193 Publications

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[193]
2017 | Journal Article | PUB-ID: 2913556
Bioinformatics for NGS-based metagenomics and the application to biogas research
Jünemann S, Kleinbölting N, Jaenicke S, Henke C, Hassa J, Nelkner J, Stolze Y, Albaum S, Schlüter A, Goesmann A, Sczyrba A, et al. (2017)
Journal of Biotechnology 261(SI): 10-23.
PUB | DOI | WoS | PubMed | Europe PMC
 
[192]
2017 | Conference Paper | PUB-ID: 2909409
Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings
Cunha L, Dantas S, Gagie T, Wittler R, Kowada L, Stoye J (2017)
In: Proceedings of CPM 2017. LIPIcs, 78. 19:1-19:9.
PUB | DOI
 
[191]
2017 | Conference Paper | PUB-ID: 2907587
Dynamic Alignment-Free and Reference-Free Read Compression
Holley G, Wittler R, Stoye J, Hach F (2017)
In: Proceedings of RECOMB 2017. Lecture Notes in Bioinformatics, 10229. 50-65.
PUB | DOI
 
[190]
2017 | Conference Paper | PUB-ID: 2913015
Algorithms for Computing the Family-Free Genomic Similarity under DCJ
Rubert DP, Medeiros GL, Hoshino EA, Dias Vieira Braga M, Stoye J, Martinez FV (2017)
In: Proceedings of RECOMB-CG 2017. Lecture Notes in Bioinformatics, 10562. Springer Verlag: 76-100.
PUB | DOI
 
[189]
2017 | Conference Paper | PUB-ID: 2913016
Finding Teams in Graphs and its Application to Spatial Gene Cluster Discovery
Schulz T, Stoye J, Dörr D (2017)
In: Proceedings of RECOMB-CG 2017. Lecture Notes in Bioinformatics, 1704. Berlin: Springer Verlag: 197-212.
PUB | DOI
 
[188]
2017 | Book Chapter | PUB-ID: 2913921
Pan-genome Storage and Analysis Techniques
Zekic T, Holley G, Stoye J (In Press)
In: Comparative Genomics: Methods and Protocols. Setubal JC, Stadler P, Stoye J (Eds); Methods in Molecular Biology, 1704. Springer Verlag.
PUB
 
[187]
2017 | Book Chapter | PUB-ID: 2913922
Family-Free Genome Comparison
Dörr D, Feijão P, Stoye J (In Press)
In: Comparative Genomics: Methods and Protocols. Setubal JC, Stadler P, Stoye J (Eds); Methods in Molecular Biology, 1704. Springer Verlag.
PUB
 
[186]
2017 | Book (Editor) | PUB-ID: 2913920
Comparative Genomics: Methods and Protocols
Setubal JC, Stadler P, Stoye J (Eds) (In Press) Methods in Molecular Biology; 1704.
Springer Verlag.
PUB
 
[185]
2017 | Journal Article | PUB-ID: 2909057
Approximating the DCJ distance of balanced genomes in linear time
Rubert DP, Feijão P, Dias Vieira Braga M, Stoye J, Martinez FHV (2017)
Algorithms for Molecular Biology 12: 3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[184]
2017 | Preprint | PUB-ID: 2908521
Faster Jumbled Indexing for Binary Run-Length Encoded Strings
Cunha L, Dantas S, Gagie T, Wittler R, Kowada L, Stoye J (2017)
arXiv: 1702.01280.
PUB
 
[183]
2017 | Journal Article | PUB-ID: 2909967
New Genome Similarity Measures based on Conserved Gene Adjacencies
Dörr D, Kowada LAB, Soares de Araujo FE, Deshpande S, Dantas S, Moret BME, Stoye J (2017)
Journal of Computational Biology 24(6): 616-634.
PUB | DOI | WoS
 
[182]
2016 | Conference Paper | PUB-ID: 2903708
A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates
Rubert DP, Feijão P, Dias Vieira Braga M, Stoye J, Martinez FV (2016)
In: Proceedings of WABI 2016. LNBI, 9838. 293-306.
PUB | DOI
 
[181]
2016 | Conference Paper | PUB-ID: 2900111
New Genome Similarity Measures based on Conserved Gene Adjacencies
Kowada LAB, Doerr D, Dantas S, Stoye J (2016)
In: Research in Computational Molecular Biology. RECOMB 2016. Singh M (Ed); Lecture Notes in Bioinformatics (LNBI), 9649. Springer: 204-224.
PUB | DOI
 
[180]
2016 | Journal Article | PUB-ID: 2905930
Finding approximate gene clusters with GECKO 3
Winter S, Jahn K, Wehner S, Kuchenbecker L, Marz M, Stoye J, Böcker S (2016)
Nucleic Acids Research 44(20): 9600-9610.
PUB | DOI | WoS | PubMed | Europe PMC
 
[179]
2016 | Journal Article | PUB-ID: 2900129
Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage
Holley G, Wittler R, Stoye J (2016)
Algorithms for Molecular Biology 11: 3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[178]
2016 | Journal Article | PUB-ID: 2900421
Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma
Krause L, Nones K, Loffler KA, Nancarrow D, Oey H, Tang YH, Wayte NJ, Patch AM, Patel K, Brosda S, Manning S, et al. (2016)
Carcinogenesis 37(4): 356-365.
PUB | DOI | WoS | PubMed | Europe PMC
 
[177]
2015 | Journal Article | PUB-ID: 2726366
On the family-free DCJ distance and similarity
Viduani Martinez FH, Feijão P, Braga MDV, Stoye J (2015)
Algorithms for Molecular Biology 10: 13.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[176]
2015 | Journal Article | PUB-ID: 2677844
Sorting linear genomes with rearrangements and indels
Braga MDV, Stoye J (2015)
IEEE/ACM Transactions on Computational Biology and Bioinformatics 12(3): 500-506.
PUB | DOI | WoS | PubMed | Europe PMC
 
[175]
2015 | Conference Paper | PUB-ID: 2757497
Bloom Filter Trie - a data structure for pan-genome storage
Holley G, Wittler R, Stoye J (2015)
In: Proceedings of WABI 2015. LNBI, 9289. 217-230.
PUB
 
[174]
2015 | Conference (Editor) | PUB-ID: 2780229 PUB
 
[173]
2015 | Conference (Editor) | PUB-ID: 2780232 PUB
 
[172]
2014 | Journal Article | PUB-ID: 2687033
Identifying Gene Clusters by Discovering Common Intervals in Indeterminate Strings
Dörr D, Stoye J, Böcker S, Jahn K (2014)
BMC Genomics 15(Suppl. 6: Proc. of RECOMB-CG 2014): S2.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[171]
2014 | Journal Article | PUB-ID: 2674387
ReadXplorer - Visualization and Analysis of Mapped Sequences
Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A (2014)
Bioinformatics 30(16): 2247-2254.
PUB | DOI | WoS | PubMed | Europe PMC
 
[170]
2014 | Journal Article | PUB-ID: 2665038
Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts
Schwientek P, Neshat A, Kalinowski J, Klein A, Rückert C, Schneiker-Bekel S, Wendler S, Stoye J, Pühler A (2014)
Journal of Biotechnology 190: 85-95.
PUB | DOI | WoS | PubMed | Europe PMC
 
[169]
2014 | Journal Article | PUB-ID: 2685988
Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing
Jakobi T, Brinkrolf K, Tauch A, Noll T, Stoye J, Pühler A, Goesmann A (2014)
Journal of Biotechnology 190: 64-75.
PUB | DOI | WoS | PubMed | Europe PMC
 
[168]
2014 | Journal Article | PUB-ID: 2685362
Orthology Detection Combining Clustering and Synteny for Very Large Datasets
Lechner M, Hernandez-Rosales M, Dörr D, Wieseke N, Thévenin A, Stoye J, Hartmann RK, Prohaska SJ, Stadler PF (2014)
PLoS ONE 9(8): e105015.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[167]
2014 | Journal Article | PUB-ID: 2693409
Metatranskriptomik der Mikrobiota aus der menschlichen Achselhöhle
Fredrich E, Ander C, Stoye J, Brune I, Tauch A (2014)
BIOspektrum 20(5): 294-296.
PUB | DOI
 
[166]
2014 | Journal Article | PUB-ID: 2665333
Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma
Henrich B, Rumming M, Sczyrba A, Velleuer E, Dietrich R, Gerlach W, Gombert M, Rahn S, Stoye J, Borkhardt A, Fischer U (2014)
PLoS ONE 9(3): e92297.
PUB | DOI | WoS | PubMed | Europe PMC
 
[165]
2014 | Journal Article | PUB-ID: 2689773
GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers
Jünemann S, Prior K, Albersmeier A, Albaum S, Kalinowski J, Goesmann A, Stoye J, Harmsen D (2014)
PLOS ONE 9(9): e107014.
PUB | DOI | WoS | PubMed | Europe PMC
 
[164]
2014 | Conference Paper | PUB-ID: 2684241
On the family-free DCJ distance
Viduani Martinez FH, Feijão P, Braga MDV, Stoye J (2014)
In: Proc. of WABI 2014. Brown D, Morgenstern B (Eds); LNBI, 8701. Springer Verlag: 174-186.
PUB | DOI
 
[163]
2014 | Journal Article | PUB-ID: 2643941
BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry
Hoffmann N, Wilhelm M, Doebbe A, Niehaus K, Stoye J (2014)
Bioinformatics 30(7): 988-995.
PUB | DOI | WoS | PubMed | Europe PMC
 
[162]
2014 | Conference Paper | PUB-ID: 2690122
Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework
Luhmann N, Chauve C, Stoye J, Wittler R (2014)
In: Proc. of BSB 2014. Sérgio C (Ed); LNBI, 8826. Springer Verlag: 135-143.
PUB | DOI
 
[161]
2014 | Encyclopedia Article | PUB-ID: 2693552
Suffix Tree Construction
Stoye J (2014)
In: Encyclopedia of Algorithms. Kao M-Y (Ed); Springer Verlag.
PUB | DOI
 
[160]
2013 | Journal Article | PUB-ID: 2548236
Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media
Schwientek P, Wendler S, Neshat A, Eirich C, Rückert C, Klein A, Wehmeier UF, Kalinowski J, Stoye J, Pühler A (2013)
Journal of Biotechnology 167(2): 166-177.
PUB | DOI | WoS | PubMed | Europe PMC
 
[159]
2013 | Book Chapter | PUB-ID: 2611648
The Potential of Family-Free Genome Comparison
Braga MDV, Chauve C, Dörr D, Jahn K, Stoye J, Thévenin A, Wittler R (2013)
In: Models and Algorithms for Genome Evolution. Chauve C, El-Mabrouk N, Tannier E (Eds); Computational Biology Series, 19. Springer Verlag: 287-307.
PUB | DOI
 
[158]
2013 | Journal Article | PUB-ID: 2575011
metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences
Ander C, Schulz-Trieglaff OB, Stoye J, Cox AJ (2013)
BMC Bioinformatics 14(Suppl 5: Proc. of RECOMB-Seq 2013): S2.
PUB | DOI | WoS | PubMed | Europe PMC
 
[157]
2013 | Journal Article | PUB-ID: 2529202
MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets
Zakrzewski M, Bekel T, Ander C, Pühler A, Rupp O, Stoye J, Schlüter A, Goesmann A (2013)
Journal of Biotechnology 167(2): 156-165.
PUB | DOI | WoS | PubMed | Europe PMC
 
[156]
2013 | Journal Article | PUB-ID: 2566922
Updating benchtop sequencing performance comparison
Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, Harmsen D (2013)
Nature Biotechnology 31(4): 294-296.
PUB | DOI | WoS | PubMed | Europe PMC
 
[155]
2013 | Journal Article | PUB-ID: 2641228
Corrigendum: Updating benchtop sequencing performance comparison
Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, Harmsen D (2013)
Nature biotechnology 31(12): 1148.
PUB | DOI | WoS | PubMed | Europe PMC
 
[154]
2013 | Journal Article | PUB-ID: 2611630
On the Inversion-Indel Distance
Willing E, Zaccaria S, Braga MDV, Stoye J (2013)
BMC Bioinformatics 14(Suppl 15: Proc. of RECOMB-CG 2013): S3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[153]
2013 | Journal Article | PUB-ID: 2575361
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
Krell P, Reuther S, Fischer U, Keller T, Weber S, Gombert M, Schuster FR, Asang C, Stepensky P, Strahm B, Meisel R, et al. (2013)
Haematologica 98(9): 1388-1396.
PUB | DOI | WoS | PubMed | Europe PMC
 
[152]
2013 | Journal Article | PUB-ID: 2611633
Statistics for approximate gene clusters
Jahn K, Winter S, Stoye J, Böcker S (2013)
BMC Bioinformatics 14(Suppl 15: Proc. of RECOMB-CG 2013): S14.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[151]
2013 | Encyclopedia Article | PUB-ID: 2577323
Taxonomic classification of metagenomic shotgun sequences with CARMA3
Gerlach W, Stoye J (2013)
In: Encyclopedia of Metagenomics. Nelson KE (Ed); Springer Verlag.
PUB | DOI
 
[150]
2013 | Book Chapter | PUB-ID: 2611643
The Genesis of the DCJ Formula
Bergeron A, Stoye J (2013)
In: Models and Algorithms for Genome Evolution. Chauve C, El-Mabrouk N, Tannier E (Eds); Computational Biology Series, 19. Springer Verlag: 63-81.
PUB | DOI
 
[149]
2013 | Conference Paper | PUB-ID: 2611641
Restricted DCJ-Indel Model Revisited
Braga MDV, Stoye J (2013)
In: Proc. of BSB 2013. Setubal JC, Almeida NF (Eds); LNBI, 8213. Springer Verlag: 36-46.
PUB | DOI
 
[148]
2013 | Conference (Editor) | PUB-ID: 2616537
Algorithms in Bioinformatics
Darling A, Stoye J (Eds) (2013)
Lecture Notes in Bioinformatics 8126.
PUB | DOI
 
[147]
2012 | Journal Article | PUB-ID: 2486060
The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110
Schwientek P, Szczepanowski R, Rückert C, Kalinowski J, Klein A, Selber K, Wehmeier UF, Stoye J, Pühler A (2012)
BMC Genomics 13(1): 112.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[146]
2012 | Journal Article | PUB-ID: 2512642
Gene family assignment-free comparative genomics
Dörr D, Thévenin A, Stoye J (2012)
BMC Bioinformatics 13(Suppl 19: Proc. of RECOMB-CG 2012): S3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[145]
2012 | Journal Article | PUB-ID: 2517239
Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets
Hoffmann N, Keck M, Neuweger H, Wilhelm M, Högy P, Niehaus K, Stoye J (2012)
BMC Bioinformatics 13(1): 21.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[144]
2012 | Journal Article | PUB-ID: 2510984
UniMoG - A unifying framework for genomic distance calculation and sorting based on DCJ
Hilker R, Sickinger C, Pedersen CNS, Stoye J (2012)
Bioinformatics 28(19): 2509-2511.
PUB | DOI | WoS | PubMed | Europe PMC
 
[143]
2012 | Journal Article | PUB-ID: 2517230
Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing
Jünemann S, Prior K, Szczepanowski R, Harks I, Ehmke B, Goesmann A, Stoye J, Harmsen D (2012)
PLoS ONE 7(8): e41606.
PUB | DOI | WoS | PubMed | Europe PMC
 
[142]
2012 | Journal Article | PUB-ID: 2512644
Multiple genome comparison based on overlap regions of pairwise local alignments
Jahn K, Sudek H, Stoye J (2012)
BMC Bioinformatics 13(Suppl. 19: Proc. of RECOMB-CG 2012): S7.
PUB | DOI | WoS | PubMed | Europe PMC
 
[141]
2012 | Book Chapter | PUB-ID: 2468382
Generic Software Frameworks for GC-MS Based Metabolomics
Hoffmann N, Stoye J (2012)
In: Metabolomics. Roessner U (Ed); InTech: 73-98.
PUB | PDF | DOI
 
[140]
2012 | Conference (Editor) | PUB-ID: 2510416
Combinatorial Pattern Matching
Kärkkäinen J, Stoye J (Eds) (2012)
Lecture Notes in Computer Science 7354.
PUB | DOI
 
[139]
2011 | Journal Article | PUB-ID: 2354746
Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology
Schwientek P, Szczepanowski R, Rückert C, Stoye J, Pühler A (2011)
Journal of Biotechnology 155(1): 68-77.
PUB | DOI | WoS | PubMed | Europe PMC
 
[138]
2011 | Journal Article | PUB-ID: 2289952
Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming
Blom J, Jakobi T, Doppmeier D, Jaenicke S, Kalinowski J, Stoye J, Goesmann A (2011)
Bioinformatics 27(10): 1351-1358.
PUB | DOI | WoS | PubMed | Europe PMC
 
[137]
2011 | Journal Article | PUB-ID: 2298170
Taxonomic classification of metagenomic shotgun sequences with CARMA3.
Gerlach W, Stoye J (2011)
Nucleic Acids Res 39(14): e91.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[136]
2011 | Journal Article | PUB-ID: 2091787
Consistency of Sequence-Based Gene Clusters
Wittler R, Maňuch J, Patterson M, Stoye J (2011)
Journal of Computational Biology 18(9): 1023-1039.
PUB | DOI | WoS | PubMed | Europe PMC
 
[135]
2011 | Journal Article | PUB-ID: 2091794
Double Cut and Join with Insertions and Deletions
Braga MDV, Willing E, Stoye J (2011)
Journal of Computational Biology 18(9): 1167-1184.
PUB | DOI | WoS | PubMed | Europe PMC
 
[134]
2011 | Journal Article | PUB-ID: 2091779
Swiftly Computing Center Strings
Hufsky F, Kuchenbecker L, Jahn K, Stoye J, Böcker S (2011)
BMC Bioinformatics 12(1): 106.
PUB | DOI | WoS | PubMed | Europe PMC
 
[133]
2011 | Journal Article | PUB-ID: 2091790
Restricted DCJ Model: Rearrangement Problems with Chromosome Reincorporation
Kováč J, Warren R, Braga MDV, Stoye J (2011)
Journal of Computational Biology 18(9): 1231-1241.
PUB | DOI | WoS | PubMed | Europe PMC
 
[132]
2011 | Journal Article | PUB-ID: 1897974
Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance
Erdős PL, Soukup L, Stoye J (2011)
Applied Mathematics Letters 24(1): 82-86.
PUB | DOI | WoS
 
[131]
2011 | Journal Article | PUB-ID: 2396509
Genomic distance under gene substitutions
Braga MDV, Machado R, Ribeiro LC, Stoye J (2011)
BMC Bioinformatics 12(Suppl 9: Proc. of RECOMB-CG 2011): S8.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[130]
2011 | Journal Article | PUB-ID: 1918550
Common Intervals of Multiple Permutations
Heber S, Mayr R, Stoye J (2011)
Algorithmica 60(2): 175-206.
PUB | DOI | WoS
 
[129]
2011 | Journal Article | PUB-ID: 2396558
On the weight of indels in genomic distances
Braga MDV, Machado R, Ribeiro LC, Stoye J (2011)
BMC Bioinformatics 12(Suppl 9: RECOMB-CG 2011): S13.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[128]
2010 | Conference Abstract | PUB-ID: 2445157
Computing the Genomic Distance in Linear Time
Bergeron A, Mixtacki J, Stoye J (2010)
In: Dagstuhl Seminar Proceedings: 10231 Abstracts Collection : Structure Discovery in Biology: Motifs, Networks & Phylogenies. Apostolico A, Dress A, Parida L (Eds); , 10231. Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik: 18.
PUB
 
[127]
2010 | Journal Article | PUB-ID: 1966439
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
Trost E, Ott L, Schneider J, Schröder J, Jaenicke S, Goesmann A, Husemann P, Stoye J, Alves Dorella F, Souza Rocha F, de Castro Soares S, et al. (2010)
BMC Genomics 11(1): 728.
PUB | DOI | WoS | PubMed | Europe PMC
 
[126]
2010 | Conference Paper | PUB-ID: 1919215
Genomic Distance with DCJ and Indels
Braga M, Willing E, Stoye J (2010)
In: Proc. of WABI 2010. LNBI, 6293. 90-101.
PUB | DOI
 
[125]
2010 | Journal Article | PUB-ID: 1893893
Phylogenetic Comparative Assembly
Husemann P, Stoye J (2010)
Algorithms for Molecular Biology 5(1): 3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[124]
2010 | Conference Paper | PUB-ID: 1919216
The Problem of Chromosome Reincorporation in DCJ Sorting and Halving
Kovac J, Braga M, Stoye J (2010)
In: Proc. of Recomb-CG 2010. LNBI, 6398. 13-24.
PUB | DOI
 
[123]
2010 | Conference Paper | PUB-ID: 1919211
Swiftly Computing Center Strings
Hufsky F, Kuchenbecker L, Jahn K, Stoye J, Böcker S (2010)
In: Proc. of WABI 2010. LNBI, 6293. 325-336.
PUB | DOI | WoS | PubMed | Europe PMC
 
[122]
2010 | Conference Paper | PUB-ID: 1893890
Repeat-aware Comparative Genome Assembly
Husemann P, Stoye J (2010)
In: Proc. of GCB 2010. LNI, P-173. 61-70.
PUB
 
[121]
2010 | Journal Article | PUB-ID: 1898025
The Solution Space of Sorting by DCJ
Braga M, Stoye J (2010)
Journal of Computational Biology 17(9): 1145-1165.
PUB | DOI | WoS | PubMed | Europe PMC
 
[120]
2010 | Conference Paper | PUB-ID: 1919217
Consistency of Sequence-based Gene Clusters
Wittler R, Stoye J (2010)
In: Proc. of Recomb-CG 2010. LNBI, 6398. Springer Verlag: 252-263.
PUB | DOI | WoS | PubMed | Europe PMC
 
[119]
2010 | Journal Article | PUB-ID: 1588556
r2cat: Synteny Plots and Comparative Assembly
Husemann P, Stoye J (2010)
Bioinformatics 26(4): 570-571.
PUB | DOI | WoS | PubMed | Europe PMC
 
[118]
2010 | Book Chapter | PUB-ID: 1918836
Indexing and Searching a Mass Spectrometry Database
Besenbacher S, Schwikowski B, Stoye J (2010)
In: Algorithms and Applications: Essays Dedicated to Esko Ukkonen on the Occasion of His 60th Birthday. Elomaa T, Mannila H, Orponen P (Eds); LNCS, 6060. 62-76.
PUB | DOI
 
[117]
2010 | Journal Article | PUB-ID: 1897997
Rearrangement Models and Single-Cut Operations
Bergeron A, Medvedev P, Stoye J (2010)
Journal of Computational Biology 17(9): 1213-1225.
PUB | DOI | WoS | PubMed | Europe PMC
 
[116]
2010 | Journal Article | PUB-ID: 1898012
Finding Nested Common Intervals Efficiently
Blin G, Faye D, Stoye J (2010)
Journal of Computational Biology 17(9): 1183-1194.
PUB | DOI | WoS | PubMed | Europe PMC
 
[115]
2010 | Report | PUB-ID: 1966434 PUB | arXiv
 
[114]
2010 | Journal Article | PUB-ID: 1795670
Partitioning Biological Data with Transitivity Clustering
Wittkop T, Emig D, Lange SJ, Rahmann S, Albrecht M, Morris JH, Böcker S, Stoye J, Baumbach J (2010)
Nature Methods 7(6): 419-420.
PUB | DOI | WoS | PubMed | Europe PMC
 
[113]
2009 | Journal Article | PUB-ID: 1634447
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
Bekel T, Henckel K, Küster H, Meyer F, Mittard-Runte V, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Pühler A, Stoye J, et al. (2009)
Journal of Biotechnology 140(1-2): 3-12.
PUB | DOI | WoS | PubMed | Europe PMC
 
[112]
2009 | Journal Article | PUB-ID: 1589098
WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads
Gerlach W, Jünemann S, Tille F, Goesmann A, Stoye J (2009)
BMC Bioinformatics 10(1): 430.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[111]
2009 | Journal Article | PUB-ID: 1591507
A Unified Approach for Reconstructing Ancient Gene Clusters
Stoye J, Wittler R (2009)
IEEE/ACM Transactions on Computational Biology and Bioinformatics 6(3): 387-400.
PUB | DOI | WoS | PubMed | Europe PMC
 
[110]
2009 | Journal Article | PUB-ID: 1898105
Computation of Median Gene Clusters
Böcker S, Jahn K, Mixtacki J, Stoye J (2009)
Journal of Computational Biology 16(8): 1085-1099.
PUB | DOI | WoS | PubMed | Europe PMC
 
[109]
2009 | Conference Paper | PUB-ID: 1919206
Counting All DCJ Sorting Scenarios
Braga M, Stoye J (2009)
In: Proc. of Recomb-CG 2009. LNBI, 5817. 36-47.
PUB | DOI
 
[108]
2009 | Conference Paper | PUB-ID: 1893884
Phylogenetic Comparative Assembly
Husemann P, Stoye J (2009)
In: Proc. of WABI 2009. LNBI, 5724. 145-156.
PUB | DOI | WoS | PubMed | Europe PMC
 
[107]
2009 | Journal Article | PUB-ID: 1898137
Approximative Gencluster und ihre Anwendung in der komparativen Genomik
Jahn K, Stoye J (2009)
Informatik-Spektrum 32(4): 288-300.
PUB | DOI
 
[106]
2009 | Journal Article | PUB-ID: 1591319
ChromA: signal-based retention time alignment for chromatography-mass spectrometry data
Hoffmann N, Stoye J (2009)
Bioinformatics 25(16): 2080-2081.
PUB | DOI | WoS | PubMed | Europe PMC
 
[105]
2009 | Conference Paper | PUB-ID: 1919207
Finding Nested Common Intervals Efficiently
Blin G, Stoye J (2009)
In: Proc. of Recomb-CG 2009. LNBI, 5817. 59-69.
PUB | DOI | WoS | PubMed | Europe PMC
 
[104]
2009 | Journal Article | PUB-ID: 1589663
A New Linear Time Algorithm to Compute the Genomic Distance via the Double Cut and Join Distance
Bergeron A, Mixtacki J, Stoye J (2009)
Theoretical Computer Science 410(51): 5300-5316.
PUB | DOI | WoS
 
[103]
2009 | Journal Article | PUB-ID: 1590204
A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG)
Brudno M, Medvedev P, Stoye J, De La Vega FM (2009)
BIOINFORMATICS 25(21): 2863-2864.
PUB | DOI | WoS | PubMed | Europe PMC
 
[102]
2009 | Conference Abstract | PUB-ID: 1918945
Computational Short Read Metagenomics
Stoye J (2009)
Presented at the JOBIM 2009, Nantes, France.
PUB
 
[101]
2009 | Conference Paper | PUB-ID: 1919209
Rearrangement Models and Single-Cut Operations
Medvedev P, Stoye J (2009)
In: Comparative Genomics : International Workshop, RECOMB-CG 2009, Budapest, Hungary, September 27-29, 2009. Proceedings. Lecture Notes in Computer Science, 5817. Berlin, Heidelberg: Springer: 84-97.
PUB | DOI
 
[100]
2008 | Journal Article | PUB-ID: 1586009
Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor
Krause L, Diaz NN, Edwards RA, Gartemann K-H, Krömeke H, Neuweger H, Pühler A, Runte KJ, Schlüter A, Stoye J, Szczepanowski R, et al. (2008)
JOURNAL OF BIOTECHNOLOGY 136(1-2): 91-101.
PUB | DOI | WoS | PubMed | Europe PMC
 
[99]
2008 | Journal Article | PUB-ID: 1636699
MeltDB: a software platform for the analysis and integration of metabolomics experiment data
Neuweger H, Albaum S, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A (2008)
Bioinformatics 24(23): 2726-2732.
PUB | DOI | WoS | PubMed | Europe PMC
 
[98]
2008 | Journal Article | PUB-ID: 1586785
Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms
Oehm S, Gilbert D, Tauch A, Stoye J, Goesmann A (2008)
NUCLEIC ACIDS RESEARCH 36(Web Server): W433-W437.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[97]
2008 | Journal Article | PUB-ID: 1783364
Phylogenetic classification of short environmental DNA fragments
Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, Stoye J (2008)
Nucleic Acids Research 36(7): 2230-2239.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[96]
2008 | Conference Paper | PUB-ID: 1919192
Computation of Median Gene Clusters
Böcker S, Jahn K, Mixtacki J, Stoye J (2008)
In: Proc. of RECOMB 2008. LNBI, 4955. 331-345.
PUB | DOI
 
[95]
2008 | Journal Article | PUB-ID: 1587078
Counting suffix arrays and strings
Schürmann K-B, Stoye J (2008)
THEORETICAL COMPUTER SCIENCE 395(2-3): 220-234.
PUB | DOI | WoS
 
[94]
2008 | Conference Paper | PUB-ID: 1919195
HP Distance via Double Cut and Join Distance
Bergeron A, Mixtacki J, Stoye J (2008)
In: Combinatorial Pattern Matching. 19th Annual Symposium, CPM 2008, Pisa, Italy, June 18-20, 2008 Proceedings. Lecture Notes in Computer Science, 5029. 56-68.
PUB | DOI
 
[93]
2008 | Encyclopedia Article | PUB-ID: 1918834
Suffix Tree Construction in RAM (1997; Farach-Colton)
Stoye J (2008)
In: Encyclopedia of Algorithms. Kao M-Y (Ed); Springer Verlag: 925-928.
PUB | DOI
 
[92]
2008 | Conference Paper | PUB-ID: 1919200
On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios
Bergeron A, Mixtacki J, Stoye J (2008)
In: Proc. of Recomb-CG 2008. LNBI, 5267. 226-240.
PUB | DOI
 
[91]
2008 | Report | PUB-ID: 1970459
A space efficient representation for sparse de Bruijn subgraphs
Quitzau JAA, Stoye J (2008) Forschungsberichte der Technischen Fakultät, Abteilung Informationstechnik / Universität Bielefeld.
Bielefeld: Technische Fakultät der Universität Bielefeld.
PUB | PDF
 
[90]
2008 | Report | PUB-ID: 1970461
Online Abelian Pattern Matching
Ejaz T, Rahmann S, Stoye J (2008) Forschungsberichte der Technischen Fakultät, Abteilung Informationstechnik / Universität Bielefeld.
Bielefeld: Technische Fakultät der Universität Bielefeld.
PUB | PDF
 
[89]
2008 | Conference Paper | PUB-ID: 1919198
Detecting Repeat Families in Incompletely Sequenced Genomes
Quitzau JAA, Stoye J (2008)
In: Proc. of WABI 2008. LNBI, 5251. 342-353.
PUB | DOI
 
[88]
2007 | Journal Article | PUB-ID: 1783345
GISMO - gene identification using a support vector machine for ORF classification
Krause L, McHardy AC, Nattkemper TW, Pühler A, Stoye J, Meyer F (2007)
Nucleic Acids Research 35(2): 540-549.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[87]
2007 | Journal Article | PUB-ID: 1918432
Character Sets of Strings
Didier G, Schmidt T, Stoye J, Tsur D (2007)
Journal of Discrete Algorithms 5(2): 330-340.
PUB | DOI
 
[86]
2007 | Journal Article | PUB-ID: 1630781
Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms
Mellmann A, Weniger T, Berssenbrügge C, Rothgänger J, Sammeth M, Stoye J, Harmsen D (2007)
BMC MICROBIOLOGY 7(1): 98.
PUB | DOI | WoS | PubMed | Europe PMC
 
[85]
2007 | Journal Article | PUB-ID: 1595253
An incomplex algorithm for fast suffix array construction
Schürmann K-B, Stoye J (2007)
SOFTWARE-PRACTICE & EXPERIENCE 37(3): 309-329.
PUB | DOI | WoS
 
[84]
2007 | Book Chapter | PUB-ID: 1918828
Chapter 12: Gecko and GhostFam - Rigorous and Efficient Gene Cluster Detection in Prokaryotic Genomes
Schmidt T, Stoye J (2007)
In: Comparative Genomics, Volume 2. Bergman NH (Ed); Methods in Molecular Biology, 396. Totowa, NJ: Humana Press Inc.: 165-182.
PUB | DOI | PubMed | Europe PMC
 
[83]
2006 | Journal Article | PUB-ID: 1631957
Finding novel genes in bacterial communities isolated from the environment
Krause L, Diaz NN, Bartels D, Edwards RA, Pühler A, Rohwer F, Meyer F, Stoye J (2006)
BIOINFORMATICS 22(14): e281-e289.
PUB | DOI | WoS | PubMed | Europe PMC
 
[82]
2006 | Journal Article | PUB-ID: 1597313
On the similarity of sets of permutations and its applications to genome comparison
Bergeron A, Stoye J (2006)
JOURNAL OF COMPUTATIONAL BIOLOGY 13(7): 1340-1354.
PUB | DOI | WoS | PubMed | Europe PMC
 
[81]
2006 | Conference Paper | PUB-ID: 1596811
A Unifying View of Genome Rearrangements
Bergeron A, Mixtacki J, Stoye J (2006)
In: Proc. of WABI 2006. LNBI, 4175. SPRINGER-VERLAG BERLIN: 163-173.
PUB | DOI | WoS
 
[80]
2006 | Journal Article | PUB-ID: 1597213
Comparing tandem repeats with duplications and excisions of variable degree
Sammeth M, Stoye J (2006)
IEEE/ACM Transactions on Computational Biology and Bioinformatics 3(4): 395-407.
PUB | DOI | WoS | PubMed | Europe PMC
 
[79]
2006 | Journal Article | PUB-ID: 1599574
On sorting by translocations
Bergeron A, Mixtacki J, Stoye J (2006)
JOURNAL OF COMPUTATIONAL BIOLOGY 13(2): 567-578.
PUB | DOI | WoS | PubMed | Europe PMC
 
[78]
2006 | Report | PUB-ID: 1970464
On Common Intervals with Errors
Chauve C, Diekmann Y, Heber S, Mixtacki J, Rahmann S, Stoye J (2006) Forschungsberichte.
Bielefeld: Technische Fakultät der Universität Bielefeld.
PUB | PDF
 
[77]
2006 | Journal Article | PUB-ID: 1599943
Panta rhei (QAlign2): an open graphical environment for sequence analysis
Sammeth M, Griebel T, Tille F, Stoye J (2006)
BIOINFORMATICS 22(7): 889-890.
PUB | DOI | WoS | PubMed | Europe PMC
 
[76]
2006 | Conference Abstract | PUB-ID: 1918946
Index Structures in Biological Sequence Analysis: From Simplicity to Complexity and Back
Stoye J (2006)
Presented at the JOBIM 2006, Bordeaux, France.
PUB
 
[75]
2006 | Journal Article | PUB-ID: 1599570
Efficient q-gram filters for finding all epsilon-matches over a given length
Rasmussen KR, Stoye J, Myers EW (2006)
JOURNAL OF COMPUTATIONAL BIOLOGY 13(2): 296-308.
PUB | DOI | WoS | PubMed | Europe PMC
 
[74]
2005 | Journal Article | PUB-ID: 1773302
BACCardI - a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison
Bartels D, Kespohl S, Albaum S, Drüke T, Goesmann A, Herold J, Kaiser O, Pühler A, Pfeiffer F, Raddatz G, Stoye J, et al. (2005)
Bioinformatics 21(7): 853-859.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[73]
2005 | Book Chapter | PUB-ID: 1918824
Chapter 10: The Inversion Distance Problem
Bergeron A, Mixtacki J, Stoye J (2005)
In: Mathematics of Evolution and Phylogeny. Gascuel O (Ed); Oxford University Press: 262-290.
PUB
 
[72]
2005 | Conference Paper | PUB-ID: 1919012
An Incomplex Algorithm for Fast Suffix Array Construction
Schürmann K-B, Stoye J (2005)
In: Proc. of ALENEX/ANALCO 2005. 77-85.
PUB
 
[71]
2005 | Report | PUB-ID: 1970470
Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI)
Sammeth M, Stoye J (2005) Forschungsberichte.
Bielefeld: Technische Fakultät der Universität Bielefeld.
PUB | PDF | DOI
 
[70]
2005 | Conference Paper | PUB-ID: 1601361
Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI)
Sammeth M, Weniger T, Harmsen D, Stoye J (2005)
In: Proc. of WABI 2005. LNBI, 3692. SPRINGER-VERLAG BERLIN: 276-290.
PUB | DOI | WoS
 
[69]
2005 | Conference Paper | PUB-ID: 1603216
Efficient q-Gram Filters for Finding All ε-Matches Over a Given Length
Rasmussen KR, Stoye J, Myers EW (2005)
In: Proc. of RECOMB 2005. LNBI, 3500. SPRINGER-VERLAG BERLIN: 189-203.
PUB | DOI | WoS
 
[68]
2005 | Conference Paper | PUB-ID: 1601348
Protein Annotation by Secondary Structure Based Alignments (PASSTA)
Bannert C, Stoye J (2005)
In: Proc. of CompLife 2005. LNBI, 3695. Springer-Verlag: 79-90.
PUB | DOI | WoS
 
[67]
2005 | Journal Article | PUB-ID: 1775168
Large scale hierarchical clustering of protein sequences
Krause A, Stoye J, Vingron M (2005)
BMC Bioinformatics 6(1): 15.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[66]
2005 | Conference Paper | PUB-ID: 1603220
On Sorting by Translocations
Bergeron A, Mixtacki J, Stoye J (2005)
In: Proc. of RECOMB 2005. LNBI, 3500. SPRINGER-VERLAG BERLIN: 615-629.
PUB | DOI | WoS
 
[65]
2005 | Report | PUB-ID: 1970472
Counting Suffix Arrays and Strings
Schürmann K-B, Stoye J (2005) Forschungsberichte.
Bielefeld: Technische Fakultät der Universität Bielefeld.
PUB | PDF
 
[64]
2005 | Conference Paper | PUB-ID: 1919026
Counting Suffix Arrays and Strings
Schürmann K-B, Stoye J (2005)
In: Proc. of SPIRE 2005. LNCS, 3772. 55-66.
PUB | DOI
 
[63]
2005 | Journal Article | PUB-ID: 1918947
Informatische Methoden zur Protein-Identifikation
Böcker S, Stoye J (2005)
LaborPraxis 29(10): 24-26.
PUB
 
[62]
2004 | Conference Paper | PUB-ID: 1607263
Reversal Distance without Hurdles and Fortresses
Bergeron A, Mixtacki J, Stoye J (2004)
In: Proc. of CPM 2004. LNCS, 3109. SPRINGER-VERLAG BERLIN: 388-399.
PUB | DOI | WoS
 
[61]
2004 | Journal Article | PUB-ID: 1773312
Benchmarking tools for the alignment of functional noncoding DNA
Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB (2004)
BMC Bioinformatics 5(1): 6.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[60]
2004 | Journal Article | PUB-ID: 1773569
Linear time algorithms for finding and representing all the tandem repeats in a string
Gusfield D, Stoye J (2004)
Journal of computer and system sciences 69(4): 525-546.
PUB | PDF | DOI | WoS
 
[59]
2004 | Journal Article | PUB-ID: 1773560
Algorithmic complexity of protein identification: combinatorics of weighted strings
Cieliebak M, Erlebach T, Lipták Z, Stoye J, Welzl E (2004)
Discrete Applied Mathematics 137(1): 27-46.
PUB | PDF | DOI | WoS
 
[58]
2004 | Journal Article | PUB-ID: 1773554
Correction: Benchmarking tools for the alignment of functional noncoding DNA
Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB (2004)
BMC Bioinformatics 5(1): 73.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[57]
2004 | Conference Paper | PUB-ID: 1606286
Suboptimal Local Alignments across Multiple Scoring Schemes
Michael M, Dieterich C, Stoye J (2004)
In: Proc. of WABI 2004. LNBI, 3240. SPRINGER-VERLAG BERLIN: 99-110.
PUB | DOI | WoS
 
[56]
2004 | Conference Paper | PUB-ID: 1607260
Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences
Schmidt T, Stoye J (2004)
In: Proc. of CPM 2004. LNCS, 3109. 347-358.
PUB | DOI | WoS
 
[55]
2004 | Conference (Editor) | PUB-ID: 1918823
Proceedings of the German Conference on Bioinformatics, GCB 2004
Giegerich R, Stoye J (Eds) (2004)
Lecture Notes in Informatics P-53.
PUB
 
[54]
2003 | Journal Article | PUB-ID: 1918949
Finden, fast ohne zu suchen: Indexstrukturen in der Bioinformatik
Giegerich R, Stoye J (2003)
Forschung an der Universität Bielefeld 26: 63-68.
PUB
 
[53]
2003 | Journal Article | PUB-ID: 1610397
Efficient implementation of lazy suffix trees
Giegerich R, Kurtz S, Stoye J (2003)
SOFTWARE-PRACTICE & EXPERIENCE 33(11): 1035-1049.
PUB | PDF | DOI | WoS
 
[52]
2003 | Conference Paper | PUB-ID: 1919005
Evaluation of the Jumping Alignment Algorithm with Artificial and Biological Data
Bannert C, Stoye J (2003)
In: Proc. of GCB 2003. 21-25.
PUB
 
[51]
2003 | Report | PUB-ID: 1970475
Suffix Tree Construction and Storage with Limited Main Memory
Schürmann K-B, Stoye J (2003) Forschungsberichte.
Bielefeld: Technische Fakultät der Universität Bielefeld.
PUB | PDF
 
[50]
2003 | Conference Paper | PUB-ID: 1610433
On the similarity of sets of permutations and its applications to genome comparison
Bergeron A, Stoye J (2003)
In: Proc. of COCOON 2003. LNCS, 2697. 68-79.
PUB | DOI | WoS
 
[49]
2003 | Journal Article | PUB-ID: 1610503
QAlign: quality-based multiple alignments with dynamic phylogenetic analysis
Sammeth M, Rothgänger J, Esser W, Albert J, Stoye J, Harmsen D (2003)
BIOINFORMATICS 19(12): 1592-1593.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[48]
2003 | Report | PUB-ID: 1970477
On the Similarity of Sets of Permutations and its Applications to Genome Comparison
Bergeron A, Stoye J (2003) Forschungsberichte.
Bielefeld: Technische Fakultät der Universität Bielefeld.
PUB | PDF
 
[47]
2003 | Journal Article | PUB-ID: 1612664
The European Conference on Computational Biology
Heber S, Stoye J (2003)
Drug Discovery Today 8(3): 113-114.
PUB | DOI | WoS | PubMed | Europe PMC
 
[46]
2003 | Journal Article | PUB-ID: 1609403
Divide-and-conquer multiple alignment with segment-based constraints
Sammeth M, Morgenstern B, Stoye J (2003)
BIOINFORMATICS 19(Suppl 2): ii189-ii195.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[45]
2002 | Journal Article | PUB-ID: 1773578
A novel approach to remote homology detection: jumping alignments
Spang R, Rehmsmeier M, Stoye J (2002)
Journal of Computational Biology 9(5): 747-760.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[44]
2002 | Conference Paper | PUB-ID: 1919000
Algorithmic Complexity of Protein Identification: Searching in Weighted Strings
Cieliebak M, Lipták Z, Welzl E, Erlebach T, Stoye J (2002)
In: Proc. of IFIP TCS 2002. 143-156.
PUB
 
[43]
2002 | Conference Abstract | PUB-ID: 1918951
Index Structures for Large Sequence Data: Suffix Trees and Affix Trees
Stoye J (2002)
In: Lecture Notes in Informatics. Schubert S, Reusch B, Jesse N (Eds); , P-20(Ergänzungsband). 67-67.
PUB
 
[42]
2002 | Journal Article | PUB-ID: 1773329
Common intervals and sorting by reversals: a marriage of necessity
Bergeron A, Heber S, Stoye J (2002)
Bioinformatics 18(Suppl 2): S54-S63.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[41]
2002 | Conference Paper | PUB-ID: 1918995
Resampling Methods in Physical Mapping
Heber S, Stoye J, Frohme M, Hoheisel J, Vingron M (2002)
In: Proc. of GfKl 2000. 437-444.
PUB
 
[40]
2002 | Journal Article | PUB-ID: 1773332
Simple and flexible detection of contiguous repeats using a suffix tree
Stoye J, Gusfield D (2002)
Theoretical Computer Science 270(1-2): 843-856.
PUB | PDF | DOI | WoS
 
[39]
2001 | Conference Paper | PUB-ID: 1880197
Algorithms for Finding Gene Clusters
Heber S, Stoye J (2001)
In: Proc. of WABI 2001. LNCS, 2149. Berlin: Sppringer: 252-263.
PUB | DOI
 
[38]
2001 | Journal Article | PUB-ID: 1773335
REPuter: the manifold applications of repeat analysis on a genomic scale
Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R (2001)
Nucleic Acids Research 29(22): 4633-4642.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[37]
2001 | Conference Paper | PUB-ID: 1918992
Finding all Common Intervals of k Permutations
Heber S, Stoye J (2001)
In: Proc. of CPM 2001. LNCS, 2089. 207-218.
PUB | DOI
 
[36]
2001 | Report | PUB-ID: 1970479
Algorithmic Complexity of Protein Identification: Combinatorics of Weighted Strings
Cieliebak M, Erlebach T, Lipták Z, Stoye J, Welzl E (2001) Technical Report.
ETH Zürich, Dept. of Computer Science.
PUB
 
[35]
2000 | Report | PUB-ID: 1970490
Affix Trees
Stoye J (2000) Forschungsberichte.
Technische Fakultät der Universität Bielefeld.
PUB | PDF
 
[34]
2000 | Conference Paper | PUB-ID: 1918988
Computation and Visualization of Degenerate Repeats in Complete Genomes
Kurtz S, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R (2000)
In: Proc. of ISMB 2000. 228-238.
PUB | PubMed | Europe PMC
 
[33]
2000 | Book Chapter | PUB-ID: 1918817
Finding Maximal Pairs with Bounded Gap
Brodal GS, Lyngsø RB, Pedersen CNS, Stoye J (2000)
In: Matching Patterns (Journal of Discrete Algorithms). Crochemore M, Gąsieniec L (Eds); 77-104.
PUB
 
[32]
2000 | Journal Article | PUB-ID: 1773572
Contig selection in physical mapping
Heber S, Stoye J, Frohme M, Hoheisel J, Vingron M (2000)
Journal of Computational Biology 7(3-4): 395-408.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[31]
2000 | Journal Article | PUB-ID: 1773345
The SYSTERS protein sequence cluster set
Krause A, Stoye J, Vingron M (2000)
Nucleic Acids Research 28(1): 270-272.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[30]
2000 | Conference Paper | PUB-ID: 1918985
Sequence Database Search Using Jumping Alignments
Spang R, Rehmsmeier M, Stoye J (2000)
In: Proc. of ISMB 2000. 367-375.
PUB | PubMed | Europe PMC
 
[29]
2000 | Journal Article | PUB-ID: 1773341
An iterative method for faster sum-of-pairs multiple sequence alignment
Reinert K, Stoye J, Will T (2000)
Bioinformatics 16(9): 808-814.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[28]
2000 | Conference Paper | PUB-ID: 1918981
Contig Selection in Physical Mapping
Heber S, Stoye J, Hoheisel J, Vingron M (2000)
In: Proc. of RECOMB 2000. 155-164.
PUB | DOI | WoS | PubMed | Europe PMC
 
[27]
2000 | Conference (Editor) | PUB-ID: 1918813
Proceedings of the German Conference on Bioinformatics, GCB 2000
Bornberg-Bauer E, Rost U, Stoye J, Vingron M (Eds) (2000)
Berlin: Logos Verlag.
PUB
 
[26]
1999 | Conference Paper | PUB-ID: 1620435
Efficient implementation of lazy suffix trees
Giegerich R, Kurtz S, Stoye J (1999)
In: Algorithm Engineering. 3rd International Workshop, WAE’99 London, UK, July 19–21, 1999 Proceedings. LNCS, 1668. 30-42.
PUB | DOI | WoS
 
[25]
1999 | Report | PUB-ID: 1970495
Consistent Equivalence Relations: A Set-Theoretical Framework for Multiple Sequence Alignment
Morgenstern B, Stoye J, Dress A (1999) Materialien/Preprints.
Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
PUB
 
[24]
1999 | Conference Paper | PUB-ID: 1918971
Finding Maximal Pairs with Bounded Gap
Brodal GS, Lyngsø RB, Pedersen CNS, Stoye J (1999)
In: Proc. of CPM 1999. LNCS, 1645. 134-149.
PUB | DOI
 
[23]
1999 | Report | PUB-ID: 1970509
Finding Maximal Pairs with Bounded Gap
Brodal GS, Lyngsø RB, Pedersen CNS, Stoye J (1999) Report.
BRICS, Department of Computer Science, University of Aarhus.
PUB
 
[22]
1999 | Conference Paper | PUB-ID: 1918978 PUB
 
[21]
1998 | Journal Article | PUB-ID: 1918538
Die Bedeutung der Zusammenarbeit der Disziplinen in der Anwendung - erläutert anhand von Beispielen
Hildebrand M, Stoye J (1998)
Der Mathematikunterricht 44(6): 34-53.
PUB
 
[20]
1998 | Report | PUB-ID: 1970515
Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree
Stoye J, Gusfield D (1998) Report.
Department of Computer Science, University of California, Davis.
PUB
 
[19]
1998 | Conference Paper | PUB-ID: 1918964
Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version)
Stoye J, Gusfield D (1998)
In: Proc. of CPM 1998. LNCS, 1448. 140-152.
PUB | DOI
 
[18]
1998 | Journal Article | PUB-ID: 1667771 PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[17]
1998 | Journal Article | PUB-ID: 1625402
Rose: generating sequence families
Stoye J, Evers D, Meyer F (1998)
BIOINFORMATICS 14(2): 157-163.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[16]
1998 | Report | PUB-ID: 1970513
Linear Time Algorithms for Finding and Representing all the Tandem Repeats in a String
Gusfield D, Stoye J (1998) Report.
Department of Computer Science, University of California, Davis.
PUB
 
[15]
1998 | Journal Article | PUB-ID: 2488102
The Number of Standard and of Effective Multiple Alignments
Dress A, Morgenstern B, Stoye J (1998)
Appl. Math. Lett. 11(4): 43-49.
PUB
 
[14]
1997 | Report | PUB-ID: 1970532
Divide-and-Conquer Multiple Sequence Alignment
Stoye J (1997) Forschungsberichte.
Technische Fakultät der Universität Bielefeld.
PUB
 
[13]
1997 | Report | PUB-ID: 1970526
On Simultaneous versus Iterative Multiple Sequence Alignment
Perrey SW, Stoye J, Moulton V, Dress A (1997) Materialien/Preprints.
Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
PUB
 
[12]
1997 | Journal Article | PUB-ID: 1773355
Improving the divide-and-conquer approach to sum-of-pairs multiple sequence alignment
Stoye J, Perrey SW, Dress A (1997)
Applied mathematics letters 10(2): 67-73.
PUB | PDF | DOI | WoS
 
[11]
1997 | Report | PUB-ID: 1970523
On the Number of Standard and Effective Multiple Alignments
Dress A, Morgenstern B, Stoye J (1997) Materialien/Preprints.
Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
PUB
 
[10]
1997 | Journal Article | PUB-ID: 1773358
Two applications of the Divide & Conquer principle in the molecular sciences
Brinkmann G, Dress A, Perrey SW, Stoye J (1997)
Mathematical programming 79(1-3): 71-97.
PUB | DOI | WoS
 
[9]
1997 | Report | PUB-ID: 1970529
Two Applications of the Divide & Conquer Principle in the Molecular Sciences
Brinkmann G, Dress A, Perrey SW, Stoye J (1997) Materialien/Preprints.
Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
PUB
 
[8]
1997 | Report | PUB-ID: 1970517
Rose: Generating Sequence Families
Stoye J, Evers D, Meyer F (1997) Forschungsberichte.
Technische Fakultät der Universität Bielefeld.
PUB
 
[7]
1997 | Report | PUB-ID: 1970520
FDCA: Fast and Accurate Approximation to Sum-of-Pairs Score Optimal Multiple Sequence Alignment
Perrey SW, Stoye J, Moulton V (1997) Materialien/Preprints.
Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
PUB
 
[6]
1997 | Journal Article | PUB-ID: 2488107 PUB
 
[5]
1997 | Conference Paper | PUB-ID: 1667885
Generating benchmarks for multiple sequence alignments and phylogenetic reconstructions
Stoye J, Evers D, Meyer F (1997)
In: Proc. of ISMB 1997. 303-306.
PUB | PubMed | Europe PMC
 
[4]
1996 | Journal Article | PUB-ID: 1773351
A general method for fast multiple sequence alignment
Tönges U, Perrey SW, Stoye J, Dress A (1996)
Gene 172(1): GC33-GC41.
PUB | DOI | WoS | PubMed | Europe PMC
 
[3]
1996 | Report | PUB-ID: 1970535
Improving the Divide-and-Conquer Approach to Sum-of-Pairs Multiple Sequence Alignment
Stoye J, Dress A, Perrey SW (1996) Materialien/Preprints.
Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
PUB
 
[2]
1996 | Report | PUB-ID: 1970537
A General Method for Fast Multiple Sequence Alignment
Tönges U, Perrey SW, Stoye J, Dress A (1996) Materialien/Preprints.
Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
PUB
 
[1]
1996 | Report | PUB-ID: 1970533
Fast Approximation to the NP-hard Problem of Multiple Sequence Alignment
Perrey SW, Stoye J (1996) Information and Mathematical Sciences Reports, Series B.
Dept. of Mathematics, Massey University, Palmerston North, New Zealand.
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[193]
2017 | Journal Article | PUB-ID: 2913556
Bioinformatics for NGS-based metagenomics and the application to biogas research
Jünemann S, Kleinbölting N, Jaenicke S, Henke C, Hassa J, Nelkner J, Stolze Y, Albaum S, Schlüter A, Goesmann A, Sczyrba A, et al. (2017)
Journal of Biotechnology 261(SI): 10-23.
PUB | DOI | WoS | PubMed | Europe PMC
 
[192]
2017 | Conference Paper | PUB-ID: 2909409
Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings
Cunha L, Dantas S, Gagie T, Wittler R, Kowada L, Stoye J (2017)
In: Proceedings of CPM 2017. LIPIcs, 78. 19:1-19:9.
PUB | DOI
 
[191]
2017 | Conference Paper | PUB-ID: 2907587
Dynamic Alignment-Free and Reference-Free Read Compression
Holley G, Wittler R, Stoye J, Hach F (2017)
In: Proceedings of RECOMB 2017. Lecture Notes in Bioinformatics, 10229. 50-65.
PUB | DOI
 
[190]
2017 | Conference Paper | PUB-ID: 2913015
Algorithms for Computing the Family-Free Genomic Similarity under DCJ
Rubert DP, Medeiros GL, Hoshino EA, Dias Vieira Braga M, Stoye J, Martinez FV (2017)
In: Proceedings of RECOMB-CG 2017. Lecture Notes in Bioinformatics, 10562. Springer Verlag: 76-100.
PUB | DOI
 
[189]
2017 | Conference Paper | PUB-ID: 2913016
Finding Teams in Graphs and its Application to Spatial Gene Cluster Discovery
Schulz T, Stoye J, Dörr D (2017)
In: Proceedings of RECOMB-CG 2017. Lecture Notes in Bioinformatics, 1704. Berlin: Springer Verlag: 197-212.
PUB | DOI
 
[188]
2017 | Book Chapter | PUB-ID: 2913921
Pan-genome Storage and Analysis Techniques
Zekic T, Holley G, Stoye J (In Press)
In: Comparative Genomics: Methods and Protocols. Setubal JC, Stadler P, Stoye J (Eds); Methods in Molecular Biology, 1704. Springer Verlag.
PUB
 
[187]
2017 | Book Chapter | PUB-ID: 2913922
Family-Free Genome Comparison
Dörr D, Feijão P, Stoye J (In Press)
In: Comparative Genomics: Methods and Protocols. Setubal JC, Stadler P, Stoye J (Eds); Methods in Molecular Biology, 1704. Springer Verlag.
PUB
 
[186]
2017 | Book (Editor) | PUB-ID: 2913920
Comparative Genomics: Methods and Protocols
Setubal JC, Stadler P, Stoye J (Eds) (In Press) Methods in Molecular Biology; 1704.
Springer Verlag.
PUB
 
[185]
2017 | Journal Article | PUB-ID: 2909057
Approximating the DCJ distance of balanced genomes in linear time
Rubert DP, Feijão P, Dias Vieira Braga M, Stoye J, Martinez FHV (2017)
Algorithms for Molecular Biology 12: 3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[184]
2017 | Preprint | PUB-ID: 2908521
Faster Jumbled Indexing for Binary Run-Length Encoded Strings
Cunha L, Dantas S, Gagie T, Wittler R, Kowada L, Stoye J (2017)
arXiv: 1702.01280.
PUB
 
[183]
2017 | Journal Article | PUB-ID: 2909967
New Genome Similarity Measures based on Conserved Gene Adjacencies
Dörr D, Kowada LAB, Soares de Araujo FE, Deshpande S, Dantas S, Moret BME, Stoye J (2017)
Journal of Computational Biology 24(6): 616-634.
PUB | DOI | WoS
 
[182]
2016 | Conference Paper | PUB-ID: 2903708
A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates
Rubert DP, Feijão P, Dias Vieira Braga M, Stoye J, Martinez FV (2016)
In: Proceedings of WABI 2016. LNBI, 9838. 293-306.
PUB | DOI
 
[181]
2016 | Conference Paper | PUB-ID: 2900111
New Genome Similarity Measures based on Conserved Gene Adjacencies
Kowada LAB, Doerr D, Dantas S, Stoye J (2016)
In: Research in Computational Molecular Biology. RECOMB 2016. Singh M (Ed); Lecture Notes in Bioinformatics (LNBI), 9649. Springer: 204-224.
PUB | DOI
 
[180]
2016 | Journal Article | PUB-ID: 2905930
Finding approximate gene clusters with GECKO 3
Winter S, Jahn K, Wehner S, Kuchenbecker L, Marz M, Stoye J, Böcker S (2016)
Nucleic Acids Research 44(20): 9600-9610.
PUB | DOI | WoS | PubMed | Europe PMC
 
[179]
2016 | Journal Article | PUB-ID: 2900129
Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage
Holley G, Wittler R, Stoye J (2016)
Algorithms for Molecular Biology 11: 3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[178]
2016 | Journal Article | PUB-ID: 2900421
Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma
Krause L, Nones K, Loffler KA, Nancarrow D, Oey H, Tang YH, Wayte NJ, Patch AM, Patel K, Brosda S, Manning S, et al. (2016)
Carcinogenesis 37(4): 356-365.
PUB | DOI | WoS | PubMed | Europe PMC
 
[177]
2015 | Journal Article | PUB-ID: 2726366
On the family-free DCJ distance and similarity
Viduani Martinez FH, Feijão P, Braga MDV, Stoye J (2015)
Algorithms for Molecular Biology 10: 13.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[176]
2015 | Journal Article | PUB-ID: 2677844
Sorting linear genomes with rearrangements and indels
Braga MDV, Stoye J (2015)
IEEE/ACM Transactions on Computational Biology and Bioinformatics 12(3): 500-506.
PUB | DOI | WoS | PubMed | Europe PMC
 
[175]
2015 | Conference Paper | PUB-ID: 2757497
Bloom Filter Trie - a data structure for pan-genome storage
Holley G, Wittler R, Stoye J (2015)
In: Proceedings of WABI 2015. LNBI, 9289. 217-230.
PUB
 
[174]
2015 | Conference (Editor) | PUB-ID: 2780229 PUB
 
[173]
2015 | Conference (Editor) | PUB-ID: 2780232 PUB
 
[172]
2014 | Journal Article | PUB-ID: 2687033
Identifying Gene Clusters by Discovering Common Intervals in Indeterminate Strings
Dörr D, Stoye J, Böcker S, Jahn K (2014)
BMC Genomics 15(Suppl. 6: Proc. of RECOMB-CG 2014): S2.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[171]
2014 | Journal Article | PUB-ID: 2674387
ReadXplorer - Visualization and Analysis of Mapped Sequences
Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A (2014)
Bioinformatics 30(16): 2247-2254.
PUB | DOI | WoS | PubMed | Europe PMC
 
[170]
2014 | Journal Article | PUB-ID: 2665038
Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts
Schwientek P, Neshat A, Kalinowski J, Klein A, Rückert C, Schneiker-Bekel S, Wendler S, Stoye J, Pühler A (2014)
Journal of Biotechnology 190: 85-95.
PUB | DOI | WoS | PubMed | Europe PMC
 
[169]
2014 | Journal Article | PUB-ID: 2685988
Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing
Jakobi T, Brinkrolf K, Tauch A, Noll T, Stoye J, Pühler A, Goesmann A (2014)
Journal of Biotechnology 190: 64-75.
PUB | DOI | WoS | PubMed | Europe PMC
 
[168]
2014 | Journal Article | PUB-ID: 2685362
Orthology Detection Combining Clustering and Synteny for Very Large Datasets
Lechner M, Hernandez-Rosales M, Dörr D, Wieseke N, Thévenin A, Stoye J, Hartmann RK, Prohaska SJ, Stadler PF (2014)
PLoS ONE 9(8): e105015.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[167]
2014 | Journal Article | PUB-ID: 2693409
Metatranskriptomik der Mikrobiota aus der menschlichen Achselhöhle
Fredrich E, Ander C, Stoye J, Brune I, Tauch A (2014)
BIOspektrum 20(5): 294-296.
PUB | DOI
 
[166]
2014 | Journal Article | PUB-ID: 2665333
Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma
Henrich B, Rumming M, Sczyrba A, Velleuer E, Dietrich R, Gerlach W, Gombert M, Rahn S, Stoye J, Borkhardt A, Fischer U (2014)
PLoS ONE 9(3): e92297.
PUB | DOI | WoS | PubMed | Europe PMC
 
[165]
2014 | Journal Article | PUB-ID: 2689773
GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers
Jünemann S, Prior K, Albersmeier A, Albaum S, Kalinowski J, Goesmann A, Stoye J, Harmsen D (2014)
PLOS ONE 9(9): e107014.
PUB | DOI | WoS | PubMed | Europe PMC
 
[164]
2014 | Conference Paper | PUB-ID: 2684241
On the family-free DCJ distance
Viduani Martinez FH, Feijão P, Braga MDV, Stoye J (2014)
In: Proc. of WABI 2014. Brown D, Morgenstern B (Eds); LNBI, 8701. Springer Verlag: 174-186.
PUB | DOI
 
[163]
2014 | Journal Article | PUB-ID: 2643941
BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry
Hoffmann N, Wilhelm M, Doebbe A, Niehaus K, Stoye J (2014)
Bioinformatics 30(7): 988-995.
PUB | DOI | WoS | PubMed | Europe PMC
 
[162]
2014 | Conference Paper | PUB-ID: 2690122
Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework
Luhmann N, Chauve C, Stoye J, Wittler R (2014)
In: Proc. of BSB 2014. Sérgio C (Ed); LNBI, 8826. Springer Verlag: 135-143.
PUB | DOI
 
[161]
2014 | Encyclopedia Article | PUB-ID: 2693552
Suffix Tree Construction
Stoye J (2014)
In: Encyclopedia of Algorithms. Kao M-Y (Ed); Springer Verlag.
PUB | DOI
 
[160]
2013 | Journal Article | PUB-ID: 2548236
Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media
Schwientek P, Wendler S, Neshat A, Eirich C, Rückert C, Klein A, Wehmeier UF, Kalinowski J, Stoye J, Pühler A (2013)
Journal of Biotechnology 167(2): 166-177.
PUB | DOI | WoS | PubMed | Europe PMC
 
[159]
2013 | Book Chapter | PUB-ID: 2611648
The Potential of Family-Free Genome Comparison
Braga MDV, Chauve C, Dörr D, Jahn K, Stoye J, Thévenin A, Wittler R (2013)
In: Models and Algorithms for Genome Evolution. Chauve C, El-Mabrouk N, Tannier E (Eds); Computational Biology Series, 19. Springer Verlag: 287-307.
PUB | DOI
 
[158]
2013 | Journal Article | PUB-ID: 2575011
metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences
Ander C, Schulz-Trieglaff OB, Stoye J, Cox AJ (2013)
BMC Bioinformatics 14(Suppl 5: Proc. of RECOMB-Seq 2013): S2.
PUB | DOI | WoS | PubMed | Europe PMC
 
[157]
2013 | Journal Article | PUB-ID: 2529202
MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets
Zakrzewski M, Bekel T, Ander C, Pühler A, Rupp O, Stoye J, Schlüter A, Goesmann A (2013)
Journal of Biotechnology 167(2): 156-165.
PUB | DOI | WoS | PubMed | Europe PMC
 
[156]
2013 | Journal Article | PUB-ID: 2566922
Updating benchtop sequencing performance comparison
Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, Harmsen D (2013)
Nature Biotechnology 31(4): 294-296.
PUB | DOI | WoS | PubMed | Europe PMC
 
[155]
2013 | Journal Article | PUB-ID: 2641228
Corrigendum: Updating benchtop sequencing performance comparison
Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, Harmsen D (2013)
Nature biotechnology 31(12): 1148.
PUB | DOI | WoS | PubMed | Europe PMC
 
[154]
2013 | Journal Article | PUB-ID: 2611630
On the Inversion-Indel Distance
Willing E, Zaccaria S, Braga MDV, Stoye J (2013)
BMC Bioinformatics 14(Suppl 15: Proc. of RECOMB-CG 2013): S3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[153]
2013 | Journal Article | PUB-ID: 2575361
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
Krell P, Reuther S, Fischer U, Keller T, Weber S, Gombert M, Schuster FR, Asang C, Stepensky P, Strahm B, Meisel R, et al. (2013)
Haematologica 98(9): 1388-1396.
PUB | DOI | WoS | PubMed | Europe PMC
 
[152]
2013 | Journal Article | PUB-ID: 2611633
Statistics for approximate gene clusters
Jahn K, Winter S, Stoye J, Böcker S (2013)
BMC Bioinformatics 14(Suppl 15: Proc. of RECOMB-CG 2013): S14.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[151]
2013 | Encyclopedia Article | PUB-ID: 2577323
Taxonomic classification of metagenomic shotgun sequences with CARMA3
Gerlach W, Stoye J (2013)
In: Encyclopedia of Metagenomics. Nelson KE (Ed); Springer Verlag.
PUB | DOI
 
[150]
2013 | Book Chapter | PUB-ID: 2611643
The Genesis of the DCJ Formula
Bergeron A, Stoye J (2013)
In: Models and Algorithms for Genome Evolution. Chauve C, El-Mabrouk N, Tannier E (Eds); Computational Biology Series, 19. Springer Verlag: 63-81.
PUB | DOI
 
[149]
2013 | Conference Paper | PUB-ID: 2611641
Restricted DCJ-Indel Model Revisited
Braga MDV, Stoye J (2013)
In: Proc. of BSB 2013. Setubal JC, Almeida NF (Eds); LNBI, 8213. Springer Verlag: 36-46.
PUB | DOI
 
[148]
2013 | Conference (Editor) | PUB-ID: 2616537
Algorithms in Bioinformatics
Darling A, Stoye J (Eds) (2013)
Lecture Notes in Bioinformatics 8126.
PUB | DOI
 
[147]
2012 | Journal Article | PUB-ID: 2486060
The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110
Schwientek P, Szczepanowski R, Rückert C, Kalinowski J, Klein A, Selber K, Wehmeier UF, Stoye J, Pühler A (2012)
BMC Genomics 13(1): 112.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[146]
2012 | Journal Article | PUB-ID: 2512642
Gene family assignment-free comparative genomics
Dörr D, Thévenin A, Stoye J (2012)
BMC Bioinformatics 13(Suppl 19: Proc. of RECOMB-CG 2012): S3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[145]
2012 | Journal Article | PUB-ID: 2517239
Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets
Hoffmann N, Keck M, Neuweger H, Wilhelm M, Högy P, Niehaus K, Stoye J (2012)
BMC Bioinformatics 13(1): 21.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[144]
2012 | Journal Article | PUB-ID: 2510984
UniMoG - A unifying framework for genomic distance calculation and sorting based on DCJ
Hilker R, Sickinger C, Pedersen CNS, Stoye J (2012)
Bioinformatics 28(19): 2509-2511.
PUB | DOI | WoS | PubMed | Europe PMC
 
[143]
2012 | Journal Article | PUB-ID: 2517230
Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing
Jünemann S, Prior K, Szczepanowski R, Harks I, Ehmke B, Goesmann A, Stoye J, Harmsen D (2012)
PLoS ONE 7(8): e41606.
PUB | DOI | WoS | PubMed | Europe PMC
 
[142]
2012 | Journal Article | PUB-ID: 2512644
Multiple genome comparison based on overlap regions of pairwise local alignments
Jahn K, Sudek H, Stoye J (2012)
BMC Bioinformatics 13(Suppl. 19: Proc. of RECOMB-CG 2012): S7.
PUB | DOI | WoS | PubMed | Europe PMC
 
[141]
2012 | Book Chapter | PUB-ID: 2468382
Generic Software Frameworks for GC-MS Based Metabolomics
Hoffmann N, Stoye J (2012)
In: Metabolomics. Roessner U (Ed); InTech: 73-98.
PUB | PDF | DOI
 
[140]
2012 | Conference (Editor) | PUB-ID: 2510416
Combinatorial Pattern Matching
Kärkkäinen J, Stoye J (Eds) (2012)
Lecture Notes in Computer Science 7354.
PUB | DOI
 
[139]
2011 | Journal Article | PUB-ID: 2354746
Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology
Schwientek P, Szczepanowski R, Rückert C, Stoye J, Pühler A (2011)
Journal of Biotechnology 155(1): 68-77.
PUB | DOI | WoS | PubMed | Europe PMC
 
[138]
2011 | Journal Article | PUB-ID: 2289952
Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming
Blom J, Jakobi T, Doppmeier D, Jaenicke S, Kalinowski J, Stoye J, Goesmann A (2011)
Bioinformatics 27(10): 1351-1358.
PUB | DOI | WoS | PubMed | Europe PMC
 
[137]
2011 | Journal Article | PUB-ID: 2298170
Taxonomic classification of metagenomic shotgun sequences with CARMA3.
Gerlach W, Stoye J (2011)
Nucleic Acids Res 39(14): e91.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[136]
2011 | Journal Article | PUB-ID: 2091787
Consistency of Sequence-Based Gene Clusters
Wittler R, Maňuch J, Patterson M, Stoye J (2011)
Journal of Computational Biology 18(9): 1023-1039.
PUB | DOI | WoS | PubMed | Europe PMC
 
[135]
2011 | Journal Article | PUB-ID: 2091794
Double Cut and Join with Insertions and Deletions
Braga MDV, Willing E, Stoye J (2011)
Journal of Computational Biology 18(9): 1167-1184.
PUB | DOI | WoS | PubMed | Europe PMC
 
[134]
2011 | Journal Article | PUB-ID: 2091779
Swiftly Computing Center Strings
Hufsky F, Kuchenbecker L, Jahn K, Stoye J, Böcker S (2011)
BMC Bioinformatics 12(1): 106.
PUB | DOI | WoS | PubMed | Europe PMC
 
[133]
2011 | Journal Article | PUB-ID: 2091790
Restricted DCJ Model: Rearrangement Problems with Chromosome Reincorporation
Kováč J, Warren R, Braga MDV, Stoye J (2011)
Journal of Computational Biology 18(9): 1231-1241.
PUB | DOI | WoS | PubMed | Europe PMC
 
[132]
2011 | Journal Article | PUB-ID: 1897974
Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance
Erdős PL, Soukup L, Stoye J (2011)
Applied Mathematics Letters 24(1): 82-86.
PUB | DOI | WoS
 
[131]
2011 | Journal Article | PUB-ID: 2396509
Genomic distance under gene substitutions
Braga MDV, Machado R, Ribeiro LC, Stoye J (2011)
BMC Bioinformatics 12(Suppl 9: Proc. of RECOMB-CG 2011): S8.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[130]
2011 | Journal Article | PUB-ID: 1918550
Common Intervals of Multiple Permutations
Heber S, Mayr R, Stoye J (2011)
Algorithmica 60(2): 175-206.
PUB | DOI | WoS
 
[129]
2011 | Journal Article | PUB-ID: 2396558
On the weight of indels in genomic distances
Braga MDV, Machado R, Ribeiro LC, Stoye J (2011)
BMC Bioinformatics 12(Suppl 9: RECOMB-CG 2011): S13.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[128]
2010 | Conference Abstract | PUB-ID: 2445157
Computing the Genomic Distance in Linear Time
Bergeron A, Mixtacki J, Stoye J (2010)
In: Dagstuhl Seminar Proceedings: 10231 Abstracts Collection : Structure Discovery in Biology: Motifs, Networks & Phylogenies. Apostolico A, Dress A, Parida L (Eds); , 10231. Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik: 18.
PUB
 
[127]
2010 | Journal Article | PUB-ID: 1966439
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
Trost E, Ott L, Schneider J, Schröder J, Jaenicke S, Goesmann A, Husemann P, Stoye J, Alves Dorella F, Souza Rocha F, de Castro Soares S, et al. (2010)
BMC Genomics 11(1): 728.
PUB | DOI | WoS | PubMed | Europe PMC
 
[126]
2010 | Conference Paper | PUB-ID: 1919215
Genomic Distance with DCJ and Indels
Braga M, Willing E, Stoye J (2010)
In: Proc. of WABI 2010. LNBI, 6293. 90-101.
PUB | DOI
 
[125]
2010 | Journal Article | PUB-ID: 1893893
Phylogenetic Comparative Assembly
Husemann P, Stoye J (2010)
Algorithms for Molecular Biology 5(1): 3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[124]
2010 | Conference Paper | PUB-ID: 1919216
The Problem of Chromosome Reincorporation in DCJ Sorting and Halving
Kovac J, Braga M, Stoye J (2010)
In: Proc. of Recomb-CG 2010. LNBI, 6398. 13-24.
PUB | DOI
 
[123]
2010 | Conference Paper | PUB-ID: 1919211
Swiftly Computing Center Strings
Hufsky F, Kuchenbecker L, Jahn K, Stoye J, Böcker S (2010)
In: Proc. of WABI 2010. LNBI, 6293. 325-336.
PUB | DOI | WoS | PubMed | Europe PMC
 
[122]
2010 | Conference Paper | PUB-ID: 1893890
Repeat-aware Comparative Genome Assembly
Husemann P, Stoye J (2010)
In: Proc. of GCB 2010. LNI, P-173. 61-70.
PUB
 
[121]
2010 | Journal Article | PUB-ID: 1898025
The Solution Space of Sorting by DCJ
Braga M, Stoye J (2010)
Journal of Computational Biology 17(9): 1145-1165.
PUB | DOI | WoS | PubMed | Europe PMC
 
[120]
2010 | Conference Paper | PUB-ID: 1919217
Consistency of Sequence-based Gene Clusters
Wittler R, Stoye J (2010)
In: Proc. of Recomb-CG 2010. LNBI, 6398. Springer Verlag: 252-263.
PUB | DOI | WoS | PubMed | Europe PMC
 
[119]
2010 | Journal Article | PUB-ID: 1588556
r2cat: Synteny Plots and Comparative Assembly
Husemann P, Stoye J (2010)
Bioinformatics 26(4): 570-571.
PUB | DOI | WoS | PubMed | Europe PMC
 
[118]
2010 | Book Chapter | PUB-ID: 1918836
Indexing and Searching a Mass Spectrometry Database
Besenbacher S, Schwikowski B, Stoye J (2010)
In: Algorithms and Applications: Essays Dedicated to Esko Ukkonen on the Occasion of His 60th Birthday. Elomaa T, Mannila H, Orponen P (Eds); LNCS, 6060. 62-76.
PUB | DOI
 
[117]
2010 | Journal Article | PUB-ID: 1897997
Rearrangement Models and Single-Cut Operations
Bergeron A, Medvedev P, Stoye J (2010)
Journal of Computational Biology 17(9): 1213-1225.
PUB | DOI | WoS | PubMed | Europe PMC
 
[116]
2010 | Journal Article | PUB-ID: 1898012
Finding Nested Common Intervals Efficiently
Blin G, Faye D, Stoye J (2010)
Journal of Computational Biology 17(9): 1183-1194.
PUB | DOI | WoS | PubMed | Europe PMC
 
[115]
2010 | Report | PUB-ID: 1966434 PUB | arXiv
 
[114]
2010 | Journal Article | PUB-ID: 1795670
Partitioning Biological Data with Transitivity Clustering
Wittkop T, Emig D, Lange SJ, Rahmann S, Albrecht M, Morris JH, Böcker S, Stoye J, Baumbach J (2010)
Nature Methods 7(6): 419-420.
PUB | DOI | WoS | PubMed | Europe PMC
 
[113]
2009 | Journal Article | PUB-ID: 1634447
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
Bekel T, Henckel K, Küster H, Meyer F, Mittard-Runte V, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Pühler A, Stoye J, et al. (2009)
Journal of Biotechnology 140(1-2): 3-12.
PUB | DOI | WoS | PubMed | Europe PMC
 
[112]
2009 | Journal Article | PUB-ID: 1589098
WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads
Gerlach W, Jünemann S, Tille F, Goesmann A, Stoye J (2009)
BMC Bioinformatics 10(1): 430.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[111]
2009 | Journal Article | PUB-ID: 1591507
A Unified Approach for Reconstructing Ancient Gene Clusters
Stoye J, Wittler R (2009)
IEEE/ACM Transactions on Computational Biology and Bioinformatics 6(3): 387-400.
PUB | DOI | WoS | PubMed | Europe PMC
 
[110]
2009 | Journal Article | PUB-ID: 1898105
Computation of Median Gene Clusters
Böcker S, Jahn K, Mixtacki J, Stoye J (2009)
Journal of Computational Biology 16(8): 1085-1099.
PUB | DOI | WoS | PubMed | Europe PMC
 
[109]
2009 | Conference Paper | PUB-ID: 1919206
Counting All DCJ Sorting Scenarios
Braga M, Stoye J (2009)
In: Proc. of Recomb-CG 2009. LNBI, 5817. 36-47.
PUB | DOI
 
[108]
2009 | Conference Paper | PUB-ID: 1893884
Phylogenetic Comparative Assembly
Husemann P, Stoye J (2009)
In: Proc. of WABI 2009. LNBI, 5724. 145-156.
PUB | DOI | WoS | PubMed | Europe PMC
 
[107]
2009 | Journal Article | PUB-ID: 1898137
Approximative Gencluster und ihre Anwendung in der komparativen Genomik
Jahn K, Stoye J (2009)
Informatik-Spektrum 32(4): 288-300.
PUB | DOI
 
[106]
2009 | Journal Article | PUB-ID: 1591319
ChromA: signal-based retention time alignment for chromatography-mass spectrometry data
Hoffmann N, Stoye J (2009)
Bioinformatics 25(16): 2080-2081.
PUB | DOI | WoS | PubMed | Europe PMC
 
[105]
2009 | Conference Paper | PUB-ID: 1919207
Finding Nested Common Intervals Efficiently
Blin G, Stoye J (2009)
In: Proc. of Recomb-CG 2009. LNBI, 5817. 59-69.
PUB | DOI | WoS | PubMed | Europe PMC
 
[104]
2009 | Journal Article | PUB-ID: 1589663
A New Linear Time Algorithm to Compute the Genomic Distance via the Double Cut and Join Distance
Bergeron A, Mixtacki J, Stoye J (2009)
Theoretical Computer Science 410(51): 5300-5316.
PUB | DOI | WoS
 
[103]
2009 | Journal Article | PUB-ID: 1590204
A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG)
Brudno M, Medvedev P, Stoye J, De La Vega FM (2009)
BIOINFORMATICS 25(21): 2863-2864.
PUB | DOI | WoS | PubMed | Europe PMC
 
[102]
2009 | Conference Abstract | PUB-ID: 1918945
Computational Short Read Metagenomics
Stoye J (2009)
Presented at the JOBIM 2009, Nantes, France.
PUB
 
[101]
2009 | Conference Paper | PUB-ID: 1919209
Rearrangement Models and Single-Cut Operations
Medvedev P, Stoye J (2009)
In: Comparative Genomics : International Workshop, RECOMB-CG 2009, Budapest, Hungary, September 27-29, 2009. Proceedings. Lecture Notes in Computer Science, 5817. Berlin, Heidelberg: Springer: 84-97.
PUB | DOI
 
[100]
2008 | Journal Article | PUB-ID: 1586009
Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor
Krause L, Diaz NN, Edwards RA, Gartemann K-H, Krömeke H, Neuweger H, Pühler A, Runte KJ, Schlüter A, Stoye J, Szczepanowski R, et al. (2008)
JOURNAL OF BIOTECHNOLOGY 136(1-2): 91-101.
PUB | DOI | WoS | PubMed | Europe PMC
 
[99]
2008 | Journal Article | PUB-ID: 1636699
MeltDB: a software platform for the analysis and integration of metabolomics experiment data
Neuweger H, Albaum S, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A (2008)
Bioinformatics 24(23): 2726-2732.
PUB | DOI | WoS | PubMed | Europe PMC
 
[98]
2008 | Journal Article | PUB-ID: 1586785
Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms
Oehm S, Gilbert D, Tauch A, Stoye J, Goesmann A (2008)
NUCLEIC ACIDS RESEARCH 36(Web Server): W433-W437.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[97]
2008 | Journal Article | PUB-ID: 1783364
Phylogenetic classification of short environmental DNA fragments
Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, Stoye J (2008)
Nucleic Acids Research 36(7): 2230-2239.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[96]
2008 | Conference Paper | PUB-ID: 1919192
Computation of Median Gene Clusters
Böcker S, Jahn K, Mixtacki J, Stoye J (2008)
In: Proc. of RECOMB 2008. LNBI, 4955. 331-345.
PUB | DOI
 
[95]
2008 | Journal Article | PUB-ID: 1587078
Counting suffix arrays and strings
Schürmann K-B, Stoye J (2008)
THEORETICAL COMPUTER SCIENCE 395(2-3): 220-234.
PUB | DOI | WoS
 
[94]
2008 | Conference Paper | PUB-ID: 1919195
HP Distance via Double Cut and Join Distance
Bergeron A, Mixtacki J, Stoye J (2008)
In: Combinatorial Pattern Matching. 19th Annual Symposium, CPM 2008, Pisa, Italy, June 18-20, 2008 Proceedings. Lecture Notes in Computer Science, 5029. 56-68.
PUB | DOI
 
[93]
2008 | Encyclopedia Article | PUB-ID: 1918834
Suffix Tree Construction in RAM (1997; Farach-Colton)
Stoye J (2008)
In: Encyclopedia of Algorithms. Kao M-Y (Ed); Springer Verlag: 925-928.
PUB | DOI
 
[92]
2008 | Conference Paper | PUB-ID: 1919200
On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios
Bergeron A, Mixtacki J, Stoye J (2008)
In: Proc. of Recomb-CG 2008. LNBI, 5267. 226-240.
PUB | DOI
 
[91]
2008 | Report | PUB-ID: 1970459
A space efficient representation for sparse de Bruijn subgraphs
Quitzau JAA, Stoye J (2008) Forschungsberichte der Technischen Fakultät, Abteilung Informationstechnik / Universität Bielefeld.
Bielefeld: Technische Fakultät der Universität Bielefeld.
PUB | PDF
 
[90]
2008 | Report | PUB-ID: 1970461
Online Abelian Pattern Matching
Ejaz T, Rahmann S, Stoye J (2008) Forschungsberichte der Technischen Fakultät, Abteilung Informationstechnik / Universität Bielefeld.
Bielefeld: Technische Fakultät der Universität Bielefeld.
PUB | PDF
 
[89]
2008 | Conference Paper | PUB-ID: 1919198
Detecting Repeat Families in Incompletely Sequenced Genomes
Quitzau JAA, Stoye J (2008)
In: Proc. of WABI 2008. LNBI, 5251. 342-353.
PUB | DOI
 
[88]
2007 | Journal Article | PUB-ID: 1783345
GISMO - gene identification using a support vector machine for ORF classification
Krause L, McHardy AC, Nattkemper TW, Pühler A, Stoye J, Meyer F (2007)
Nucleic Acids Research 35(2): 540-549.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[87]
2007 | Journal Article | PUB-ID: 1918432
Character Sets of Strings
Didier G, Schmidt T, Stoye J, Tsur D (2007)
Journal of Discrete Algorithms 5(2): 330-340.
PUB | DOI
 
[86]
2007 | Journal Article | PUB-ID: 1630781
Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms
Mellmann A, Weniger T, Berssenbrügge C, Rothgänger J, Sammeth M, Stoye J, Harmsen D (2007)
BMC MICROBIOLOGY 7(1): 98.
PUB | DOI | WoS | PubMed | Europe PMC
 
[85]
2007 | Journal Article | PUB-ID: 1595253
An incomplex algorithm for fast suffix array construction
Schürmann K-B, Stoye J (2007)
SOFTWARE-PRACTICE & EXPERIENCE 37(3): 309-329.
PUB | DOI | WoS
 
[84]
2007 | Book Chapter | PUB-ID: 1918828
Chapter 12: Gecko and GhostFam - Rigorous and Efficient Gene Cluster Detection in Prokaryotic Genomes
Schmidt T, Stoye J (2007)
In: Comparative Genomics, Volume 2. Bergman NH (Ed); Methods in Molecular Biology, 396. Totowa, NJ: Humana Press Inc.: 165-182.
PUB | DOI | PubMed | Europe PMC
 
[83]
2006 | Journal Article | PUB-ID: 1631957
Finding novel genes in bacterial communities isolated from the environment
Krause L, Diaz NN, Bartels D, Edwards RA, Pühler A, Rohwer F, Meyer F, Stoye J (2006)
BIOINFORMATICS 22(14): e281-e289.
PUB | DOI | WoS | PubMed | Europe PMC
 
[82]
2006 | Journal Article | PUB-ID: 1597313
On the similarity of sets of permutations and its applications to genome comparison
Bergeron A, Stoye J (2006)
JOURNAL OF COMPUTATIONAL BIOLOGY 13(7): 1340-1354.
PUB | DOI | WoS | PubMed | Europe PMC
 
[81]
2006 | Conference Paper | PUB-ID: 1596811
A Unifying View of Genome Rearrangements
Bergeron A, Mixtacki J, Stoye J (2006)
In: Proc. of WABI 2006. LNBI, 4175. SPRINGER-VERLAG BERLIN: 163-173.
PUB | DOI | WoS
 
[80]
2006 | Journal Article | PUB-ID: 1597213
Comparing tandem repeats with duplications and excisions of variable degree
Sammeth M, Stoye J (2006)
IEEE/ACM Transactions on Computational Biology and Bioinformatics 3(4): 395-407.
PUB | DOI | WoS | PubMed | Europe PMC
 
[79]
2006 | Journal Article | PUB-ID: 1599574
On sorting by translocations
Bergeron A, Mixtacki J, Stoye J (2006)
JOURNAL OF COMPUTATIONAL BIOLOGY 13(2): 567-578.
PUB | DOI | WoS | PubMed | Europe PMC
 
[78]
2006 | Report | PUB-ID: 1970464
On Common Intervals with Errors
Chauve C, Diekmann Y, Heber S, Mixtacki J, Rahmann S, Stoye J (2006) Forschungsberichte.
Bielefeld: Technische Fakultät der Universität Bielefeld.
PUB | PDF
 
[77]
2006 | Journal Article | PUB-ID: 1599943
Panta rhei (QAlign2): an open graphical environment for sequence analysis
Sammeth M, Griebel T, Tille F, Stoye J (2006)
BIOINFORMATICS 22(7): 889-890.
PUB | DOI | WoS | PubMed | Europe PMC
 
[76]
2006 | Conference Abstract | PUB-ID: 1918946
Index Structures in Biological Sequence Analysis: From Simplicity to Complexity and Back
Stoye J (2006)
Presented at the JOBIM 2006, Bordeaux, France.
PUB
 
[75]
2006 | Journal Article | PUB-ID: 1599570
Efficient q-gram filters for finding all epsilon-matches over a given length
Rasmussen KR, Stoye J, Myers EW (2006)
JOURNAL OF COMPUTATIONAL BIOLOGY 13(2): 296-308.
PUB | DOI | WoS | PubMed | Europe PMC
 
[74]
2005 | Journal Article | PUB-ID: 1773302
BACCardI - a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison
Bartels D, Kespohl S, Albaum S, Drüke T, Goesmann A, Herold J, Kaiser O, Pühler A, Pfeiffer F, Raddatz G, Stoye J, et al. (2005)
Bioinformatics 21(7): 853-859.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[73]
2005 | Book Chapter | PUB-ID: 1918824
Chapter 10: The Inversion Distance Problem
Bergeron A, Mixtacki J, Stoye J (2005)
In: Mathematics of Evolution and Phylogeny. Gascuel O (Ed); Oxford University Press: 262-290.
PUB
 
[72]
2005 | Conference Paper | PUB-ID: 1919012
An Incomplex Algorithm for Fast Suffix Array Construction
Schürmann K-B, Stoye J (2005)
In: Proc. of ALENEX/ANALCO 2005. 77-85.
PUB
 
[71]
2005 | Report | PUB-ID: 1970470
Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI)
Sammeth M, Stoye J (2005) Forschungsberichte.
Bielefeld: Technische Fakultät der Universität Bielefeld.
PUB | PDF | DOI
 
[70]
2005 | Conference Paper | PUB-ID: 1601361
Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI)
Sammeth M, Weniger T, Harmsen D, Stoye J (2005)
In: Proc. of WABI 2005. LNBI, 3692. SPRINGER-VERLAG BERLIN: 276-290.
PUB | DOI | WoS
 
[69]
2005 | Conference Paper | PUB-ID: 1603216
Efficient q-Gram Filters for Finding All ε-Matches Over a Given Length
Rasmussen KR, Stoye J, Myers EW (2005)
In: Proc. of RECOMB 2005. LNBI, 3500. SPRINGER-VERLAG BERLIN: 189-203.
PUB | DOI | WoS
 
[68]
2005 | Conference Paper | PUB-ID: 1601348
Protein Annotation by Secondary Structure Based Alignments (PASSTA)
Bannert C, Stoye J (2005)
In: Proc. of CompLife 2005. LNBI, 3695. Springer-Verlag: 79-90.
PUB | DOI | WoS
 
[67]
2005 | Journal Article | PUB-ID: 1775168
Large scale hierarchical clustering of protein sequences
Krause A, Stoye J, Vingron M (2005)
BMC Bioinformatics 6(1): 15.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[66]
2005 | Conference Paper | PUB-ID: 1603220
On Sorting by Translocations
Bergeron A, Mixtacki J, Stoye J (2005)
In: Proc. of RECOMB 2005. LNBI, 3500. SPRINGER-VERLAG BERLIN: 615-629.
PUB | DOI | WoS
 
[65]
2005 | Report | PUB-ID: 1970472
Counting Suffix Arrays and Strings
Schürmann K-B, Stoye J (2005) Forschungsberichte.
Bielefeld: Technische Fakultät der Universität Bielefeld.
PUB | PDF
 
[64]
2005 | Conference Paper | PUB-ID: 1919026
Counting Suffix Arrays and Strings
Schürmann K-B, Stoye J (2005)
In: Proc. of SPIRE 2005. LNCS, 3772. 55-66.
PUB | DOI
 
[63]
2005 | Journal Article | PUB-ID: 1918947
Informatische Methoden zur Protein-Identifikation
Böcker S, Stoye J (2005)
LaborPraxis 29(10): 24-26.
PUB
 
[62]
2004 | Conference Paper | PUB-ID: 1607263
Reversal Distance without Hurdles and Fortresses
Bergeron A, Mixtacki J, Stoye J (2004)
In: Proc. of CPM 2004. LNCS, 3109. SPRINGER-VERLAG BERLIN: 388-399.
PUB | DOI | WoS
 
[61]
2004 | Journal Article | PUB-ID: 1773312
Benchmarking tools for the alignment of functional noncoding DNA
Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB (2004)
BMC Bioinformatics 5(1): 6.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[60]
2004 | Journal Article | PUB-ID: 1773569
Linear time algorithms for finding and representing all the tandem repeats in a string
Gusfield D, Stoye J (2004)
Journal of computer and system sciences 69(4): 525-546.
PUB | PDF | DOI | WoS
 
[59]
2004 | Journal Article | PUB-ID: 1773560
Algorithmic complexity of protein identification: combinatorics of weighted strings
Cieliebak M, Erlebach T, Lipták Z, Stoye J, Welzl E (2004)
Discrete Applied Mathematics 137(1): 27-46.
PUB | PDF | DOI | WoS
 
[58]
2004 | Journal Article | PUB-ID: 1773554
Correction: Benchmarking tools for the alignment of functional noncoding DNA
Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB (2004)
BMC Bioinformatics 5(1): 73.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[57]
2004 | Conference Paper | PUB-ID: 1606286
Suboptimal Local Alignments across Multiple Scoring Schemes
Michael M, Dieterich C, Stoye J (2004)
In: Proc. of WABI 2004. LNBI, 3240. SPRINGER-VERLAG BERLIN: 99-110.
PUB | DOI | WoS
 
[56]
2004 | Conference Paper | PUB-ID: 1607260
Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences
Schmidt T, Stoye J (2004)
In: Proc. of CPM 2004. LNCS, 3109. 347-358.
PUB | DOI | WoS
 
[55]
2004 | Conference (Editor) | PUB-ID: 1918823
Proceedings of the German Conference on Bioinformatics, GCB 2004
Giegerich R, Stoye J (Eds) (2004)
Lecture Notes in Informatics P-53.
PUB
 
[54]
2003 | Journal Article | PUB-ID: 1918949
Finden, fast ohne zu suchen: Indexstrukturen in der Bioinformatik
Giegerich R, Stoye J (2003)
Forschung an der Universität Bielefeld 26: 63-68.
PUB
 
[53]
2003 | Journal Article | PUB-ID: 1610397
Efficient implementation of lazy suffix trees
Giegerich R, Kurtz S, Stoye J (2003)
SOFTWARE-PRACTICE & EXPERIENCE 33(11): 1035-1049.
PUB | PDF | DOI | WoS
 
[52]
2003 | Conference Paper | PUB-ID: 1919005
Evaluation of the Jumping Alignment Algorithm with Artificial and Biological Data
Bannert C, Stoye J (2003)
In: Proc. of GCB 2003. 21-25.
PUB
 
[51]
2003 | Report | PUB-ID: 1970475
Suffix Tree Construction and Storage with Limited Main Memory
Schürmann K-B, Stoye J (2003) Forschungsberichte.
Bielefeld: Technische Fakultät der Universität Bielefeld.
PUB | PDF
 
[50]
2003 | Conference Paper | PUB-ID: 1610433
On the similarity of sets of permutations and its applications to genome comparison
Bergeron A, Stoye J (2003)
In: Proc. of COCOON 2003. LNCS, 2697. 68-79.
PUB | DOI | WoS
 
[49]
2003 | Journal Article | PUB-ID: 1610503
QAlign: quality-based multiple alignments with dynamic phylogenetic analysis
Sammeth M, Rothgänger J, Esser W, Albert J, Stoye J, Harmsen D (2003)
BIOINFORMATICS 19(12): 1592-1593.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[48]
2003 | Report | PUB-ID: 1970477
On the Similarity of Sets of Permutations and its Applications to Genome Comparison
Bergeron A, Stoye J (2003) Forschungsberichte.
Bielefeld: Technische Fakultät der Universität Bielefeld.
PUB | PDF
 
[47]
2003 | Journal Article | PUB-ID: 1612664
The European Conference on Computational Biology
Heber S, Stoye J (2003)
Drug Discovery Today 8(3): 113-114.
PUB | DOI | WoS | PubMed | Europe PMC
 
[46]
2003 | Journal Article | PUB-ID: 1609403
Divide-and-conquer multiple alignment with segment-based constraints
Sammeth M, Morgenstern B, Stoye J (2003)
BIOINFORMATICS 19(Suppl 2): ii189-ii195.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[45]
2002 | Journal Article | PUB-ID: 1773578
A novel approach to remote homology detection: jumping alignments
Spang R, Rehmsmeier M, Stoye J (2002)
Journal of Computational Biology 9(5): 747-760.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[44]
2002 | Conference Paper | PUB-ID: 1919000
Algorithmic Complexity of Protein Identification: Searching in Weighted Strings
Cieliebak M, Lipták Z, Welzl E, Erlebach T, Stoye J (2002)
In: Proc. of IFIP TCS 2002. 143-156.
PUB
 
[43]
2002 | Conference Abstract | PUB-ID: 1918951
Index Structures for Large Sequence Data: Suffix Trees and Affix Trees
Stoye J (2002)
In: Lecture Notes in Informatics. Schubert S, Reusch B, Jesse N (Eds); , P-20(Ergänzungsband). 67-67.
PUB
 
[42]
2002 | Journal Article | PUB-ID: 1773329
Common intervals and sorting by reversals: a marriage of necessity
Bergeron A, Heber S, Stoye J (2002)
Bioinformatics 18(Suppl 2): S54-S63.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[41]
2002 | Conference Paper | PUB-ID: 1918995
Resampling Methods in Physical Mapping
Heber S, Stoye J, Frohme M, Hoheisel J, Vingron M (2002)
In: Proc. of GfKl 2000. 437-444.
PUB
 
[40]
2002 | Journal Article | PUB-ID: 1773332
Simple and flexible detection of contiguous repeats using a suffix tree
Stoye J, Gusfield D (2002)
Theoretical Computer Science 270(1-2): 843-856.
PUB | PDF | DOI | WoS
 
[39]
2001 | Conference Paper | PUB-ID: 1880197
Algorithms for Finding Gene Clusters
Heber S, Stoye J (2001)
In: Proc. of WABI 2001. LNCS, 2149. Berlin: Sppringer: 252-263.
PUB | DOI
 
[38]
2001 | Journal Article | PUB-ID: 1773335
REPuter: the manifold applications of repeat analysis on a genomic scale
Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R (2001)
Nucleic Acids Research 29(22): 4633-4642.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[37]
2001 | Conference Paper | PUB-ID: 1918992
Finding all Common Intervals of k Permutations
Heber S, Stoye J (2001)
In: Proc. of CPM 2001. LNCS, 2089. 207-218.
PUB | DOI
 
[36]
2001 | Report | PUB-ID: 1970479
Algorithmic Complexity of Protein Identification: Combinatorics of Weighted Strings
Cieliebak M, Erlebach T, Lipták Z, Stoye J, Welzl E (2001) Technical Report.
ETH Zürich, Dept. of Computer Science.
PUB
 
[35]
2000 | Report | PUB-ID: 1970490
Affix Trees
Stoye J (2000) Forschungsberichte.
Technische Fakultät der Universität Bielefeld.
PUB | PDF
 
[34]
2000 | Conference Paper | PUB-ID: 1918988
Computation and Visualization of Degenerate Repeats in Complete Genomes
Kurtz S, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R (2000)
In: Proc. of ISMB 2000. 228-238.
PUB | PubMed | Europe PMC
 
[33]
2000 | Book Chapter | PUB-ID: 1918817
Finding Maximal Pairs with Bounded Gap
Brodal GS, Lyngsø RB, Pedersen CNS, Stoye J (2000)
In: Matching Patterns (Journal of Discrete Algorithms). Crochemore M, Gąsieniec L (Eds); 77-104.
PUB
 
[32]
2000 | Journal Article | PUB-ID: 1773572
Contig selection in physical mapping
Heber S, Stoye J, Frohme M, Hoheisel J, Vingron M (2000)
Journal of Computational Biology 7(3-4): 395-408.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[31]
2000 | Journal Article | PUB-ID: 1773345
The SYSTERS protein sequence cluster set
Krause A, Stoye J, Vingron M (2000)
Nucleic Acids Research 28(1): 270-272.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[30]
2000 | Conference Paper | PUB-ID: 1918985
Sequence Database Search Using Jumping Alignments
Spang R, Rehmsmeier M, Stoye J (2000)
In: Proc. of ISMB 2000. 367-375.
PUB | PubMed | Europe PMC
 
[29]
2000 | Journal Article | PUB-ID: 1773341
An iterative method for faster sum-of-pairs multiple sequence alignment
Reinert K, Stoye J, Will T (2000)
Bioinformatics 16(9): 808-814.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[28]
2000 | Conference Paper | PUB-ID: 1918981
Contig Selection in Physical Mapping
Heber S, Stoye J, Hoheisel J, Vingron M (2000)
In: Proc. of RECOMB 2000. 155-164.
PUB | DOI | WoS | PubMed | Europe PMC
 
[27]
2000 | Conference (Editor) | PUB-ID: 1918813
Proceedings of the German Conference on Bioinformatics, GCB 2000
Bornberg-Bauer E, Rost U, Stoye J, Vingron M (Eds) (2000)
Berlin: Logos Verlag.
PUB
 
[26]
1999 | Conference Paper | PUB-ID: 1620435
Efficient implementation of lazy suffix trees
Giegerich R, Kurtz S, Stoye J (1999)
In: Algorithm Engineering. 3rd International Workshop, WAE’99 London, UK, July 19–21, 1999 Proceedings. LNCS, 1668. 30-42.
PUB | DOI | WoS
 
[25]
1999 | Report | PUB-ID: 1970495
Consistent Equivalence Relations: A Set-Theoretical Framework for Multiple Sequence Alignment
Morgenstern B, Stoye J, Dress A (1999) Materialien/Preprints.
Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
PUB
 
[24]
1999 | Conference Paper | PUB-ID: 1918971
Finding Maximal Pairs with Bounded Gap
Brodal GS, Lyngsø RB, Pedersen CNS, Stoye J (1999)
In: Proc. of CPM 1999. LNCS, 1645. 134-149.
PUB | DOI
 
[23]
1999 | Report | PUB-ID: 1970509
Finding Maximal Pairs with Bounded Gap
Brodal GS, Lyngsø RB, Pedersen CNS, Stoye J (1999) Report.
BRICS, Department of Computer Science, University of Aarhus.
PUB
 
[22]
1999 | Conference Paper | PUB-ID: 1918978 PUB
 
[21]
1998 | Journal Article | PUB-ID: 1918538
Die Bedeutung der Zusammenarbeit der Disziplinen in der Anwendung - erläutert anhand von Beispielen
Hildebrand M, Stoye J (1998)
Der Mathematikunterricht 44(6): 34-53.
PUB
 
[20]
1998 | Report | PUB-ID: 1970515
Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree
Stoye J, Gusfield D (1998) Report.
Department of Computer Science, University of California, Davis.
PUB
 
[19]
1998 | Conference Paper | PUB-ID: 1918964
Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version)
Stoye J, Gusfield D (1998)
In: Proc. of CPM 1998. LNCS, 1448. 140-152.
PUB | DOI
 
[18]
1998 | Journal Article | PUB-ID: 1667771 PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[17]
1998 | Journal Article | PUB-ID: 1625402
Rose: generating sequence families
Stoye J, Evers D, Meyer F (1998)
BIOINFORMATICS 14(2): 157-163.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[16]
1998 | Report | PUB-ID: 1970513
Linear Time Algorithms for Finding and Representing all the Tandem Repeats in a String
Gusfield D, Stoye J (1998) Report.
Department of Computer Science, University of California, Davis.
PUB
 
[15]
1998 | Journal Article | PUB-ID: 2488102
The Number of Standard and of Effective Multiple Alignments
Dress A, Morgenstern B, Stoye J (1998)
Appl. Math. Lett. 11(4): 43-49.
PUB
 
[14]
1997 | Report | PUB-ID: 1970532
Divide-and-Conquer Multiple Sequence Alignment
Stoye J (1997) Forschungsberichte.
Technische Fakultät der Universität Bielefeld.
PUB
 
[13]
1997 | Report | PUB-ID: 1970526
On Simultaneous versus Iterative Multiple Sequence Alignment
Perrey SW, Stoye J, Moulton V, Dress A (1997) Materialien/Preprints.
Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
PUB
 
[12]
1997 | Journal Article | PUB-ID: 1773355
Improving the divide-and-conquer approach to sum-of-pairs multiple sequence alignment
Stoye J, Perrey SW, Dress A (1997)
Applied mathematics letters 10(2): 67-73.
PUB | PDF | DOI | WoS
 
[11]
1997 | Report | PUB-ID: 1970523
On the Number of Standard and Effective Multiple Alignments
Dress A, Morgenstern B, Stoye J (1997) Materialien/Preprints.
Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
PUB
 
[10]
1997 | Journal Article | PUB-ID: 1773358
Two applications of the Divide & Conquer principle in the molecular sciences
Brinkmann G, Dress A, Perrey SW, Stoye J (1997)
Mathematical programming 79(1-3): 71-97.
PUB | DOI | WoS
 
[9]
1997 | Report | PUB-ID: 1970529
Two Applications of the Divide & Conquer Principle in the Molecular Sciences
Brinkmann G, Dress A, Perrey SW, Stoye J (1997) Materialien/Preprints.
Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
PUB
 
[8]
1997 | Report | PUB-ID: 1970517
Rose: Generating Sequence Families
Stoye J, Evers D, Meyer F (1997) Forschungsberichte.
Technische Fakultät der Universität Bielefeld.
PUB
 
[7]
1997 | Report | PUB-ID: 1970520
FDCA: Fast and Accurate Approximation to Sum-of-Pairs Score Optimal Multiple Sequence Alignment
Perrey SW, Stoye J, Moulton V (1997) Materialien/Preprints.
Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
PUB
 
[6]
1997 | Journal Article | PUB-ID: 2488107 PUB
 
[5]
1997 | Conference Paper | PUB-ID: 1667885
Generating benchmarks for multiple sequence alignments and phylogenetic reconstructions
Stoye J, Evers D, Meyer F (1997)
In: Proc. of ISMB 1997. 303-306.
PUB | PubMed | Europe PMC
 
[4]
1996 | Journal Article | PUB-ID: 1773351
A general method for fast multiple sequence alignment
Tönges U, Perrey SW, Stoye J, Dress A (1996)
Gene 172(1): GC33-GC41.
PUB | DOI | WoS | PubMed | Europe PMC
 
[3]
1996 | Report | PUB-ID: 1970535
Improving the Divide-and-Conquer Approach to Sum-of-Pairs Multiple Sequence Alignment
Stoye J, Dress A, Perrey SW (1996) Materialien/Preprints.
Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
PUB
 
[2]
1996 | Report | PUB-ID: 1970537
A General Method for Fast Multiple Sequence Alignment
Tönges U, Perrey SW, Stoye J, Dress A (1996) Materialien/Preprints.
Forschungsschwerpunkt Mathematisierung, Universität Bielefeld.
PUB
 
[1]
1996 | Report | PUB-ID: 1970533
Fast Approximation to the NP-hard Problem of Multiple Sequence Alignment
Perrey SW, Stoye J (1996) Information and Mathematical Sciences Reports, Series B.
Dept. of Mathematics, Massey University, Palmerston North, New Zealand.
PUB
 

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