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ORCIDJens Stoye
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- affiliation: Bielefeld University, Germany
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2020 – today
- 2024
[j73]Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, Jens Stoye:
Investigating the complexity of the double distance problems. Algorithms Mol. Biol. 19(1): 1 (2024)- [c59]Leonard Bohnenkämper, Jens Stoye, Daniel Dörr:
Reconstructing Rearrangement Phylogenies of Natural Genomes. WABI 2024: 12:1-12:16 - 2023
- [c58]Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, Jens Stoye
:
On the Class of Double Distance Problems. RECOMB-CG 2023: 35-50 - [i9]Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, Jens Stoye:
Investigating the complexity of the double distance problems. CoRR abs/2303.04205 (2023) - 2022
- [j72]Paola Bonizzoni, Matteo Costantini, Clelia de Felice, Alessia Petescia, Yuri Pirola, Marco Previtali, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza:
Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches. Inf. Sci. 607: 458-476 (2022) - [c57]Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, Jens Stoye:
A Linear Time Algorithm for an Extended Version of the Breakpoint Double Distance. WABI 2022: 13:1-13:16 - [i8]Paola Bonizzoni, Matteo Costantini, Clelia De Felice, Alessia Petescia, Yuri Pirola, Marco Previtali, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza:
Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches. CoRR abs/2202.13884 (2022) - 2021
- [j71]Tizian Schulz, Roland Wittler, Sven Rahmann, Faraz Hach, Jens Stoye:
Detecting high-scoring local alignments in pangenome graphs. Bioinform. 37(16): 2266-2274 (2021) - [j70]Leonard Bohnenkämper, Marília D. V. Braga, Daniel Doerr, Jens Stoye:
Computing the Rearrangement Distance of Natural Genomes. J. Comput. Biol. 28(4): 410-431 (2021) - [j69]Linda K. Sundermann, Jeff Wintersinger, Gunnar Rätsch, Jens Stoye, Quaid Morris:
Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine. PLoS Comput. Biol. 17(1) (2021) - [j68]Eyla Willing, Jens Stoye, Marília D. V. Braga:
Computing the Inversion-Indel Distance. IEEE ACM Trans. Comput. Biol. Bioinform. 18(6): 2314-2326 (2021) - [c56]Paola Bonizzoni, Clelia De Felice, Alessia Petescia, Yuri Pirola, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza:
Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning. AlCoB 2021: 16-28 - 2020
- [j67]Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, Jens Stoye:
Finding all maximal perfect haplotype blocks in linear time. Algorithms Mol. Biol. 15(1): 2 (2020) - [j66]Diego P. Rubert, Eloi Araujo, Marco Aurelio Stefanes, Jens Stoye, Fábio Viduani Martinez:
Searching and inferring colorful topological motifs in vertex-colored graphs. J. Comb. Optim. 40(2): 379-411 (2020) - [c55]Leonard Bohnenkämper, Marília D. V. Braga, Daniel Doerr, Jens Stoye:
Computing the Rearrangement Distance of Natural Genomes. RECOMB 2020: 3-18 - [i7]Leonard Bohnenkämper, Marília D. V. Braga, Daniel Doerr, Jens Stoye:
Computing the rearrangement distance of natural genomes. CoRR abs/2001.02139 (2020) - [i6]Diego P. Rubert, Eloi Araujo, Marco Aurelio Stefanes, Jens Stoye, Fábio Viduani Martinez:
On motifs in colored graphs. CoRR abs/2005.13634 (2020)
2010 – 2019
- 2019
- [c54]Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, Jens Stoye:
Finding All Maximal Perfect Haplotype Blocks in Linear Time. WABI 2019: 8:1-8:9 - [i5]Eyla Willing, Jens Stoye, Marília D. V. Braga:
Computing the Inversion-Indel Distance. CoRR abs/1909.12877 (2019) - [i4]Travis Gagie, Giovanni Manzini, Gonzalo Navarro, Jens Stoye:
25 Years of the Burrows-Wheeler Transform (Dagstuhl Seminar 19241). Dagstuhl Reports 9(6): 55-68 (2019) - 2018
- [j65]Diego P. Rubert, Edna Ayako Hoshino, Marília D. V. Braga, Jens Stoye, Fábio Viduani Martinez:
Computing the family-free DCJ similarity. BMC Bioinform. 19-S(6): 31-42 (2018) - [j64]Guillaume Holley, Roland Wittler, Jens Stoye, Faraz Hach:
Dynamic Alignment-Free and Reference-Free Read Compression. J. Comput. Biol. 25(7): 825-836 (2018) - [j63]Nina Luhmann, Cédric Chauve, Jens Stoye, Roland Wittler:
Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework. IEEE ACM Trans. Comput. Biol. Bioinform. 15(6): 2094-2100 (2018) - [c53]Luís Felipe I. Cunha, Yoan Diekmann, Luis Antonio Brasil Kowada, Jens Stoye:
Identifying Maximal Perfect Haplotype Blocks. BSB 2018: 26-37 - 2017
- [j62]Diego P. Rubert, Pedro Feijão, Marília Dias Vieira Braga, Jens Stoye, Fábio Viduani Martinez:
Approximating the DCJ distance of balanced genomes in linear time. Algorithms Mol. Biol. 12(1): 3:1-3:13 (2017) - [j61]Daniel Doerr, Luis Antonio Brasil Kowada, Eloi Araujo, Shachi Deshpande, Simone Dantas, Bernard M. E. Moret, Jens Stoye:
New Genome Similarity Measures based on Conserved Gene Adjacencies. J. Comput. Biol. 24(6): 616-634 (2017) - [c52]Luís Felipe I. Cunha, Simone Dantas, Travis Gagie, Roland Wittler, Luis Antonio Brasil Kowada, Jens Stoye:
Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings. CPM 2017: 19:1-19:9 - [c51]Guillaume Holley, Roland Wittler, Jens Stoye, Faraz Hach:
Dynamic Alignment-Free and Reference-Free Read Compression. RECOMB 2017: 50-65 - [c50]Diego P. Rubert, Gabriela Medeiros, Edna Ayako Hoshino, Marília D. V. Braga, Jens Stoye, Fábio Viduani Martinez:
Algorithms for Computing the Family-Free Genomic Similarity Under DCJ. RECOMB-CG 2017: 76-100 - [c49]Tizian Schulz, Jens Stoye, Daniel Doerr:
Finding Teams in Graphs and Its Application to Spatial Gene Cluster Discovery. RECOMB-CG 2017: 197-212 - [i3]Luís Felipe I. Cunha, Simone Dantas, Travis Gagie, Roland Wittler, Luis Antonio Brasil Kowada, Jens Stoye:
Fast and Simple Jumbled Indexing for Binary RLE Strings. CoRR abs/1702.01280 (2017) - 2016
- [j60]Guillaume Holley, Roland Wittler, Jens Stoye:
Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage. Algorithms Mol. Biol. 11: 3 (2016) - [c48]Luis Antonio Brasil Kowada, Daniel Doerr, Simone Dantas, Jens Stoye:
New Genome Similarity Measures Based on Conserved Gene Adjacencies. RECOMB 2016: 204-224 - [c47]Diego P. Rubert, Pedro Feijão, Marília D. V. Braga, Jens Stoye, Fábio Viduani Martinez:
A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates. WABI 2016: 293-306 - [r2]Jens Stoye:
Suffix Tree Construction. Encyclopedia of Algorithms 2016: 2144-2149 - 2015
- [j59]Fábio Viduani Martinez, Pedro Feijão, Marília D. V. Braga, Jens Stoye:
On the family-free DCJ distance and similarity. Algorithms Mol. Biol. 10: 13 (2015) - [j58]Marília D. V. Braga, Jens Stoye:
Sorting Linear Genomes with Rearrangements and Indels. IEEE ACM Trans. Comput. Biol. Bioinform. 12(3): 500-506 (2015) - [c46]Guillaume Holley, Roland Wittler, Jens Stoye:
Bloom Filter Trie - A Data Structure for Pan-Genome Storage. WABI 2015: 217-230 - 2014
- [j57]Nils Hoffmann, Mathias Wilhelm, Anja Doebbe, Karsten Niehaus, Jens Stoye:
BiPACE 2D - graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry. Bioinform. 30(7): 988-995 (2014) - [j56]Rolf Hilker, Kai Bernd Stadermann, Daniel Doppmeier, Jörn Kalinowski, Jens Stoye, Jasmin Straube, Jörn Winnebald, Alexander Goesmann:
ReadXplorer - visualization and analysis of mapped sequences. Bioinform. 30(16): 2247-2254 (2014) - [j55]Jens Stoye, Juha Kärkkäinen:
Editorial. J. Discrete Algorithms 25: 1 (2014) - [c45]Fábio Viduani Martinez, Pedro Feijão, Marília D. V. Braga, Jens Stoye:
On the Family-Free DCJ Distance. WABI 2014: 174-186 - [c44]Nina Luhmann, Cédric Chauve, Jens Stoye, Roland Wittler:
Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework. BSB 2014: 135-143 - 2013
- [j54]Katharina Jahn, Sascha Winter, Jens Stoye, Sebastian Böcker:
Statistics for approximate gene clusters. BMC Bioinform. 14(S-15): S14 (2013) - [j53]Eyla Willing, Simone Zaccaria, Marília D. V. Braga, Jens Stoye:
On the inversion-indel distance. BMC Bioinform. 14(S-15): S3 (2013) - [j52]Christina Ander, Ole Schulz-Trieglaff, Jens Stoye, Anthony J. Cox:
metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences. BMC Bioinform. 14(S-5): S2 (2013) - [c43]Marília D. V. Braga, Jens Stoye:
Restricted DCJ-Indel Model Revisited. BSB 2013: 36-46 - [p3]Anne Bergeron, Jens Stoye:
The Genesis of the DCJ Formula. Models and Algorithms for Genome Evolution 2013: 63-81 - [p2]Marília D. V. Braga, Cédric Chauve, Daniel Doerr, Katharina Jahn, Jens Stoye, Annelyse Thévenin, Roland Wittler:
The Potential of Family-Free Genome Comparison. Models and Algorithms for Genome Evolution 2013: 287-307 - [e4]Aaron E. Darling, Jens Stoye:
Algorithms in Bioinformatics - 13th International Workshop, WABI 2013, Sophia Antipolis, France, September 2-4, 2013. Proceedings. Lecture Notes in Computer Science 8126, Springer 2013, ISBN 978-3-642-40452-8 [contents] - 2012
- [j51]Rolf Hilker, Corinna Sickinger, Christian N. S. Pedersen, Jens Stoye:
UniMoG - a unifying framework for genomic distance calculation and sorting based on DCJ. Bioinform. 28(19): 2509-2511 (2012) - [j50]Nils Hoffmann, Matthias Keck, Heiko Neuweger, Mathias Wilhelm, Petra Högy, Karsten Niehaus, Jens Stoye:
Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets. BMC Bioinform. 13: 214 (2012) - [j49]Daniel Doerr, Annelyse Thévenin, Jens Stoye:
Gene family assignment-free comparative genomics. BMC Bioinform. 13(S-19): S3 (2012) - [j48]Katharina Jahn, Henner Sudek, Jens Stoye:
Multiple genome comparison based on overlap regions of pairwise local alignments. BMC Bioinform. 13(S-19): S7 (2012) - [e3]Juha Kärkkäinen, Jens Stoye:
Combinatorial Pattern Matching - 23rd Annual Symposium, CPM 2012, Helsinki, Finland, July 3-5, 2012. Proceedings. Lecture Notes in Computer Science 7354, Springer 2012, ISBN 978-3-642-31264-9 [contents] - 2011
- [j47]Steffen Heber, Richard Mayr, Jens Stoye:
Common Intervals of Multiple Permutations. Algorithmica 60(2): 175-206 (2011) - [j46]Péter L. Erdös, Lajos Soukup, Jens Stoye:
Balanced vertices in trees and a simpler algorithm to compute the genomic distance. Appl. Math. Lett. 24(1): 82-86 (2011) - [j45]Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jörn Kalinowski, Jens Stoye, Alexander Goesmann:
Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. Bioinform. 27(10): 1351-1358 (2011) - [j44]Franziska Hufsky, Léon Kuchenbecker, Katharina Jahn, Jens Stoye, Sebastian Böcker:
Swiftly Computing Center Strings. BMC Bioinform. 12: 106 (2011) - [j43]Marília D. V. Braga, Raphael Machado, Leonardo Costa Ribeiro, Jens Stoye:
On the weight of indels in genomic distances. BMC Bioinform. 12(S-9): S13 (2011) - [j42]Marília D. V. Braga, Raphael Machado, Leonardo Costa Ribeiro, Jens Stoye:
Genomic distance under gene substitutions. BMC Bioinform. 12(S-9): S8 (2011) - [j41]Roland Wittler, Ján Manuch, Murray Patterson, Jens Stoye:
Consistency of Sequence-Based Gene Clusters. J. Comput. Biol. 18(9): 1023-1039 (2011) - [j40]Marília D. V. Braga, Eyla Willing, Jens Stoye:
Double Cut and Join with Insertions and Deletions. J. Comput. Biol. 18(9): 1167-1184 (2011) - [j39]Jakub Kovác, Robert Warren, Marília D. V. Braga, Jens Stoye:
Restricted DCJ Model: Rearrangement Problems with Chromosome Reincorporation. J. Comput. Biol. 18(9): 1231-1241 (2011) - 2010
- [j38]Peter Husemann, Jens Stoye:
Phylogenetic comparative assembly. Algorithms Mol. Biol. 5: 3 (2010) - [j37]Peter Husemann, Jens Stoye:
r2cat: synteny plots and comparative assembly. Bioinform. 26(4): 570-571 (2010) - [j36]Marília D. V. Braga, Jens Stoye:
The Solution Space of Sorting by DCJ. J. Comput. Biol. 17(9): 1145-1165 (2010) - [j35]Guillaume Blin, David C. Faye, Jens Stoye:
Finding Nested Common Intervals Efficiently. J. Comput. Biol. 17(9): 1183-1194 (2010) - [j34]Anne Bergeron, Paul Medvedev, Jens Stoye:
Rearrangement Models and Single-Cut Operations. J. Comput. Biol. 17(9): 1213-1225 (2010) - [c42]Søren Besenbacher, Benno Schwikowski, Jens Stoye:
Indexing and Searching a Mass Spectrometry Database. Algorithms and Applications 2010: 62-76 - [c41]Peter Husemann, Jens Stoye:
Repeat-aware Comparative Genome Assembly. GCB 2010: 61-70 - [c40]Jakub Kovác, Marília D. V. Braga, Jens Stoye:
The Problem of Chromosome Reincorporation in DCJ Sorting and Halving. RECOMB-CG 2010: 13-24 - [c39]Roland Wittler, Jens Stoye:
Consistency of Sequence-Based Gene Clusters. RECOMB-CG 2010: 252-263 - [c38]Marília D. V. Braga, Eyla Willing, Jens Stoye:
Genomic Distance with DCJ and Indels. WABI 2010: 90-101 - [c37]Franziska Hufsky, Léon Kuchenbecker, Katharina Jahn, Jens Stoye, Sebastian Böcker:
Swiftly Computing Center Strings. WABI 2010: 325-336 - [i2]Anne Bergeron, Julia Mixtacki, Jens Stoye:
A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance. Structure Discovery in Biology: Motifs, Networks & Phylogenies 2010 - [i1]Péter L. Erdös, Lajos Soukup, Jens Stoye:
Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance. CoRR abs/1004.2735 (2010)
2000 – 2009
- 2009
- [j33]Nils Hoffmann, Jens Stoye:
ChromA: signal-based retention time alignment for chromatography-mass spectrometry data. Bioinform. 25(16): 2080-2081 (2009) - [j32]Michael Brudno, Paul Medvedev, Jens Stoye, Francisco M. de la Vega:
A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG). Bioinform. 25(21): 2863-2864 (2009) - [j31]Wolfgang Gerlach, Sebastian Jünemann, Felix Tille, Alexander Goesmann, Jens Stoye:
WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinform. 10: 430 (2009) - [j30]Katharina Jahn, Jens Stoye:
Approximative Gencluster und ihre Anwendung in der komparativen Genomik. Inform. Spektrum 32(4): 288-300 (2009) - [j29]Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye:
Computation of Median Gene Clusters. J. Comput. Biol. 16(8): 1085-1099 (2009) - [j28]Jens Stoye, Roland Wittler:
A Unified Approach for Reconstructing Ancient Gene Clusters. IEEE ACM Trans. Comput. Biol. Bioinform. 6(3): 387-400 (2009) - [j27]Anne Bergeron, Julia Mixtacki, Jens Stoye:
A new linear time algorithm to compute the genomic distance via the double cut and join distance. Theor. Comput. Sci. 410(51): 5300-5316 (2009) - [c36]Marília D. V. Braga, Jens Stoye:
Counting All DCJ Sorting Scenarios. RECOMB-CG 2009: 36-47 - [c35]Guillaume Blin, Jens Stoye:
Finding Nested Common Intervals Efficiently. RECOMB-CG 2009: 59-69 - [c34]Paul Medvedev, Jens Stoye:
Rearrangement Models and Single-Cut Operations. RECOMB-CG 2009: 84-97 - [c33]Peter Husemann, Jens Stoye:
Phylogenetic Comparative Assembly. WABI 2009: 145-156 - 2008
- [j26]Heiko Neuweger, Stefan P. Albaum, Michael Dondrup, Marcus Persicke, Tony Watt, Karsten Niehaus, Jens Stoye, Alexander Goesmann:
MeltDB: a software platform for the analysis and integration of metabolomics experiment data. Bioinform. 24(23): 2726-2732 (2008) - [j25]Sebastian Oehm, David R. Gilbert, Andreas Tauch, Jens Stoye, Alexander Goesmann:
Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. Nucleic Acids Res. 36(Web-Server-Issue): 433-437 (2008) - [j24]Klaus-Bernd Schürmann, Jens Stoye:
Counting suffix arrays and strings. Theor. Comput. Sci. 395(2-3): 220-234 (2008) - [c32]Anne Bergeron, Julia Mixtacki, Jens Stoye:
HP Distance Via Double Cut and Join Distance. CPM 2008: 56-68 - [c31]Anne Bergeron, Julia Mixtacki, Jens Stoye:
On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios. RECOMB-CG 2008: 226-240 - [c30]Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye:
Computation of Median Gene Clusters. RECOMB 2008: 331-345 - [c29]José Augusto Amgarten Quitzau, Jens Stoye:
Detecting Repeat Families in Incompletely Sequenced Genomes. WABI 2008: 342-353 - [r1]Jens Stoye:
Suffix Tree Construction in RAM. Encyclopedia of Algorithms 2008 - 2007
- [j23]Gilles Didier, Thomas Schmidt, Jens Stoye, Dekel Tsur:
Character sets of strings. J. Discrete Algorithms 5(2): 330-340 (2007) - [j22]Klaus-Bernd Schürmann, Jens Stoye:
An incomplex algorithm for fast suffix array construction. Softw. Pract. Exp. 37(3): 309-329 (2007) - [p1]Anne Bergeron, Julia Mixtacki, Jens Stoye:
The inversion distance problem. Mathematics of Evolution and Phylogeny 2007 - 2006
- [j21]Michael Sammeth, Thasso Griebel, Felix Tille, Jens Stoye:
Panta rhei (QAlign2): an open graphical environment for sequence analysis. Bioinform. 22(7): 889-890 (2006) - [j20]Kim R. Rasmussen, Jens Stoye, Eugene W. Myers:
Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length. J. Comput. Biol. 13(2): 296-308 (2006) - [j19]Anne Bergeron, Julia Mixtacki, Jens Stoye:
On Sorting by Translocations. J. Comput. Biol. 13(2): 567-578 (2006) - [j18]Anne Bergeron, Jens Stoye:
On the Similarity of Sets of Permutations and Its Applications to Genome Comparison. J. Comput. Biol. 13(7): 1340-1354 (2006) - [j17]Michael Sammeth, Jens Stoye:
Comparing Tandem Repeats with Duplications and Excisions of Variable Degree. IEEE ACM Trans. Comput. Biol. Bioinform. 3(4): 395-407 (2006) - [c28]Lutz Krause, Naryttza N. Diaz, Daniela Bartels, Robert A. Edwards, Alfred Pühler, Forest Rohwer, Folker Meyer, Jens Stoye:
Finding novel genes in bacterial communities isolated from the environment. ISMB (Supplement of Bioinformatics) 2006: 281-289 - [c27]Anne Bergeron, Julia Mixtacki, Jens Stoye:
A Unifying View of Genome Rearrangements. WABI 2006: 163-173 - 2005
- [j16]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:
BACCardI-a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. Bioinform. 21(7): 853-859 (2005) - [j15]Antje Krause, Jens Stoye, Martin Vingron:
Large scale hierarchical clustering of protein sequences. BMC Bioinform. 6: 15 (2005) - [c26]Klaus-Bernd Schürmann, Jens Stoye:
An Incomplex Algorithm for Fast Suffix Array Construction. ALENEX/ANALCO 2005: 78-85 - [c25]Constantin Bannert, Jens Stoye:
Protein Annotation by Secondary Structure Based Alignments (PASSTA). CompLife 2005: 79-90 - [c24]Kim R. Rasmussen, Jens Stoye, Eugene W. Myers:
Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length. RECOMB 2005: 189-203 - [c23]Anne Bergeron, Julia Mixtacki, Jens Stoye:
On Sorting by Translocations. RECOMB 2005: 615-629 - [c22]Klaus-Bernd Schürmann