Jens Stoye

According to our database, Jens Stoye authored at least 129 papers between 1997 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Investigating the complexity of the double distance problems.

Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, Jens Stoye

Algorithms Mol. Biol., December, 2024

Closing the complexity gap of the double distance problem.

Luís Cunha, Thiago Lopes, Uéverton S. Souza, Marília D. V. Braga, Jens Stoye

CoRR, 2024

Reconstructing Rearrangement Phylogenies of Natural Genomes.

Leonard Bohnenkämper, Jens Stoye, Daniel Dörr

Proceedings of the 24th International Workshop on Algorithms in Bioinformatics, 2024

2023

On the Class of Double Distance Problems.

Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, Jens Stoye

Proceedings of the Comparative Genomics - 20th International Conference, 2023

2022

Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches.

Paola Bonizzoni, Matteo Costantini, Clelia de Felice, Alessia Petescia, Yuri Pirola, Marco Previtali, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza

Inf. Sci., 2022

A Linear Time Algorithm for an Extended Version of the Breakpoint Double Distance.

Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, Jens Stoye

Proceedings of the 22nd International Workshop on Algorithms in Bioinformatics, 2022

2021

Computing the Inversion-Indel Distance.

Eyla Willing, Jens Stoye, Marília D. V. Braga

IEEE ACM Trans. Comput. Biol. Bioinform., 2021

Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine.

Linda K. Sundermann, Jeff Wintersinger, Gunnar Rätsch, Jens Stoye, Quaid Morris

PLoS Comput. Biol., 2021

Computing the Rearrangement Distance of Natural Genomes.

Leonard Bohnenkämper, Marília D. V. Braga, Daniel Doerr, Jens Stoye

J. Comput. Biol., 2021

Detecting high-scoring local alignments in pangenome graphs.

Tizian Schulz, Roland Wittler, Sven Rahmann, Faraz Hach, Jens Stoye

Bioinform., 2021

Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning.

Paola Bonizzoni, Clelia De Felice, Alessia Petescia, Yuri Pirola, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza

Proceedings of the Algorithms for Computational Biology - 8th International Conference, 2021

2020

Searching and inferring colorful topological motifs in vertex-colored graphs.

Diego P. Rubert, Eloi Araujo, Marco Aurelio Stefanes, Jens Stoye, Fábio Viduani Martinez

J. Comb. Optim., 2020

On motifs in colored graphs.

Diego P. Rubert, Eloi Araujo, Marco Aurelio Stefanes, Jens Stoye, Fábio Viduani Martinez

CoRR, 2020

Finding all maximal perfect haplotype blocks in linear time.

Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, Jens Stoye

Algorithms Mol. Biol., 2020

2019

25 Years of the Burrows-Wheeler Transform (Dagstuhl Seminar 19241).

Travis Gagie, Giovanni Manzini, Gonzalo Navarro, Jens Stoye

Dagstuhl Reports, 2019

2018

Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework.

Nina Luhmann, Cédric Chauve, Jens Stoye, Roland Wittler

IEEE ACM Trans. Comput. Biol. Bioinform., 2018

Dynamic Alignment-Free and Reference-Free Read Compression.

Guillaume Holley, Roland Wittler, Jens Stoye, Faraz Hach

J. Comput. Biol., 2018

Computing the family-free DCJ similarity.

Diego P. Rubert, Edna Ayako Hoshino, Marília D. V. Braga, Jens Stoye, Fábio Viduani Martinez

BMC Bioinform., 2018

Identifying Maximal Perfect Haplotype Blocks.

Luís Felipe I. Cunha, Yoan Diekmann, Luis Antonio Brasil Kowada, Jens Stoye

Proceedings of the Advances in Bioinformatics and Computational Biology, 2018

2017

New Genome Similarity Measures based on Conserved Gene Adjacencies.

Daniel Doerr, Luis Antonio Brasil Kowada, Eloi Araujo, Shachi Deshpande, Simone Dantas, Bernard M. E. Moret, Jens Stoye

J. Comput. Biol., 2017

Fast and Simple Jumbled Indexing for Binary RLE Strings.

Luís Felipe I. Cunha, Simone Dantas, Travis Gagie, Roland Wittler, Luis Antonio Brasil Kowada, Jens Stoye

CoRR, 2017

Approximating the DCJ distance of balanced genomes in linear time.

Diego P. Rubert, Pedro Feijão, Marília Dias Vieira Braga, Jens Stoye, Fábio Viduani Martinez

Algorithms Mol. Biol., 2017

Finding Teams in Graphs and Its Application to Spatial Gene Cluster Discovery.

Tizian Schulz, Jens Stoye, Daniel Doerr

Proceedings of the Comparative Genomics - 15th International Workshop, 2017

Algorithms for Computing the Family-Free Genomic Similarity Under DCJ.

Diego P. Rubert, Gabriela Medeiros, Edna Ayako Hoshino, Marília D. V. Braga, Jens Stoye, Fábio Viduani Martinez

Proceedings of the Comparative Genomics - 15th International Workshop, 2017

Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings.

Luís Felipe I. Cunha, Simone Dantas, Travis Gagie, Roland Wittler, Luis Antonio Brasil Kowada, Jens Stoye

Proceedings of the 28th Annual Symposium on Combinatorial Pattern Matching, 2017

2016

Suffix Tree Construction.

Jens Stoye

Encyclopedia of Algorithms, 2016

Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage.

Guillaume Holley, Roland Wittler, Jens Stoye

Algorithms Mol. Biol., 2016

A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates.

Diego P. Rubert, Pedro Feijão, Marília D. V. Braga, Jens Stoye, Fábio Viduani Martinez

Proceedings of the Algorithms in Bioinformatics - 16th International Workshop, 2016

New Genome Similarity Measures Based on Conserved Gene Adjacencies.

Luis Antonio Brasil Kowada, Daniel Doerr, Simone Dantas, Jens Stoye

Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

2015

Sorting Linear Genomes with Rearrangements and Indels.

Marília D. V. Braga, Jens Stoye

IEEE ACM Trans. Comput. Biol. Bioinform., 2015

On the family-free DCJ distance and similarity.

Fábio Viduani Martinez, Pedro Feijão, Marília D. V. Braga, Jens Stoye

Algorithms Mol. Biol., 2015

Bloom Filter Trie - A Data Structure for Pan-Genome Storage.

Guillaume Holley, Roland Wittler, Jens Stoye

Proceedings of the Algorithms in Bioinformatics - 15th International Workshop, 2015

2014

Editorial.

Jens Stoye, Juha Kärkkäinen

J. Discrete Algorithms, 2014

BiPACE 2D - graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry.

Nils Hoffmann, Mathias Wilhelm, Anja Doebbe, Karsten Niehaus, Jens Stoye

Bioinform., 2014

ReadXplorer - visualization and analysis of mapped sequences.

Rolf Hilker, Kai Bernd Stadermann, Daniel Doppmeier, Jörn Kalinowski, Jens Stoye, Jasmin Straube, Jörn Winnebald, Alexander Goesmann

Bioinform., 2014

On the Family-Free DCJ Distance.

Fábio Viduani Martinez, Pedro Feijão, Marília D. V. Braga, Jens Stoye

Proceedings of the Algorithms in Bioinformatics - 14th International Workshop, 2014

2013

On the inversion-indel distance.

Eyla Willing, Simone Zaccaria, Marília D. V. Braga, Jens Stoye

BMC Bioinform., 2013

Statistics for approximate gene clusters.

Katharina Jahn, Sascha Winter, Jens Stoye, Sebastian Böcker

BMC Bioinform., 2013

metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences.

Christina Ander, Ole Schulz-Trieglaff, Jens Stoye, Anthony J. Cox

BMC Bioinform., 2013

Restricted DCJ-Indel Model Revisited.

Marília D. V. Braga, Jens Stoye

Proceedings of the Advances in Bioinformatics and Computational Biology, 2013

The Potential of Family-Free Genome Comparison.

Marília D. V. Braga, Cédric Chauve, Daniel Doerr, Katharina Jahn, Jens Stoye, Annelyse Thévenin, Roland Wittler

Proceedings of the Models and Algorithms for Genome Evolution, 2013

The Genesis of the DCJ Formula.

Anne Bergeron, Jens Stoye

Proceedings of the Models and Algorithms for Genome Evolution, 2013

2012

Multiple genome comparison based on overlap regions of pairwise local alignments.

Katharina Jahn, Henner Sudek, Jens Stoye

BMC Bioinform., 2012

Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets.

Nils Hoffmann, Matthias Keck, Heiko Neuweger, Mathias Wilhelm, Petra Högy, Karsten Niehaus, Jens Stoye

BMC Bioinform., 2012

Gene family assignment-free comparative genomics.

Daniel Doerr, Annelyse Thévenin, Jens Stoye

BMC Bioinform., 2012

UniMoG - a unifying framework for genomic distance calculation and sorting based on DCJ.

Rolf Hilker, Corinna Sickinger, Christian N. S. Pedersen, Jens Stoye

Bioinform., 2012

2011

Consistency of Sequence-Based Gene Clusters.

Roland Wittler, Ján Manuch, Murray Patterson, Jens Stoye

J. Comput. Biol., 2011

Restricted DCJ Model: Rearrangement Problems with Chromosome Reincorporation.

Jakub Kovác, Robert Warren, Marília D. V. Braga, Jens Stoye

J. Comput. Biol., 2011

Double Cut and Join with Insertions and Deletions.

Marília D. V. Braga, Eyla Willing, Jens Stoye

J. Comput. Biol., 2011

Swiftly Computing Center Strings.

Franziska Hufsky, Léon Kuchenbecker, Katharina Jahn, Jens Stoye, Sebastian Böcker

BMC Bioinform., 2011

On the weight of indels in genomic distances.

Marília D. V. Braga, Raphael Machado, Leonardo Costa Ribeiro, Jens Stoye

BMC Bioinform., 2011

Genomic distance under gene substitutions.

Marília D. V. Braga, Raphael Machado, Leonardo Costa Ribeiro, Jens Stoye

BMC Bioinform., 2011

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming.

Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jörn Kalinowski, Jens Stoye, Alexander Goesmann

Bioinform., 2011

Balanced vertices in trees and a simpler algorithm to compute the genomic distance.

Péter L. Erdös, Lajos Soukup, Jens Stoye

Appl. Math. Lett., 2011

Common Intervals of Multiple Permutations.

Steffen Heber, Richard Mayr, Jens Stoye

Algorithmica, 2011

2010

The Solution Space of Sorting by DCJ.

Marília D. V. Braga, Jens Stoye

J. Comput. Biol., 2010

Finding Nested Common Intervals Efficiently.

Guillaume Blin, David C. Faye, Jens Stoye

J. Comput. Biol., 2010

Rearrangement Models and Single-Cut Operations.

Anne Bergeron, Paul Medvedev, Jens Stoye

J. Comput. Biol., 2010

r2cat: synteny plots and comparative assembly.

Peter Husemann, Jens Stoye

Bioinform., 2010

Phylogenetic comparative assembly.

Peter Husemann, Jens Stoye

Algorithms Mol. Biol., 2010

Genomic Distance with DCJ and Indels.

Marília D. V. Braga, Eyla Willing, Jens Stoye

Proceedings of the Algorithms in Bioinformatics, 10th International Workshop, 2010

Consistency of Sequence-Based Gene Clusters.

Roland Wittler, Jens Stoye

Proceedings of the Comparative Genomics - International Workshop, 2010

The Problem of Chromosome Reincorporation in DCJ Sorting and Halving.

Jakub Kovác, Marília D. V. Braga, Jens Stoye

Proceedings of the Comparative Genomics - International Workshop, 2010

Repeat-aware Comparative Genome Assembly.

Peter Husemann, Jens Stoye

Proceedings of the German Conference on Bioinformatics 2010, 2010

Indexing and Searching a Mass Spectrometry Database.

Søren Besenbacher, Benno Schwikowski, Jens Stoye

Proceedings of the Algorithms and Applications, 2010

2009

A new linear time algorithm to compute the genomic distance via the double cut and join distance.

Anne Bergeron, Julia Mixtacki, Jens Stoye

Theor. Comput. Sci., 2009

A Unified Approach for Reconstructing Ancient Gene Clusters.

Jens Stoye, Roland Wittler

IEEE ACM Trans. Comput. Biol. Bioinform., 2009

Computation of Median Gene Clusters.

Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye

J. Comput. Biol., 2009

Approximative Gencluster und ihre Anwendung in der komparativen Genomik.

Katharina Jahn, Jens Stoye

Inform. Spektrum, 2009

WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads.

Wolfgang Gerlach, Sebastian Jünemann, Felix Tille, Alexander Goesmann, Jens Stoye

BMC Bioinform., 2009

ChromA: signal-based retention time alignment for chromatography-mass spectrometry data.

Nils Hoffmann, Jens Stoye

Bioinform., 2009

A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG).

Michael Brudno, Paul Medvedev, Jens Stoye, Francisco M. de la Vega

Bioinform., 2009

Rearrangement Models and Single-Cut Operations.

Paul Medvedev, Jens Stoye

Proceedings of the Comparative Genomics, International Workshop, 2009

Counting All DCJ Sorting Scenarios.

Marília D. V. Braga, Jens Stoye

Proceedings of the Comparative Genomics, International Workshop, 2009

Finding Nested Common Intervals Efficiently.

Guillaume Blin, Jens Stoye

Proceedings of the Comparative Genomics, International Workshop, 2009

2008

Suffix Tree Construction in RAM.

Jens Stoye

Proceedings of the Encyclopedia of Algorithms - 2008 Edition, 2008

Counting suffix arrays and strings.

Klaus-Bernd Schürmann, Jens Stoye

Theor. Comput. Sci., 2008

Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms.

Sebastian Oehm, David R. Gilbert, Andreas Tauch, Jens Stoye, Alexander Goesmann

Nucleic Acids Res., 2008

MeltDB: a software platform for the analysis and integration of metabolomics experiment data.

Heiko Neuweger, Stefan P. Albaum, Michael Dondrup, Marcus Persicke, Tony Watt, Karsten Niehaus, Jens Stoye, Alexander Goesmann

Bioinform., 2008

Detecting Repeat Families in Incompletely Sequenced Genomes.

José Augusto Amgarten Quitzau, Jens Stoye

Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios.

Anne Bergeron, Julia Mixtacki, Jens Stoye

Proceedings of the Comparative Genomics, International Workshop, 2008

HP Distance Via Double Cut and Join Distance.

Anne Bergeron, Julia Mixtacki, Jens Stoye

Proceedings of the Combinatorial Pattern Matching, 19th Annual Symposium, 2008

2007

An incomplex algorithm for fast suffix array construction.

Klaus-Bernd Schürmann, Jens Stoye

Softw. Pract. Exp., 2007

Character sets of strings.

Gilles Didier, Thomas Schmidt, Jens Stoye, Dekel Tsur

J. Discrete Algorithms, 2007

The inversion distance problem.

Anne Bergeron, Julia Mixtacki, Jens Stoye

Proceedings of the Mathematics of Evolution and Phylogeny., 2007

2006

Comparing Tandem Repeats with Duplications and Excisions of Variable Degree.

Michael Sammeth, Jens Stoye

IEEE ACM Trans. Comput. Biol. Bioinform., 2006

Efficient <i>q</i>-Gram Filters for Finding All <i>epsilon</i>-Matches over a Given Length.

Kim R. Rasmussen, Jens Stoye, Eugene W. Myers

J. Comput. Biol., 2006

On the Similarity of Sets of Permutations and Its Applications to Genome Comparison.

Anne Bergeron, Jens Stoye

J. Comput. Biol., 2006

On Sorting by Translocations.

Anne Bergeron, Julia Mixtacki, Jens Stoye

J. Comput. Biol., 2006

<i>Panta rhei</i> (QAlign2): an open graphical environment for sequence analysis.

Michael Sammeth, Thasso Griebel, Felix Tille, Jens Stoye

Bioinform., 2006

A Unifying View of Genome Rearrangements.

Anne Bergeron, Julia Mixtacki, Jens Stoye

Proceedings of the Algorithms in Bioinformatics, 6th International Workshop, 2006

Finding novel genes in bacterial communities isolated from the environment.

Lutz Krause, Naryttza N. Diaz, Daniela Bartels, Robert A. Edwards, Alfred Pühler, Forest Rohwer, Folker Meyer, Jens Stoye

Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

2005

Large scale hierarchical clustering of protein sequences.

Antje Krause, Jens Stoye, Martin Vingron

BMC Bioinform., 2005

BACCardI-a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison.

Daniela Bartels, Sebastian Kespohl, Stefan P. Albaum, Tanja Drüke, Alexander Goesmann, Julia Herold, Olaf Kaiser, Alfred Pühler, Friedhelm Pfeiffer, Günter Raddatz, Jens Stoye, Folker Meyer, Stephan C. Schuster

Bioinform., 2005

Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI).

Michael Sammeth, Thomas Weniger, Dag Harmsen, Jens Stoye

Proceedings of the Algorithms in Bioinformatics, 5th International Workshop, 2005

Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length.

Kim R. Rasmussen, Jens Stoye, Eugene W. Myers

Proceedings of the Research in Computational Molecular Biology, 2005

Protein Annotation by Secondary Structure Based Alignments (PASSTA).

Constantin Bannert, Jens Stoye

Proceedings of the Computational Life Sciences, First International Symposium, 2005

2004

Linear time algorithms for finding and representing all the tandem repeats in a string.

Dan Gusfield, Jens Stoye

J. Comput. Syst. Sci., 2004

Algorithmic complexity of protein identification: combinatorics of weighted strings.

Mark Cieliebak, Thomas Erlebach, Zsuzsanna Lipták, Jens Stoye, Emo Welzl

Discret. Appl. Math., 2004

Correction: Benchmarking tools for the alignment of functional noncodingDNA.

Daniel A. Pollard, Casey M. Bergman, Jens Stoye, Susan E. Celniker, Michael B. Eisen

BMC Bioinform., 2004

Benchmarking tools for the alignment of functional noncoding DNA.

Daniel A. Pollard, Casey M. Bergman, Jens Stoye, Susan E. Celniker, Michael B. Eisen

BMC Bioinform., 2004

Suboptimal Local Alignments Across Multiple Scoring Schemes.

Morris Michael, Christoph Dieterich, Jens Stoye

Proceedings of the Algorithms in Bioinformatics, 4th International Workshop, 2004

Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences.

Thomas Schmidt, Jens Stoye

Proceedings of the Combinatorial Pattern Matching, 15th Annual Symposium, 2004

Reversal Distance without Hurdles and Fortresses.

Anne Bergeron, Julia Mixtacki, Jens Stoye

Proceedings of the Combinatorial Pattern Matching, 15th Annual Symposium, 2004

2003

Efficient implementation of lazy suffix trees.

Robert Giegerich, Stefan Kurtz, Jens Stoye

Softw. Pract. Exp., 2003

Digital extractor: analysis of digital differential display output.

Michael Sammeth, Jörg Rothgänger, W. Esser, Jürgen Albert, Jens Stoye, Dag Harmsen

Bioinform., 2003

Evaluation of the Jumping Alignment algorithm with artificial and biological data.

Constantin Bannert, Jens Stoye

Proceedings of the German Conference on Bioinformatics, 2003

Divide-and-conquer multiple alignment with segment-based constraints.

Michael Sammeth, Burkhard Morgenstern, Jens Stoye

Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003

2002

Simple and flexible detection of contiguous repeats using a suffix tree.

Jens Stoye, Dan Gusfield

Theor. Comput. Sci., 2002

A Novel Approach to Remote Homology Detection: Jumping Alignments.

Rainer Spang, Marc Rehmsmeier, Jens Stoye

J. Comput. Biol., 2002

Algorithmic Complexity of Protein Identification: Searching in Weighted Strings.

Mark Cieliebak, Thomas Erlebach, Zsuzsanna Lipták, Jens Stoye, Emo Welzl

Proceedings of the Foundations of Information Technology in the Era of Networking and Mobile Computing, 2002

Index Structures for Large Sequence Data: Suffix Trees and Affix Trees.

Jens Stoye

Proceedings of the 32. Jahrestagung der Gesellschaft für Informatik, Informatik bewegt, INFORMATIK 2002, Dortmund, Germany, September 30, 2002

Common intervals and sorting by reversals: a marriage of necessity.

Anne Bergeron, Steffen Heber, Jens Stoye

Proceedings of the European Conference on Computational Biology (ECCB 2002), 2002

2001

Algorithms for Finding Gene Clusters.

Steffen Heber, Jens Stoye

Proceedings of the Algorithms in Bioinformatics, First International Workshop, 2001

Sequence Database Search Using Jumping Alignments.

Constantin Bannert, Marc Rehmsmeier, Rainer Spang, Jens Stoye

Proceedings of the Computer science and biology: Proceedings of the German Conference on Bioinformatics, 2001

Finding All Common Intervals of k Permutations.

Steffen Heber, Jens Stoye

Proceedings of the Combinatorial Pattern Matching, 12th Annual Symposium, 2001

2000

The SYSTERS protein sequence cluster set.

Antje Krause, Jens Stoye, Martin Vingron

Nucleic Acids Res., 2000

Contig Selection in Physical Mapping.

Steffen Heber, Jens Stoye, Marcus Frohme, Jörg D. Hoheisel, Martin Vingron

J. Comput. Biol., 2000

An iterative method for faster sum-of-pairs multiple sequence alignment.

Knut Reinert, Jens Stoye, Torsten Will

Bioinform., 2000

Contig selection in physical mapping.

Steffen Heber, Jens Stoye, Jörg D. Hoheisel, Martin Vingron

Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 2000

Sequence Database Search Using Jumping Alignments.

Rainer Spang, Marc Rehmsmeier, Jens Stoye

Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000

Computation and Visualization of Degenerate Repeats in Complete Genomes.

Stefan Kurtz, Enno Ohlebusch, Chris Schleiermacher, Jens Stoye, Robert Giegerich

Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000

1999

Combining Divide-and-Conquer, the A^*-Algorithm, and Successive Realignment Approaches to Speed Multiple Sequence Alignment.

Knut Reinert, Jens Stoye, Torsten Will

Proceedings of the German Conference on Bioinformatics, 1999

Finding Maximal Pairs with Bounded Gap.

Gerth Stølting Brodal, Rune B. Lyngsø, Christian N. S. Pedersen, Jens Stoye

Proceedings of the Combinatorial Pattern Matching, 10th Annual Symposium, 1999

1998

Rose: generating sequence families.

Jens Stoye, Dirk Evers, Folker Meyer

Bioinform., 1998

Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version).

Jens Stoye, Dan Gusfield

Proceedings of the Combinatorial Pattern Matching, 9th Annual Symposium, 1998

1997

Two applications of the Divide&Conquer principle in the molecular sciences.

Gunnar Brinkmann, Andreas W. M. Dress, Sören Perrey, Jens Stoye

Math. Program., 1997

DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment.

Jens Stoye, Vincent Moulton, Andreas W. M. Dress

Comput. Appl. Biosci., 1997

Generating Benchmarks for Multiple Sequence Alignments and Phylogenic Reconstructions.

Jens Stoye, Dirk Evers, Folker Meyer

Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997