205 Publikationen

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[205]
2019 | Zeitschriftenaufsatz | Im Druck | PUB-ID: 2937712
D. Rubert, et al., “Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants”, BMC Genomics, In Press.
PUB
 
[204]
2019 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2937148
J. Alanko, et al., “Finding All Maximal Perfect Haplotype Blocks in Linear Time”, Proceedings of WABI 2019, Leibniz International Proceedings in Informatics. LIPIcs, vol. 143, Dagstuhl: Schloss Dagstuhl, Leibniz-Zentrum für Informatik , 2019, pp.8:1-8:9.
PUB | DOI
 
[203]
2019 | Herausgeber*in Sammelwerk | Veröffentlicht | PUB-ID: 2935998
J.C. Setubal, J. Stoye, and B.E. Dutilh, eds., Computational Methods for Microbiome Analysis, Frontiers Research Topics, Lausanne: Frontiers Media, 2019.
PUB | Download (ext.)
 
[202]
2019 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2932883
D. Dörr and J. Stoye, “A Perspective on Comparative and Functional Genomics”, Bioinformatics and Phylogenetics, T. Warnow, ed., Computational Biology, vol. 29, Cham: Springer , 2019, pp.361-372.
PUB | DOI
 
[201]
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2932884
H. Oey, et al., “Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium”, PLOS Pathogens, vol. 15, 2019, : e1007513.
PUB | DOI | WoS | PubMed | Europe PMC
 
[200]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919005
T. Schulz, J. Stoye, and D. Dörr, “GraphTeams. A method for discovering spatial gene clusters in Hi-C sequencing data”, BMC Genomics, vol. 19, 2018, : 308.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[199]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919006
D. Rubert, et al., “Computing the family-free DCJ similarity”, BMC Bioinformatics, vol. 19, 2018, : 152.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[198]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2918481
N. Luhmann, et al., “Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 15, 2018, pp. 2094-2100.
PUB | DOI | WoS | PubMed | Europe PMC
 
[197]
2018 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2930445
L. Cunha, et al., “Identifying Maximal Perfect Haplotype Blocks”, Proceedings of BSB 2018, LNBI, vol. 11228, Springer Verlag, 2018, pp.26-37.
PUB | DOI
 
[196]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2930268
G. Holley, et al., “Dynamic Alignment-Free and Reference-Free Read Compression”, JOURNAL OF COMPUTATIONAL BIOLOGY, vol. 25, 2018, pp. 825-836.
PUB | DOI | WoS | PubMed | Europe PMC
 
[195]
2018 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2913921
T. Zekic, G. Holley, and J. Stoye, “Pan-genome Storage and Analysis Techniques”, Comparative Genomics. Methods and Protocols, J.C. Setubal, P. Stadler, and J. Stoye, eds., Methods in Molecular Biology, vol. 1704, New York: Springer Verlag, 2018, pp.29-53.
PUB
 
[194]
2018 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2913922
D. Dörr, P. Feijão, and J. Stoye, “Family-Free Genome Comparison”, Comparative Genomics: Methods and Protocols, J.C. Setubal, P. Stadler, and J. Stoye, eds., Methods in Molecular Biology, vol. 1704, New York: Springer Verlag, 2018, pp.331-342.
PUB
 
[193]
2018 | Herausgeber*in Sammelwerk | Veröffentlicht | PUB-ID: 2913920
J.C. Setubal, P. Stadler, and J. Stoye, eds., Comparative Genomics: Methods and Protocols, Methods in Molecular Biology, vol. 1704, New York: Springer Verlag, 2018.
PUB
 
[192]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919012
S. Jaenicke, et al., “Flexible metagenome analysis using the MGX framework”, Microbiome, vol. 6, 2018, : 76.
PUB | DOI | WoS | PubMed | Europe PMC
 
[191]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2913556
S. Jünemann, et al., “Bioinformatics for NGS-based metagenomics and the application to biogas research”, Journal of Biotechnology, vol. 261, 2017, pp. 10-23.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[190]
2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2913015
D. Rubert, et al., “Algorithms for Computing the Family-Free Genomic Similarity under DCJ”, Comparative Genomics. RECOMB-CG 2017, J. Meidanis and L. Nakhleh, eds., Lecture Notes in Bioinformatics, vol. 10562, Cham: Springer Verlag, 2017, pp.76-100.
PUB | DOI
 
[189]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909057
D. Rubert, et al., “Approximating the DCJ distance of balanced genomes in linear time”, Algorithms for Molecular Biology, vol. 12, 2017, : 3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[188]
2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2909409
L. Cunha, et al., “Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings”, Proceedings of CPM 2017, LIPIcs, vol. 78, 2017, pp.19:1-19:9.
PUB | DOI
 
[187]
2017 | Preprint | Veröffentlicht | PUB-ID: 2908521
L. Cunha, et al., “Faster Jumbled Indexing for Binary Run-Length Encoded Strings”, arXiv: 1702.01280, 2017.
PUB
 
[186]
2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2907587
G. Holley, et al., “Dynamic Alignment-Free and Reference-Free Read Compression”, Proceedings of RECOMB 2017, Lecture Notes in Bioinformatics, vol. 10229, 2017, pp.50-65.
PUB | DOI
 
[185]
2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2913016
T. Schulz, J. Stoye, and D. Dörr, “Finding Teams in Graphs and its Application to Spatial Gene Cluster Discovery”, Proceedings of RECOMB-CG 2017, Lecture Notes in Bioinformatics, vol. 1704, Berlin: Springer Verlag, 2017, pp.197-212.
PUB | DOI
 
[184]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909967
D. Dörr, et al., “New Genome Similarity Measures based on Conserved Gene Adjacencies”, Journal of Computational Biology, vol. 24, 2017, pp. 616-634.
PUB | DOI | WoS | PubMed | Europe PMC
 
[183]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2905930
S. Winter, et al., “Finding approximate gene clusters with GECKO 3”, Nucleic Acids Research, vol. 44, 2016, pp. 9600-9610.
PUB | DOI | WoS | PubMed | Europe PMC
 
[182]
2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2903708
D. Rubert, et al., “A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates”, Algorithms in Bioinformatics. WABI 2016, M. Frith and C.N. Storm Pedersen, eds., Lecture Notes in Bioinformatics, vol. 9838, Cham: Springer, 2016, pp.293-306.
PUB | DOI
 
[181]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900129
G. Holley, R. Wittler, and J. Stoye, “Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage”, Algorithms for Molecular Biology, vol. 11, 2016, : 3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[180]
2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2900111
L.A.B. Kowada, et al., “New Genome Similarity Measures based on Conserved Gene Adjacencies”, Research in Computational Molecular Biology. RECOMB 2016, M. Singh, ed., Lecture Notes in Bioinformatics (LNBI), vol. 9649, Springer, 2016, pp.204-224.
PUB | DOI
 
[179]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900421
L. Krause, et al., “Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma”, Carcinogenesis, vol. 37, 2016, pp. 356-365.
PUB | DOI | WoS | PubMed | Europe PMC
 
[178]
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2677844
M. Dias Vieira Braga and J. Stoye, “Sorting linear genomes with rearrangements and indels”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 12, 2015, pp. 500-506.
PUB | DOI | WoS | PubMed | Europe PMC
 
[177]
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726366
F.H. Viduani Martinez, et al., “On the family-free DCJ distance and similarity”, Algorithms for Molecular Biology, vol. 10, 2015, : 13.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[176]
2015 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2757497
G. Holley, R. Wittler, and J. Stoye, “Bloom Filter Trie - a data structure for pan-genome storage”, Proceedings of WABI 2015, LNBI, vol. 9289, 2015, pp.217-230.
PUB
 
[175]
2015 | Konferenzband | Veröffentlicht | PUB-ID: 2780229
J. Meidanis and J. Stoye, eds., “Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Bioinformatics”, BMC Bioinformatics, vol. 16, 2015.
PUB | Download (ext.)
 
[174]
2015 | Konferenzband | Veröffentlicht | PUB-ID: 2780232
J. Meidanis and J. Stoye, eds., “Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Genomics”, BMC Genomics, vol. 16, 2015.
PUB | Download (ext.)
 
[173]
2014 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2684241
F.H. Viduani Martinez, et al., “On the family-free DCJ distance”, Algorithms in Bioinformatics. WABI 2014, D. Brown and B. Morgenstern, eds., Lecture Notes in Bioinformatics, vol. 8701, Berlin ; Heidelberg: Springer Verlag, 2014, pp.174-186.
PUB | DOI
 
[172]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2687033
D. Dörr, et al., “Identifying Gene Clusters by Discovering Common Intervals in Indeterminate Strings”, BMC Genomics, vol. 15, 2014, pp. S2.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[171]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685362
M. Lechner, et al., “Orthology Detection Combining Clustering and Synteny for Very Large Datasets”, PLoS ONE, vol. 9, 2014, pp. e105015.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[170]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2689773
S. Jünemann, et al., “GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers”, PLOS ONE, vol. 9, 2014, pp. e107014.
PUB | DOI | WoS | PubMed | Europe PMC
 
[169]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2674387
R. Hilker, et al., “ReadXplorer - Visualization and Analysis of Mapped Sequences”, Bioinformatics, vol. 30, 2014, pp. 2247-2254.
PUB | DOI | WoS | PubMed | Europe PMC
 
[168]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665038
P. Schwientek, et al., “Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts”, Journal of Biotechnology, vol. 190, 2014, pp. 85-95.
PUB | DOI | WoS | PubMed | Europe PMC
 
[167]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685988
T. Jakobi, et al., “Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing”, Journal of Biotechnology, vol. 190, 2014, pp. 64-75.
PUB | DOI | WoS | PubMed | Europe PMC
 
[166]
2014 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2690122
N. Luhmann, et al., “Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework”, Proc. of BSB 2014, C. Sérgio, ed., LNBI, vol. 8826, Springer Verlag, 2014, pp.135-143.
PUB | DOI
 
[165]
2014 | Lexikoneintrag | Veröffentlicht | PUB-ID: 2693552
J. Stoye, “Suffix Tree Construction”, Encyclopedia of Algorithms, M.-Y. Kao, ed., Springer Verlag, 2014.
PUB | DOI
 
[164]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2693409
E. Fredrich, et al., “Metatranskriptomik der Mikrobiota aus der menschlichen Achselhöhle”, BIOspektrum, vol. 20, 2014, pp. 294-296.
PUB | DOI
 
[163]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2643941
N. Hoffmann, et al., “BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry”, Bioinformatics, vol. 30, 2014, pp. 988-995.
PUB | DOI | WoS | PubMed | Europe PMC
 
[162]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665333
B. Henrich, et al., “Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma”, PLoS ONE, vol. 9, 2014, pp. e92297.
PUB | DOI | WoS | PubMed | Europe PMC
 
[161]
2013 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2611641
M. Dias Vieira Braga and J. Stoye, “Restricted DCJ-Indel Model Revisited”, Advances in Bioinformatics and Computational Biology. BSB 2013, J.C. Setubal and N.F. Almeida, eds., Lecture Notes in Bioinformatics, vol. 8213, Cham: Springer Verlag, 2013, pp.36-46.
PUB | DOI
 
[160]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2611630
E. Willing, et al., “On the Inversion-Indel Distance”, BMC Bioinformatics, vol. 14, 2013, : S3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[159]
2013 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2611648
M. Dias Vieira Braga, et al., “The Potential of Family-Free Genome Comparison”, Models and Algorithms for Genome Evolution, C. Chauve, N. El-Mabrouk, and E. Tannier, eds., Computational Biology Series, vol. 19, Springer Verlag, 2013, pp.287-307.
PUB | DOI
 
[158]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2575011
C. Ander, et al., “metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences”, BMC Bioinformatics, vol. 14, 2013, pp. S2.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[157]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2641228
S. Jünemann, et al., “Corrigendum: Updating benchtop sequencing performance comparison”, Nature biotechnology, vol. 31, 2013, pp. 1148.
PUB | DOI | WoS | PubMed | Europe PMC
 
[156]
2013 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2611643
A. Bergeron and J. Stoye, “The Genesis of the DCJ Formula”, Models and Algorithms for Genome Evolution, C. Chauve, N. El-Mabrouk, and E. Tannier, eds., Computational Biology Series, vol. 19, Springer Verlag, 2013, pp.63-81.
PUB | DOI
 
[155]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2575361
P. Krell, et al., “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”, Haematologica, vol. 98, 2013, pp. 1388-1396.
PUB | DOI | WoS | PubMed | Europe PMC
 
[154]
2013 | Lexikoneintrag | Veröffentlicht | PUB-ID: 2577323
W. Gerlach and J. Stoye, “Taxonomic classification of metagenomic shotgun sequences with CARMA3”, Encyclopedia of Metagenomics, K.E. Nelson, ed., Springer Verlag, 2013.
PUB | DOI
 
[153]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2566922
S. Jünemann, et al., “Updating benchtop sequencing performance comparison”, Nature Biotechnology, vol. 31, 2013, pp. 294-296.
PUB | DOI | WoS | PubMed | Europe PMC
 
[152]
2013 | Konferenzband | Veröffentlicht | PUB-ID: 2616537
A. Darling and J. Stoye, eds., “Algorithms in Bioinformatics”, Lecture Notes in Bioinformatics, vol. 8126, 2013.
PUB | DOI
 
[151]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2611633
K. Jahn, et al., “Statistics for approximate gene clusters”, BMC Bioinformatics, vol. 14, 2013, pp. S14.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[150]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2548236
P. Schwientek, et al., “Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media”, Journal of Biotechnology, vol. 167, 2013, pp. 166-177.
PUB | DOI | WoS | PubMed | Europe PMC
 
[149]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2529202
M. Zakrzewski, et al., “MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets”, Journal of Biotechnology, vol. 167, 2013, pp. 156-165.
PUB | DOI | WoS | PubMed | Europe PMC
 
[148]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2512642
D. Dörr, A. Thévenin, and J. Stoye, “Gene family assignment-free comparative genomics”, BMC Bioinformatics, vol. 13, 2012, pp. S3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[147]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2517239
N. Hoffmann, et al., “Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets”, BMC Bioinformatics, vol. 13, 2012, pp. 21.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[146]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2512644
K. Jahn, H. Sudek, and J. Stoye, “Multiple genome comparison based on overlap regions of pairwise local alignments”, BMC Bioinformatics, vol. 13, 2012, pp. S7.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[145]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2486060
P. Schwientek, et al., “The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110”, BMC Genomics, vol. 13, 2012, : 112.
PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[144]
2012 | Konferenzband | Veröffentlicht | PUB-ID: 2510416
J. Kärkkäinen and J. Stoye, eds., “Combinatorial Pattern Matching”, Lecture Notes in Computer Science, vol. 7354, 2012.
PUB | DOI
 
[143]
2012 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2468382
N. Hoffmann and J. Stoye, “Generic Software Frameworks for GC-MS Based Metabolomics”, Metabolomics, U. Roessner, ed., InTech, 2012, pp.73-98.
PUB | PDF | DOI | Download (ext.)
 
[142]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2510984
R. Hilker, et al., “UniMoG - A unifying framework for genomic distance calculation and sorting based on DCJ”, Bioinformatics, vol. 28, 2012, pp. 2509-2511.
PUB | DOI | WoS | PubMed | Europe PMC
 
[141]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2517230
S. Jünemann, et al., “Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing”, PLoS ONE, vol. 7, 2012, pp. e41606.
PUB | DOI | WoS | PubMed | Europe PMC
 
[140]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2396558
M. Dias Vieira Braga, et al., “On the weight of indels in genomic distances”, BMC Bioinformatics, vol. 12, 2011, : S13.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[139]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2396509
M. Dias Vieira Braga, et al., “Genomic distance under gene substitutions”, BMC Bioinformatics, vol. 12, 2011, : S8.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[138]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091794
M. Dias Vieira Braga, E. Willing, and J. Stoye, “Double Cut and Join with Insertions and Deletions”, Journal of Computational Biology, vol. 18, 2011, pp. 1167-1184.
PUB | DOI | WoS | PubMed | Europe PMC
 
[137]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091790
J. Kovac, et al., “Restricted DCJ Model. Rearrangement Problems with Chromosome Reincorporation”, Journal of Computational Biology, vol. 18, 2011, pp. 1231-1241.
PUB | DOI | WoS | PubMed | Europe PMC
 
[136]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2354746
P. Schwientek, et al., “Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology”, Journal of Biotechnology, vol. 155, 2011, pp. 68-77.
PUB | DOI | WoS | PubMed | Europe PMC
 
[135]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2289952
J. Blom, et al., “Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming”, Bioinformatics, vol. 27, 2011, pp. 1351-1358.
PUB | DOI | WoS | PubMed | Europe PMC
 
[134]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918550
S. Heber, R. Mayr, and J. Stoye, “Common Intervals of Multiple Permutations”, Algorithmica, vol. 60, 2011, pp. 175-206.
PUB | DOI | WoS
 
[133]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2298170
W. Gerlach and J. Stoye, “Taxonomic classification of metagenomic shotgun sequences with CARMA3.”, Nucleic Acids Res, vol. 39, 2011, pp. e91.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[132]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897974
P.L. Erdős, L. Soukup, and J. Stoye, “Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance”, Applied Mathematics Letters, vol. 24, 2011, pp. 82-86.
PUB | DOI | WoS
 
[131]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091787
R. Wittler, et al., “Consistency of Sequence-Based Gene Clusters”, Journal of Computational Biology, vol. 18, 2011, pp. 1023-1039.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[130]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091779
F. Hufsky, et al., “Swiftly Computing Center Strings”, BMC Bioinformatics, vol. 12, 2011, pp. 106.
PUB | DOI | WoS | PubMed | Europe PMC
 
[129]
2010 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2907492
A. Bergeron, J. Mixtacki, and J. Stoye, “A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance”, Structure Discovery in Biology: Motifs, Networks & Phylogenies, A. Apostolico, A. Dress, and L. Parida, eds., Dagstuhl Seminar Proceedings, vol. 10231, Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany, 2010.
PUB | Download (ext.)
 
[128]
2010 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2445157
A. Bergeron, J. Mixtacki, and J. Stoye, “Computing the Genomic Distance in Linear Time”, Dagstuhl Seminar Proceedings: 10231 Abstracts Collection : Structure Discovery in Biology: Motifs, Networks & Phylogenies, A. Apostolico, A. Dress, and L. Parida, eds., vol. 10231, Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp.18.
PUB | Download (ext.)
 
[127]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1893893
P. Husemann and J. Stoye, “Phylogenetic Comparative Assembly”, Algorithms for Molecular Biology, vol. 5, 2010, pp. 3.
PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[126]
2010 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 1918836
S. Besenbacher, B. Schwikowski, and J. Stoye, “Indexing and Searching a Mass Spectrometry Database”, Algorithms and Applications: Essays Dedicated to Esko Ukkonen on the Occasion of His 60th Birthday, T. Elomaa, H. Mannila, and P. Orponen, eds., LNCS, vol. 6060, 2010, pp.62-76.
PUB | DOI
 
[125]
2010 | Report | Veröffentlicht | PUB-ID: 1966434
P.L. Erdős, L. Soukup, and J. Stoye, Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance, 2010.
PUB | arXiv
 
[124]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1966439
E. Trost, et al., “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”, BMC Genomics, vol. 11, 2010, : 728.
PUB | DOI | WoS | PubMed | Europe PMC
 
[123]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1795670
T. Wittkop, et al., “Partitioning Biological Data with Transitivity Clustering”, Nature Methods, vol. 7, 2010, pp. 419-420.
PUB | DOI | WoS | PubMed | Europe PMC
 
[122]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898012
G. Blin, D. Faye, and J. Stoye, “Finding Nested Common Intervals Efficiently”, Journal of Computational Biology, vol. 17, 2010, pp. 1183-1194.
PUB | DOI | WoS | PubMed | Europe PMC
 
[121]
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919217
R. Wittler and J. Stoye, “Consistency of Sequence-based Gene Clusters”, Proc. of Recomb-CG 2010, LNBI, vol. 6398, Springer Verlag, 2010, pp.252-263.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[120]
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1893890
P. Husemann and J. Stoye, “Repeat-aware Comparative Genome Assembly”, Proc. of GCB 2010, LNI, vol. P-173, 2010, pp.61-70.
PUB | Download (ext.)
 
[119]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1588556
P. Husemann and J. Stoye, “r2cat: Synteny Plots and Comparative Assembly”, Bioinformatics, vol. 26, 2010, pp. 570-571.
PUB | DOI | WoS | PubMed | Europe PMC
 
[118]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897997
A. Bergeron, P. Medvedev, and J. Stoye, “Rearrangement Models and Single-Cut Operations”, Journal of Computational Biology, vol. 17, 2010, pp. 1213-1225.
PUB | DOI | WoS | PubMed | Europe PMC
 
[117]
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919211
F. Hufsky, et al., “Swiftly Computing Center Strings”, Proc. of WABI 2010, LNBI, vol. 6293, 2010, pp.325-336.
PUB | DOI | WoS | PubMed | Europe PMC
 
[116]
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919216
J. Kovac, M. Dias Vieira Braga, and J. Stoye, “The Problem of Chromosome Reincorporation in DCJ Sorting and Halving”, Proc. of Recomb-CG 2010, LNBI, vol. 6398, 2010, pp.13-24.
PUB | DOI
 
[115]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898025
M. Dias Vieira Braga and J. Stoye, “The Solution Space of Sorting by DCJ”, Journal of Computational Biology, vol. 17, 2010, pp. 1145-1165.
PUB | DOI | WoS | PubMed | Europe PMC
 
[114]
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919215
M. Dias Vieira Braga, E. Willing, and J. Stoye, “Genomic Distance with DCJ and Indels”, Proc. of WABI 2010, LNBI, vol. 6293, 2010, pp.90-101.
PUB | DOI
 
[113]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1589663
A. Bergeron, J. Mixtacki, and J. Stoye, “A New Linear Time Algorithm to Compute the Genomic Distance via the Double Cut and Join Distance”, Theoretical Computer Science, vol. 410, 2009, pp. 5300-5316.
PUB | DOI | WoS
 
[112]
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919206
M. Dias Vieira Braga and J. Stoye, “Counting All DCJ Sorting Scenarios”, Proc. of Recomb-CG 2009, LNBI, vol. 5817, 2009, pp.36-47.
PUB | DOI
 
[111]
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919207
G. Blin and J. Stoye, “Finding Nested Common Intervals Efficiently”, Proc. of Recomb-CG 2009, LNBI, vol. 5817, 2009, pp.59-69.
PUB | DOI | WoS | PubMed | Europe PMC
 
[110]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898137
K. Jahn and J. Stoye, “Approximative Gencluster und ihre Anwendung in der komparativen Genomik”, Informatik-Spektrum, vol. 32, 2009, pp. 288-300.
PUB | DOI
 
[109]
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1893884
P. Husemann and J. Stoye, “Phylogenetic Comparative Assembly”, Proc. of WABI 2009, LNBI, vol. 5724, 2009, pp.145-156.
PUB | DOI | WoS | PubMed | Europe PMC
 
[108]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1591507
J. Stoye and R. Wittler, “A Unified Approach for Reconstructing Ancient Gene Clusters”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, 2009, pp. 387-400.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[107]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1589098
W. Gerlach, et al., “WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads”, BMC Bioinformatics, vol. 10, 2009, pp. 430.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[106]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1590204
M. Brudno, et al., “A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG)”, BIOINFORMATICS, vol. 25, 2009, pp. 2863-2864.
PUB | DOI | WoS | PubMed | Europe PMC
 
[105]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898105
S. Böcker, et al., “Computation of Median Gene Clusters”, Journal of Computational Biology, vol. 16, 2009, pp. 1085-1099.
PUB | DOI | WoS | PubMed | Europe PMC
 
[104]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1591319
N. Hoffmann and J. Stoye, “ChromA: signal-based retention time alignment for chromatography-mass spectrometry data”, Bioinformatics, vol. 25, 2009, pp. 2080-2081.
PUB | DOI | WoS | PubMed | Europe PMC
 
[103]
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919209
P. Medvedev and J. Stoye, “Rearrangement Models and Single-Cut Operations”, Comparative Genomics : International Workshop, RECOMB-CG 2009, Budapest, Hungary, September 27-29, 2009. Proceedings, Lecture Notes in Computer Science, vol. 5817, Berlin, Heidelberg: Springer, 2009, pp.84-97.
PUB | DOI
 
[102]
2009 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 1918945
J. Stoye, “Computational Short Read Metagenomics”, Presented at the JOBIM 2009, Nantes, France, 2009.
PUB
 
[101]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1634447
T. Bekel, et al., “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”, Journal of Biotechnology, vol. 140, 2009, pp. 3-12.
PUB | DOI | WoS | PubMed | Europe PMC
 
[100]
2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919198
J.A.A. Quitzau and J. Stoye, “Detecting Repeat Families in Incompletely Sequenced Genomes”, Proc. of WABI 2008, LNBI, vol. 5251, 2008, pp.342-353.
PUB | DOI
 
[99]
2008 | Report | PUB-ID: 1970459
J.A.A. Quitzau and J. Stoye, A space efficient representation for sparse de Bruijn subgraphs, Forschungsberichte der Technischen Fakultät, Abteilung Informationstechnik / Universität Bielefeld, Bielefeld: Technische Fakultät der Universität Bielefeld, 2008.
PUB | PDF
 
[98]
2008 | Report | PUB-ID: 1970461
T. Ejaz, S. Rahmann, and J. Stoye, Online Abelian Pattern Matching, Forschungsberichte der Technischen Fakultät, Abteilung Informationstechnik / Universität Bielefeld, Bielefeld: Technische Fakultät der Universität Bielefeld, 2008.
PUB | PDF
 
[97]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1636699
H. Neuweger, et al., “MeltDB: a software platform for the analysis and integration of metabolomics experiment data”, Bioinformatics, vol. 24, 2008, pp. 2726-2732.
PUB | DOI | WoS | PubMed | Europe PMC
 
[96]
2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919192
S. Böcker, et al., “Computation of Median Gene Clusters”, Proc. of RECOMB 2008, LNBI, vol. 4955, 2008, pp.331-345.
PUB | DOI
 
[95]
2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919200
A. Bergeron, J. Mixtacki, and J. Stoye, “On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios”, Proc. of Recomb-CG 2008, LNBI, vol. 5267, 2008, pp.226-240.
PUB | DOI
 
[94]
2008 | Lexikoneintrag | Veröffentlicht | PUB-ID: 1918834
J. Stoye, “Suffix Tree Construction in RAM (1997; Farach-Colton)”, Encyclopedia of Algorithms, M.-Y. Kao, ed., Springer Verlag, 2008, pp.925-928.
PUB | DOI
 
[93]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1587078
K.-B. Schürmann and J. Stoye, “Counting suffix arrays and strings”, THEORETICAL COMPUTER SCIENCE, vol. 395, 2008, pp. 220-234.
PUB | DOI | WoS
 
[92]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1586009
L. Krause, et al., “Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor”, JOURNAL OF BIOTECHNOLOGY, vol. 136, 2008, pp. 91-101.
PUB | DOI | WoS | PubMed | Europe PMC
 
[91]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1586785
S. Oehm, et al., “Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms”, NUCLEIC ACIDS RESEARCH, vol. 36, 2008, pp. W433-W437.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[90]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1783364
L. Krause, et al., “Phylogenetic classification of short environmental DNA fragments”, Nucleic Acids Research, vol. 36, 2008, pp. 2230-2239.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[89]
2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919195
A. Bergeron, J. Mixtacki, and J. Stoye, “HP Distance via Double Cut and Join Distance”, Combinatorial Pattern Matching. 19th Annual Symposium, CPM 2008, Pisa, Italy, June 18-20, 2008 Proceedings, Lecture Notes in Computer Science, 5029, 2008, pp.56-68.
PUB | DOI
 
[88]
2007 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 1918828
T. Schmidt and J. Stoye, “Chapter 12: Gecko and GhostFam - Rigorous and Efficient Gene Cluster Detection in Prokaryotic Genomes”, Comparative Genomics, Volume 2, N.H. Bergman, ed., Methods in Molecular Biology, vol. 396, Totowa, NJ: Humana Press Inc., 2007, pp.165-182.
PUB | DOI | PubMed | Europe PMC
 
[87]
2007 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918432
G. Didier, et al., “Character Sets of Strings”, Journal of Discrete Algorithms, vol. 5, 2007, pp. 330-340.
PUB | DOI
 
[86]
2007 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1595253
K.-B. Schürmann and J. Stoye, “An incomplex algorithm for fast suffix array construction”, SOFTWARE-PRACTICE & EXPERIENCE, vol. 37, 2007, pp. 309-329.
PUB | DOI | WoS
 
[85]
2007 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1783345
L. Krause, et al., “GISMO - gene identification using a support vector machine for ORF classification”, Nucleic Acids Research, vol. 35, 2007, pp. 540-549.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[84]
2007 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1630781
A. Mellmann, et al., “Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms”, BMC MICROBIOLOGY, vol. 7, 2007, pp. 98.
PUB | DOI | WoS | PubMed | Europe PMC
 
[83]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1599943
M. Sammeth, et al., “Panta rhei (QAlign2): an open graphical environment for sequence analysis”, BIOINFORMATICS, vol. 22, 2006, pp. 889-890.
PUB | DOI | WoS | PubMed | Europe PMC
 
[82]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1599570
K.R. Rasmussen, J. Stoye, and E.W. Myers, “Efficient q-gram filters for finding all epsilon-matches over a given length”, JOURNAL OF COMPUTATIONAL BIOLOGY, vol. 13, 2006, pp. 296-308.
PUB | DOI | WoS | PubMed | Europe PMC
 
[81]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1599574
A. Bergeron, J. Mixtacki, and J. Stoye, “On sorting by translocations”, JOURNAL OF COMPUTATIONAL BIOLOGY, vol. 13, 2006, pp. 567-578.
PUB | DOI | WoS | PubMed | Europe PMC
 
[80]
2006 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1596811
A. Bergeron, J. Mixtacki, and J. Stoye, “A Unifying View of Genome Rearrangements”, Proc. of WABI 2006, LNBI, vol. 4175, SPRINGER-VERLAG BERLIN, 2006, pp.163-173.
PUB | DOI | WoS
 
[79]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1597213
M. Sammeth and J. Stoye, “Comparing tandem repeats with duplications and excisions of variable degree”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 3, 2006, pp. 395-407.
PUB | DOI | WoS | PubMed | Europe PMC
 
[78]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1597313
A. Bergeron and J. Stoye, “On the similarity of sets of permutations and its applications to genome comparison”, JOURNAL OF COMPUTATIONAL BIOLOGY, vol. 13, 2006, pp. 1340-1354.
PUB | DOI | WoS | PubMed | Europe PMC
 
[77]
2006 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 1918946
J. Stoye, “Index Structures in Biological Sequence Analysis: From Simplicity to Complexity and Back”, Presented at the JOBIM 2006, Bordeaux, France, 2006.
PUB
 
[76]
2006 | Report | PUB-ID: 1970464
C. Chauve, et al., On Common Intervals with Errors, Forschungsberichte, Bielefeld: Technische Fakultät der Universität Bielefeld, 2006.
PUB | PDF
 
[75]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1631957
L. Krause, et al., “Finding novel genes in bacterial communities isolated from the environment”, BIOINFORMATICS, vol. 22, 2006, pp. e281-e289.
PUB | DOI | WoS | PubMed | Europe PMC
 
[74]
2005 | Report | PUB-ID: 1970470
M. Sammeth and J. Stoye, Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI), Forschungsberichte, Bielefeld: Technische Fakultät der Universität Bielefeld, 2005.
PUB | PDF | DOI
 
[73]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919012
K.-B. Schürmann and J. Stoye, “An Incomplex Algorithm for Fast Suffix Array Construction”, Proc. of ALENEX/ANALCO 2005, 2005, pp.77-85.
PUB
 
[72]
2005 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 1918824
A. Bergeron, J. Mixtacki, and J. Stoye, “Chapter 10: The Inversion Distance Problem”, Mathematics of Evolution and Phylogeny, O. Gascuel, ed., Oxford University Press, 2005, pp.262-290.
PUB
 
[71]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1603220
A. Bergeron, J. Mixtacki, and J. Stoye, “On Sorting by Translocations”, Proc. of RECOMB 2005, LNBI, vol. 3500, SPRINGER-VERLAG BERLIN, 2005, pp.615-629.
PUB | DOI | WoS
 
[70]
2005 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1775168
A. Krause, J. Stoye, and M. Vingron, “Large scale hierarchical clustering of protein sequences”, BMC Bioinformatics, vol. 6, 2005, pp. 15.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[69]
2005 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773302
D. Bartels, et al., “BACCardI - a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison”, Bioinformatics, vol. 21, 2005, pp. 853-859.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[68]
2005 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918947
S. Böcker and J. Stoye, “Informatische Methoden zur Protein-Identifikation”, LaborPraxis, vol. 29, 2005, pp. 24-26.
PUB
 
[67]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1601348
C. Bannert and J. Stoye, “Protein Annotation by Secondary Structure Based Alignments (PASSTA)”, Proc. of CompLife 2005, LNBI, vol. 3695, Springer-Verlag, 2005, pp.79-90.
PUB | DOI | WoS
 
[66]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1603216
K.R. Rasmussen, J. Stoye, and E.W. Myers, “Efficient q-Gram Filters for Finding All ε-Matches Over a Given Length”, Proc. of RECOMB 2005, LNBI, vol. 3500, SPRINGER-VERLAG BERLIN, 2005, pp.189-203.
PUB | DOI | WoS
 
[65]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1601361
M. Sammeth, et al., “Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI)”, Proc. of WABI 2005, LNBI, vol. 3692, SPRINGER-VERLAG BERLIN, 2005, pp.276-290.
PUB | DOI | WoS
 
[64]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919026
K.-B. Schürmann and J. Stoye, “Counting Suffix Arrays and Strings”, Proc. of SPIRE 2005, LNCS, vol. 3772, 2005, pp.55-66.
PUB | DOI
 
[63]
2005 | Report | PUB-ID: 1970472
K.-B. Schürmann and J. Stoye, Counting Suffix Arrays and Strings, Forschungsberichte, Bielefeld: Technische Fakultät der Universität Bielefeld, 2005.
PUB | PDF
 
[62]
2004 | Konferenzband | Veröffentlicht | PUB-ID: 1918823
R. Giegerich and J. Stoye, eds., “Proceedings of the German Conference on Bioinformatics, GCB 2004”, Lecture Notes in Informatics, vol. P-53, 2004.
PUB
 
[61]
2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1606286
M. Michael, C. Dieterich, and J. Stoye, “Suboptimal Local Alignments across Multiple Scoring Schemes”, Proc. of WABI 2004, LNBI, vol. 3240, SPRINGER-VERLAG BERLIN, 2004, pp.99-110.
PUB | DOI | WoS
 
[60]
2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1607260
T. Schmidt and J. Stoye, “Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences”, Proc. of CPM 2004, LNCS, vol. 3109, 2004, pp.347-358.
PUB | DOI | WoS
 
[59]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773554
D.A. Pollard, et al., “Correction: Benchmarking tools for the alignment of functional noncoding DNA”, BMC Bioinformatics, vol. 5, 2004, pp. 73.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[58]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773560
M. Cieliebak, et al., “Algorithmic complexity of protein identification: combinatorics of weighted strings”, Discrete Applied Mathematics, vol. 137, 2004, pp. 27-46.
PUB | PDF | DOI | WoS
 
[57]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773312
D.A. Pollard, et al., “Benchmarking tools for the alignment of functional noncoding DNA”, BMC Bioinformatics, vol. 5, 2004, pp. 6.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[56]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773569
D. Gusfield and J. Stoye, “Linear time algorithms for finding and representing all the tandem repeats in a string”, Journal of computer and system sciences, vol. 69, 2004, pp. 525-546.
PUB | PDF | DOI | WoS
 
[55]
2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1607263
A. Bergeron, J. Mixtacki, and J. Stoye, “Reversal Distance without Hurdles and Fortresses”, Proc. of CPM 2004, LNCS, vol. 3109, SPRINGER-VERLAG BERLIN, 2004, pp.388-399.
PUB | DOI | WoS
 
[54]
2003 | Report | PUB-ID: 1970475
K.-B. Schürmann and J. Stoye, Suffix Tree Construction and Storage with Limited Main Memory, Forschungsberichte, Bielefeld: Technische Fakultät der Universität Bielefeld, 2003.
PUB | PDF
 
[53]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1612664
S. Heber and J. Stoye, “The European Conference on Computational Biology”, Drug Discovery Today, vol. 8, 2003, pp. 113-114.
PUB | DOI | WoS | PubMed | Europe PMC
 
[52]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918949
R. Giegerich and J. Stoye, “Finden, fast ohne zu suchen: Indexstrukturen in der Bioinformatik”, Forschung an der Universität Bielefeld, vol. 26, 2003, pp. 63-68.
PUB
 
[51]
2003 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919005
C. Bannert and J. Stoye, “Evaluation of the Jumping Alignment Algorithm with Artificial and Biological Data”, Proc. of GCB 2003, 2003, pp.21-25.
PUB
 
[50]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1610397
R. Giegerich, S. Kurtz, and J. Stoye, “Efficient implementation of lazy suffix trees”, SOFTWARE-PRACTICE & EXPERIENCE, vol. 33, 2003, pp. 1035-1049.
PUB | PDF | DOI | WoS
 
[49]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1609403
M. Sammeth, B. Morgenstern, and J. Stoye, “Divide-and-conquer multiple alignment with segment-based constraints”, BIOINFORMATICS, vol. 19, 2003, pp. ii189-ii195.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[48]
2003 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1610433
A. Bergeron and J. Stoye, “On the similarity of sets of permutations and its applications to genome comparison”, Proc. of COCOON 2003, LNCS, vol. 2697, 2003, pp.68-79.
PUB | DOI | WoS
 
[47]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1610503
M. Sammeth, et al., “QAlign: quality-based multiple alignments with dynamic phylogenetic analysis”, BIOINFORMATICS, vol. 19, 2003, pp. 1592-1593.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[46]
2003 | Report | PUB-ID: 1970477
A. Bergeron and J. Stoye, On the Similarity of Sets of Permutations and its Applications to Genome Comparison, Forschungsberichte, Bielefeld: Technische Fakultät der Universität Bielefeld, 2003.
PUB | PDF
 
[45]
2002 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 1918951
J. Stoye, “Index Structures for Large Sequence Data: Suffix Trees and Affix Trees”, Lecture Notes in Informatics, S. Schubert, B. Reusch, and N. Jesse, eds., vol. P-20, 2002, pp.67-67.
PUB
 
[44]
2002 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919000
M. Cieliebak, et al., “Algorithmic Complexity of Protein Identification: Searching in Weighted Strings”, Proc. of IFIP TCS 2002, 2002, pp.143-156.
PUB
 
[43]
2002 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773578
R. Spang, M. Rehmsmeier, and J. Stoye, “A novel approach to remote homology detection: jumping alignments”, Journal of Computational Biology, vol. 9, 2002, pp. 747-760.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[42]
2002 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773332
J. Stoye and D. Gusfield, “Simple and flexible detection of contiguous repeats using a suffix tree”, Theoretical Computer Science, vol. 270, 2002, pp. 843-856.
PUB | PDF | DOI | WoS
 
[41]
2002 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773329
A. Bergeron, S. Heber, and J. Stoye, “Common intervals and sorting by reversals: a marriage of necessity”, Bioinformatics, vol. 18, 2002, pp. S54-S63.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[40]
2002 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918995
S. Heber, et al., “Resampling Methods in Physical Mapping”, Proc. of GfKl 2000, 2002, pp.437-444.
PUB
 
[39]
2001 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773335
S. Kurtz, et al., “REPuter: the manifold applications of repeat analysis on a genomic scale”, Nucleic Acids Research, vol. 29, 2001, pp. 4633-4642.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[38]
2001 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918992
S. Heber and J. Stoye, “Finding all Common Intervals of k Permutations”, Proc. of CPM 2001, LNCS, vol. 2089, 2001, pp.207-218.
PUB | DOI
 
[37]
2001 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1880197
S. Heber and J. Stoye, “Algorithms for Finding Gene Clusters”, Proc. of WABI 2001, LNCS, vol. 2149, Berlin: Sppringer, 2001, pp.252-263.
PUB | DOI
 
[36]
2001 | Report | PUB-ID: 1970479
M. Cieliebak, et al., Algorithmic Complexity of Protein Identification: Combinatorics of Weighted Strings, Technical Report, ETH Zürich, Dept. of Computer Science: 2001.
PUB
 
[35]
2000 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918981
S. Heber, et al., “Contig Selection in Physical Mapping”, Proc. of RECOMB 2000, 2000, pp.155-164.
PUB | DOI | WoS | PubMed | Europe PMC
 
[34]
2000 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 1918817
G.S. Brodal, et al., “Finding Maximal Pairs with Bounded Gap”, Matching Patterns (Journal of Discrete Algorithms), M. Crochemore and L. Gąsieniec, eds., 2000, pp.77-104.
PUB
 
[33]
2000 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773345
A. Krause, J. Stoye, and M. Vingron, “The SYSTERS protein sequence cluster set”, Nucleic Acids Research, vol. 28, 2000, pp. 270-272.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[32]
2000 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773572
S. Heber, et al., “Contig selection in physical mapping”, Journal of Computational Biology, vol. 7, 2000, pp. 395-408.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[31]
2000 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918985
R. Spang, M. Rehmsmeier, and J. Stoye, “Sequence Database Search Using Jumping Alignments”, Proc. of ISMB 2000, 2000, pp.367-375.
PUB | PubMed | Europe PMC
 
[30]
2000 | Report | PUB-ID: 1970490
J. Stoye, Affix Trees, Forschungsberichte, Technische Fakultät der Universität Bielefeld: 2000.
PUB | PDF
 
[29]
2000 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773341
K. Reinert, J. Stoye, and T. Will, “An iterative method for faster sum-of-pairs multiple sequence alignment”, Bioinformatics, vol. 16, 2000, pp. 808-814.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[28]
2000 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918988
S. Kurtz, et al., “Computation and Visualization of Degenerate Repeats in Complete Genomes”, Proc. of ISMB 2000, 2000, pp.228-238.
PUB | PubMed | Europe PMC
 
[27]
2000 | Konferenzband | Veröffentlicht | PUB-ID: 1918813
E. Bornberg-Bauer, et al., eds., Proceedings of the German Conference on Bioinformatics, GCB 2000, Berlin: Logos Verlag, 2000.
PUB
 
[26]
1999 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1620435
R. Giegerich, S. Kurtz, and J. Stoye, “Efficient implementation of lazy suffix trees”, Algorithm Engineering. 3rd International Workshop, WAE’99 London, UK, July 19–21, 1999 Proceedings, LNCS, vol. 1668, 1999, pp.30-42.
PUB | DOI | WoS
 
[25]
1999 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918978
K. Reinert, T. Will, and J. Stoye, “Combining Divide-and-Conquer, the A*-Algorithm, and Successive Realignment Approaches to Speed up Multiple Sequence Alignment”, Proc. of GCB 1999, 1999, pp.17-24.
PUB | Download (ext.)
 
[24]
1999 | Report | PUB-ID: 1970495
B. Morgenstern, J. Stoye, and A. Dress, Consistent Equivalence Relations: A Set-Theoretical Framework for Multiple Sequence Alignment, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld: 1999.
PUB
 
[23]
1999 | Report | PUB-ID: 1970509
G.S. Brodal, et al., Finding Maximal Pairs with Bounded Gap, Report, BRICS, Department of Computer Science, University of Aarhus: 1999.
PUB
 
[22]
1999 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918971
G.S. Brodal, et al., “Finding Maximal Pairs with Bounded Gap”, Proc. of CPM 1999, LNCS, vol. 1645, 1999, pp.134-149.
PUB | DOI
 
[21]
1998 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2488102
A. Dress, B. Morgenstern, and J. Stoye, “The Number of Standard and of Effective Multiple Alignments”, Appl. Math. Lett., vol. 11, 1998, pp. 43-49.
PUB
 
[20]
1998 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918538
M. Hildebrand and J. Stoye, “Die Bedeutung der Zusammenarbeit der Disziplinen in der Anwendung - erläutert anhand von Beispielen”, Der Mathematikunterricht, vol. 44, 1998, pp. 34-53.
PUB
 
[19]
1998 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1667771
J. Stoye, “Multiple sequence alignment with the Divide-and-Conquer method.”, Gene, vol. 211, 1998, pp. GC45-GC56.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[18]
1998 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1625402
J. Stoye, D. Evers, and F. Meyer, “Rose: generating sequence families”, BIOINFORMATICS, vol. 14, 1998, pp. 157-163.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[17]
1998 | Report | PUB-ID: 1970515
J. Stoye and D. Gusfield, Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree, Report, Department of Computer Science, University of California, Davis: 1998.
PUB
 
[16]
1998 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918964
J. Stoye and D. Gusfield, “Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version)”, Proc. of CPM 1998, LNCS, vol. 1448, 1998, pp.140-152.
PUB | DOI
 
[15]
1998 | Report | PUB-ID: 1970513
D. Gusfield and J. Stoye, Linear Time Algorithms for Finding and Representing all the Tandem Repeats in a String, Report, Department of Computer Science, University of California, Davis: 1998.
PUB
 
[14]
1997 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2488107
J. Stoye, V. Moulton, and A. Dress, “DCA: An efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment”, CABIOS, vol. 13, 1997, pp. 625-626.
PUB
 
[13]
1997 | Report | PUB-ID: 1970526
S.W. Perrey, et al., On Simultaneous versus Iterative Multiple Sequence Alignment, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld: 1997.
PUB
 
[12]
1997 | Report | PUB-ID: 1970517
J. Stoye, D. Evers, and F. Meyer, Rose: Generating Sequence Families, Forschungsberichte, Technische Fakultät der Universität Bielefeld: 1997.
PUB
 
[11]
1997 | Report | PUB-ID: 1970529
G. Brinkmann, et al., Two Applications of the Divide & Conquer Principle in the Molecular Sciences, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld: 1997.
PUB
 
[10]
1997 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1667885
J. Stoye, D. Evers, and F. Meyer, “Generating benchmarks for multiple sequence alignments and phylogenetic reconstructions”, Proc. of ISMB 1997, 1997, pp.303-306.
PUB | PubMed | Europe PMC
 
[9]
1997 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773355
J. Stoye, S.W. Perrey, and A. Dress, “Improving the divide-and-conquer approach to sum-of-pairs multiple sequence alignment”, Applied mathematics letters, vol. 10, 1997, pp. 67-73.
PUB | PDF | DOI | WoS
 
[8]
1997 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773358
G. Brinkmann, et al., “Two applications of the Divide & Conquer principle in the molecular sciences”, Mathematical programming, vol. 79, 1997, pp. 71-97.
PUB | DOI | WoS
 
[7]
1997 | Report | PUB-ID: 1970523
A. Dress, B. Morgenstern, and J. Stoye, On the Number of Standard and Effective Multiple Alignments, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld: 1997.
PUB
 
[6]
1997 | Report | PUB-ID: 1970520
S.W. Perrey, J. Stoye, and V. Moulton, FDCA: Fast and Accurate Approximation to Sum-of-Pairs Score Optimal Multiple Sequence Alignment, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld: 1997.
PUB
 
[5]
1997 | Report | PUB-ID: 1970532
J. Stoye, Divide-and-Conquer Multiple Sequence Alignment, Forschungsberichte, Technische Fakultät der Universität Bielefeld: 1997.
PUB
 
[4]
1996 | Report | PUB-ID: 1970533
S.W. Perrey and J. Stoye, Fast Approximation to the NP-hard Problem of Multiple Sequence Alignment, Information and Mathematical Sciences Reports, Series B, Dept. of Mathematics, Massey University, Palmerston North, New Zealand: 1996.
PUB
 
[3]
1996 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773351
U. Tönges, et al., “A general method for fast multiple sequence alignment”, Gene, vol. 172, 1996, pp. GC33-GC41.
PUB | DOI | WoS | PubMed | Europe PMC
 
[2]
1996 | Report | PUB-ID: 1970535
J. Stoye, A. Dress, and S.W. Perrey, Improving the Divide-and-Conquer Approach to Sum-of-Pairs Multiple Sequence Alignment, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld: 1996.
PUB
 
[1]
1996 | Report | PUB-ID: 1970537
U. Tönges, et al., A General Method for Fast Multiple Sequence Alignment, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld: 1996.
PUB
 

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[205]
2019 | Zeitschriftenaufsatz | Im Druck | PUB-ID: 2937712
D. Rubert, et al., “Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants”, BMC Genomics, In Press.
PUB
 
[204]
2019 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2937148
J. Alanko, et al., “Finding All Maximal Perfect Haplotype Blocks in Linear Time”, Proceedings of WABI 2019, Leibniz International Proceedings in Informatics. LIPIcs, vol. 143, Dagstuhl: Schloss Dagstuhl, Leibniz-Zentrum für Informatik , 2019, pp.8:1-8:9.
PUB | DOI
 
[203]
2019 | Herausgeber*in Sammelwerk | Veröffentlicht | PUB-ID: 2935998
J.C. Setubal, J. Stoye, and B.E. Dutilh, eds., Computational Methods for Microbiome Analysis, Frontiers Research Topics, Lausanne: Frontiers Media, 2019.
PUB | Download (ext.)
 
[202]
2019 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2932883
D. Dörr and J. Stoye, “A Perspective on Comparative and Functional Genomics”, Bioinformatics and Phylogenetics, T. Warnow, ed., Computational Biology, vol. 29, Cham: Springer , 2019, pp.361-372.
PUB | DOI
 
[201]
2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2932884
H. Oey, et al., “Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium”, PLOS Pathogens, vol. 15, 2019, : e1007513.
PUB | DOI | WoS | PubMed | Europe PMC
 
[200]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919005
T. Schulz, J. Stoye, and D. Dörr, “GraphTeams. A method for discovering spatial gene clusters in Hi-C sequencing data”, BMC Genomics, vol. 19, 2018, : 308.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[199]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919006
D. Rubert, et al., “Computing the family-free DCJ similarity”, BMC Bioinformatics, vol. 19, 2018, : 152.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[198]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2918481
N. Luhmann, et al., “Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 15, 2018, pp. 2094-2100.
PUB | DOI | WoS | PubMed | Europe PMC
 
[197]
2018 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2930445
L. Cunha, et al., “Identifying Maximal Perfect Haplotype Blocks”, Proceedings of BSB 2018, LNBI, vol. 11228, Springer Verlag, 2018, pp.26-37.
PUB | DOI
 
[196]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2930268
G. Holley, et al., “Dynamic Alignment-Free and Reference-Free Read Compression”, JOURNAL OF COMPUTATIONAL BIOLOGY, vol. 25, 2018, pp. 825-836.
PUB | DOI | WoS | PubMed | Europe PMC
 
[195]
2018 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2913921
T. Zekic, G. Holley, and J. Stoye, “Pan-genome Storage and Analysis Techniques”, Comparative Genomics. Methods and Protocols, J.C. Setubal, P. Stadler, and J. Stoye, eds., Methods in Molecular Biology, vol. 1704, New York: Springer Verlag, 2018, pp.29-53.
PUB
 
[194]
2018 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2913922
D. Dörr, P. Feijão, and J. Stoye, “Family-Free Genome Comparison”, Comparative Genomics: Methods and Protocols, J.C. Setubal, P. Stadler, and J. Stoye, eds., Methods in Molecular Biology, vol. 1704, New York: Springer Verlag, 2018, pp.331-342.
PUB
 
[193]
2018 | Herausgeber*in Sammelwerk | Veröffentlicht | PUB-ID: 2913920
J.C. Setubal, P. Stadler, and J. Stoye, eds., Comparative Genomics: Methods and Protocols, Methods in Molecular Biology, vol. 1704, New York: Springer Verlag, 2018.
PUB
 
[192]
2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919012
S. Jaenicke, et al., “Flexible metagenome analysis using the MGX framework”, Microbiome, vol. 6, 2018, : 76.
PUB | DOI | WoS | PubMed | Europe PMC
 
[191]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2913556
S. Jünemann, et al., “Bioinformatics for NGS-based metagenomics and the application to biogas research”, Journal of Biotechnology, vol. 261, 2017, pp. 10-23.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[190]
2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2913015
D. Rubert, et al., “Algorithms for Computing the Family-Free Genomic Similarity under DCJ”, Comparative Genomics. RECOMB-CG 2017, J. Meidanis and L. Nakhleh, eds., Lecture Notes in Bioinformatics, vol. 10562, Cham: Springer Verlag, 2017, pp.76-100.
PUB | DOI
 
[189]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909057
D. Rubert, et al., “Approximating the DCJ distance of balanced genomes in linear time”, Algorithms for Molecular Biology, vol. 12, 2017, : 3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[188]
2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2909409
L. Cunha, et al., “Fast and Simple Jumbled Indexing for Binary Run-Length Encoded Strings”, Proceedings of CPM 2017, LIPIcs, vol. 78, 2017, pp.19:1-19:9.
PUB | DOI
 
[187]
2017 | Preprint | Veröffentlicht | PUB-ID: 2908521
L. Cunha, et al., “Faster Jumbled Indexing for Binary Run-Length Encoded Strings”, arXiv: 1702.01280, 2017.
PUB
 
[186]
2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2907587
G. Holley, et al., “Dynamic Alignment-Free and Reference-Free Read Compression”, Proceedings of RECOMB 2017, Lecture Notes in Bioinformatics, vol. 10229, 2017, pp.50-65.
PUB | DOI
 
[185]
2017 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2913016
T. Schulz, J. Stoye, and D. Dörr, “Finding Teams in Graphs and its Application to Spatial Gene Cluster Discovery”, Proceedings of RECOMB-CG 2017, Lecture Notes in Bioinformatics, vol. 1704, Berlin: Springer Verlag, 2017, pp.197-212.
PUB | DOI
 
[184]
2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2909967
D. Dörr, et al., “New Genome Similarity Measures based on Conserved Gene Adjacencies”, Journal of Computational Biology, vol. 24, 2017, pp. 616-634.
PUB | DOI | WoS | PubMed | Europe PMC
 
[183]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2905930
S. Winter, et al., “Finding approximate gene clusters with GECKO 3”, Nucleic Acids Research, vol. 44, 2016, pp. 9600-9610.
PUB | DOI | WoS | PubMed | Europe PMC
 
[182]
2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2903708
D. Rubert, et al., “A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates”, Algorithms in Bioinformatics. WABI 2016, M. Frith and C.N. Storm Pedersen, eds., Lecture Notes in Bioinformatics, vol. 9838, Cham: Springer, 2016, pp.293-306.
PUB | DOI
 
[181]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900129
G. Holley, R. Wittler, and J. Stoye, “Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage”, Algorithms for Molecular Biology, vol. 11, 2016, : 3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[180]
2016 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2900111
L.A.B. Kowada, et al., “New Genome Similarity Measures based on Conserved Gene Adjacencies”, Research in Computational Molecular Biology. RECOMB 2016, M. Singh, ed., Lecture Notes in Bioinformatics (LNBI), vol. 9649, Springer, 2016, pp.204-224.
PUB | DOI
 
[179]
2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900421
L. Krause, et al., “Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma”, Carcinogenesis, vol. 37, 2016, pp. 356-365.
PUB | DOI | WoS | PubMed | Europe PMC
 
[178]
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2677844
M. Dias Vieira Braga and J. Stoye, “Sorting linear genomes with rearrangements and indels”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 12, 2015, pp. 500-506.
PUB | DOI | WoS | PubMed | Europe PMC
 
[177]
2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2726366
F.H. Viduani Martinez, et al., “On the family-free DCJ distance and similarity”, Algorithms for Molecular Biology, vol. 10, 2015, : 13.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[176]
2015 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2757497
G. Holley, R. Wittler, and J. Stoye, “Bloom Filter Trie - a data structure for pan-genome storage”, Proceedings of WABI 2015, LNBI, vol. 9289, 2015, pp.217-230.
PUB
 
[175]
2015 | Konferenzband | Veröffentlicht | PUB-ID: 2780229
J. Meidanis and J. Stoye, eds., “Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Bioinformatics”, BMC Bioinformatics, vol. 16, 2015.
PUB | Download (ext.)
 
[174]
2015 | Konferenzband | Veröffentlicht | PUB-ID: 2780232
J. Meidanis and J. Stoye, eds., “Proceedings of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics: Genomics”, BMC Genomics, vol. 16, 2015.
PUB | Download (ext.)
 
[173]
2014 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2684241
F.H. Viduani Martinez, et al., “On the family-free DCJ distance”, Algorithms in Bioinformatics. WABI 2014, D. Brown and B. Morgenstern, eds., Lecture Notes in Bioinformatics, vol. 8701, Berlin ; Heidelberg: Springer Verlag, 2014, pp.174-186.
PUB | DOI
 
[172]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2687033
D. Dörr, et al., “Identifying Gene Clusters by Discovering Common Intervals in Indeterminate Strings”, BMC Genomics, vol. 15, 2014, pp. S2.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[171]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685362
M. Lechner, et al., “Orthology Detection Combining Clustering and Synteny for Very Large Datasets”, PLoS ONE, vol. 9, 2014, pp. e105015.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[170]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2689773
S. Jünemann, et al., “GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers”, PLOS ONE, vol. 9, 2014, pp. e107014.
PUB | DOI | WoS | PubMed | Europe PMC
 
[169]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2674387
R. Hilker, et al., “ReadXplorer - Visualization and Analysis of Mapped Sequences”, Bioinformatics, vol. 30, 2014, pp. 2247-2254.
PUB | DOI | WoS | PubMed | Europe PMC
 
[168]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665038
P. Schwientek, et al., “Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts”, Journal of Biotechnology, vol. 190, 2014, pp. 85-95.
PUB | DOI | WoS | PubMed | Europe PMC
 
[167]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2685988
T. Jakobi, et al., “Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing”, Journal of Biotechnology, vol. 190, 2014, pp. 64-75.
PUB | DOI | WoS | PubMed | Europe PMC
 
[166]
2014 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2690122
N. Luhmann, et al., “Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework”, Proc. of BSB 2014, C. Sérgio, ed., LNBI, vol. 8826, Springer Verlag, 2014, pp.135-143.
PUB | DOI
 
[165]
2014 | Lexikoneintrag | Veröffentlicht | PUB-ID: 2693552
J. Stoye, “Suffix Tree Construction”, Encyclopedia of Algorithms, M.-Y. Kao, ed., Springer Verlag, 2014.
PUB | DOI
 
[164]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2693409
E. Fredrich, et al., “Metatranskriptomik der Mikrobiota aus der menschlichen Achselhöhle”, BIOspektrum, vol. 20, 2014, pp. 294-296.
PUB | DOI
 
[163]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2643941
N. Hoffmann, et al., “BiPACE 2D – Graph-based multiple alignment for comprehensive two-dimensional gas chromatography–mass spectrometry”, Bioinformatics, vol. 30, 2014, pp. 988-995.
PUB | DOI | WoS | PubMed | Europe PMC
 
[162]
2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2665333
B. Henrich, et al., “Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma”, PLoS ONE, vol. 9, 2014, pp. e92297.
PUB | DOI | WoS | PubMed | Europe PMC
 
[161]
2013 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2611641
M. Dias Vieira Braga and J. Stoye, “Restricted DCJ-Indel Model Revisited”, Advances in Bioinformatics and Computational Biology. BSB 2013, J.C. Setubal and N.F. Almeida, eds., Lecture Notes in Bioinformatics, vol. 8213, Cham: Springer Verlag, 2013, pp.36-46.
PUB | DOI
 
[160]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2611630
E. Willing, et al., “On the Inversion-Indel Distance”, BMC Bioinformatics, vol. 14, 2013, : S3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[159]
2013 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2611648
M. Dias Vieira Braga, et al., “The Potential of Family-Free Genome Comparison”, Models and Algorithms for Genome Evolution, C. Chauve, N. El-Mabrouk, and E. Tannier, eds., Computational Biology Series, vol. 19, Springer Verlag, 2013, pp.287-307.
PUB | DOI
 
[158]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2575011
C. Ander, et al., “metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences”, BMC Bioinformatics, vol. 14, 2013, pp. S2.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[157]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2641228
S. Jünemann, et al., “Corrigendum: Updating benchtop sequencing performance comparison”, Nature biotechnology, vol. 31, 2013, pp. 1148.
PUB | DOI | WoS | PubMed | Europe PMC
 
[156]
2013 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2611643
A. Bergeron and J. Stoye, “The Genesis of the DCJ Formula”, Models and Algorithms for Genome Evolution, C. Chauve, N. El-Mabrouk, and E. Tannier, eds., Computational Biology Series, vol. 19, Springer Verlag, 2013, pp.63-81.
PUB | DOI
 
[155]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2575361
P. Krell, et al., “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”, Haematologica, vol. 98, 2013, pp. 1388-1396.
PUB | DOI | WoS | PubMed | Europe PMC
 
[154]
2013 | Lexikoneintrag | Veröffentlicht | PUB-ID: 2577323
W. Gerlach and J. Stoye, “Taxonomic classification of metagenomic shotgun sequences with CARMA3”, Encyclopedia of Metagenomics, K.E. Nelson, ed., Springer Verlag, 2013.
PUB | DOI
 
[153]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2566922
S. Jünemann, et al., “Updating benchtop sequencing performance comparison”, Nature Biotechnology, vol. 31, 2013, pp. 294-296.
PUB | DOI | WoS | PubMed | Europe PMC
 
[152]
2013 | Konferenzband | Veröffentlicht | PUB-ID: 2616537
A. Darling and J. Stoye, eds., “Algorithms in Bioinformatics”, Lecture Notes in Bioinformatics, vol. 8126, 2013.
PUB | DOI
 
[151]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2611633
K. Jahn, et al., “Statistics for approximate gene clusters”, BMC Bioinformatics, vol. 14, 2013, pp. S14.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[150]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2548236
P. Schwientek, et al., “Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media”, Journal of Biotechnology, vol. 167, 2013, pp. 166-177.
PUB | DOI | WoS | PubMed | Europe PMC
 
[149]
2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2529202
M. Zakrzewski, et al., “MetaSAMS - A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets”, Journal of Biotechnology, vol. 167, 2013, pp. 156-165.
PUB | DOI | WoS | PubMed | Europe PMC
 
[148]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2512642
D. Dörr, A. Thévenin, and J. Stoye, “Gene family assignment-free comparative genomics”, BMC Bioinformatics, vol. 13, 2012, pp. S3.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[147]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2517239
N. Hoffmann, et al., “Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets”, BMC Bioinformatics, vol. 13, 2012, pp. 21.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[146]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2512644
K. Jahn, H. Sudek, and J. Stoye, “Multiple genome comparison based on overlap regions of pairwise local alignments”, BMC Bioinformatics, vol. 13, 2012, pp. S7.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[145]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2486060
P. Schwientek, et al., “The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110”, BMC Genomics, vol. 13, 2012, : 112.
PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[144]
2012 | Konferenzband | Veröffentlicht | PUB-ID: 2510416
J. Kärkkäinen and J. Stoye, eds., “Combinatorial Pattern Matching”, Lecture Notes in Computer Science, vol. 7354, 2012.
PUB | DOI
 
[143]
2012 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2468382
N. Hoffmann and J. Stoye, “Generic Software Frameworks for GC-MS Based Metabolomics”, Metabolomics, U. Roessner, ed., InTech, 2012, pp.73-98.
PUB | PDF | DOI | Download (ext.)
 
[142]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2510984
R. Hilker, et al., “UniMoG - A unifying framework for genomic distance calculation and sorting based on DCJ”, Bioinformatics, vol. 28, 2012, pp. 2509-2511.
PUB | DOI | WoS | PubMed | Europe PMC
 
[141]
2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2517230
S. Jünemann, et al., “Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing”, PLoS ONE, vol. 7, 2012, pp. e41606.
PUB | DOI | WoS | PubMed | Europe PMC
 
[140]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2396558
M. Dias Vieira Braga, et al., “On the weight of indels in genomic distances”, BMC Bioinformatics, vol. 12, 2011, : S13.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[139]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2396509
M. Dias Vieira Braga, et al., “Genomic distance under gene substitutions”, BMC Bioinformatics, vol. 12, 2011, : S8.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[138]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091794
M. Dias Vieira Braga, E. Willing, and J. Stoye, “Double Cut and Join with Insertions and Deletions”, Journal of Computational Biology, vol. 18, 2011, pp. 1167-1184.
PUB | DOI | WoS | PubMed | Europe PMC
 
[137]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091790
J. Kovac, et al., “Restricted DCJ Model. Rearrangement Problems with Chromosome Reincorporation”, Journal of Computational Biology, vol. 18, 2011, pp. 1231-1241.
PUB | DOI | WoS | PubMed | Europe PMC
 
[136]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2354746
P. Schwientek, et al., “Sequencing of high G + C microbial genomes using the ultrafast pyrosequencing technology”, Journal of Biotechnology, vol. 155, 2011, pp. 68-77.
PUB | DOI | WoS | PubMed | Europe PMC
 
[135]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2289952
J. Blom, et al., “Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming”, Bioinformatics, vol. 27, 2011, pp. 1351-1358.
PUB | DOI | WoS | PubMed | Europe PMC
 
[134]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918550
S. Heber, R. Mayr, and J. Stoye, “Common Intervals of Multiple Permutations”, Algorithmica, vol. 60, 2011, pp. 175-206.
PUB | DOI | WoS
 
[133]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2298170
W. Gerlach and J. Stoye, “Taxonomic classification of metagenomic shotgun sequences with CARMA3.”, Nucleic Acids Res, vol. 39, 2011, pp. e91.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[132]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897974
P.L. Erdős, L. Soukup, and J. Stoye, “Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance”, Applied Mathematics Letters, vol. 24, 2011, pp. 82-86.
PUB | DOI | WoS
 
[131]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091787
R. Wittler, et al., “Consistency of Sequence-Based Gene Clusters”, Journal of Computational Biology, vol. 18, 2011, pp. 1023-1039.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[130]
2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091779
F. Hufsky, et al., “Swiftly Computing Center Strings”, BMC Bioinformatics, vol. 12, 2011, pp. 106.
PUB | DOI | WoS | PubMed | Europe PMC
 
[129]
2010 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2907492
A. Bergeron, J. Mixtacki, and J. Stoye, “A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance”, Structure Discovery in Biology: Motifs, Networks & Phylogenies, A. Apostolico, A. Dress, and L. Parida, eds., Dagstuhl Seminar Proceedings, vol. 10231, Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany, 2010.
PUB | Download (ext.)
 
[128]
2010 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 2445157
A. Bergeron, J. Mixtacki, and J. Stoye, “Computing the Genomic Distance in Linear Time”, Dagstuhl Seminar Proceedings: 10231 Abstracts Collection : Structure Discovery in Biology: Motifs, Networks & Phylogenies, A. Apostolico, A. Dress, and L. Parida, eds., vol. 10231, Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp.18.
PUB | Download (ext.)
 
[127]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1893893
P. Husemann and J. Stoye, “Phylogenetic Comparative Assembly”, Algorithms for Molecular Biology, vol. 5, 2010, pp. 3.
PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[126]
2010 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 1918836
S. Besenbacher, B. Schwikowski, and J. Stoye, “Indexing and Searching a Mass Spectrometry Database”, Algorithms and Applications: Essays Dedicated to Esko Ukkonen on the Occasion of His 60th Birthday, T. Elomaa, H. Mannila, and P. Orponen, eds., LNCS, vol. 6060, 2010, pp.62-76.
PUB | DOI
 
[125]
2010 | Report | Veröffentlicht | PUB-ID: 1966434
P.L. Erdős, L. Soukup, and J. Stoye, Balanced Vertices in Trees and a Simpler Algorithm to Compute the Genomic Distance, 2010.
PUB | arXiv
 
[124]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1966439
E. Trost, et al., “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”, BMC Genomics, vol. 11, 2010, : 728.
PUB | DOI | WoS | PubMed | Europe PMC
 
[123]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1795670
T. Wittkop, et al., “Partitioning Biological Data with Transitivity Clustering”, Nature Methods, vol. 7, 2010, pp. 419-420.
PUB | DOI | WoS | PubMed | Europe PMC
 
[122]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898012
G. Blin, D. Faye, and J. Stoye, “Finding Nested Common Intervals Efficiently”, Journal of Computational Biology, vol. 17, 2010, pp. 1183-1194.
PUB | DOI | WoS | PubMed | Europe PMC
 
[121]
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919217
R. Wittler and J. Stoye, “Consistency of Sequence-based Gene Clusters”, Proc. of Recomb-CG 2010, LNBI, vol. 6398, Springer Verlag, 2010, pp.252-263.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[120]
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1893890
P. Husemann and J. Stoye, “Repeat-aware Comparative Genome Assembly”, Proc. of GCB 2010, LNI, vol. P-173, 2010, pp.61-70.
PUB | Download (ext.)
 
[119]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1588556
P. Husemann and J. Stoye, “r2cat: Synteny Plots and Comparative Assembly”, Bioinformatics, vol. 26, 2010, pp. 570-571.
PUB | DOI | WoS | PubMed | Europe PMC
 
[118]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1897997
A. Bergeron, P. Medvedev, and J. Stoye, “Rearrangement Models and Single-Cut Operations”, Journal of Computational Biology, vol. 17, 2010, pp. 1213-1225.
PUB | DOI | WoS | PubMed | Europe PMC
 
[117]
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919211
F. Hufsky, et al., “Swiftly Computing Center Strings”, Proc. of WABI 2010, LNBI, vol. 6293, 2010, pp.325-336.
PUB | DOI | WoS | PubMed | Europe PMC
 
[116]
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919216
J. Kovac, M. Dias Vieira Braga, and J. Stoye, “The Problem of Chromosome Reincorporation in DCJ Sorting and Halving”, Proc. of Recomb-CG 2010, LNBI, vol. 6398, 2010, pp.13-24.
PUB | DOI
 
[115]
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898025
M. Dias Vieira Braga and J. Stoye, “The Solution Space of Sorting by DCJ”, Journal of Computational Biology, vol. 17, 2010, pp. 1145-1165.
PUB | DOI | WoS | PubMed | Europe PMC
 
[114]
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919215
M. Dias Vieira Braga, E. Willing, and J. Stoye, “Genomic Distance with DCJ and Indels”, Proc. of WABI 2010, LNBI, vol. 6293, 2010, pp.90-101.
PUB | DOI
 
[113]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1589663
A. Bergeron, J. Mixtacki, and J. Stoye, “A New Linear Time Algorithm to Compute the Genomic Distance via the Double Cut and Join Distance”, Theoretical Computer Science, vol. 410, 2009, pp. 5300-5316.
PUB | DOI | WoS
 
[112]
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919206
M. Dias Vieira Braga and J. Stoye, “Counting All DCJ Sorting Scenarios”, Proc. of Recomb-CG 2009, LNBI, vol. 5817, 2009, pp.36-47.
PUB | DOI
 
[111]
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919207
G. Blin and J. Stoye, “Finding Nested Common Intervals Efficiently”, Proc. of Recomb-CG 2009, LNBI, vol. 5817, 2009, pp.59-69.
PUB | DOI | WoS | PubMed | Europe PMC
 
[110]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898137
K. Jahn and J. Stoye, “Approximative Gencluster und ihre Anwendung in der komparativen Genomik”, Informatik-Spektrum, vol. 32, 2009, pp. 288-300.
PUB | DOI
 
[109]
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1893884
P. Husemann and J. Stoye, “Phylogenetic Comparative Assembly”, Proc. of WABI 2009, LNBI, vol. 5724, 2009, pp.145-156.
PUB | DOI | WoS | PubMed | Europe PMC
 
[108]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1591507
J. Stoye and R. Wittler, “A Unified Approach for Reconstructing Ancient Gene Clusters”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, 2009, pp. 387-400.
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
[107]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1589098
W. Gerlach, et al., “WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads”, BMC Bioinformatics, vol. 10, 2009, pp. 430.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[106]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1590204
M. Brudno, et al., “A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG)”, BIOINFORMATICS, vol. 25, 2009, pp. 2863-2864.
PUB | DOI | WoS | PubMed | Europe PMC
 
[105]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898105
S. Böcker, et al., “Computation of Median Gene Clusters”, Journal of Computational Biology, vol. 16, 2009, pp. 1085-1099.
PUB | DOI | WoS | PubMed | Europe PMC
 
[104]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1591319
N. Hoffmann and J. Stoye, “ChromA: signal-based retention time alignment for chromatography-mass spectrometry data”, Bioinformatics, vol. 25, 2009, pp. 2080-2081.
PUB | DOI | WoS | PubMed | Europe PMC
 
[103]
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919209
P. Medvedev and J. Stoye, “Rearrangement Models and Single-Cut Operations”, Comparative Genomics : International Workshop, RECOMB-CG 2009, Budapest, Hungary, September 27-29, 2009. Proceedings, Lecture Notes in Computer Science, vol. 5817, Berlin, Heidelberg: Springer, 2009, pp.84-97.
PUB | DOI
 
[102]
2009 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 1918945
J. Stoye, “Computational Short Read Metagenomics”, Presented at the JOBIM 2009, Nantes, France, 2009.
PUB
 
[101]
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1634447
T. Bekel, et al., “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”, Journal of Biotechnology, vol. 140, 2009, pp. 3-12.
PUB | DOI | WoS | PubMed | Europe PMC
 
[100]
2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919198
J.A.A. Quitzau and J. Stoye, “Detecting Repeat Families in Incompletely Sequenced Genomes”, Proc. of WABI 2008, LNBI, vol. 5251, 2008, pp.342-353.
PUB | DOI
 
[99]
2008 | Report | PUB-ID: 1970459
J.A.A. Quitzau and J. Stoye, A space efficient representation for sparse de Bruijn subgraphs, Forschungsberichte der Technischen Fakultät, Abteilung Informationstechnik / Universität Bielefeld, Bielefeld: Technische Fakultät der Universität Bielefeld, 2008.
PUB | PDF
 
[98]
2008 | Report | PUB-ID: 1970461
T. Ejaz, S. Rahmann, and J. Stoye, Online Abelian Pattern Matching, Forschungsberichte der Technischen Fakultät, Abteilung Informationstechnik / Universität Bielefeld, Bielefeld: Technische Fakultät der Universität Bielefeld, 2008.
PUB | PDF
 
[97]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1636699
H. Neuweger, et al., “MeltDB: a software platform for the analysis and integration of metabolomics experiment data”, Bioinformatics, vol. 24, 2008, pp. 2726-2732.
PUB | DOI | WoS | PubMed | Europe PMC
 
[96]
2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919192
S. Böcker, et al., “Computation of Median Gene Clusters”, Proc. of RECOMB 2008, LNBI, vol. 4955, 2008, pp.331-345.
PUB | DOI
 
[95]
2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919200
A. Bergeron, J. Mixtacki, and J. Stoye, “On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios”, Proc. of Recomb-CG 2008, LNBI, vol. 5267, 2008, pp.226-240.
PUB | DOI
 
[94]
2008 | Lexikoneintrag | Veröffentlicht | PUB-ID: 1918834
J. Stoye, “Suffix Tree Construction in RAM (1997; Farach-Colton)”, Encyclopedia of Algorithms, M.-Y. Kao, ed., Springer Verlag, 2008, pp.925-928.
PUB | DOI
 
[93]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1587078
K.-B. Schürmann and J. Stoye, “Counting suffix arrays and strings”, THEORETICAL COMPUTER SCIENCE, vol. 395, 2008, pp. 220-234.
PUB | DOI | WoS
 
[92]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1586009
L. Krause, et al., “Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor”, JOURNAL OF BIOTECHNOLOGY, vol. 136, 2008, pp. 91-101.
PUB | DOI | WoS | PubMed | Europe PMC
 
[91]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1586785
S. Oehm, et al., “Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms”, NUCLEIC ACIDS RESEARCH, vol. 36, 2008, pp. W433-W437.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[90]
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1783364
L. Krause, et al., “Phylogenetic classification of short environmental DNA fragments”, Nucleic Acids Research, vol. 36, 2008, pp. 2230-2239.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[89]
2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919195
A. Bergeron, J. Mixtacki, and J. Stoye, “HP Distance via Double Cut and Join Distance”, Combinatorial Pattern Matching. 19th Annual Symposium, CPM 2008, Pisa, Italy, June 18-20, 2008 Proceedings, Lecture Notes in Computer Science, 5029, 2008, pp.56-68.
PUB | DOI
 
[88]
2007 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 1918828
T. Schmidt and J. Stoye, “Chapter 12: Gecko and GhostFam - Rigorous and Efficient Gene Cluster Detection in Prokaryotic Genomes”, Comparative Genomics, Volume 2, N.H. Bergman, ed., Methods in Molecular Biology, vol. 396, Totowa, NJ: Humana Press Inc., 2007, pp.165-182.
PUB | DOI | PubMed | Europe PMC
 
[87]
2007 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918432
G. Didier, et al., “Character Sets of Strings”, Journal of Discrete Algorithms, vol. 5, 2007, pp. 330-340.
PUB | DOI
 
[86]
2007 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1595253
K.-B. Schürmann and J. Stoye, “An incomplex algorithm for fast suffix array construction”, SOFTWARE-PRACTICE & EXPERIENCE, vol. 37, 2007, pp. 309-329.
PUB | DOI | WoS
 
[85]
2007 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1783345
L. Krause, et al., “GISMO - gene identification using a support vector machine for ORF classification”, Nucleic Acids Research, vol. 35, 2007, pp. 540-549.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[84]
2007 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1630781
A. Mellmann, et al., “Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms”, BMC MICROBIOLOGY, vol. 7, 2007, pp. 98.
PUB | DOI | WoS | PubMed | Europe PMC
 
[83]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1599943
M. Sammeth, et al., “Panta rhei (QAlign2): an open graphical environment for sequence analysis”, BIOINFORMATICS, vol. 22, 2006, pp. 889-890.
PUB | DOI | WoS | PubMed | Europe PMC
 
[82]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1599570
K.R. Rasmussen, J. Stoye, and E.W. Myers, “Efficient q-gram filters for finding all epsilon-matches over a given length”, JOURNAL OF COMPUTATIONAL BIOLOGY, vol. 13, 2006, pp. 296-308.
PUB | DOI | WoS | PubMed | Europe PMC
 
[81]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1599574
A. Bergeron, J. Mixtacki, and J. Stoye, “On sorting by translocations”, JOURNAL OF COMPUTATIONAL BIOLOGY, vol. 13, 2006, pp. 567-578.
PUB | DOI | WoS | PubMed | Europe PMC
 
[80]
2006 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1596811
A. Bergeron, J. Mixtacki, and J. Stoye, “A Unifying View of Genome Rearrangements”, Proc. of WABI 2006, LNBI, vol. 4175, SPRINGER-VERLAG BERLIN, 2006, pp.163-173.
PUB | DOI | WoS
 
[79]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1597213
M. Sammeth and J. Stoye, “Comparing tandem repeats with duplications and excisions of variable degree”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 3, 2006, pp. 395-407.
PUB | DOI | WoS | PubMed | Europe PMC
 
[78]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1597313
A. Bergeron and J. Stoye, “On the similarity of sets of permutations and its applications to genome comparison”, JOURNAL OF COMPUTATIONAL BIOLOGY, vol. 13, 2006, pp. 1340-1354.
PUB | DOI | WoS | PubMed | Europe PMC
 
[77]
2006 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 1918946
J. Stoye, “Index Structures in Biological Sequence Analysis: From Simplicity to Complexity and Back”, Presented at the JOBIM 2006, Bordeaux, France, 2006.
PUB
 
[76]
2006 | Report | PUB-ID: 1970464
C. Chauve, et al., On Common Intervals with Errors, Forschungsberichte, Bielefeld: Technische Fakultät der Universität Bielefeld, 2006.
PUB | PDF
 
[75]
2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1631957
L. Krause, et al., “Finding novel genes in bacterial communities isolated from the environment”, BIOINFORMATICS, vol. 22, 2006, pp. e281-e289.
PUB | DOI | WoS | PubMed | Europe PMC
 
[74]
2005 | Report | PUB-ID: 1970470
M. Sammeth and J. Stoye, Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI), Forschungsberichte, Bielefeld: Technische Fakultät der Universität Bielefeld, 2005.
PUB | PDF | DOI
 
[73]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919012
K.-B. Schürmann and J. Stoye, “An Incomplex Algorithm for Fast Suffix Array Construction”, Proc. of ALENEX/ANALCO 2005, 2005, pp.77-85.
PUB
 
[72]
2005 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 1918824
A. Bergeron, J. Mixtacki, and J. Stoye, “Chapter 10: The Inversion Distance Problem”, Mathematics of Evolution and Phylogeny, O. Gascuel, ed., Oxford University Press, 2005, pp.262-290.
PUB
 
[71]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1603220
A. Bergeron, J. Mixtacki, and J. Stoye, “On Sorting by Translocations”, Proc. of RECOMB 2005, LNBI, vol. 3500, SPRINGER-VERLAG BERLIN, 2005, pp.615-629.
PUB | DOI | WoS
 
[70]
2005 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1775168
A. Krause, J. Stoye, and M. Vingron, “Large scale hierarchical clustering of protein sequences”, BMC Bioinformatics, vol. 6, 2005, pp. 15.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[69]
2005 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773302
D. Bartels, et al., “BACCardI - a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison”, Bioinformatics, vol. 21, 2005, pp. 853-859.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[68]
2005 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918947
S. Böcker and J. Stoye, “Informatische Methoden zur Protein-Identifikation”, LaborPraxis, vol. 29, 2005, pp. 24-26.
PUB
 
[67]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1601348
C. Bannert and J. Stoye, “Protein Annotation by Secondary Structure Based Alignments (PASSTA)”, Proc. of CompLife 2005, LNBI, vol. 3695, Springer-Verlag, 2005, pp.79-90.
PUB | DOI | WoS
 
[66]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1603216
K.R. Rasmussen, J. Stoye, and E.W. Myers, “Efficient q-Gram Filters for Finding All ε-Matches Over a Given Length”, Proc. of RECOMB 2005, LNBI, vol. 3500, SPRINGER-VERLAG BERLIN, 2005, pp.189-203.
PUB | DOI | WoS
 
[65]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1601361
M. Sammeth, et al., “Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI)”, Proc. of WABI 2005, LNBI, vol. 3692, SPRINGER-VERLAG BERLIN, 2005, pp.276-290.
PUB | DOI | WoS
 
[64]
2005 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919026
K.-B. Schürmann and J. Stoye, “Counting Suffix Arrays and Strings”, Proc. of SPIRE 2005, LNCS, vol. 3772, 2005, pp.55-66.
PUB | DOI
 
[63]
2005 | Report | PUB-ID: 1970472
K.-B. Schürmann and J. Stoye, Counting Suffix Arrays and Strings, Forschungsberichte, Bielefeld: Technische Fakultät der Universität Bielefeld, 2005.
PUB | PDF
 
[62]
2004 | Konferenzband | Veröffentlicht | PUB-ID: 1918823
R. Giegerich and J. Stoye, eds., “Proceedings of the German Conference on Bioinformatics, GCB 2004”, Lecture Notes in Informatics, vol. P-53, 2004.
PUB
 
[61]
2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1606286
M. Michael, C. Dieterich, and J. Stoye, “Suboptimal Local Alignments across Multiple Scoring Schemes”, Proc. of WABI 2004, LNBI, vol. 3240, SPRINGER-VERLAG BERLIN, 2004, pp.99-110.
PUB | DOI | WoS
 
[60]
2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1607260
T. Schmidt and J. Stoye, “Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences”, Proc. of CPM 2004, LNCS, vol. 3109, 2004, pp.347-358.
PUB | DOI | WoS
 
[59]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773554
D.A. Pollard, et al., “Correction: Benchmarking tools for the alignment of functional noncoding DNA”, BMC Bioinformatics, vol. 5, 2004, pp. 73.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[58]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773560
M. Cieliebak, et al., “Algorithmic complexity of protein identification: combinatorics of weighted strings”, Discrete Applied Mathematics, vol. 137, 2004, pp. 27-46.
PUB | PDF | DOI | WoS
 
[57]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773312
D.A. Pollard, et al., “Benchmarking tools for the alignment of functional noncoding DNA”, BMC Bioinformatics, vol. 5, 2004, pp. 6.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[56]
2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773569
D. Gusfield and J. Stoye, “Linear time algorithms for finding and representing all the tandem repeats in a string”, Journal of computer and system sciences, vol. 69, 2004, pp. 525-546.
PUB | PDF | DOI | WoS
 
[55]
2004 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1607263
A. Bergeron, J. Mixtacki, and J. Stoye, “Reversal Distance without Hurdles and Fortresses”, Proc. of CPM 2004, LNCS, vol. 3109, SPRINGER-VERLAG BERLIN, 2004, pp.388-399.
PUB | DOI | WoS
 
[54]
2003 | Report | PUB-ID: 1970475
K.-B. Schürmann and J. Stoye, Suffix Tree Construction and Storage with Limited Main Memory, Forschungsberichte, Bielefeld: Technische Fakultät der Universität Bielefeld, 2003.
PUB | PDF
 
[53]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1612664
S. Heber and J. Stoye, “The European Conference on Computational Biology”, Drug Discovery Today, vol. 8, 2003, pp. 113-114.
PUB | DOI | WoS | PubMed | Europe PMC
 
[52]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918949
R. Giegerich and J. Stoye, “Finden, fast ohne zu suchen: Indexstrukturen in der Bioinformatik”, Forschung an der Universität Bielefeld, vol. 26, 2003, pp. 63-68.
PUB
 
[51]
2003 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919005
C. Bannert and J. Stoye, “Evaluation of the Jumping Alignment Algorithm with Artificial and Biological Data”, Proc. of GCB 2003, 2003, pp.21-25.
PUB
 
[50]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1610397
R. Giegerich, S. Kurtz, and J. Stoye, “Efficient implementation of lazy suffix trees”, SOFTWARE-PRACTICE & EXPERIENCE, vol. 33, 2003, pp. 1035-1049.
PUB | PDF | DOI | WoS
 
[49]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1609403
M. Sammeth, B. Morgenstern, and J. Stoye, “Divide-and-conquer multiple alignment with segment-based constraints”, BIOINFORMATICS, vol. 19, 2003, pp. ii189-ii195.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[48]
2003 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1610433
A. Bergeron and J. Stoye, “On the similarity of sets of permutations and its applications to genome comparison”, Proc. of COCOON 2003, LNCS, vol. 2697, 2003, pp.68-79.
PUB | DOI | WoS
 
[47]
2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1610503
M. Sammeth, et al., “QAlign: quality-based multiple alignments with dynamic phylogenetic analysis”, BIOINFORMATICS, vol. 19, 2003, pp. 1592-1593.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[46]
2003 | Report | PUB-ID: 1970477
A. Bergeron and J. Stoye, On the Similarity of Sets of Permutations and its Applications to Genome Comparison, Forschungsberichte, Bielefeld: Technische Fakultät der Universität Bielefeld, 2003.
PUB | PDF
 
[45]
2002 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 1918951
J. Stoye, “Index Structures for Large Sequence Data: Suffix Trees and Affix Trees”, Lecture Notes in Informatics, S. Schubert, B. Reusch, and N. Jesse, eds., vol. P-20, 2002, pp.67-67.
PUB
 
[44]
2002 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919000
M. Cieliebak, et al., “Algorithmic Complexity of Protein Identification: Searching in Weighted Strings”, Proc. of IFIP TCS 2002, 2002, pp.143-156.
PUB
 
[43]
2002 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773578
R. Spang, M. Rehmsmeier, and J. Stoye, “A novel approach to remote homology detection: jumping alignments”, Journal of Computational Biology, vol. 9, 2002, pp. 747-760.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[42]
2002 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773332
J. Stoye and D. Gusfield, “Simple and flexible detection of contiguous repeats using a suffix tree”, Theoretical Computer Science, vol. 270, 2002, pp. 843-856.
PUB | PDF | DOI | WoS
 
[41]
2002 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773329
A. Bergeron, S. Heber, and J. Stoye, “Common intervals and sorting by reversals: a marriage of necessity”, Bioinformatics, vol. 18, 2002, pp. S54-S63.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[40]
2002 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918995
S. Heber, et al., “Resampling Methods in Physical Mapping”, Proc. of GfKl 2000, 2002, pp.437-444.
PUB
 
[39]
2001 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773335
S. Kurtz, et al., “REPuter: the manifold applications of repeat analysis on a genomic scale”, Nucleic Acids Research, vol. 29, 2001, pp. 4633-4642.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[38]
2001 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918992
S. Heber and J. Stoye, “Finding all Common Intervals of k Permutations”, Proc. of CPM 2001, LNCS, vol. 2089, 2001, pp.207-218.
PUB | DOI
 
[37]
2001 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1880197
S. Heber and J. Stoye, “Algorithms for Finding Gene Clusters”, Proc. of WABI 2001, LNCS, vol. 2149, Berlin: Sppringer, 2001, pp.252-263.
PUB | DOI
 
[36]
2001 | Report | PUB-ID: 1970479
M. Cieliebak, et al., Algorithmic Complexity of Protein Identification: Combinatorics of Weighted Strings, Technical Report, ETH Zürich, Dept. of Computer Science: 2001.
PUB
 
[35]
2000 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918981
S. Heber, et al., “Contig Selection in Physical Mapping”, Proc. of RECOMB 2000, 2000, pp.155-164.
PUB | DOI | WoS | PubMed | Europe PMC
 
[34]
2000 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 1918817
G.S. Brodal, et al., “Finding Maximal Pairs with Bounded Gap”, Matching Patterns (Journal of Discrete Algorithms), M. Crochemore and L. Gąsieniec, eds., 2000, pp.77-104.
PUB
 
[33]
2000 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773345
A. Krause, J. Stoye, and M. Vingron, “The SYSTERS protein sequence cluster set”, Nucleic Acids Research, vol. 28, 2000, pp. 270-272.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[32]
2000 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773572
S. Heber, et al., “Contig selection in physical mapping”, Journal of Computational Biology, vol. 7, 2000, pp. 395-408.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[31]
2000 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918985
R. Spang, M. Rehmsmeier, and J. Stoye, “Sequence Database Search Using Jumping Alignments”, Proc. of ISMB 2000, 2000, pp.367-375.
PUB | PubMed | Europe PMC
 
[30]
2000 | Report | PUB-ID: 1970490
J. Stoye, Affix Trees, Forschungsberichte, Technische Fakultät der Universität Bielefeld: 2000.
PUB | PDF
 
[29]
2000 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773341
K. Reinert, J. Stoye, and T. Will, “An iterative method for faster sum-of-pairs multiple sequence alignment”, Bioinformatics, vol. 16, 2000, pp. 808-814.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[28]
2000 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918988
S. Kurtz, et al., “Computation and Visualization of Degenerate Repeats in Complete Genomes”, Proc. of ISMB 2000, 2000, pp.228-238.
PUB | PubMed | Europe PMC
 
[27]
2000 | Konferenzband | Veröffentlicht | PUB-ID: 1918813
E. Bornberg-Bauer, et al., eds., Proceedings of the German Conference on Bioinformatics, GCB 2000, Berlin: Logos Verlag, 2000.
PUB
 
[26]
1999 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1620435
R. Giegerich, S. Kurtz, and J. Stoye, “Efficient implementation of lazy suffix trees”, Algorithm Engineering. 3rd International Workshop, WAE’99 London, UK, July 19–21, 1999 Proceedings, LNCS, vol. 1668, 1999, pp.30-42.
PUB | DOI | WoS
 
[25]
1999 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918978
K. Reinert, T. Will, and J. Stoye, “Combining Divide-and-Conquer, the A*-Algorithm, and Successive Realignment Approaches to Speed up Multiple Sequence Alignment”, Proc. of GCB 1999, 1999, pp.17-24.
PUB | Download (ext.)
 
[24]
1999 | Report | PUB-ID: 1970495
B. Morgenstern, J. Stoye, and A. Dress, Consistent Equivalence Relations: A Set-Theoretical Framework for Multiple Sequence Alignment, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld: 1999.
PUB
 
[23]
1999 | Report | PUB-ID: 1970509
G.S. Brodal, et al., Finding Maximal Pairs with Bounded Gap, Report, BRICS, Department of Computer Science, University of Aarhus: 1999.
PUB
 
[22]
1999 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918971
G.S. Brodal, et al., “Finding Maximal Pairs with Bounded Gap”, Proc. of CPM 1999, LNCS, vol. 1645, 1999, pp.134-149.
PUB | DOI
 
[21]
1998 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2488102
A. Dress, B. Morgenstern, and J. Stoye, “The Number of Standard and of Effective Multiple Alignments”, Appl. Math. Lett., vol. 11, 1998, pp. 43-49.
PUB
 
[20]
1998 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1918538
M. Hildebrand and J. Stoye, “Die Bedeutung der Zusammenarbeit der Disziplinen in der Anwendung - erläutert anhand von Beispielen”, Der Mathematikunterricht, vol. 44, 1998, pp. 34-53.
PUB
 
[19]
1998 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1667771
J. Stoye, “Multiple sequence alignment with the Divide-and-Conquer method.”, Gene, vol. 211, 1998, pp. GC45-GC56.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[18]
1998 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1625402
J. Stoye, D. Evers, and F. Meyer, “Rose: generating sequence families”, BIOINFORMATICS, vol. 14, 1998, pp. 157-163.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[17]
1998 | Report | PUB-ID: 1970515
J. Stoye and D. Gusfield, Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree, Report, Department of Computer Science, University of California, Davis: 1998.
PUB
 
[16]
1998 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1918964
J. Stoye and D. Gusfield, “Simple and Flexible Detection of Contiguous Repeats Using a Suffix Tree (Preliminary Version)”, Proc. of CPM 1998, LNCS, vol. 1448, 1998, pp.140-152.
PUB | DOI
 
[15]
1998 | Report | PUB-ID: 1970513
D. Gusfield and J. Stoye, Linear Time Algorithms for Finding and Representing all the Tandem Repeats in a String, Report, Department of Computer Science, University of California, Davis: 1998.
PUB
 
[14]
1997 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2488107
J. Stoye, V. Moulton, and A. Dress, “DCA: An efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment”, CABIOS, vol. 13, 1997, pp. 625-626.
PUB
 
[13]
1997 | Report | PUB-ID: 1970526
S.W. Perrey, et al., On Simultaneous versus Iterative Multiple Sequence Alignment, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld: 1997.
PUB
 
[12]
1997 | Report | PUB-ID: 1970517
J. Stoye, D. Evers, and F. Meyer, Rose: Generating Sequence Families, Forschungsberichte, Technische Fakultät der Universität Bielefeld: 1997.
PUB
 
[11]
1997 | Report | PUB-ID: 1970529
G. Brinkmann, et al., Two Applications of the Divide & Conquer Principle in the Molecular Sciences, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld: 1997.
PUB
 
[10]
1997 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1667885
J. Stoye, D. Evers, and F. Meyer, “Generating benchmarks for multiple sequence alignments and phylogenetic reconstructions”, Proc. of ISMB 1997, 1997, pp.303-306.
PUB | PubMed | Europe PMC
 
[9]
1997 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773355
J. Stoye, S.W. Perrey, and A. Dress, “Improving the divide-and-conquer approach to sum-of-pairs multiple sequence alignment”, Applied mathematics letters, vol. 10, 1997, pp. 67-73.
PUB | PDF | DOI | WoS
 
[8]
1997 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773358
G. Brinkmann, et al., “Two applications of the Divide & Conquer principle in the molecular sciences”, Mathematical programming, vol. 79, 1997, pp. 71-97.
PUB | DOI | WoS
 
[7]
1997 | Report | PUB-ID: 1970523
A. Dress, B. Morgenstern, and J. Stoye, On the Number of Standard and Effective Multiple Alignments, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld: 1997.
PUB
 
[6]
1997 | Report | PUB-ID: 1970520
S.W. Perrey, J. Stoye, and V. Moulton, FDCA: Fast and Accurate Approximation to Sum-of-Pairs Score Optimal Multiple Sequence Alignment, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld: 1997.
PUB
 
[5]
1997 | Report | PUB-ID: 1970532
J. Stoye, Divide-and-Conquer Multiple Sequence Alignment, Forschungsberichte, Technische Fakultät der Universität Bielefeld: 1997.
PUB
 
[4]
1996 | Report | PUB-ID: 1970533
S.W. Perrey and J. Stoye, Fast Approximation to the NP-hard Problem of Multiple Sequence Alignment, Information and Mathematical Sciences Reports, Series B, Dept. of Mathematics, Massey University, Palmerston North, New Zealand: 1996.
PUB
 
[3]
1996 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773351
U. Tönges, et al., “A general method for fast multiple sequence alignment”, Gene, vol. 172, 1996, pp. GC33-GC41.
PUB | DOI | WoS | PubMed | Europe PMC
 
[2]
1996 | Report | PUB-ID: 1970535
J. Stoye, A. Dress, and S.W. Perrey, Improving the Divide-and-Conquer Approach to Sum-of-Pairs Multiple Sequence Alignment, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld: 1996.
PUB
 
[1]
1996 | Report | PUB-ID: 1970537
U. Tönges, et al., A General Method for Fast Multiple Sequence Alignment, Materialien/Preprints, Forschungsschwerpunkt Mathematisierung, Universität Bielefeld: 1996.
PUB
 

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