| 2019 | RECOMB | ModHMM: A Modular Supra-Bayesian Genome Segmentation Method. | Philipp Benner, Martin Vingron |
| 2011 | CPM | Computational Regulatory Genomics. | Martin Vingron |
| 2009 | WABI | Exact Score Distribution Computation for Similarity Searches in Ontologies. | Marcel H. Schulz, Sebastian Khler, Sebastian Bauer, Martin Vingron, Peter N. Robinson |
| 2008 | WABI | Fast and Adaptive Variable Order Markov Chain Construction. | Marcel H. Schulz, David Weese, Tobias Rausch, Andreas Dring, Knut Reinert, Martin Vingron |
| 2007 | ISMB | A physical model for tiling array analysis. | Ho-Ryun Chung, Dennis Kostka, Martin Vingron |
| 2006 | CPM | An Improved Algorithm for the Macro-evolutionary Phylogeny Problem. | Behshad Behzadi, Martin Vingron |
| 2006 | RECOMB | Reconstructing Domain Compositions of Ancestral Multi-domain Proteins. | Behshad Behzadi, Martin Vingron |
| 2006 | RECOMB | An Improved Statistic for Detecting Over-Represented Gene Ontology Annotations in Gene Sets. | Steffen Grossmann, Sebastian Bauer, Peter N. Robinson, Martin Vingron |
| 2006 | RECOMB | Alignment Statistics for Long-Range Correlated Genomic Sequences. | Philipp W. Messer, Ralf Bundschuh, Martin Vingron, Peter F. Arndt |
| 2004 | ISMB | Functional inference from non-random distributions of conserved predicted transcription factor binding sites. | Christoph Dieterich, Sven Rahmann, Martin Vingron |
| 2004 | ISMB | Optimal robust non-unique probe selection using Integer Linear Programming. | Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, Knut Reinert |
| 2004 | RECOMB | Detecting Functional Modules of Transcription Factor Binding Sites in the Human Genome. | Thomas Manke, Christoph Dieterich, Martin Vingron |
| 2003 | ECCB | Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites. | Christoph Dieterich, Ralf Herwig, Martin Vingron |
| 2003 | IDA | Gaussian Mixture Density Estimation Applied to Microarray Data. | Christine Steinhoff, Tobias Mller, Ulrike A. Nuber, Martin Vingron |
| 2002 | ECCB | Theoretical analysis of alternative splice forms using computational methods. | Stphanie Bou, Martin Vingron, Evgenia V. Kriventseva, Ina Koch |
| 2002 | ECCB | Annotating regulatory DNA based on man-mouse genomic comparison. | Christoph Dieterich, Brian Cusack, Haiyan Wang, Katja Rateitschak, Antje Krause, Martin Vingron |
| 2002 | ECCB | Proteome analysis based on motif statistics. | Pierre Nicodme, T. Doerks, Martin Vingron |
| 2002 | ISMB | Variance stabilization applied to microarray data calibration and to the quantification of differential expression. | Wolfgang Huber, Anja von Heydebreck, Holger Sltmann, Annemarie Poustka, Martin Vingron |
| 2001 | ISMB | Identifying splits with clear separation: a new class discovery method for gene expression data. | Anja von Heydebreck, Wolfgang Huber, Annemarie Poustka, Martin Vingron |
| 2000 | RECOMB | Tree fitting: an algebraic approach using profile distances. | Richard Desper, Martin Vingron |
| 2000 | RECOMB | Contig selection in physical mapping. | Steffen Heber, Jens Stoye, Jrg D. Hoheisel, Martin Vingron |
| 1999 | RECOMB | Untitled record | Stefan Burkhardt, Andreas Crauser, Paolo Ferragina, Hans-Peter Lenhof, Eric Rivals, Martin Vingron |
| 1998 | RECOMB | A polyhedral approach to RNA sequence structure alignment. | Hans-Peter Lenhof, Knut Reinert, Martin Vingron |
| 1997 | RECOMB | The deferred path heuristic for the generalized tree alignment problem. | Benno Schwikowski, Martin Vingron |
| 1993 | CPM | Multiple Sequence Comparison and n-Dimensional Image Reconstruction. | Martin Vingron, Pavel A. Pevzner |