Universität Bielefeld - Technische Fakultät - AG Genominformatik

Jens Stoye's Publications (consortium papers, preprints and unpublished material below)

Upcoming

Methods for Pangenomic Core Detection
T. Schulz, L. Parmigiani, A. Rempel, J. Stoye
In: J. C. Setubal, P. Stadler, J. Stoye (eds.): Comparative Genomics: Methods and Protocols, volume 2. Methods in Molecular Biology, in press.

Family-Free Genome Comparison
M. D. V. Braga, D. Doerr, D. P. Rubert, J. Stoye
In: J. C. Setubal, P. Stadler, J. Stoye (eds.): Comparative Genomics: Methods and Protocols, volume 2. Methods in Molecular Biology, in press.

2024

Faster method for estimating the openness of species (recommendation, arXiv version)
L. Parmigiani, R. Wittler, J. Stoye
PCI Math. & Comp. Biol., recommended.

Investigating the complexity of the double distance problems (open access, conference version 1, conference version 2, arXiv version)
M. D. V. Braga, L. R. Brockmann, K. Klerx, J. Stoye
Algorithms Mol. Biol. 19: 1, 2024.

2023

On the class of double distance problems (preview, publisher website, journal version, arXiv version)
M. D. V. Braga, L. R. Brockmann, K. Klerx, J. Stoye
Proceedings of RECOMB-CG 2023, Springer Verlag, LNBI 13883, 35-50, 2023.

HaploBlocks: efficient detection of positive selection in large population genomic datasets (publisher website)
B. Kirsch-Gerweck, L. Bohnenkämper, M. T. Henrichs, J. N. Alanko, H. Bannai, B. Cazaux, P. Peterlongo, J. Burger, J. Stoye, Y. Diekmann
Mol. Biol. Evol. 4(3): msad027, 2023.

2022

A Linear Time Algorithm for an Extended Version of the Breakpoint Double Distance (open access, journal version, arXiv version)
M. D. V. Braga, L. R. Brockmann, K. Klerx, J. Stoye
Proceedings of WABI 2022, LIPIcs 242, 13:1-13:16, 2022.

Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches (publisher website, conference version, arXiv version)
P. Bonizzoni, M. Costantini, C. De Felice, A. Petescia, Y. Pirola, M. Previtali, R. Rizzi, J. Stoye, R. Zaccagnino, R. Zizza
Information Sciences 607: 458-476, 2022.

Sequence-based Pangenomic Core Detection (open access)
T. Schulz, R. Wittler, J. Stoye
iScience 25(6), 104413, 2022. (Presented at Recomb-Seq 2022.)

2021

Computing the Inversion-Indel Distance (publisher website, arXiv version)
E. Willing, J. Stoye, M. D. V. Braga
IEEE/ACM Trans. Comput. Biol. Bioinf. 18(6): 2314-2326, 2021.

Detecting High Scoring Local Alignments in Pangenome Graphs (open access, bioRxiv version)
T. Schulz, R. Wittler, S. Rahmann, F. Hach, J. Stoye
Bioinformatics 37(16): 2266-2274, 2021.

Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning (preview, publisher website, journal version, arXiv version)
P. Bonizzoni, C. De Felice, A. Petescia, Y. Pirola, R. Rizzi, J. Stoye, R. Zaccagnino, R. Zizza
Proceedings of AlCoB 2020 & 2021, Springer Verlag, LNBI 12715, 16-28, 2021.

Computing the rearrangement distance of natural genomes (open access, conference version, arXiv version)
L. Bohnenkämper, M. D. V. Braga, D. Doerr, J. Stoye
J. Comp. Biol. 28(4): 410-431, 2021.

Computational Methods for Microbiome Analysis (publisher website, editorial)
J. C. Setubal, J. Stoye, B. E. Dutilh (eds.)
Frontiers Research Topic.

Reconstructing Tumor Evolutionary Histories and Clone Trees in Polynomial-time with SubMARine (open access, bioRxiv version)
L. Sundermann, J. Wintersinger, G. Rätsch, J. Stoye, Q. Morris
PLOS Computational Biology, 17(1): e1008400, 2021. (Presented at Recomb-CCB 2020.)

2020

HASLR: Fast Hybrid Assembly of Long Reads (open access, bioRxiv version)
E. Haghshenas, H. Asghari, J. Stoye, C. Chauve, F. Hach
iScience 23(8), 101389, 2020. (Presented at Recomb-Seq 2020.)

Searching and Inferring Colorful Topological Motifs in Vertex-Colored Graphs (publisher website, arXiv version)
D. P. Rubert, E. Araujo, M. A. Stefanes, J. Stoye, F. V. Martinez
J. Comb. Opt. 40, 379-411, 2020.

Horizontal gene transfer phylogenetics: A random walk approach (publisher website)
G. Sevillya, D. Doerr, Y. Lerner, J. Stoye, M. Steel, S. Snir
Mol. Biol. Evol. 37(5): 1470-1479, 2020.

Computing the rearrangement distance of natural genomes (preview, publisher website, journal version, arXiv version)
L. Bohnenkämper, M. D. V. Braga, D. Doerr, J. Stoye
Proceedings of RECOMB 2020, Springer Verlag, LNBI 12074, 3-18, 2020.

Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants (open access)
D. P. Rubert, F. H. V. Martinez, J. Stoye, D. Doerr
BMC Genomics 21(Suppl. 2): 273, 2020.

Finding all maximal perfect haplotype blocks in linear time (open access, conference version)
J. Alanko, H. Bannai, B. Cazaux, P. Peterlongo, J. Stoye
Algorithms Mol. Biol. 15: 2, 2020.

2019

25 Years of the Burrows-Wheeler Transform (Dagstuhl Seminar 19241) (invited report) (publisher website)
T. Gagie, G. Manzini, G. Navarro, J. Stoye
Dagstuhl Reports, 259(6), 55-68, 2019.

Finding all maximal perfect haplotype blocks in linear time (open access, journal version)
J. Alanko, H. Bannai, B. Cazaux, P. Peterlongo, J. Stoye
Proceedings of WABI 2019, LIPIcs 143, 8:1-8:9, 2019.

A Perspective on Comparative and Functional Genomics (publisher website)
D. Doerr, J. Stoye
In: T. Warnow (ed.): Bioinformatics and Phylogenetics. Computational Biology, vol. 29, Chapter 14, pp. 361-372. Springer Verlag, 2019.

Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium (publisher website)
H. Oey, M. Zakrzewski, K. Gravermann, N. D. Young, P. K. Korhonen, G. N. Gobert, S. Nawaratna, S. Hasan, D. M. Martínez, H. You, M. Lavin, M. Jones, M. A. Ragan, J. Stoye, A. Oleaga, A. M. Emery, B. Webster, D. Rollinson, R. B. Gasser, D. P. McManus, L. Krause
PLOS Pathogens 15(1): e1007513, 2019.

2018

Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework (publisher website, conference version)
N. Luhmann, C. Chauve, J. Stoye, R. Wittler
IEEE/ACM Trans. Comput. Biol. Bioinf. 15(6): 2094-2100, 2018.

Identifying Maximal Perfect Haplotype Blocks (preview, publisher website)
L. Cunha, Y. Diekmann, L. Kowada, J. Stoye
Proceedings of BSB 2018, Springer Verlag, LNBI 11228, 26-37, 2018.

Dynamic Alignment-Free and Reference-Free Read Compression (publisher website, conference version)
G. Holley, R. Wittler, J. Stoye, F. Hach
J. Comp. Biol. 25(7): 825-836, 2018.

Flexible metagenome analysis using the MGX framework (open access)
S. Jaenicke, S. P. Albaum, P. Blumenkamp, B. Linke, J. Stoye, A. Goesmann
Microbiome 6: 76, 2018.

Computing the family-free DCJ similarity (open access, conference version)
D. P. Rubert, E. A. Hoshino, M. D. V. Braga, J. Stoye, F. V. Martinez
BMC Bioinformatics 19(Suppl. 6): 152, 2018.

GraphTeams: a method for discovering spatial gene clusters in Hi-C sequencing data (open access, conference version)
T. Schulz, J. Stoye, D. Doerr
BMC Genomics 19(Suppl. 5): 308, 2018.

Family-Free Genome Comparison (publisher website)
D. Doerr, P. Feijão, J. Stoye
In: J. C. Setubal, P. Stadler, J. Stoye (eds.): Comparative Genomics: Methods and Protocols. Methods in Molecular Biology, vol. 1704, Chapter 12, pp. 331-342. Springer Verlag, 2018.

Pan-genome Storage and Analysis Techniques (publisher website)
T. Zekic, G. Holley, J. Stoye
In: J. C. Setubal, P. Stadler, J. Stoye (eds.): Comparative Genomics: Methods and Protocols. Methods in Molecular Biology, vol. 1704, Chapter 2, pp. 29-53. Springer Verlag, 2018.

Comparative Genomics: Methods and Protocols (publisher website)
J. C. Setubal, P. Stadler, J. Stoye (eds.)
Methods in Molecular Biology, vol. 1704. Springer Verlag, 2018.

2017

Finding Teams in Graphs and its Application to Spatial Gene Cluster Discovery (preview, publisher website, journal version)
T. Schulz, J. Stoye, D. Doerr
Proceedings of RECOMB-CG 2017, Springer Verlag, LNBI 10562, 197-212, 2017.

Algorithms for Computing the Family-Free Genomic Similarity under DCJ (preview, publisher website, journal version)
D. P. Rubert, G. L. Medeiros, E. A. Hoshino, M. D. V. Braga, J. Stoye, F. V. Martinez
Proceedings of RECOMB-CG 2017, Springer Verlag, LNBI 10562, 76-100, 2017.

Bioinformatics for NGS-based Metagenomics and the Application to Biogas Research (publisher website)
S. Jünemann, N. Kleinbölting, S. Jaenicke, C. Henke, J. Hassa, J. Nelkner, Y. Stolze, S. P. Albaum, A. Schlüter, A. Goesmann, A. Sczyrba, J. Stoye
J. Biotechnol. 261, 10-23, 2017.

Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings (open access, arXiv version)
L. Cunha, S. Dantas, T. Gagie, R. Wittler, L. Kowada, J. Stoye
Proceedings of CPM 2017, LIPIcs 78, 19:1-19:9, 2017.

New Genome Similarity Measures based on Conserved Gene Adjacencies (publisher website, conference version)
D. Doerr, L. A. B. Kowada, E. Araujo, S. Deshpande, S. Dantas, B. M. E. Moret, J. Stoye
J. Comp. Biol. 24(6): 616-634, 2017.

Dynamic Alignment-Free and Reference-Free Read Compression (preview, publisher website, journal version)
G. Holley, R. Wittler, J. Stoye, F. Hach
Proceedings of RECOMB 2017, Springer Verlag, LNBI 10229, 50-65, 2017.

Approximating the DCJ distance of balanced genomes in linear time (open access, conference version)
D. Rubert, P. Feijão, M. D. V. Braga, J. Stoye, F. H. V. Martinez
Algorithms Mol. Biol. 12: 3, 2017.

2016

Finding Approximate Gene Clusters with GECKO 3 (open access)
S. Winter, K. Jahn, S. Wehner, L. Kuchenbecker, M. Marz, J. Stoye, S. Böcker
Nucleic Acids Res. 44(20): 9600-9610, 2016.

A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates (preview, publisher website, journal version)
D. P. Rubert, P. Feijão, M. D. V. Braga, J. Stoye, F. V. Martinez
Proceedings of WABI 2016, Springer Verlag, LNBI 9838, 293-306, 2016.

New Genome Similarity Measures based on Conserved Gene Adjacencies (preview, publisher website, journal version)
L. A. B. Kowada, D. Doerr, S. Dantas, J. Stoye
Proceedings of RECOMB 2016, Springer Verlag, LNBI 9649, 204-224, 2016.

Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage (open access, conference version)
G. Holley, R. Wittler, J. Stoye
Algorithms Mol. Biol. 11: 3, 2016.

Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma (open access)
L. Krause, K. Nones, K. A. Loffler, D. Nancarrow, H. Oey, Y. H. Tang, N. J. Wayte, A. M. Patch, K. Patel, S. Brosda, S. Manning, G. Lampe, A. Clouston, J. Thomas, J. Stoye, D. J. Hussey, D. I. Watson, R. V. Lord, W. A Phillips, D. Gotley, B. M. Smithers, D. C. Whiteman, N. K. Hayward, S. M. Grimmond, N. Waddell, A. P. Barbour
Carcinogenesis 37(4): 356-365, 2016.

2015

Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Genomics (open access)
J. Meidanis, J. Stoye (eds.)
BMC Genomics, 16(Suppl. 10), 2015.

Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Bioinformatics (open access)
J. Meidanis, J. Stoye (eds.)
BMC Bioinformatics, 16(Suppl. 14), 2015.

Bloom Filter Trie - a data structure for pan-genome storage (preview, publisher website, journal version)
G. Holley, R. Wittler, J. Stoye
Proceedings of WABI 2015, Springer Verlag, LNBI 9289, 217-230, 2015.

Sorting linear genomes with rearrangements and indels (publisher website, conference version)
M. D. V. Braga, J. Stoye
IEEE/ACM Trans. Comput. Biol. Bioinf. 12(3): 500-506, 2015.

On the family-free DCJ distance and similarity (open access, conference version)
F. V. Martinez, P. Feijão, M. D. V. Braga, J. Stoye
Algorithms Mol. Biol. 10: 13, 2015.

2014

Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts (publisher website)
P. Schwientek, A. Neshat, J. Kalinowski, A. Klein, C. Rückert, S. Schneiker-Bekel, S. Wendler, J. Stoye, A. Pühler
J. Biotechnol. 190: 85-95, 2014.

Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing (publisher website)
T. Jakobi, K. Brinkrolf, A. Tauch, T. Noll, J. Stoye, A. Pühler, A. Goesmann
J. Biotechnol. 190: 64-75, 2014.

Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework (preview, publisher website, journal version)
N. Luhmann, C. Chauve, J. Stoye, R. Wittler
Proceedings of BSB 2014, Springer Verlag, LNBI 8826, 135-143, 2014.

Identifying Gene Clusters by Discovering Common Intervals in Indeterminate Strings (open access)
D. Doerr, J. Stoye, S. Böcker, K. Jahn
BMC Genomics 15(Suppl. 6): S2, 2014. (Proceedings of RECOMB-CG 2014)

Suffix Tree Construction (publisher website)
J. Stoye
In: M.-Y. Kao (ed.): Encyclopedia of Algorithms. Springer Verlag, 2014.

GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers (open access)
S. Jünemann, K. Prior, A. Albersmeier, S. Albaum, J. Kalinowski, A. Goesmann, J. Stoye, D. Harmsen
PLOS ONE 9(9): e107014, 2014.

Metatranskriptomik der Mikrobiota der menschlichen Achselhöhle (invited article, in German)
E. Fredrich, C. Ander, J. Stoye, I. Brune, A. Tauch
BIOSpektrum 20(5): 294-296, 2014.

Orthology Detection Combining Clustering and Synteny for Very Large Datasets (open access)
M. Lechner, M. Hernandez-Rosales, D. Doerr, N. Wieseke, A. Thévenin, J. Stoye, R. K. Hartmann, S. J. Prohaska, P. F. Stadler
PLOS ONE 9(8): e105015, 2014.

On the family-free DCJ distance (preview, publisher website, journal version)
F. V. Martinez, P. Feijão, M. D. V. Braga, J. Stoye
Proceedings of WABI 2014, Springer Verlag, LNBI 8701, 174-186, 2014.

ReadXplorer - Visualization and Analysis of Mapped Sequences (open access)
R. Hilker, K. B. Stadermann, D. Doppmeier, J. Kalinowski, J. Stoye, J. Straube, J. Winnebald, A. Goesmann
Bioinformatics 30(16): 2247-2254, 2014.

Mycoplasma salivarium as a dominant coloniser of Fanconi anaemia associated oral carcinoma (open access)
B. Henrich, M. Rumming, A. Sczyrba, E. Velleuer, R. Dietrich, W. Gerlach, M. Gombert, S. Rahn, J. Stoye, A. Borkhardt, U. Fischer
PLOS ONE 9(3): e92297, 2014.

BiPACE 2D - Graph-based multiple alignment for comprehensive two-dimensional gas chromatography-mass spectrometry (publisher website)
N. Hoffmann, M. Wilhelm, A. Doebbe, K. Niehaus, J. Stoye
Bioinformatics 30(7): 988-995, 2014.

2013

Restricted DCJ-Indel Model Revisited (preview, publisher website, journal version)
M. D. V. Braga, J. Stoye
Proceedings of BSB 2013, Springer Verlag, LNBI 8213, 36-46, 2013.

Statistics for approximate gene clusters (open access)
K. Jahn, S. Winter, J. Stoye, S. Böcker
BMC Bioinformatics 14(Suppl. 15): S14, 2013. (Proceedings of RECOMB-CG 2013)

On the Inversion-Indel Distance (open access)
E. Willing, S. Zaccaria, M. D. V. Braga, J. Stoye
BMC Bioinformatics 14(Suppl. 15): S3, 2013. (Proceedings of RECOMB-CG 2013)

The Potential of Family-Free Genome Comparison (preview, publisher website)
M. D. V. Braga, C. Chauve, D. Doerr, K. Jahn, J. Stoye, A. Thévenin, R. Wittler
In: C. Chauve, N. El-Mabrouk, E. Tannier (eds.): Models and Algorithms for Genome Evolution, Springer Verlag, Computational Biology Series, Vol. 19, 287-307, 2013.

The Genesis of the DCJ Formula (preview, publisher website)
A. Bergeron, J. Stoye
In: C. Chauve, N. El-Mabrouk, E. Tannier (eds.): Models and Algorithms for Genome Evolution, Springer Verlag, Computational Biology Series, Vol. 19, 63-81, 2013.

Next-generation-sequencing-spectratyping reveals public T-cell receptor repertoires in pediatric very severe aplastic anemia and identifies a beta chain CDR3 sequence associated with hepatitis-induced pathogenesis (publisher website)
P. F. I. Krell, S. Reuther, U. Fischer, T. Keller, S. Weber, M. Gombert, F. R. Schuster, C. Asang, P. Stepensky, B. Strahm, R. Meisel, J. Stoye, A. Borkhardt
Haematologica 98(9): 1388-1396, 2013.

Proceedings of the 13th International Workshop on Algorithms in Bioinformatics, WABI 2013 (publisher website)
A. Darling, J. Stoye (eds.)
Lecture Notes in Bioinformatics 8126, Springer Verlag, Heidelberg, 2013.

Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media (publisher website)
P. Schwientek, S. Wendler, A. Neshat, C. Eirich, C. Rückert, A. Klein, U. F. Wehmeier, J. Kalinowski, J. Stoye, A. Pühler
J. Biotechnol. 167(2): 166-177, 2013.

MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets (publisher website)
M. Zakrzewski, T. Bekel, C. Ander, A. Pühler, O. Rupp, J. Stoye, A. Schlüter, A. Goesmann
J. Biotechnol. 167(2): 156-165, 2013.

Taxonomic classification of metagenomic shotgun sequences with CARMA3 (publisher website)
W. Gerlach, J. Stoye
In: K. E. Nelson (ed.): Encyclopedia of Metagenomics. pp. 1-8. Springer Verlag, 2013.

metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences (open access)
C. Ander, O. B. Schulz-Trieglaff, J. Stoye, A. J. Cox
BMC Bioinformatics 14(Suppl. 5): S2, 2013. (Proceedings of RECOMB-Seq 2013)

Updating benchtop sequencing performance comparison (publisher website)
S. Jünemann, F. J. Sedlazeck, K. Prior, A. Albersmeier, U. John, J. Kalinowski, A. Mellmann, A. Goesmann, A. v. Haeseler, J. Stoye, D. Harmsen
Nat. Biotechnol. 31(4): 294-296, 2013. (Corrigendum: Nat. Biotechnology 31(12): 1148, 2013; publisher website)

2012

Multiple genome comparison based on overlap regions of pairwise local alignments (open access)
K. Jahn, H. Sudek, J. Stoye
BMC Bioinformatics 13(Suppl. 19): S7, 2012. (Proceedings of RECOMB-CG 2012)

Gene Family Assignment-Free Comparative Genomics (open access)
D. Doerr, A. Thévenin, J. Stoye
BMC Bioinformatics 13(Suppl. 19): S3, 2012. (Proceedings of RECOMB-CG 2012)

UniMoG - A unifying framework for genomic distance calculation and sorting based on DCJ (open access)
R. Hilker, C. Sickinger, C. N. S. Pedersen, J. Stoye
Bioinformatics 28(9): 2509-2511, 2012.

Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets (open access)
N. Hoffmann, M. Keck, H. Neuweger, M. Wilhelm, P. Högy, K. Niehaus, J. Stoye
BMC Bioinformatics 13: 214, 2012.

Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing (open access)
S. Jünemann, K. Prior, R. Szczepanowski, I. Harks, B. Ehmke, A. Goesmann, J. Stoye, D. Harmsen
PLOS ONE 7(8): e41606, 2012.

Proceedings of the 23rd Annual Symposium on Combinatorial Pattern Matching, CPM 2012 (publisher website)
J. Kärkkäinen, J. Stoye (eds.)
Lecture Notes in Computer Science 7354, Springer Verlag, Heidelberg, 2012.

The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110 (open access)
P. Schwientek, R. Szczepanowski, C. Rückert, J. Kalinowski, A. Klein, K. Selber, U. F. Wehmeier, J. Stoye, A. Pühler
BMC Genomics 13: 112, 2012.

Generic Software Frameworks for GC-MS Based Metabolomics (open access)
N. Hoffmann, J. Stoye
In: U. Roessner (ed.): Metabolomics. Chapter 4, pp. 73-98. InTech, 2012.


2011

On the weight of indels in genomic distances (open access)
M. D. V. Braga, R. Machado, L. C. Ribeiro, J. Stoye
BMC Bioinformatics 12(Suppl. 9): S13, 2011. (Proceedings of RECOMB-CG 2011)

Genomic distance under gene substitutions (open access)
M. D. V. Braga, R. Machado, L. C. Ribeiro, J. Stoye
BMC Bioinformatics 12(Suppl. 9): S8, 2011. (Proceedings of RECOMB-CG 2011)

Restricted DCJ Model: Rearrangement Problems with Chromosome Reincorporation (publisher website, conference version)
J. Kováč, R. Warren, M. D. V. Braga, J. Stoye
J. Comp. Biol. 18(9), 1231-1241, 2011.

Double Cut and Join with Insertions and Deletions (publisher website, conference version)
M. D. V. Braga, E. Willing, J. Stoye
J. Comp. Biol. 18(9), 1167-1184, 2011.

Consistency of Sequence-Based Gene Clusters (publisher website, conference version)
R. Wittler, J. Maňuch, M. Patterson, J. Stoye
J. Comp. Biol. 18(9), 1023-1039, 2011.

Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology (publisher website)
P. Schwientek, R. Szczepanowski, C. Rückert, J. Stoye, A. Pühler
J. Biotechnol. 155(1), 68-77, 2011.

Taxonomic classification of metagenomic shotgun sequences with CARMA3 (open access)
W. Gerlach, J. Stoye
Nucleic Acids Res. 39(14), e91, 2011.

Common Intervals of Multiple Permutations (publisher website, conference version)
S. Heber, R. Mayr, J. Stoye
Algorithmica 60(2), 175-206, 2011.

Exact and complete short read alignment to microbial genomes using GPU programming (open access)
J. Blom, T. Jakobi, D. Doppmeier, S. Jaenicke, J. Kalinowski, J. Stoye, A. Goesmann
Bioinformatics 27(10), 1351-1358, 2011.

Swiftly Computing Center Strings (open access, conference version)
F. Hufsky, L. Kuchenbecker, K. Jahn, J. Stoye, S. Böcker
BMC Bioinformatics 12: 106, 2011.

Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance (publisher website, arXiv version)
P. L. Erdős, L. Soukup, J. Stoye
Appl. Math. Lett. 24(1), 82-86, 2011.


2010

The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence (open access)
E. Trost, L. Ott, J. Schneider, J. Schröder, S. Jaenicke, A. Goesmann, P. Husemann, J. Stoye, F. Alves Dorella, F. Souza Rocha, S. de Castro Soares, V. D'Afonseca, A. Miyoshi, J. Ruiz, A. Silva, V. Azevedo, A. Burkovski, N. Guiso, O. F. Join-Lambert, S. Kayal, A. Tauch
BMC Genomics 11: 728, 2010.

Consistency of Sequence-based Gene Clusters (preview, publisher website, journal version)
R. Wittler, J. Stoye
Proceedings of RECOMB-CG 2010, Springer Verlag, LNBI 6398, 252-263, 2010.

The Problem of Chromosome Reincorporation in DCJ Sorting and Halving (preview, publisher website, journal version)
J. Kováč, M. D. V. Braga, J. Stoye
Proceedings of RECOMB-CG 2010, Springer Verlag, LNBI 6398, 13-24, 2010.

Rearrangement Models and Single-Cut Operations (publisher website, conference version)
A. Bergeron, P. Medvedev, J. Stoye
J. Comp. Biol. 17(9), 1213-1225, 2010.

Finding Nested Common Intervals Efficiently (publisher website, conference version)
G. Blin, D. Faye, J. Stoye
J. Comp. Biol. 17(9), 1183-1194, 2010.

The Solution Space of Sorting by DCJ (publisher website, conference version)
M. D. V. Braga, J. Stoye
J. Comp. Biol. 17(9), 1145-1165, 2010.

Repeat-aware Comparative Genome Assembly (open access)
P. Husemann, J. Stoye
Proceedings of GCB 2010, LNI P-173, 61-70, 2010.

Swiftly Computing Center Strings (preview, publisher website, journal version)
F. Hufsky, L. Kuchenbecker, K. Jahn, J. Stoye, S. Böcker
Proceedings of WABI 2010, Springer Verlag, LNBI 6293, 325-336, 2010.

Genomic Distance with DCJ and Indels (preview, publisher website, journal version)
M. D. V. Braga, E. Willing, J. Stoye
Proceedings of WABI 2010, Springer Verlag, LNBI 6293, 90-101, 2010.

Partitioning Biological Data with Transitivity Clustering (publisher website)
T. Wittkop, D. Emig, S. J. Lange, S. Rahmann, M. Albrecht, J. H. Morris, S. Böcker, J. Stoye, J. Baumbach
Nature Methods 7(6), 419-420, 2010.

r2cat: Synteny Plots and Comparative Assembly (open access)
P. Husemann, J. Stoye
Bioinformatics 26(4), 570-571, 2010.

Indexing and Searching a Mass Spectrometry Database (preview, publisher website)
S. Besenbacher, B. Schwikowski, J. Stoye
In: T. Elomaa, H. Mannila, P. Orponen (eds.): Algorithms and Applications: Essays Dedicated to Esko Ukkonen on the Occasion of His 60th Birthday, Springer Verlag, LNCS 6060, 62-76, 2010.

Phylogenetic Comparative Assembly (open access, conference version)
P. Husemann, J. Stoye
Algorithms Mol. Biol. 5: 3, 2010.


2009

WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads (open access)
W. Gerlach, S. Jünemann, F. Tille, A. Goesmann, J. Stoye
BMC Bioinformatics 10: 430, 2009.

A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance (publisher website, conference version)
A. Bergeron, J. Mixtacki, J. Stoye
Theor. Comput. Sci. 410(51), 5300-5316, 2009.

A Report on the 2009 SIG on Short Read Sequencing and Algorithms (Short-SIG) (invited report) (publisher website)
M. Brudno, P. Medvedev, J. Stoye, F. De La Vega
Bioinformatics, 25(21), 2863-2864, 2009.

Rearrangement Models and Single-Cut Operations (preview, publisher website, journal version)
P. Medvedev, J. Stoye
Proceedings of RECOMB-CG 2009, Springer Verlag, LNBI 5817, 84-97, 2009.

Finding Nested Common Intervals Efficiently (preview, publisher website, journal version)
G. Blin, J. Stoye
Proceedings of RECOMB-CG 2009, Springer Verlag, LNBI 5817, 59-69, 2009.

Counting All DCJ Sorting Scenarios (preview, publisher website, journal version)
M. D. V. Braga, J. Stoye
Proceedings of RECOMB-CG 2009, Springer Verlag, LNBI 5817, 36-47, 2009.

A Unified Approach for Reconstructing Ancient Gene Clusters (publisher website)
J. Stoye, R. Wittler
IEEE/ACM Trans. Comput. Biol. Bioinf. 6(3), 387-400, 2009.

Phylogenetic Comparative Assembly (preview, publisher website, journal version)
P. Husemann, J. Stoye
Proceedings of WABI 2009, Springer Verlag, LNBI 5724, 145-156, 2009.

Computation of Median Gene Clusters (publisher website, conference version)
S. Böcker, K. Jahn, J. Mixtacki, J. Stoye
J. Comp. Biol. 16(8), 1085-1099, 2009.

ChromA: Signal Based Retention Time Alignment for Chromatography-Mass Spectrometry Data (open access)
N. Hoffmann, J. Stoye
Bioinformatics 25(16), 2080-2081, 2009.

Computational Short Read Metagenomics (invited abstract)
J. Stoye
Proceedings of JOBIM 2009, 3-4, 2009.

Approximative Gencluster und ihre Anwendung in der komparativen Genomik (in German) (publisher website)
K. Jahn, J. Stoye
Informatik-Spektrum 32(4), 288-300, 2009.

The Sequence Analysis and Management System - SAMS-2.0: Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies (publisher website)
T. Bekel, K. Henckel, H. Küster, V. Mittard Runte, H. Neuweger, D. Paarmann, O. Rupp, M. Zakrzewski, A. Pühler, J. Stoye, A. Goesmann
J. Biotechnol. 140(1-2), 3-12, 2009.


2008

MeltDB: A software Platform for the Analysis and Integration of Metabolomics Experiment Data (open access)
H. Neuweger, S. P. Albaum, M. Dondrup, M. Persicke, T. Watt, K. Niehaus, J. Stoye, A. Goesmann
Bioinformatics 24(23), 2726-2732, 2008.

On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios (preview)
A. Bergeron, J. Mixtacki, J. Stoye
Proceedings of RECOMB-CG 2008, Springer Verlag, LNBI 5267, 226-240, 2008.

Detecting Repeat Families in Incompletely Sequenced Genomes (technical report, preview)
J. A. A. Quitzau, J. Stoye
Proceedings of WABI 2008, Springer Verlag, LNBI 5251, 342-353, 2008.

Taxonomic Composition and Gene Content of a Methane-producing Microbial Community Isolated from a Biogas Reactor (publisher website)
L. Krause, N. N. Diaz, R. A. Edwards, K.-H. Gartemann, H. Krömeke, H. Neuweger, A. Pühler, K. Runte, A. Schlüter, J. Stoye, R. Szczepanowski, A. Tauch, A. Goesmann
J. Biotechnol. 136(1-2), 91-101, 2008.

Suffix Tree Construction in RAM (1997; Farach-Colton) (publisher website)
J. Stoye
In: M.-Y. Kao (ed.): Encyclopedia of Algorithms. pp. 925-928. Springer Verlag, 2008.

Comparative Pathway Analyzer - CPA - A Web Server for Comparative Analysis, Clustering and Visualization of Metabolomic Networks in Multiple Organisms (open access)
S. Oehm, D. Gilbert, A. Tauch, J. Stoye, A. Goesmann
Nucleic Acids Res. 36(Supplement 2), W433-W437, 2008. (Web Server Issue 2008)

HP Distance via Double Cut and Join (preview, journal version)
A. Bergeron, J. Mixtacki, J. Stoye
Proceedings of CPM 2008, Springer Verlag, LNCS 5029, 56-68, 2008.

Counting Suffix Arrays and Strings (publisher website, conference version, technical report)
K.-B. Schürmann, J. Stoye
Theor. Comput. Sci. 395(2-3), 220-234, 2008.

Phylogenetic Classification of Short Environmental DNA Fragments (open access)
L. Krause, N. N. Diaz, A. Goesmann, S. Kelley, T. W. Nattkemper, F. Rohwer, R. A. Edwards, J. Stoye
Nucleic Acids Res. 36(7), 2230-2239, 2008.

Computation of Median Gene Clusters (preview, journal version)
S. Böcker, K. Jahn, J. Mixtacki, J. Stoye
Proceedings of RECOMB 2008, Springer Verlag, LNBI 4955, 331-345, 2008.


2007

Gecko and GhostFam - Rigorous and Efficient Gene Cluster Detection in Prokaryotic Genomes (publisher website)
T. Schmidt, J. Stoye
In: N. H. Bergman (ed.): Methods in Molecular Biology, vol. 396: Comparative Genomics, Volume 2. Chapter 12, pp. 165-182. Humana Press Inc., Totowa, NJ, 2007.

Based Upon Repeat Pattern (BURP): An Algorithm to Characterize the Long-term Evolution of Staphylococcus aureus Populations based on spa Polymorphisms (open access)
A. Mellmann, T. Weniger, C. Berssenbrügge, J. Rothgänger, M. Sammeth, J. Stoye, D. Harmsen
BMC Microbiology 7: 98, 2007.

Character Sets of Strings (publisher website, conference version)
G. Didier, T. Schmidt, J. Stoye, D. Tsur
J. Discr. Alg. 5(2), 330-340, 2007.

An Incomplex Algorithm for Fast Suffix Array Construction (publisher website, conference version)
K.-B. Schürmann, J. Stoye
Softw. Pract. Exper. 37(3), 309-329, 2007.

GISMO - Gene Identification using a Support Vector Machine for ORF Classification (open access)
L. Krause, A. McHardy, T. Nattkemper, A. Pühler, J. Stoye, F. Meyer
Nucleic Acids Res. 35(2), 540-549, 2007.


2006

Comparing Tandem Repeats with Duplications and Excisions of Variable Degree (publisher website, conference version, technical report)
M. Sammeth, J. Stoye
IEEE/ACM Trans. Comput. Biol. Bioinf. 3(4), 395-407, 2006.

On the Similarity of Sets of Permutations and its Applications to Genome Comparison (publisher website, conference version, technical report)
A. Bergeron, J. Stoye
J. Comp. Biol. 13(7), 1340-1354, 2006.

A Unifying View of Genome Rearrangements (publisher website, preview)
A. Bergeron, J. Mixtacki, J. Stoye
Proceedings of WABI 2006, Springer Verlag, LNBI 4175, 163-173, 2006.

Finding Novel Genes in Bacterial Communities Isolated from the Environment (open access)
L. Krause, N. N. Diaz, D. Bartels, R. A. Edwards, A. Pühler, F. Rohwer, F. Meyer, J. Stoye
Bioinformatics 22(14), e281-e289, 2006. (Proceedings of ISMB 2006)

Index Structures in Biological Sequence Analysis: From Simplicity to Complexity and Back (invited abstract)
J. Stoye
Proceedings of JOBIM 2006, 3, 2006.

On Sorting by Translocations (publisher website, conference version)
A. Bergeron, J. Mixtacki, J. Stoye
J. Comp. Biol. 13(2), 567-578, 2006.

Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length (publisher website, conference version)
K. R. Rasmussen, J. Stoye, E. W. Myers
J. Comp. Biol. 13(2), 296-308, 2006.

Panta rhei (QAlign2): an Open Graphical Environment for Sequence Analysis (open access)
M. Sammeth, T. Griebel, F. Tille, J. Stoye
Bioinformatics 22(7), 889-890, 2006.


2005

Counting Suffix Arrays and Strings (journal version, technical report)
K.-B. Schürmann, J. Stoye
Proceedings of SPIRE 2005, Springer Verlag, LNCS 3772, 55-66, 2005.

Informatische Methoden zur Protein-Identifikation (invited article, in German) (publisher website)
S. Böcker, J. Stoye
LaborPraxis 29(10), 24-26, 2005.

Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI) (preview, technical report, journal version)
M. Sammeth, T. Weniger, D. Harmsen, J. Stoye
Proceedings of WABI 2005, Springer Verlag, LNBI 3692, 276-290, 2005.

Protein Annotation by Secondary Structure Based Alignments (PASSTA) (preview, publisher website)
C. Bannert, J. Stoye
Proceedings of CompLife 2005, Springer Verlag, LNBI 3695, 79-90, 2005.

On Sorting by Translocations (preview, publisher website, journal version)
A. Bergeron, J. Mixtacki, J. Stoye
Proceedings of RECOMB 2005, Springer Verlag, LNBI 3500, 615-629, 2005.

Efficient q-Gram Filters for Finding All ε-Matches Over a Given Length (preview, publisher website, journal version)
K. R. Rasmussen, J. Stoye, E. W. Myers
Proceedings of RECOMB 2005, Springer Verlag, LNBI 3500, 189-203, 2005.

The Inversion Distance Problem (conference version)
A. Bergeron, J. Mixtacki, J. Stoye
In: O. Gascuel (ed.): Mathematics of Evolution and Phylogeny. Chapter 10, pp. 262-290. Oxford University Press, 2005.

BACCardI - A Tool for the Validation of Genomic Assemblies, Assisting Genome Finishing and Intergenome Comparison (open access, repository)
D. Bartels, S. Kespohl, S. Albaum, T. Drüke, A. Goesmann, J. Herold, O. Kaiser, A. Pühler, F. Pfeiffer, G. Raddatz, J. Stoye, F. Meyer, S. C. Schuster
Bioinformatics 21(7), 853-859, 2005.

Large Scale Hierarchical Clustering of Protein Sequences (open access)
A. Krause, J. Stoye, M. Vingron
BMC Bioinformatics 6:15, 2005.

An Incomplex Algorithm for Fast Suffix Array Construction (preview, journal version)
K.-B. Schürmann, J. Stoye
Proceedings of ALENEX/ANALCO 2005, 77-85, 2005.


2004

Linear Time Algorithms for Finding and Representing all the Tandem Repeats in a String (publisher website, technical report)
D. Gusfield, J. Stoye
J. Comput. Syst. Sci. 69(4), 525-546, 2004.

Proceedings of the German Conference on Bioinformatics, GCB 2004
R. Giegerich, J. Stoye (eds.)
Lecture Notes in Informatics, P-53, Bonn, 2004.

Suboptimal Local Alignments across Multiple Scoring Schemes (preview)
M. Michael, C. Dieterich, J. Stoye
Proceedings of WABI 2004, Springer Verlag, LNBI 3240, 99-110, 2004.

Reversal Distance without Hurdles and Fortresses (preview, publisher website, book chapter version)
A. Bergeron, J. Mixtacki, J. Stoye
Proceedings of CPM 2004, Springer Verlag, LNCS 3109, 388-399, 2004.

Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences (preview, publisher website, journal version)
T. Schmidt, J. Stoye
Proceedings of CPM 2004, Springer Verlag, LNCS 3109, 347-359, 2004.

Algorithmic Complexity of Protein Identification: Combinatorics of Weighted Strings (publisher website, conference version, technical report)
M. Cieliebak, T. Erlebach, Zs. Lipták, J. Stoye, E. Welzl
Discr. Appl. Math. 137(1), 27-46, 2004.

Benchmarking Tools for the Alignment of Functional Noncoding DNA (open access, repository)
D. A. Pollard, C. M. Bergman, J. Stoye, S. E. Celniker, M. B. Eisen
BMC Bioinformatics 5: 6, 2004. (Correction: BMC Bioinformatics, 5: 73, 2004; open access)


2003

The European Conference on Computational Biology (invited report)
S. Heber, J. Stoye
Drug Discovery Today 8(3), 113-114, 2003.

Evaluation of the Jumping Alignment Algorithm with Artificial and Biological Data
C. Bannert, J. Stoye
Proceedings of GCB 2003, 21-25, 2003.

Divide-and-conquer Multiple Alignment with Segment-based Constraints (open access, repository)
M. Sammeth, B. Morgenstern, J. Stoye
Bioinformatics 19(Supplement 2), ii189-ii195, 2003. (Proceedings of ECCB 2003)

Efficient Implementation of Lazy Suffix Trees (publisher website, conference version)
R. Giegerich, S. Kurtz, J. Stoye
Softw. Pract. Exper. 33(11), 1035-1049, 2003.

QAlign: Quality-Based Multiple Alignments with Dynamic Phylogenetic Analysis (open access, repository)
M. Sammeth, J. Rothgänger, W. Esser, J. Albert, J. Stoye, D. Harmsen
Bioinformatics 19(12), 1592-1593, 2003.

Finden, fast ohne zu suchen: Indexstrukturen in der Bioinformatik (invited article, in German)
R. Giegerich, J. Stoye
Forschung an der Universität Bielefeld 26, 63-68, 2003.

On the Similarity of Sets of Permutations and its Applications to Genome Comparison (preview, publisher website, technical report, journal version)
A. Bergeron, J. Stoye
Proceedings of COCOON 2003, Springer Verlag, LNCS 2697, 68-79, 2003.


2002

A Novel Approach to Remote Homology Detection: Jumping Alignments (publisher website, conference version)
R. Spang, M. Rehmsmeier, J. Stoye
J. Comp. Biol. 9(5), 747-760, 2002.

Common Intervals and Sorting by Reversals: A Marriage of Necessity (publisher website, repository)
A. Bergeron, S. Heber, J. Stoye
Bioinformatics 18(Supplement 2), S54-S63, 2002. (Proceedings of ECCB 2002)

Index Structures for Large Sequence Data: Suffix Trees and Affix Trees (invited abstract)
J. Stoye
GI Jahrestagung (Ergänzungsband), LNI P-20, 67, 2002.

Algorithmic Complexity of Protein Identification: Searching in Weighted Strings (journal version, technical report)
M. Cieliebak, Zs. Lipták, E. Welzl, T. Erlebach, J. Stoye
Proceedings of IFIP TCS 2002, 143-156, 2002.

Resampling Methods in Physical Mapping
S. Heber, J. Stoye, M. Frohme, J. Hoheisel, M. Vingron
Proceedings of GfKl 2000, 437-444, 2002.

Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (publisher website, repository, conference version, technical report)
J. Stoye, D. Gusfield
Theor. Comput. Sci. 270(1-2), 843-856, 2002.


2001

Algorithms for Finding Gene Clusters (publisher website, preview)
S. Heber, J. Stoye
Proceedings of WABI 2001, Springer Verlag, LNCS 2149, 252-263, 2001.

Finding all Common Intervals of k Permutations (publisher website, preview)
S. Heber, J. Stoye
Proceedings of CPM 2001, Springer Verlag, LNCS 2089, 207-218, 2001.

REPuter: the Manifold Applications of Repeat Analysis on a Genomic Scale (open access, repository, conference version)
S. Kurtz, J. V. Choudhuri, E. Ohlebusch, C. Schleiermacher, J. Stoye, R. Giegerich
Nucleic Acids Res. 29(22), 4633-4642, 2001.


2000

Finding Maximal Pairs with Bounded Gap (conference version, technical report)
G. S. Brodal, R. B. Lyngsø, C. N. S. Pedersen, J. Stoye
In: M. Crochemore, L. Gąsieniec (eds.): Matching Patterns (Journal of Discrete Algorithms), 77-104, 2000.

Proceedings of the German Conference on Bioinformatics, GCB 2000
E. Bornberg-Bauer, U. Rost, J. Stoye, M. Vingron (eds.)
Logos Verlag, Berlin, 2000.

An Iterative Method for Faster Sum-of-Pairs Multiple Sequence Alignment (open access, repository, conference version)
K. Reinert, J. Stoye, T. Will
Bioinformatics 16(9), 808-814, 2000.

Contig Selection in Physical Mapping (publisher website, conference version)
S. Heber, J. Stoye, M. Frohme, J. Hoheisel, M. Vingron
J. Comp. Biol. 7(3-4), 395-408, 2000.

Computation and Visualization of Degenerate Repeats in Complete Genomes (preview, journal version)
S. Kurtz, E. Ohlebusch, C. Schleiermacher, J. Stoye, R. Giegerich
Proceedings of ISMB 2000, 228-238, 2000.

Sequence Database Search Using Jumping Alignments (preview, journal version)
R. Spang, M. Rehmsmeier, J. Stoye
Proceedings of ISMB 2000, 367-375, 2000.

Contig Selection in Physical Mapping (journal version)
S. Heber, J. Stoye, J. Hoheisel, M. Vingron
Proceedings of RECOMB 2000, 155-164, 2000.

The SYSTERS Protein Sequence Cluster Set (open access, repository)
A. Krause, J. Stoye, M. Vingron
Nucleic Acids Res. 28(1), 270-272, 2000.


1999

Combining Divide-and-Conquer, the A*-Algorithm, and Successive Realignment Approaches to Speed up Multiple Sequence Alignment (online proceedings)
K. Reinert, J. Stoye, T. Will
Proceedings of GCB 1999, 17-24, 1999.

Finding Maximal Pairs with Bounded Gap (publisher website, bookchapter version, technical report)
G. S. Brodal, R. B. Lyngsø, C. N. S. Pedersen, J. Stoye
Proceedings of CPM 1999, Springer Verlag, LNCS 1645, 134-149, 1999.

Efficient Implementation of Lazy Suffix Trees (preview, publisher website)
R. Giegerich, S. Kurtz, J. Stoye
Proceedings of WAE 1999, Springer Verlag, LNCS 1668, 30-42, 1999.


1998

Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version) (preview, publisher website, technical report, journal version)
J. Stoye, D. Gusfield
Proceedings of CPM 1998, Springer Verlag, LNCS 1448, 140-152, 1998.

The Number of Standard and of Effective Multiple Alignments (publisher website, repository, preprint)
A. Dress, B. Morgenstern, J. Stoye
Appl. Math. Lett. 11(4), 43-49, 1998.

Die Bedeutung der Zusammenarbeit der Disziplinen in der Anwendung - erläutert anhand von Beispielen (in German)
M. Hildebrand, J. Stoye
Der Mathematikunterricht 44(6), 34-53, 1998.

Multiple Sequence Alignment with the Divide-and-Conquer Method (publisher website, repository)
J. Stoye
Gene 211(2), GC45-GC56, 1998.

Rose: Generating Sequence Families (open access, repository, poster, technical report, conference version)
J. Stoye, D. Evers, F. Meyer
Bioinformatics 14(2), 157-163, 1998.


1997

DCA: An Efficient Implementation of the Divide-and-Conquer Approach to Simultaneous Multiple Sequence Alignment (open access, repository)
J. Stoye, V. Moulton, A. W. M. Dress
CABIOS 13(6), 625-626, 1997.

Generating Benchmarks for Multiple Sequence Alignments and Phylogenetic Reconstructions (poster, technical report, journal version)
J. Stoye, D. Evers, F. Meyer
Proceedings of ISMB 1997, 303-306, 1997.

Two Applications of the Divide&Conquer Principle in the Molecular Sciences (publisher website, preprint)
G. Brinkmann, A. W. M. Dress, S. W. Perrey, J. Stoye
Math. Program. 79, 71-97, 1997.

Improving the Divide-and-Conquer Approach to Sum-of-Pairs Multiple Sequence Alignment (publisher website, preprint)
J. Stoye, S. W. Perrey, A. W. M. Dress
Appl. Math. Lett. 10(2), 67-73, 1997.

Divide-and-Conquer Multiple Sequence Alignment (pdf)
J. Stoye
Dissertation Thesis. Universität Bielefeld, Forschungsbericht der Technischen Fakultät, Abteilung Informationstechnik. Report 97-02, 1997. (ISSN 0946-7831)


1996

A General Method for Fast Multiple Sequence Alignment (publisher website, preprint)
U. Tönges, S. W. Perrey, J. Stoye, A. W. M. Dress
Gene 172(1), GC33-GC41, 1996.


Consortium Papers, Preprints, Posters and Other Material

NFDI4Microbiota – national research data infrastructure for microbiota research (open access)
K. U. Förstner, A. Becker, J. Blom, P. Bork, T. Clavel, M. Dieckmann, A. Goesmann, B. Götz, T. Gübitz, F. Hufsky, S. Jünemann, M.-L. Körner, M. Marz, U. Nunes Da Rocha, J. Overmann, A. Pühler, D. Rebholz-Schuhmann, A. Sczyrba, J. Stoye, J. Vandendorpe, T. Van Rossum, A. McHardy
Research Ideas and Outcomes 9: e110501, 2023.

Investigating the complexity of the double distance problems (arXiv, conference version 1, conference version 2, journal version)
M. D, V. Braga, L. R. Brockmann, K. Klerx, J. Stoye
arXiv:2303.04205, 2023.

Revisiting pangenome openness with k-mers (bioRxiv, journal version)
L. Parmigiani, R. Wittler, J. Stoye
bioRxiv:2022.11.15.516472, 2022.

Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021 (open access, medRxiv version)
T. Houwaart et al., German COVID-19 OMICS Initiative (DeCOI)
Eurosurveillance 27:43, 2022.

Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches (arXiv, journal version, conference version)
P. Bonizzoni, M. Costantini, C. De Felice, A. Petescia, Y. Pirola, M. Previtali, R. Rizzi, J. Stoye, R. Zaccagnino, R. Zizza
arXiv:2202.13884, 2022.

The Bielefeld Institute for Bioinformatics Infrastructure (publisher website)
J. Stoye, R. Wittler (eds.)
Bielefeld: Universität Bielefeld, Technische Fakultät, 2021.

Integrated Genomic Surveillance reveals extensive onward transmission of travel-imported SARS-CoV-2 infections in the community (medRxiv, journal version)
T. Houwaart et al., German COVID-19 OMICS Initiative (DeCOI)
medRxiv:2021.10.18.21264530, 2021.

Characterization of SARS-CoV-2 infection clusters based on integrated genomic surveillance, outbreak analysis and contact tracing in an urban setting (open access)
A. Walker et al., German COVID-19 OMICS Initiative (DeCOI)
Clinical Infectious Diseases, ciab588, 2021.

Editorial: Computational Methods for Microbiome Analysis (open acccess, research topic)
J. C. Setubal, J. Stoye, B. E. Dutilh (eds.)
Front. Genet. 11: 623897, 2020.

Detecting High Scoring Local Alignments in Pangenome Graphs (bioRxiv, journal version)
T. Schulz, R. Wittler, S. Rahmann, F. Hach, J. Stoye
bioRxiv:2020.09.03.280958, 2020.

Severe COVID-19 is marked by a dysregulated myeloid cell compartment (open access)
J. Schulte-Schrepping et al., Deutsche COVID-19 OMICS Initiative (DeCOI)
Cell 182, 1419-1440, 2020.

Swarm Learning as a privacy-preserving machine learning approach for disease classification (bioRrxiv)
S. Warnat-Herresthal et al., German COVID-19 OMICS Initiative (DeCOI)
bioRxiv:2020.06.25.171009, 2020.

NFDI4BioDiversity - A Consortium for the National Research Data Infrastructure (NFDI) (open access)
F. O. Glöckner, M. Diepenbroek, J. Felden, A. Güntsch, J. Stoye, J. Overmann, K. Wimmers, I. Kostadinov, R. Yahyapour, W. Müller, U. Scholz, D. Triebel, M. Frenzel, B. Gemeinholzer, A. Goesmann, B. König-Ries, A. Bonn, B. Seeger
Zenodo, 2020.

Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine (bioRrxiv, journal version)
L. K. Sundermann, J. Wintersinger, G. Rätsch, J. Stoye, Q. Morris
bioRxiv:2020.06.11.146100, 2020.

On motifs in colored graphs (arXiv, journal version)
D. P. Rubert, E. Araujo, M. A. Stefanes, J. Stoye, F. V. Martinez
arXiv:2005.13634, 2020.

HASLR: Fast Hybrid Assembly of Long Reads (bioRrxiv, journal version)
E. Haghshenas, H. Asghari, J. Stoye, C. Chauve, F. Hach
bioRxiv:2020.01.27.921817, 2020.

Computing the rearrangement distance of natural genomes (arXiv, journal version, conference version)
L. Bohnenkämper, M. D. V. Braga, D. Doerr, J. Stoye
arXiv:2001.02139, 2020.

Computing the Inversion-Indel Distance (arXiv, journal version)
E. Willing, J. Stoye, M. D. V. Braga
arXiv:1909.12877, 2019.

Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings (arXiv, conference version)
L. Cunha, S. Dantas, T. Gagie, R. Wittler, L. Kowada, J. Stoye
arXiv:1702.01280, 2017.

Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distace (arXiv, journal version)
P. Erdős, L. Soukup, J. Stoye
arXiv:1004.2735, 2010.

A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance (repository)
A. Bergeron, J. Mixtacki, J. Stoye
In: A. Apostolico, A. Dress, L. Parida (eds.): Dagstuhl Seminar Proceedings, number 10231: Structure Discovery in Biology: Motifs, Networks & Phylogenies, June 7-11, 2010.

Maltcms - an Application Framework for Processing of Metabolomics-Data (pdf)
N. Hoffmann, M. Wilhelm, M. Keck, A. Döbbe, K. Niehaus, J. Stoye
Poster presented at GCB 2009, Halle/Saale, Germany, September 28-30, 2009.

A Space Efficient Representation for Sparse de Bruijn Subgraphs (repository)
J. A. A. Quitzau, J. Stoye
Universität Bielefeld, Forschungsbericht der Technischen Fakultät, Abteilung Informationstechnik. Report 2008-02, 2008. (ISSN 0946-7831)

Online Abelian Pattern Matching (repository)
T. Ejaz, S. Rahmann, J. Stoye
Universität Bielefeld, Forschungsbericht der Technischen Fakultät, Abteilung Informationstechnik. Report 2008-01, 2008. (ISSN 0946-7831)

Transforming the Mouse Genome into the Human Genome with only 6 Breakpoint Reuses (movie)
A. Bergeron, A. Gués, B. Stoye, F. Stoye, J. Stoye, L. Stoye
Animated video with three kids and 281 post-it notes, 2007. The original photos can be found here.

On Common Intervals with Errors (repository)
C. Chauve, Y. Diekmann, S. Heber, J. Mixtacki, S. Rahmann, J. Stoye
Universität Bielefeld, Forschungsbericht der Technischen Fakultät, Abteilung Informationstechnik. Report 2006-02, 2006. (ISSN 0946-7831)

Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI) (repository, conference version, journal version)
M. Sammeth, J. Stoye
Universität Bielefeld, Forschungsbericht der Technischen Fakultät, Abteilung Informationstechnik. Report 2005-05, 2005. (ISSN 0946-7831)

Counting Suffix Arrays and Strings (repository, journal version, conference version)
K.-B. Schürmann, J. Stoye
Universität Bielefeld, Forschungsbericht der Technischen Fakultät, Abteilung Informationstechnik. Report 2005-04, 2005. (ISSN 0946-7831)

Suffix Tree Construction and Storage with Limited Main Memory (repository)
K.-B. Schürmann, J. Stoye
Universität Bielefeld, Forschungsbericht der Technischen Fakultät, Abteilung Informationstechnik. Report 2003-06, 2003. (ISSN 0946-7831)

On the Similarity of Sets of Permutations and its Applications to Genome Comparison (repository, journal version, conference version)
A. Bergeron, J. Stoye
Universität Bielefeld, Forschungsbericht der Technischen Fakultät, Abteilung Informationstechnik. Report 2003-01, 2003. (ISSN 0946-7831)

Sequence Database Search Using Jumping Alignments (pdf)
C. Bannert, R. Spang, M. Rehmsmeier, J. Stoye
Poster presented at GCB 01, Braunschweig, Germany, October 7-10, 2001.

Algorithmic Complexity of Protein Identification: Combinatorics of Weighted Strings (pdf, conference version, journal version)
M. Cieliebak, T. Erlebach, Zs. Lipták, J. Stoye, E. Welzl
Technical Report no. 361, ETH Zürich, Dept. of Computer Science, 2001.

Affix Trees (pdf)
J. Stoye
Diploma thesis. Universität Bielefeld, Forschungsbericht der Technischen Fakultät, Abteilung Informationstechnik. Report 2000-04, 2000. (ISSN 0946-7831)
English translation. Original title in German: Affixbäume. Bielefeld, 1995.

Consistent Equivalence Relations: A Set-Theoretical Framework for Multiple Sequence Alignment (pdf)
B. Morgenstern, J. Stoye, A. Dress
Universität Bielefeld, Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse. Materialien/Preprints 133, 1999.

Finding Maximal Pairs with Bounded Gap (pdf, bookchapter version, journal version)
G. S. Brodal, R. B. Lyngsø, C. N. S. Pedersen, J. Stoye
BRICS, Department of Computer Science, University of Aarhus, Ny Munkegade, 8000 Århus C, Denmark. Report RS-99-12, 1999.

Linear Time Algorithms for Finding and Representing all the Tandem Repeats in a String (pdf)
D. Gusfield, J. Stoye
Department of Computer Science, University of California, Davis. Report CSE-98-4, 1998.

Sorting Leaf-Lists in a Tree (pdf)
C. N. S. Pedersen, J. Stoye
Unpublished manuscript, 1998.

On the Number of Standard and of Effective Alignments (pdf)
A.W.M. Dress, B. Morgenstern, J. Stoye
Poster presented at RECOMB 98, New York, NY, USA, March 22-25, 1998.

Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (pdf, conference version, journal version)
J. Stoye, D. Gusfield
Department of Computer Science, University of California, Davis. Report CSE-98-2, 1998.

FDCA: Fast and Accurate Approximation to Sum-of-Pairs Score Optimal Multiple Sequence Alignment
S.W. Perrey, J. Stoye, V. Moulton
Universität Bielefeld, Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse. Materialien/Preprints 114, 1997.

On the Number of Standard and Effective Multiple Alignments (pdf, journal version)
A. Dress, B. Morgenstern, J. Stoye
Universität Bielefeld, Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse. Materialien/Preprints 112, 1997.

On Simultaneous versus Iterative Multiple Sequence Alignment (pdf)
S.W. Perrey, J. Stoye, V. Moulton, A.W.M. Dress
Universität Bielefeld, Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse. Materialien/Preprints 111, 1997.

Rose: Generating Sequence Families (pdf, poster, conference version, journal version)
J. Stoye, D. Evers, F. Meyer
Universität Bielefeld, Forschungsbericht der Technischen Fakultät, Abteilung Informationstechnik. Report 97-04, 1997. (ISSN 0946-7831)

Generating Benchmarks for Multiple Sequence Alignments and Phylogenetic Reconstructions (pdf, technical report, conference version, journal version)
J. Stoye, D. Evers, F. Meyer
Poster presented at ISMB 97, Halkidiki, Greece, June 21-25, 1997.

Two Applications of the Divide & Conquer Principle in the Molecular Sciences (pdf, journal version)
G. Brinkmann, A.W.M. Dress, S.W. Perrey, J. Stoye
Universität Bielefeld, Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse. Materialien/Preprints 109, 1997.
(Also appeared as: Research Report 151, University of Canterbury, Christchurch, New Zealand. Department of Mathematics and Statistics, March, 1997.)

Fast Approximation to the NP-hard Problem of Multiple Sequence Alignment (pdf)
S.W. Perrey, J. Stoye
Information and Mathematical Sciences Reports, Series B:96/06. Dept. of Mathematics, Massey University, Palmerston North, New Zealand. May, 1996. (ISSN 1171-7637)

Improving the Divide-and-Conquer Approach to Sum-of-Pairs Multiple Sequence Alignment (pdf, journal version)
J. Stoye, A.W.M. Dress, S.W. Perrey
Universität Bielefeld, Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse. Materialien/Preprints 102, 1996.

A General Method for Fast Multiple Sequence Alignment (pdf, journal version)
U. Tönges, S.W. Perrey, J. Stoye, A.W.M. Dress
Universität Bielefeld, Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse. Materialien/Preprints XCIX, 1996.

Divide-and-Conquer Multiple Sequence Alignment (pdf)
J. Stoye, S.W. Perrey, A.W.M. Dress
Poster and talk presented at the Winter Seminar on Molecular Biology and Biophysical Chemistry of the Cell, Klosters, Switzerland, Jan. 11-25, 1997.

Statistics for Fragment Comparison - A Biologically Motivated Approach to Sequence Alignment (pdf)
S.W. Perrey, J. Stoye, A.W.M. Dress
Talk presented by S.W. Perrey at the German Conference on Bioinformatics, Braunschweig, 1995.

Affixbäume (pdf, in German)
J. Stoye
Diploma thesis, 1995.

Jens Stoye