| 2026 | WABI | On the Complexity of the (ℓ, k)-Median Problems. | Lus Cunha, Thiago Nascimento, Marlia D. V. Braga, Jens Stoye |
| 2024 | WABI | Reconstructing Rearrangement Phylogenies of Natural Genomes. | Leonard Bohnenkmper, Jens Stoye, Daniel Drr |
| 2022 | WABI | A Linear Time Algorithm for an Extended Version of the Breakpoint Double Distance. | Marlia D. V. Braga, Leonie R. Brockmann, Katharina Klerx, Jens Stoye |
| 2020 | RECOMB | Computing the Rearrangement Distance of Natural Genomes. | Leonard Bohnenkmper, Marlia D. V. Braga, Daniel Doerr, Jens Stoye |
| 2019 | WABI | Finding All Maximal Perfect Haplotype Blocks in Linear Time. | Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, Jens Stoye |
| 2017 | CPM | Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings. | Lus Felipe I. Cunha, Simone Dantas, Travis Gagie, Roland Wittler, Luis A. B. Kowada, Jens Stoye |
| 2017 | RECOMB | Dynamic Alignment-Free and Reference-Free Read Compression. | Guillaume Holley, Roland Wittler, Jens Stoye, Faraz Hach |
| 2017 | RECOMB | Algorithms for Computing the Family-Free Genomic Similarity Under DCJ. | Diego P. Rubert, Gabriela Medeiros, Edna Ayako Hoshino, Marlia D. V. Braga, Jens Stoye, Fbio Viduani Martinez |
| 2017 | RECOMB | Finding Teams in Graphs and Its Application to Spatial Gene Cluster Discovery. | Tizian Schulz, Jens Stoye, Daniel Doerr |
| 2016 | RECOMB | New Genome Similarity Measures Based on Conserved Gene Adjacencies. | Luis Antonio Brasil Kowada, Daniel Doerr, Simone Dantas, Jens Stoye |
| 2016 | WABI | A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates. | Diego P. Rubert, Pedro Feijo, Marlia D. V. Braga, Jens Stoye, Fbio Viduani Martinez |
| 2015 | WABI | Bloom Filter Trie - A Data Structure for Pan-Genome Storage. | Guillaume Holley, Roland Wittler, Jens Stoye |
| 2014 | WABI | On the Family-Free DCJ Distance. | Fbio Viduani Martinez, Pedro Feijo, Marlia D. V. Braga, Jens Stoye |
| 2010 | RECOMB | The Problem of Chromosome Reincorporation in DCJ Sorting and Halving. | Jakub Kovc, Marlia D. V. Braga, Jens Stoye |
| 2010 | RECOMB | Consistency of Sequence-Based Gene Clusters. | Roland Wittler, Jens Stoye |
| 2010 | WABI | Genomic Distance with DCJ and Indels. | Marlia D. V. Braga, Eyla Willing, Jens Stoye |
| 2010 | WABI | Swiftly Computing Center Strings. | Franziska Hufsky, Lon Kuchenbecker, Katharina Jahn, Jens Stoye, Sebastian Bcker |
| 2009 | RECOMB | Finding Nested Common Intervals Efficiently. | Guillaume Blin, Jens Stoye |
| 2009 | RECOMB | Counting All DCJ Sorting Scenarios. | Marlia D. V. Braga, Jens Stoye |
| 2009 | RECOMB | Rearrangement Models and Single-Cut Operations. | Paul Medvedev, Jens Stoye |
| 2009 | WABI | Phylogenetic Comparative Assembly. | Peter Husemann, Jens Stoye |
| 2008 | CPM | HP Distance Via Double Cut and Join Distance. | Anne Bergeron, Julia Mixtacki, Jens Stoye |
| 2008 | RECOMB | On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios. | Anne Bergeron, Julia Mixtacki, Jens Stoye |
| 2008 | RECOMB | Computation of Median Gene Clusters. | Sebastian Bcker, Katharina Jahn, Julia Mixtacki, Jens Stoye |
| 2008 | WABI | Detecting Repeat Families in Incompletely Sequenced Genomes. | Jos Augusto Amgarten Quitzau, Jens Stoye |
| 2006 | ISMB | Finding novel genes in bacterial communities isolated from the environment. | Lutz Krause, Naryttza N. Diaz, Daniela Bartels, Robert A. Edwards, Alfred Phler, Forest Rohwer, Folker Meyer, Jens Stoye |
| 2006 | WABI | A Unifying View of Genome Rearrangements. | Anne Bergeron, Julia Mixtacki, Jens Stoye |
| 2005 | ALENEX | An Incomplex Algorithm for Fast Suffix Array Construction. | Klaus-Bernd Schrmann, Jens Stoye |
| 2005 | RECOMB | On Sorting by Translocations. | Anne Bergeron, Julia Mixtacki, Jens Stoye |
| 2005 | RECOMB | Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length. | Kim R. Rasmussen, Jens Stoye, Eugene W. Myers |
| 2005 | SPIRE | Counting Suffix Arrays and Strings. | Klaus-Bernd Schrmann, Jens Stoye |
| 2005 | WABI | Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI). | Michael Sammeth, Thomas Weniger, Dag Harmsen, Jens Stoye |
| 2004 | CPM | Reversal Distance without Hurdles and Fortresses. | Anne Bergeron, Julia Mixtacki, Jens Stoye |
| 2004 | CPM | Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences. | Thomas Schmidt, Jens Stoye |
| 2004 | WABI | Suboptimal Local Alignments Across Multiple Scoring Schemes. | Morris Michael, Christoph Dieterich, Jens Stoye |
| 2003 | COCOON | On the Similarity of Sets of Permutations and Its Applications to Genome Comparison. | Anne Bergeron, Jens Stoye |
| 2003 | ECCB | Divide-and-conquer multiple alignment with segment-based constraints. | Michael Sammeth, Burkhard Morgenstern, Jens Stoye |
| 2002 | ECCB | Common intervals and sorting by reversals: a marriage of necessity. | Anne Bergeron, Steffen Heber, Jens Stoye |
| 2002 | GI | Index Structures for Large Sequence Data: Suffix Trees and Affix Trees. | Jens Stoye |
| 2001 | CPM | Finding All Common Intervals of k Permutations. | Steffen Heber, Jens Stoye |
| 2001 | WABI | Algorithms for Finding Gene Clusters. | Steffen Heber, Jens Stoye |
| 2000 | ISMB | Computation and Visualization of Degenerate Repeats in Complete Genomes. | Stefan Kurtz, Enno Ohlebusch, Chris Schleiermacher, Jens Stoye, Robert Giegerich |
| 2000 | ISMB | Sequence Database Search Using Jumping Alignments. | Rainer Spang, Marc Rehmsmeier, Jens Stoye |
| 2000 | RECOMB | Contig selection in physical mapping. | Steffen Heber, Jens Stoye, Jrg D. Hoheisel, Martin Vingron |
| 1999 | CPM | Finding Maximal Pairs with Bounded Gap. | Gerth Stlting Brodal, Rune B. Lyngs, Christian N. S. Pedersen, Jens Stoye |
| 1998 | CPM | Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version). | Jens Stoye, Dan Gusfield |
| 1997 | ISMB | Generating Benchmarks for Multiple Sequence Alignments and Phylogenic Reconstructions. | Jens Stoye, Dirk Evers, Folker Meyer |