Jens Stoye - RankMe

154 papers A 3B 15C 18Misc 1Journal 84Unranked 25

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Closing the Complexity Gap of the Double Distance Problem. IEEE Trans. Comput. Biol. Bioinform. Luís Cunha, Thiago Lopes, Uéverton S. Souza, Leonard Bohnenkämper, Marília D. V. Braga, Jens Stoye
2025	—	`ed.`	Information Theory and Related Fields - Festschrift in Memory of Ning Cai Information Theory and Related Fields Christian Deppe, Andreas J. Winter, Raymond W. Yeung, Holger Boche, Ingo Althöfer, Jens Stoye, Ulrich Tamm, Rami Ezzine
2025	J	`jnl`	Reconstructing rearrangement phylogenies of natural genomes. Algorithms Mol. Biol. Leonard Bohnenkämper, Jens Stoye, Daniel Doerr
2024	J	`jnl`	Closing the complexity gap of the double distance problem. CoRR Luís Cunha, Thiago Lopes, Uéverton S. Souza, Marília D. V. Braga, Jens Stoye
2024	J	`jnl`	Investigating the complexity of the double distance problems. Algorithms Mol. Biol. Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, Jens Stoye
2024	J	`jnl`	Panacus: fast and exact pangenome growth and core size estimation. Bioinform. Luca Parmigiani, Erik Garrison, Jens Stoye, Tobias Marschall, Daniel Doerr
2024	C	`conf`	Reconstructing Rearrangement Phylogenies of Natural Genomes. WABI Leonard Bohnenkämper, Jens Stoye, Daniel Dörr
2023	J	`jnl`	Investigating the complexity of the double distance problems. CoRR Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, Jens Stoye
2023	—	`conf`	On the Class of Double Distance Problems. RECOMB-CG Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, Jens Stoye
2022	C	`conf`	A Linear Time Algorithm for an Extended Version of the Breakpoint Double Distance. WABI Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, Jens Stoye
2022	J	`jnl`	Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches. CoRR Paola Bonizzoni, Matteo Costantini, Clelia De Felice, Alessia Petescia, Yuri Pirola, Marco Previtali, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza
2022	J	`jnl`	Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches. Inf. Sci. Paola Bonizzoni, Matteo Costantini, Clelia De Felice, Alessia Petescia, Yuri Pirola, Marco Previtali, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza
2021	—	`conf`	Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning. AlCoB Paola Bonizzoni, Clelia De Felice, Alessia Petescia, Yuri Pirola, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza
2021	J	`jnl`	Computing the Inversion-Indel Distance. IEEE ACM Trans. Comput. Biol. Bioinform. Eyla Willing, Jens Stoye, Marília D. V. Braga
2021	J	`jnl`	Computing the Rearrangement Distance of Natural Genomes. J. Comput. Biol. Leonard Bohnenkämper, Marília D. V. Braga, Daniel Doerr, Jens Stoye
2021	J	`jnl`	Detecting high-scoring local alignments in pangenome graphs. Bioinform. Tizian Schulz, Roland Wittler, Sven Rahmann, Faraz Hach, Jens Stoye
2021	J	`jnl`	Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine. PLoS Comput. Biol. Linda K. Sundermann, Jeff Wintersinger, Gunnar Rätsch, Jens Stoye, Quaid Morris
2020	B	`conf`	Computing the Rearrangement Distance of Natural Genomes. RECOMB Leonard Bohnenkämper, Marília D. V. Braga, Daniel Doerr, Jens Stoye
2020	J	`jnl`	Computing the rearrangement distance of natural genomes. CoRR Leonard Bohnenkämper, Marília D. V. Braga, Daniel Doerr, Jens Stoye
2020	J	`jnl`	Finding all maximal perfect haplotype blocks in linear time. Algorithms Mol. Biol. Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, Jens Stoye
2020	J	`jnl`	On motifs in colored graphs. CoRR Diego P. Rubert, Eloi Araujo, Marco Aurelio Stefanes, Jens Stoye, Fábio Viduani Martinez
2020	J	`jnl`	Searching and inferring colorful topological motifs in vertex-colored graphs. J. Comb. Optim. Diego P. Rubert, Eloi Araujo, Marco Aurelio Stefanes, Jens Stoye, Fábio Viduani Martinez
2019	J	`jnl`	25 Years of the Burrows-Wheeler Transform (Dagstuhl Seminar 19241). Dagstuhl Reports Travis Gagie, Giovanni Manzini, Gonzalo Navarro, Jens Stoye
2019	J	`jnl`	Computing the Inversion-Indel Distance. CoRR Eyla Willing, Jens Stoye, Marília D. V. Braga
2019	C	`conf`	Finding All Maximal Perfect Haplotype Blocks in Linear Time. WABI Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, Jens Stoye
2018	J	`jnl`	Computing the family-free DCJ similarity. BMC Bioinform. Diego P. Rubert, Edna Ayako Hoshino, Marília D. V. Braga, Jens Stoye, Fábio Viduani Martinez
2018	J	`jnl`	Dynamic Alignment-Free and Reference-Free Read Compression. J. Comput. Biol. Guillaume Holley, Roland Wittler, Jens Stoye, Faraz Hach
2018	—	`conf`	Identifying Maximal Perfect Haplotype Blocks. BSB Luís Felipe I. Cunha, Yoan Diekmann, Luis A. B. Kowada, Jens Stoye
2018	J	`jnl`	Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework. IEEE ACM Trans. Comput. Biol. Bioinform. Nina Luhmann, Cédric Chauve, Jens Stoye, Roland Wittler
2017	—	`conf`	Algorithms for Computing the Family-Free Genomic Similarity Under DCJ. RECOMB-CG Diego P. Rubert, Gabriela Medeiros, Edna Ayako Hoshino, Marília D. V. Braga, Jens Stoye, Fábio Viduani Martinez
2017	J	`jnl`	Approximating the DCJ distance of balanced genomes in linear time. Algorithms Mol. Biol. Diego P. Rubert, Pedro Feijão, Marília Dias Vieira Braga, Jens Stoye, Fábio Viduani Martinez
2017	B	`conf`	Dynamic Alignment-Free and Reference-Free Read Compression. RECOMB Guillaume Holley, Roland Wittler, Jens Stoye, Faraz Hach
2017	J	`jnl`	Fast and Simple Jumbled Indexing for Binary RLE Strings. CoRR Luís Felipe I. Cunha, Simone Dantas, Travis Gagie, Roland Wittler, Luis A. B. Kowada, Jens Stoye
2017	B	`conf`	Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings. CPM Luís Felipe I. Cunha, Simone Dantas, Travis Gagie, Roland Wittler, Luis A. B. Kowada, Jens Stoye
2017	—	`conf`	Finding Teams in Graphs and Its Application to Spatial Gene Cluster Discovery. RECOMB-CG Tizian Schulz, Jens Stoye, Daniel Doerr
2017	J	`jnl`	New Genome Similarity Measures based on Conserved Gene Adjacencies. J. Comput. Biol. Daniel Doerr, Luis Antonio Brasil Kowada, Eloi Araujo, Shachi Deshpande, Simone Dantas, Bernard M. E. Moret, Jens Stoye
2016	C	`conf`	A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates. WABI Diego P. Rubert, Pedro Feijão, Marília D. V. Braga, Jens Stoye, Fábio Viduani Martinez
2016	J	`jnl`	Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage. Algorithms Mol. Biol. Guillaume Holley, Roland Wittler, Jens Stoye
2016	B	`conf`	New Genome Similarity Measures Based on Conserved Gene Adjacencies. RECOMB Luis Antonio Brasil Kowada, Daniel Doerr, Simone Dantas, Jens Stoye
2016	—	`ch.`	Suffix Tree Construction. Encyclopedia of Algorithms Jens Stoye
2015	C	`conf`	Bloom Filter Trie - A Data Structure for Pan-Genome Storage. WABI Guillaume Holley, Roland Wittler, Jens Stoye
2015	J	`jnl`	On the family-free DCJ distance and similarity. Algorithms Mol. Biol. Fábio Viduani Martinez, Pedro Feijão, Marília D. V. Braga, Jens Stoye
2015	J	`jnl`	Sorting Linear Genomes with Rearrangements and Indels. IEEE ACM Trans. Comput. Biol. Bioinform. Marília D. V. Braga, Jens Stoye
2014	J	`jnl`	BiPACE 2D - graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry. Bioinform. Nils Hoffmann, Mathias Wilhelm, Anja Doebbe, Karsten Niehaus, Jens Stoye
2014	J	`jnl`	Editorial. J. Discrete Algorithms Jens Stoye, Juha Kärkkäinen
2014	C	`conf`	On the Family-Free DCJ Distance. WABI Fábio Viduani Martinez, Pedro Feijão, Marília D. V. Braga, Jens Stoye
2014	J	`jnl`	ReadXplorer - visualization and analysis of mapped sequences. Bioinform. Rolf Hilker, Kai Bernd Stadermann, Daniel Doppmeier, Jörn Kalinowski, Jens Stoye, Jasmin Straube, Jörn Winnebald, Alexander Goesmann
2014	—	`conf`	Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework. BSB Nina Luhmann, Cédric Chauve, Jens Stoye, Roland Wittler
2013	C	`ed.`	Algorithms in Bioinformatics - 13th International Workshop, WABI 2013, Sophia Antipolis, France, September 2-4, 2013. Proceedings WABI Aaron E. Darling, Jens Stoye
2013	J	`jnl`	On the inversion-indel distance. BMC Bioinform. Eyla Willing, Simone Zaccaria, Marília D. V. Braga, Jens Stoye
2013	—	`conf`	Restricted DCJ-Indel Model Revisited. BSB Marília D. V. Braga, Jens Stoye
2013	J	`jnl`	Statistics for approximate gene clusters. BMC Bioinform. Katharina Jahn, Sascha Winter, Jens Stoye, Sebastian Böcker
2013	—	`ch.`	The Genesis of the DCJ Formula. Models and Algorithms for Genome Evolution Anne Bergeron, Jens Stoye
2013	—	`ch.`	The Potential of Family-Free Genome Comparison. Models and Algorithms for Genome Evolution Marília D. V. Braga, Cédric Chauve, Daniel Doerr, Katharina Jahn, Jens Stoye, Annelyse Thévenin, Roland Wittler
2013	J	`jnl`	metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences. BMC Bioinform. Christina Ander, Ole Schulz-Trieglaff, Jens Stoye, Anthony J. Cox
2012	B	`ed.`	Combinatorial Pattern Matching - 23rd Annual Symposium, CPM 2012, Helsinki, Finland, July 3-5, 2012. Proceedings CPM Juha Kärkkäinen, Jens Stoye
2012	J	`jnl`	Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets. BMC Bioinform. Nils Hoffmann, Matthias Keck, Heiko Neuweger, Mathias Wilhelm, Petra Högy, Karsten Niehaus, Jens Stoye
2012	J	`jnl`	Gene family assignment-free comparative genomics. BMC Bioinform. Daniel Doerr, Annelyse Thévenin, Jens Stoye
2012	J	`jnl`	Multiple genome comparison based on overlap regions of pairwise local alignments. BMC Bioinform. Katharina Jahn, Henner Sudek, Jens Stoye
2012	J	`jnl`	UniMoG - a unifying framework for genomic distance calculation and sorting based on DCJ. Bioinform. Rolf Hilker, Corinna Sickinger, Christian N. S. Pedersen, Jens Stoye
2011	J	`jnl`	Balanced vertices in trees and a simpler algorithm to compute the genomic distance. Appl. Math. Lett. Péter L. Erdös, Lajos Soukup, Jens Stoye
2011	J	`jnl`	Common Intervals of Multiple Permutations. Algorithmica Steffen Heber, Richard Mayr, Jens Stoye
2011	J	`jnl`	Consistency of Sequence-Based Gene Clusters. J. Comput. Biol. Roland Wittler, Ján Manuch, Murray Patterson, Jens Stoye
2011	J	`jnl`	Double Cut and Join with Insertions and Deletions. J. Comput. Biol. Marília D. V. Braga, Eyla Willing, Jens Stoye
2011	J	`jnl`	Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. Bioinform. Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jörn Kalinowski, Jens Stoye, Alexander Goesmann
2011	J	`jnl`	Genomic distance under gene substitutions. BMC Bioinform. Marília D. V. Braga, Raphael Machado, Leonardo Costa Ribeiro, Jens Stoye
2011	J	`jnl`	On the weight of indels in genomic distances. BMC Bioinform. Marília D. V. Braga, Raphael Machado, Leonardo Costa Ribeiro, Jens Stoye
2011	J	`jnl`	Restricted DCJ Model: Rearrangement Problems with Chromosome Reincorporation. J. Comput. Biol. Jakub Kovác, Robert Warren, Marília D. V. Braga, Jens Stoye
2011	J	`jnl`	Swiftly Computing Center Strings. BMC Bioinform. Franziska Hufsky, Léon Kuchenbecker, Katharina Jahn, Jens Stoye, Sebastian Böcker
2010	—	`conf`	A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance. Structure Discovery in Biology: Motifs, Networks & Phylogenies Anne Bergeron, Julia Mixtacki, Jens Stoye
2010	J	`jnl`	Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance CoRR Péter L. Erdös, Lajos Soukup, Jens Stoye
2010	—	`conf`	Consistency of Sequence-Based Gene Clusters. RECOMB-CG Roland Wittler, Jens Stoye
2010	J	`jnl`	Finding Nested Common Intervals Efficiently. J. Comput. Biol. Guillaume Blin, David C. Faye, Jens Stoye
2010	C	`conf`	Genomic Distance with DCJ and Indels. WABI Marília D. V. Braga, Eyla Willing, Jens Stoye
2010	—	`conf`	Indexing and Searching a Mass Spectrometry Database. Algorithms and Applications Søren Besenbacher, Benno Schwikowski, Jens Stoye
2010	J	`jnl`	Phylogenetic comparative assembly. Algorithms Mol. Biol. Peter Husemann, Jens Stoye
2010	J	`jnl`	Rearrangement Models and Single-Cut Operations. J. Comput. Biol. Anne Bergeron, Paul Medvedev, Jens Stoye
2010	—	`conf`	Repeat-aware Comparative Genome Assembly. GCB Peter Husemann, Jens Stoye
2010	C	`conf`	Swiftly Computing Center Strings. WABI Franziska Hufsky, Léon Kuchenbecker, Katharina Jahn, Jens Stoye, Sebastian Böcker
2010	—	`conf`	The Problem of Chromosome Reincorporation in DCJ Sorting and Halving. RECOMB-CG Jakub Kovác, Marília D. V. Braga, Jens Stoye
2010	J	`jnl`	The Solution Space of Sorting by DCJ. J. Comput. Biol. Marília D. V. Braga, Jens Stoye
2010	J	`jnl`	r2cat: synteny plots and comparative assembly. Bioinform. Peter Husemann, Jens Stoye
2009	J	`jnl`	A Unified Approach for Reconstructing Ancient Gene Clusters. IEEE ACM Trans. Comput. Biol. Bioinform. Jens Stoye, Roland Wittler
2009	J	`jnl`	A new linear time algorithm to compute the genomic distance via the double cut and join distance. Theor. Comput. Sci. Anne Bergeron, Julia Mixtacki, Jens Stoye
2009	J	`jnl`	A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG). Bioinform. Michael Brudno, Paul Medvedev, Jens Stoye, Francisco M. de la Vega
2009	J	`jnl`	Approximative Gencluster und ihre Anwendung in der komparativen Genomik. Inform. Spektrum Katharina Jahn, Jens Stoye
2009	J	`jnl`	ChromA: signal-based retention time alignment for chromatography-mass spectrometry data. Bioinform. Nils Hoffmann, Jens Stoye
2009	J	`jnl`	Computation of Median Gene Clusters. J. Comput. Biol. Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye
2009	—	`conf`	Counting All DCJ Sorting Scenarios. RECOMB-CG Marília D. V. Braga, Jens Stoye
2009	—	`conf`	Finding Nested Common Intervals Efficiently. RECOMB-CG Guillaume Blin, Jens Stoye
2009	C	`conf`	Phylogenetic Comparative Assembly. WABI Peter Husemann, Jens Stoye
2009	—	`conf`	Rearrangement Models and Single-Cut Operations. RECOMB-CG Paul Medvedev, Jens Stoye
2009	J	`jnl`	WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinform. Wolfgang Gerlach, Sebastian Jünemann, Felix Tille, Alexander Goesmann, Jens Stoye
2008	J	`jnl`	Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. Nucleic Acids Res. Sebastian Oehm, David R. Gilbert, Andreas Tauch, Jens Stoye, Alexander Goesmann
2008	B	`conf`	Computation of Median Gene Clusters. RECOMB Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye
2008	J	`jnl`	Counting suffix arrays and strings. Theor. Comput. Sci. Klaus-Bernd Schürmann, Jens Stoye
2008	C	`conf`	Detecting Repeat Families in Incompletely Sequenced Genomes. WABI José Augusto Amgarten Quitzau, Jens Stoye
2008	B	`conf`	HP Distance Via Double Cut and Join Distance. CPM Anne Bergeron, Julia Mixtacki, Jens Stoye
2008	J	`jnl`	MeltDB: a software platform for the analysis and integration of metabolomics experiment data. Bioinform. Heiko Neuweger, Stefan P. Albaum, Michael Dondrup, Marcus Persicke, Tony Watt, Karsten Niehaus, Jens Stoye, Alexander Goesmann
2008	—	`conf`	On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios. RECOMB-CG Anne Bergeron, Julia Mixtacki, Jens Stoye
2008	—	`ch.`	Suffix Tree Construction in RAM. Encyclopedia of Algorithms Jens Stoye
2007	J	`jnl`	An incomplex algorithm for fast suffix array construction. Softw. Pract. Exp. Klaus-Bernd Schürmann, Jens Stoye
2007	J	`jnl`	Character sets of strings. J. Discrete Algorithms Gilles Didier, Thomas Schmidt, Jens Stoye, Dekel Tsur
2007	—	`ch.`	The inversion distance problem. Mathematics of Evolution and Phylogeny Anne Bergeron, Julia Mixtacki, Jens Stoye
2006	C	`conf`	A Unifying View of Genome Rearrangements. WABI Anne Bergeron, Julia Mixtacki, Jens Stoye
2006	J	`jnl`	Comparing Tandem Repeats with Duplications and Excisions of Variable Degree. IEEE ACM Trans. Comput. Biol. Bioinform. Michael Sammeth, Jens Stoye
2006	J	`jnl`	Efficient J. Comput. Biol. Kim R. Rasmussen, Jens Stoye, Eugene W. Myers
2006	—	`conf`	Finding novel genes in bacterial communities isolated from the environment. ISMB (Supplement of Bioinformatics) Lutz Krause, Naryttza N. Diaz, Daniela Bartels, Robert A. Edwards, Alfred Pühler, Forest Rohwer, Folker Meyer, Jens Stoye
2006	J	`jnl`	On Sorting by Translocations. J. Comput. Biol. Anne Bergeron, Julia Mixtacki, Jens Stoye
2006	J	`jnl`	On the Similarity of Sets of Permutations and Its Applications to Genome Comparison. J. Comput. Biol. Anne Bergeron, Jens Stoye
2005	C	`conf`	Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI). WABI Michael Sammeth, Thomas Weniger, Dag Harmsen, Jens Stoye
2005	—	`conf`	An Incomplex Algorithm for Fast Suffix Array Construction. ALENEX/ANALCO Klaus-Bernd Schürmann, Jens Stoye
2005	J	`jnl`	BACCardI-a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. Bioinform. 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
2005	C	`conf`	Counting Suffix Arrays and Strings. SPIRE Klaus-Bernd Schürmann, Jens Stoye
2005	B	`conf`	Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length. RECOMB Kim R. Rasmussen, Jens Stoye, Eugene W. Myers
2005	J	`jnl`	Large scale hierarchical clustering of protein sequences. BMC Bioinform. Antje Krause, Jens Stoye, Martin Vingron
2005	B	`conf`	On Sorting by Translocations. RECOMB Anne Bergeron, Julia Mixtacki, Jens Stoye
2005	—	`conf`	Protein Annotation by Secondary Structure Based Alignments (PASSTA). CompLife Constantin Bannert, Jens Stoye
2004	J	`jnl`	Algorithmic complexity of protein identification: combinatorics of weighted strings. Discret. Appl. Math. Mark Cieliebak, Thomas Erlebach, Zsuzsanna Lipták, Jens Stoye, Emo Welzl
2004	J	`jnl`	Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinform. Daniel A. Pollard, Casey M. Bergman, Jens Stoye, Susan E. Celniker, Michael B. Eisen
2004	J	`jnl`	Correction: Benchmarking tools for the alignment of functional noncodingDNA. BMC Bioinform. Daniel A. Pollard, Casey M. Bergman, Jens Stoye, Susan E. Celniker, Michael B. Eisen
2004	J	`jnl`	Linear time algorithms for finding and representing all the tandem repeats in a string. J. Comput. Syst. Sci. Dan Gusfield, Jens Stoye
2004	—	`ed.`	Proceedings of the German Conference on Bioinformatics (GCB 2004), Bielefeld, Germany, October 4-6, 2004 German Conference on Bioinformatics Robert Giegerich, Jens Stoye
2004	B	`conf`	Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences. CPM Thomas Schmidt, Jens Stoye
2004	B	`conf`	Reversal Distance without Hurdles and Fortresses. CPM Anne Bergeron, Julia Mixtacki, Jens Stoye
2004	C	`conf`	Suboptimal Local Alignments Across Multiple Scoring Schemes. WABI Morris Michael, Christoph Dieterich, Jens Stoye
2003	J	`jnl`	Digital extractor: analysis of digital differential display output. Bioinform. Michael Sammeth, Jörg Rothgänger, W. Esser, Jürgen Albert, Jens Stoye, Dag Harmsen
2003	C	`conf`	Divide-and-conquer multiple alignment with segment-based constraints. ECCB Michael Sammeth, Burkhard Morgenstern, Jens Stoye
2003	J	`jnl`	Efficient implementation of lazy suffix trees. Softw. Pract. Exp. Robert Giegerich, Stefan Kurtz, Jens Stoye
2003	—	`conf`	Evaluation of the Jumping Alignment algorithm with artificial and biological data. German Conference on Bioinformatics Constantin Bannert, Jens Stoye
2003	Misc	`conf`	On the Similarity of Sets of Permutations and Its Applications to Genome Comparison. COCOON Anne Bergeron, Jens Stoye
2002	J	`jnl`	A Novel Approach to Remote Homology Detection: Jumping Alignments. J. Comput. Biol. Rainer Spang, Marc Rehmsmeier, Jens Stoye
2002	—	`conf`	Algorithmic Complexity of Protein Identification: Searching in Weighted Strings. IFIP TCS Mark Cieliebak, Thomas Erlebach, Zsuzsanna Lipták, Jens Stoye, Emo Welzl
2002	C	`conf`	Common intervals and sorting by reversals: a marriage of necessity. ECCB Anne Bergeron, Steffen Heber, Jens Stoye
2002	—	`conf`	Index Structures for Large Sequence Data: Suffix Trees and Affix Trees. GI Jahrestagung (Ergänzungsband) Jens Stoye
2002	J	`jnl`	Simple and flexible detection of contiguous repeats using a suffix tree. Theor. Comput. Sci. Jens Stoye, Dan Gusfield
2001	C	`conf`	Algorithms for Finding Gene Clusters. WABI Steffen Heber, Jens Stoye
2001	B	`conf`	Finding All Common Intervals of k Permutations. CPM Steffen Heber, Jens Stoye
2001	—	`conf`	Sequence Database Search Using Jumping Alignments. German Conference on Bioinformatics Constantin Bannert, Marc Rehmsmeier, Rainer Spang, Jens Stoye
2000	J	`jnl`	An iterative method for faster sum-of-pairs multiple sequence alignment. Bioinform. Knut Reinert, Jens Stoye, Torsten Will
2000	A	`conf`	Computation and Visualization of Degenerate Repeats in Complete Genomes. ISMB Stefan Kurtz, Enno Ohlebusch, Chris Schleiermacher, Jens Stoye, Robert Giegerich
2000	J	`jnl`	Contig Selection in Physical Mapping. J. Comput. Biol. Steffen Heber, Jens Stoye, Marcus Frohme, Jörg D. Hoheisel, Martin Vingron
2000	B	`conf`	Contig selection in physical mapping. RECOMB Steffen Heber, Jens Stoye, Jörg D. Hoheisel, Martin Vingron
2000	—	`ed.`	Proceedings of the German Conference on Bioinformatics (GCB 2000), Heidelberg, October 5-7, 2000 German Conference on Bioinformatics Erich Bornberg-Bauer, Ursula Rost, Jens Stoye
2000	A	`conf`	Sequence Database Search Using Jumping Alignments. ISMB Rainer Spang, Marc Rehmsmeier, Jens Stoye
2000	J	`jnl`	The SYSTERS protein sequence cluster set. Nucleic Acids Res. Antje Krause, Jens Stoye, Martin Vingron
1999	—	`conf`	Combining Divide-and-Conquer, the A German Conference on Bioinformatics Knut Reinert, Jens Stoye, Torsten Will
1999	—	`conf`	Efficient Implementation of Lazy Suffix Trees. WAE Robert Giegerich, Stefan Kurtz, Jens Stoye
1999	B	`conf`	Finding Maximal Pairs with Bounded Gap. CPM Gerth Stølting Brodal, Rune B. Lyngsø, Christian N. S. Pedersen, Jens Stoye
1998	J	`jnl`	Rose: generating sequence families. Bioinform. Jens Stoye, Dirk Evers, Folker Meyer
1998	B	`conf`	Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version). CPM Jens Stoye, Dan Gusfield
1997	J	`jnl`	DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment. Comput. Appl. Biosci. Jens Stoye, Vincent Moulton, Andreas W. M. Dress
1997	A	`conf`	Generating Benchmarks for Multiple Sequence Alignments and Phylogenic Reconstructions. ISMB Jens Stoye, Dirk Evers, Folker Meyer
1997	J	`jnl`	Two applications of the Divide&Conquer principle in the molecular sciences. Math. Program. Gunnar Brinkmann, Andreas W. M. Dress, Sören Perrey, Jens Stoye