Jens Stoye

ORCID

Publication Activity (10 Years)

Years Active: 1997-2024
Publications (10 Years): 37

Top Venues

CoRR

WABI

Algorithms Mol. Biol.

Bioinform.

Publications

Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, Jens Stoye
Investigating the complexity of the double distance problems. Algorithms Mol. Biol. 19 (1) (2024)
Leonard Bohnenkämper, Jens Stoye, Daniel Dörr
Reconstructing Rearrangement Phylogenies of Natural Genomes. WABI (2024)
Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, Jens Stoye
Investigating the complexity of the double distance problems. CoRR (2023)
Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, Jens Stoye
On the Class of Double Distance Problems. RECOMB-CG (2023)
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 (2022)
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 (2022)
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)
Leonard Bohnenkämper, Marília D. V. Braga, Daniel Doerr, Jens Stoye
Computing the Rearrangement Distance of Natural Genomes. J. Comput. Biol. 28 (4) (2021)
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)
Tizian Schulz, Roland Wittler, Sven Rahmann, Faraz Hach, Jens Stoye
Detecting high-scoring local alignments in pangenome graphs. Bioinform. 37 (16) (2021)
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)
Eyla Willing, Jens Stoye, Marília D. V. Braga
Computing the Inversion-Indel Distance. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (6) (2021)
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) (2020)
Leonard Bohnenkämper, Marília D. V. Braga, Daniel Doerr, Jens Stoye
Computing the rearrangement distance of natural genomes. CoRR (2020)
Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, Jens Stoye
Finding all maximal perfect haplotype blocks in linear time. Algorithms Mol. Biol. 15 (1) (2020)
Diego P. Rubert, Eloi Araujo, Marco Aurelio Stefanes, Jens Stoye, Fábio Viduani Martinez
On motifs in colored graphs. CoRR (2020)
Leonard Bohnenkämper, Marília D. V. Braga, Daniel Doerr, Jens Stoye
Computing the Rearrangement Distance of Natural Genomes. RECOMB (2020)
Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, Jens Stoye
Finding All Maximal Perfect Haplotype Blocks in Linear Time. WABI (2019)
Travis Gagie, Giovanni Manzini, Gonzalo Navarro, Jens Stoye
25 Years of the Burrows-Wheeler Transform (Dagstuhl Seminar 19241). Dagstuhl Reports 9 (6) (2019)
Eyla Willing, Jens Stoye, Marília D. V. Braga
Computing the Inversion-Indel Distance. CoRR (2019)
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) (2018)
Diego P. Rubert, Edna Ayako Hoshino, Marília D. V. Braga, Jens Stoye, Fábio Viduani Martinez
Computing the family-free DCJ similarity. BMC Bioinform. (6) (2018)
Guillaume Holley, Roland Wittler, Jens Stoye, Faraz Hach
Dynamic Alignment-Free and Reference-Free Read Compression. J. Comput. Biol. 25 (7) (2018)
Luís Felipe I. Cunha, Yoan Diekmann, Luis Antonio Brasil Kowada, Jens Stoye
Identifying Maximal Perfect Haplotype Blocks. BSB (2018)
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) (2017)
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 (2017)
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)
Tizian Schulz, Jens Stoye, Daniel Doerr
Finding Teams in Graphs and Its Application to Spatial Gene Cluster Discovery. RECOMB-CG (2017)
Guillaume Holley, Roland Wittler, Jens Stoye, Faraz Hach
Dynamic Alignment-Free and Reference-Free Read Compression. RECOMB (2017)
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) (2017)
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)
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 (2016)
Luis Antonio Brasil Kowada, Daniel Doerr, Simone Dantas, Jens Stoye
New Genome Similarity Measures Based on Conserved Gene Adjacencies. RECOMB (2016)
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)
Marília D. V. Braga, Jens Stoye
Sorting Linear Genomes with Rearrangements and Indels. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (3) (2015)
Guillaume Holley, Roland Wittler, Jens Stoye
Bloom Filter Trie - A Data Structure for Pan-Genome Storage. WABI (2015)
Fábio Viduani Martinez, Pedro Feijão, Marília D. V. Braga, Jens Stoye
On the family-free DCJ distance and similarity. Algorithms Mol. Biol. 10 (2015)
Nina Luhmann, Cédric Chauve, Jens Stoye, Roland Wittler
Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework. BSB (2014)
Fábio Viduani Martinez, Pedro Feijão, Marília D. V. Braga, Jens Stoye
On the Family-Free DCJ Distance. WABI (2014)
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) (2014)
Jens Stoye, Juha Kärkkäinen
Editorial. J. Discrete Algorithms 25 (2014)
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) (2014)
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) (2013)
Marília D. V. Braga, Jens Stoye
Restricted DCJ-Indel Model Revisited. BSB (2013)
Katharina Jahn, Sascha Winter, Jens Stoye, Sebastian Böcker
Statistics for approximate gene clusters. BMC Bioinform. 14 (S-15) (2013)
Eyla Willing, Simone Zaccaria, Marília D. V. Braga, Jens Stoye
On the inversion-indel distance. BMC Bioinform. 14 (S-15) (2013)
Katharina Jahn, Henner Sudek, Jens Stoye
Multiple genome comparison based on overlap regions of pairwise local alignments. BMC Bioinform. 13 (S-19) (2012)
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) (2012)
Daniel Doerr, Annelyse Thévenin, Jens Stoye
Gene family assignment-free comparative genomics. BMC Bioinform. 13 (S-19) (2012)
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 (2012)
Jakub Kovác, Robert Warren, Marília D. V. Braga, Jens Stoye
Restricted DCJ Model: Rearrangement Problems with Chromosome Reincorporation. J. Comput. Biol. 18 (9) (2011)
Marília D. V. Braga, Raphael Machado, Leonardo Costa Ribeiro, Jens Stoye
On the weight of indels in genomic distances. BMC Bioinform. 12 (S-9) (2011)
Roland Wittler, Ján Manuch, Murray Patterson, Jens Stoye
Consistency of Sequence-Based Gene Clusters. J. Comput. Biol. 18 (9) (2011)
Franziska Hufsky, Léon Kuchenbecker, Katharina Jahn, Jens Stoye, Sebastian Böcker
Swiftly Computing Center Strings. BMC Bioinform. 12 (2011)
Marília D. V. Braga, Eyla Willing, Jens Stoye
Double Cut and Join with Insertions and Deletions. J. Comput. Biol. 18 (9) (2011)
Steffen Heber, Richard Mayr, Jens Stoye
Common Intervals of Multiple Permutations. Algorithmica 60 (2) (2011)
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) (2011)
Marília D. V. Braga, Raphael Machado, Leonardo Costa Ribeiro, Jens Stoye
Genomic distance under gene substitutions. BMC Bioinform. 12 (S-9) (2011)
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) (2011)
Péter L. Erdös, Lajos Soukup, Jens Stoye
Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance CoRR (2010)
Guillaume Blin, David Faye, Jens Stoye
Finding Nested Common Intervals Efficiently. J. Comput. Biol. 17 (9) (2010)
Søren Besenbacher, Benno Schwikowski, Jens Stoye
Indexing and Searching a Mass Spectrometry Database. Algorithms and Applications (2010)
Marília D. V. Braga, Eyla Willing, Jens Stoye
Genomic Distance with DCJ and Indels. WABI (2010)
Jakub Kovác, Marília D. V. Braga, Jens Stoye
The Problem of Chromosome Reincorporation in DCJ Sorting and Halving. RECOMB-CG (2010)
Peter Husemann, Jens Stoye
Repeat-aware Comparative Genome Assembly. GCB (2010)
Peter Husemann, Jens Stoye
Phylogenetic comparative assembly. Algorithms Mol. Biol. 5 (2010)
Franziska Hufsky, Léon Kuchenbecker, Katharina Jahn, Jens Stoye, Sebastian Böcker
Swiftly Computing Center Strings. WABI (2010)
Anne Bergeron, Paul Medvedev, Jens Stoye
Rearrangement Models and Single-Cut Operations. J. Comput. Biol. 17 (9) (2010)
Roland Wittler, Jens Stoye
Consistency of Sequence-Based Gene Clusters. RECOMB-CG (2010)
Peter Husemann, Jens Stoye
r2cat: synteny plots and comparative assembly. Bioinform. 26 (4) (2010)
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)
Marília D. V. Braga, Jens Stoye
The Solution Space of Sorting by DCJ. J. Comput. Biol. 17 (9) (2010)
Marília D. V. Braga, Jens Stoye
Counting All DCJ Sorting Scenarios. RECOMB-CG (2009)
Peter Husemann, Jens Stoye
Phylogenetic Comparative Assembly. WABI (2009)
Paul Medvedev, Jens Stoye
Rearrangement Models and Single-Cut Operations. RECOMB-CG (2009)
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) (2009)
Nils Hoffmann, Jens Stoye
ChromA: signal-based retention time alignment for chromatography-mass spectrometry data. Bioinform. 25 (16) (2009)
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) (2009)
Jens Stoye, Roland Wittler
A Unified Approach for Reconstructing Ancient Gene Clusters. IEEE ACM Trans. Comput. Biol. Bioinform. 6 (3) (2009)
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 (2009)
Katharina Jahn, Jens Stoye
Approximative Gencluster und ihre Anwendung in der komparativen Genomik. Inform. Spektrum 32 (4) (2009)
Guillaume Blin, Jens Stoye
Finding Nested Common Intervals Efficiently. RECOMB-CG (2009)
Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye
Computation of Median Gene Clusters. J. Comput. Biol. 16 (8) (2009)
Anne Bergeron, Julia Mixtacki, Jens Stoye
HP Distance Via Double Cut and Join Distance. CPM (2008)
Klaus-Bernd Schürmann, Jens Stoye
Counting suffix arrays and strings. Theor. Comput. Sci. 395 (2-3) (2008)
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) (2008)
Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye
Computation of Median Gene Clusters. RECOMB (2008)
José Augusto Amgarten Quitzau, Jens Stoye
Detecting Repeat Families in Incompletely Sequenced Genomes. WABI (2008)
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) (2008)
Anne Bergeron, Julia Mixtacki, Jens Stoye
On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios. RECOMB-CG (2008)
Klaus-Bernd Schürmann, Jens Stoye
An incomplex algorithm for fast suffix array construction. Softw. Pract. Exp. 37 (3) (2007)
Gilles Didier, Thomas Schmidt, Jens Stoye, Dekel Tsur
Character sets of strings. J. Discrete Algorithms 5 (2) (2007)
Michael Sammeth, Jens Stoye
Comparing Tandem Repeats with Duplications and Excisions of Variable Degree. IEEE ACM Trans. Comput. Biol. Bioinform. 3 (4) (2006)
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)
Anne Bergeron, Julia Mixtacki, Jens Stoye
A Unifying View of Genome Rearrangements. WABI (2006)
Anne Bergeron, Jens Stoye
On the Similarity of Sets of Permutations and Its Applications to Genome Comparison. J. Comput. Biol. 13 (7) (2006)
Kim R. Rasmussen, Jens Stoye, Eugene W. Myers
-Matches over a Given Length. J. Comput. Biol. 13 (2) (2006)
Anne Bergeron, Julia Mixtacki, Jens Stoye
On Sorting by Translocations. J. Comput. Biol. 13 (2) (2006)
Michael Sammeth, Thasso Griebel, Felix Tille, Jens Stoye
(QAlign2): an open graphical environment for sequence analysis. Bioinform. 22 (7) (2006)
Klaus-Bernd Schürmann, Jens Stoye
An Incomplex Algorithm for Fast Suffix Array Construction. ALENEX/ANALCO (2005)

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Publication Activity (10 Years)

Top Topics

Top Venues

Jens Stoye