, Peter Steffen |
| 2002 | GI | Towards A Discipline of Dynamic Programming. | Robert Giegerich |
| 2002 | MPC | Implementing Algebraic Dynamic Programming in the Functional and the Imperative Programming Paradigm. | Robert Giegerich, Peter Steffen |
| 2000 | CPM | Explaining and Controlling Ambiguity in Dynamic Programming. | Robert Giegerich |
| 2000 | ISMB | Computation and Visualization of Degenerate Repeats in Complete Genomes. | Stefan Kurtz, Enno Ohlebusch, Chris Schleiermacher, Jens Stoye, Robert Giegerich |
| 1999 | PSB | Prediction and Visualization of Structural Switches in RNA. | Robert Giegerich, Dirk Haase, Marc Rehmsmeier |
| 1998 | GI | ViSeL - An interactive course in DNA Sequencing. | Robert Giegerich, Dieter Lorenz |
| 1997 | ISMB | RIFLE: Rapid Identification of Microorganisms by Fragment Length Evaluation. | Henning Hermjakob, Robert Giegerich, Walter Arnold |
| 1996 | ISMB | GeneFisher-Software Support for the Detection of Postulated Genes. | Robert Giegerich, Folker Meyer, Chris Schleiermacher |
| 1994 | ESOP | Suffix Trees in the Functional Programming Paradigm. | Robert Giegerich, Stefan Kurtz |
| 1990 | PLDI | On the Structure of Verifiable Code Generator Specifications. | Robert Giegerich |
| 1988 | ESOP | Code Selection Techniques: Pattern Matching, Tree Parsing, and Inversion of Derivors. | Robert Giegerich, Karl Schmal |
| 1982 | POPL | Automatic Generation of Machine Specific Code Optimizers. | Robert Giegerich |
| 1981 | GI | Invariance of Approximate Semantics with Respect to Program Transformations. | Robert Giegerich, Ulrich Mncke, Reinhard Wilhelm |
| 1977 | GI | Implementierbarkeit attributierter Grammatiken. | Robert Giegerich, Reinhard Wilhelm |