Jens Stoye - Publications

Affiliations: 
Faculty of Technology Bielefeld University, Bielefeld, Nordrhein-Westfalen, Germany 

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Year Citation  Score
2022 Schulz T, Wittler R, Stoye J. Sequence-based pangenomic core detection. Iscience. 25: 104413. PMID 35663029 DOI: 10.1016/j.isci.2022.104413  0.308
2021 Schulz T, Wittler R, Rahmann S, Hach F, Stoye J. Detecting High Scoring Local Alignments in Pangenome Graphs. Bioinformatics (Oxford, England). PMID 33532821 DOI: 10.1093/bioinformatics/btab077  0.305
2021 Sundermann LK, Wintersinger J, Rätsch G, Stoye J, Morris Q. Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine. Plos Computational Biology. 17: e1008400. PMID 33465079 DOI: 10.7490/F1000Research.1118307.1  0.377
2020 Bohnenkämper L, Braga MDV, Doerr D, Stoye J. Computing the Rearrangement Distance of Natural Genomes. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 33393848 DOI: 10.1089/cmb.2020.0434  0.346
2020 Haghshenas E, Asghari H, Stoye J, Chauve C, Hach F. HASLR: Fast Hybrid Assembly of Long Reads. Iscience. 23: 101389. PMID 32781410 DOI: 10.1016/J.Isci.2020.101389  0.385
2020 Willing E, Stoye J, Braga M. Computing the Inversion-Indel Distance. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 32324562 DOI: 10.1109/Tcbb.2020.2988950  0.422
2020 Rubert DP, Martinez FV, Stoye J, Doerr D. Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants. Bmc Genomics. 21: 273. PMID 32299356 DOI: 10.1186/S12864-020-6609-X  0.376
2020 Alanko J, Bannai H, Cazaux B, Peterlongo P, Stoye J. Finding all maximal perfect haplotype blocks in linear time. Algorithms For Molecular Biology : Amb. 15: 2. PMID 32055252 DOI: 10.1186/S13015-020-0163-6  0.457
2019 Sevillya G, Doerr D, Lerner Y, Stoye J, Steel M, Snir S. Horizontal Gene Transfer Phylogenetics: A Random Walk Approach. Molecular Biology and Evolution. PMID 31845962 DOI: 10.1093/Molbev/Msz302  0.426
2019 Oey H, Zakrzewski M, Gravermann K, Young ND, Korhonen PK, Gobert GN, Nawaratna S, Hasan S, Martínez DM, You H, Lavin M, Jones MK, Ragan MA, Stoye J, Oleaga A, et al. Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium. Plos Pathogens. 15: e1007513. PMID 30673782 DOI: 10.1371/Journal.Ppat.1007513  0.425
2018 Holley G, Wittler R, Stoye J, Hach F. Dynamic Alignment-Free and Reference-Free Read Compression. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 25: 825-836. PMID 30011247 DOI: 10.1089/Cmb.2018.0068  0.449
2018 Luhmann N, Chauve C, Stoye J, Wittler R. Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 29993816 DOI: 10.1109/TCBB.2018.2816034  0.358
2018 Rubert DP, Hoshino EA, Braga MDV, Stoye J, Martinez FV. Computing the family-free DCJ similarity. Bmc Bioinformatics. 19: 152. PMID 29745861 DOI: 10.1186/S12859-018-2130-5  0.389
2018 Schulz T, Stoye J, Doerr D. GraphTeams: a method for discovering spatial gene clusters in Hi-C sequencing data. Bmc Genomics. 19: 308. PMID 29745835 DOI: 10.1186/S12864-018-4622-0  0.349
2018 Jaenicke S, Albaum SP, Blumenkamp P, Linke B, Stoye J, Goesmann A. Flexible metagenome analysis using the MGX framework. Microbiome. 6: 76. PMID 29690922 DOI: 10.1186/S40168-018-0460-1  0.431
2018 Doerr D, Feijão P, Stoye J. Family-Free Genome Comparison. Methods in Molecular Biology (Clifton, N.J.). 1704: 331-342. PMID 29277872 DOI: 10.1007/978-1-4939-7463-4_12  0.436
2018 Zekic T, Holley G, Stoye J. Pan-Genome Storage and Analysis Techniques. Methods in Molecular Biology (Clifton, N.J.). 1704: 29-53. PMID 29277862 DOI: 10.1007/978-1-4939-7463-4_2  0.456
2017 Jünemann S, Kleinbölting N, Jaenicke S, Henke C, Hassa J, Nelkner J, Stolze Y, Albaum SP, Schlüter A, Goesmann A, Sczyrba A, Stoye J. Bioinformatics for NGS-based Metagenomics and the Application to Biogas Research. Journal of Biotechnology. PMID 28823476 DOI: 10.1016/J.Jbiotec.2017.08.012  0.38
2017 Doerr D, Kowada LAB, Araujo E, Deshpande S, Dantas S, Moret BME, Stoye J. New Genome Similarity Measures based on Conserved Gene Adjacencies. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 24: 616-634. PMID 28590847 DOI: 10.1089/Cmb.2017.0065  0.425
2017 Rubert DP, Feijão P, Braga MD, Stoye J, Martinez FH. Approximating the DCJ distance of balanced genomes in linear time. Algorithms For Molecular Biology : Amb. 12: 3. PMID 28293275 DOI: 10.1186/S13015-017-0095-Y  0.407
2016 Winter S, Jahn K, Wehner S, Kuchenbecker L, Marz M, Stoye J, Böcker S. Finding approximate gene clusters with Gecko 3. Nucleic Acids Research. PMID 27679480 DOI: 10.1093/Nar/Gkw843  0.415
2016 Holley G, Wittler R, Stoye J. Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage. Algorithms For Molecular Biology : Amb. 11: 3. PMID 27087830 DOI: 10.1186/S13015-016-0066-8  0.477
2016 Kowada LAB, Doerr D, Dantas S, Stoye J. New genome similarity measures based on conserved gene adjacencies Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9649: 204-224. DOI: 10.1007/978-3-319-31957-5_15  0.32
2015 Braga MD, Stoye J. Sorting Linear Genomes with Rearrangements and Indels. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 12: 500-6. PMID 26357261 DOI: 10.1109/Tcbb.2014.2329297  0.402
2015 Mager DL, Stoye JP. Mammalian Endogenous Retroviruses. Microbiology Spectrum. 3. PMID 26104559 DOI: 10.1128/microbiolspec.MDNA3-0009-2014  0.303
2015 Martinez FV, Feijão P, Braga MD, Stoye J. On the family-free DCJ distance and similarity. Algorithms For Molecular Biology : Amb. 10: 13. PMID 25859276 DOI: 10.1186/S13015-015-0041-9  0.42
2014 Doerr D, Stoye J, Böcker S, Jahn K. Identifying gene clusters by discovering common intervals in indeterminate strings. Bmc Genomics. 15: S2. PMID 25571793 DOI: 10.1186/1471-2164-15-S6-S2  0.367
2014 Jünemann S, Prior K, Albersmeier A, Albaum S, Kalinowski J, Goesmann A, Stoye J, Harmsen D. GABenchToB: a genome assembly benchmark tuned on bacteria and benchtop sequencers. Plos One. 9: e107014. PMID 25198770 DOI: 10.1371/Journal.Pone.0107014  0.476
2014 Lechner M, Hernandez-Rosales M, Doerr D, Wieseke N, Thévenin A, Stoye J, Hartmann RK, Prohaska SJ, Stadler PF. Orthology detection combining clustering and synteny for very large datasets. Plos One. 9: e105015. PMID 25137074 DOI: 10.1371/Journal.Pone.0105015  0.461
2014 Jakobi T, Brinkrolf K, Tauch A, Noll T, Stoye J, Pühler A, Goesmann A. Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing. Journal of Biotechnology. 190: 64-75. PMID 25086342 DOI: 10.1016/J.Jbiotec.2014.07.437  0.442
2014 Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A. ReadXplorer--visualization and analysis of mapped sequences. Bioinformatics (Oxford, England). 30: 2247-54. PMID 24790157 DOI: 10.1093/Bioinformatics/Btu205  0.337
2014 Schwientek P, Neshat A, Kalinowski J, Klein A, Rückert C, Schneiker-Bekel S, Wendler S, Stoye J, Pühler A. Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts. Journal of Biotechnology. 190: 85-95. PMID 24642337 DOI: 10.1016/J.Jbiotec.2014.03.013  0.378
2014 Hoffmann N, Wilhelm M, Doebbe A, Niehaus K, Stoye J. BiPACE 2D--graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry. Bioinformatics (Oxford, England). 30: 988-95. PMID 24363380 DOI: 10.1093/Bioinformatics/Btt738  0.333
2014 Jünemann S, Prior K, Albersmeier A, Albaum S, Kalinowski J, Goesmann A, Stoye J, Harmsen D. Overview of the data sets used in this study and their sequencing yield. Plos One. DOI: 10.1371/Journal.Pone.0107014.T001  0.402
2014 Luhmann N, Chauve C, Stoye J, Wittler R. Scaffolding of ancient contigs and ancestral reconstruction in a phylogenetic framework Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8826: 135-143. DOI: 10.1109/Tcbb.2018.2816034  0.459
2013 Jahn K, Winter S, Stoye J, Böcker S. Statistics for approximate gene clusters. Bmc Bioinformatics. 14: S14. PMID 24564620 DOI: 10.1186/1471-2105-14-S15-S14  0.361
2013 Willing E, Zaccaria S, Braga MD, Stoye J. On the inversion-indel distance. Bmc Bioinformatics. 14: S3. PMID 24564182 DOI: 10.1186/1471-2105-14-S15-S3  0.442
2013 Ander C, Schulz-Trieglaff OB, Stoye J, Cox AJ. metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences. Bmc Bioinformatics. 14: S2. PMID 23734710 DOI: 10.1186/1471-2105-14-S5-S2  0.493
2013 Krell PF, Reuther S, Fischer U, Keller T, Weber S, Gombert M, Schuster FR, Asang C, Stepensky P, Strahm B, Meisel R, Stoye J, Borkhardt A. Next-generation-sequencing-spectratyping reveals public T-cell receptor repertoires in pediatric very severe aplastic anemia and identifies a β chain CDR3 sequence associated with hepatitis-induced pathogenesis. Haematologica. 98: 1388-96. PMID 23716544 DOI: 10.3324/Haematol.2012.069708  0.382
2013 Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, Harmsen D. Updating benchtop sequencing performance comparison. Nature Biotechnology. 31: 294-6. PMID 23563421 DOI: 10.1038/Nbt.2522  0.422
2013 Zakrzewski M, Bekel T, Ander C, Pühler A, Rupp O, Stoye J, Schlüter A, Goesmann A. MetaSAMS--a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets. Journal of Biotechnology. 167: 156-65. PMID 23026555 DOI: 10.1016/J.Jbiotec.2012.09.013  0.425
2013 Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, Harmsen D. Correction: Corrigendum: Updating benchtop sequencing performance comparison Nature Biotechnology. 31: 1148-1148. DOI: 10.1038/Nbt1213-1148E  0.348
2012 Jahn K, Sudek H, Stoye J. Multiple genome comparison based on overlap regions of pairwise local alignments. Bmc Bioinformatics. 13: S7. PMID 23281942 DOI: 10.1186/1471-2105-13-S19-S7  0.432
2012 Doerr D, Thévenin A, Stoye J. Gene family assignment-free comparative genomics. Bmc Bioinformatics. 13: S3. PMID 23281826 DOI: 10.1186/1471-2105-13-S19-S3  0.431
2012 Hoffmann N, Keck M, Neuweger H, Wilhelm M, Högy P, Niehaus K, Stoye J. Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets. Bmc Bioinformatics. 13: 214. PMID 22920415 DOI: 10.1186/1471-2105-13-214  0.356
2012 Jünemann S, Prior K, Szczepanowski R, Harks I, Ehmke B, Goesmann A, Stoye J, Harmsen D. Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing. Plos One. 7: e41606. PMID 22870235 DOI: 10.1371/Journal.Pone.0041606  0.393
2012 Hilker R, Sickinger C, Pedersen CN, Stoye J. UniMoG--a unifying framework for genomic distance calculation and sorting based on DCJ. Bioinformatics (Oxford, England). 28: 2509-11. PMID 22815356 DOI: 10.1093/Bioinformatics/Bts440  0.435
2012 Schwientek P, Szczepanowski R, Rückert C, Kalinowski J, Klein A, Selber K, Wehmeier UF, Stoye J, Pühler A. The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110. Bmc Genomics. 13: 112. PMID 22443545 DOI: 10.1186/1471-2164-13-112  0.476
2012 Hoffmann N, Stoye J. Generic Software Frameworks for GC-MS Based Metabolomics Metabolomics. DOI: 10.5772/31224  0.349
2011 Braga MD, Machado R, Ribeiro LC, Stoye J. On the weight of indels in genomic distances. Bmc Bioinformatics. 12: S13. PMID 22151784 DOI: 10.1186/1471-2105-12-S9-S13  0.435
2011 Braga MD, Machado R, Ribeiro LC, Stoye J. Genomic distance under gene substitutions. Bmc Bioinformatics. 12: S8. PMID 22151231 DOI: 10.1186/1471-2105-12-S9-S8  0.441
2011 Kováč J, Warren R, Braga MD, Stoye J. Restricted DCJ model: rearrangement problems with chromosome reincorporation. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 1231-41. PMID 21899428 DOI: 10.1089/Cmb.2011.0116  0.379
2011 Braga MD, Willing E, Stoye J. Double cut and join with insertions and deletions. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 1167-84. PMID 21899423 DOI: 10.1089/Cmb.2011.0118  0.468
2011 Wittler R, Ma?uch J, Patterson M, Stoye J. Consistency of sequence-based gene clusters. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 1023-39. PMID 21899413 DOI: 10.1089/Cmb.2011.0083  0.395
2011 Gerlach W, Stoye J. Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic Acids Research. 39: e91. PMID 21586583 DOI: 10.1093/Nar/Gkr225  0.468
2011 Schwientek P, Szczepanowski R, Rückert C, Stoye J, Pühler A. Sequencing of high G+C microbial genomes using the ultrafast pyrosequencing technology. Journal of Biotechnology. 155: 68-77. PMID 21536083 DOI: 10.1016/J.Jbiotec.2011.04.010  0.505
2011 Hufsky F, Kuchenbecker L, Jahn K, Stoye J, Böcker S. Swiftly computing center strings. Bmc Bioinformatics. 12: 106. PMID 21504573 DOI: 10.1186/1471-2105-12-106  0.317
2011 Blom J, Jakobi T, Doppmeier D, Jaenicke S, Kalinowski J, Stoye J, Goesmann A. Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. Bioinformatics (Oxford, England). 27: 1351-8. PMID 21450712 DOI: 10.1093/Bioinformatics/Btr151  0.514
2011 Krell PFI, Weber S, Reuther S, Gombert M, Keller T, Schuster FR, Asang C, Stoye J, Borkhardt A, Fischer U. Next Generation Sequencing Spectratyping (NGS-S) Comprehensively Monitors T Cell Receptor Diversity in Children with T Cell Abnormalities Blood. 118: 2173-2173. DOI: 10.1182/Blood.V118.21.2173.2173  0.389
2011 Erdos PL, Soukup L, Stoye J. Balanced vertices in trees and a simpler algorithm to compute the genomic distance Applied Mathematics Letters. 24: 82-86. DOI: 10.1016/J.Aml.2010.08.021  0.399
2010 Trost E, Ott L, Schneider J, Schröder J, Jaenicke S, Goesmann A, Husemann P, Stoye J, Dorella FA, Rocha FS, Soares Sde C, D'Afonseca V, Miyoshi A, Ruiz J, Silva A, 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. 11: 728. PMID 21192786 DOI: 10.1186/1471-2164-11-728  0.404
2010 Bergeron A, Medvedev P, Stoye J. Rearrangement models and single-cut operations. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 1213-25. PMID 20874405 DOI: 10.1089/Cmb.2010.0091  0.358
2010 Blin G, Faye D, Stoye J. Finding nested common intervals efficiently. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 1183-94. PMID 20874403 DOI: 10.1089/Cmb.2010.0089  0.416
2010 Braga MD, Stoye J. The solution space of sorting by DCJ. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 1145-65. PMID 20874401 DOI: 10.1089/Cmb.2010.0109  0.476
2010 Husemann P, Stoye J. Phylogenetic comparative assembly. Algorithms For Molecular Biology : Amb. 5: 3. PMID 20047659 DOI: 10.1186/1748-7188-5-3  0.498
2010 Husemann P, Stoye J. r2cat: synteny plots and comparative assembly. Bioinformatics (Oxford, England). 26: 570-1. PMID 20015948 DOI: 10.1093/Bioinformatics/Btp690  0.472
2010 Besenbacher S, Schwikowski B, Stoye J. Indexing and searching a mass spectrometry database Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6060: 62-76. DOI: 10.1007/978-3-642-12476-1_4  0.336
2009 Gerlach W, Jünemann S, Tille F, Goesmann A, Stoye J. WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. Bmc Bioinformatics. 10: 430. PMID 20021646 DOI: 10.1186/1471-2105-10-430  0.391
2009 Brudno M, Medvedev P, Stoye J, De La Vega FM. A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG). Bioinformatics (Oxford, England). 25: 2863-4. PMID 19783529 DOI: 10.1093/Bioinformatics/Btp525  0.441
2009 Böcker S, Jahn K, Mixtacki J, Stoye J. Computation of median gene clusters. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 1085-99. PMID 19689215 DOI: 10.1089/Cmb.2009.0098  0.391
2009 Stoye J, Wittler R. A unified approach for reconstructing ancient gene clusters. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 6: 387-400. PMID 19644167 DOI: 10.1109/Tcbb.2008.135  0.395
2009 Hoffmann N, Stoye J. ChromA: signal-based retention time alignment for chromatography-mass spectrometry data. Bioinformatics (Oxford, England). 25: 2080-1. PMID 19505941 DOI: 10.1093/Bioinformatics/Btp343  0.341
2009 Bekel T, Henckel K, Küster H, Meyer F, Mittard Runte V, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Pühler A, Stoye J, Goesmann A. 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. 140: 3-12. PMID 19297685 DOI: 10.1016/J.Jbiotec.2009.01.006  0.492
2009 Bergeron A, Mixtacki J, Stoye J. A new linear time algorithm to compute the genomic distance via the double cut and join distance Theoretical Computer Science. 410: 5300-5316. DOI: 10.1016/J.Tcs.2009.09.008  0.424
2009 Jahn K, Stoye J. Approximate gene clusters and their application in comparative genomics | Approximative Gencluster und ihre Anwendung in der komparativen Genomik Informatik-Spektrum. 32: 288-300. DOI: 10.1007/S00287-009-0350-9  0.376
2008 Neuweger H, Albaum SP, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A. MeltDB: a software platform for the analysis and integration of metabolomics experiment data. Bioinformatics (Oxford, England). 24: 2726-32. PMID 18765459 DOI: 10.1093/Bioinformatics/Btn452  0.35
2008 Krause L, Diaz NN, Edwards RA, Gartemann KH, Krömeke H, Neuweger H, Pühler A, Runte KJ, Schlüter A, Stoye J, Szczepanowski R, Tauch A, Goesmann A. Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor. Journal of Biotechnology. 136: 91-101. PMID 18611419 DOI: 10.1016/J.Jbiotec.2008.06.003  0.329
2008 Oehm S, Gilbert D, Tauch A, Stoye J, Goesmann A. Comparative Pathway Analyzer--a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. Nucleic Acids Research. 36: W433-7. PMID 18539612 DOI: 10.1093/Nar/Gkn284  0.309
2008 Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, Stoye J. Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Research. 36: 2230-9. PMID 18285365 DOI: 10.1093/Nar/Gkn038  0.434
2008 Amgarten Quitzau JA, Stoye J. Detecting repeat families in incompletely sequenced genomes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5251: 342-353. DOI: 10.1007/978-3-540-87361-7_29  0.32
2007 Schmidt T, Stoye J. Gecko and GhostFam: rigorous and efficient gene cluster detection in prokaryotic genomes. Methods in Molecular Biology (Clifton, N.J.). 396: 165-82. PMID 18025693 DOI: 10.1007/978-1-59745-515-2_12  0.395
2007 Mellmann A, Weniger T, Berssenbrügge C, Rothgänger J, Sammeth M, Stoye J, Harmsen D. Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms. Bmc Microbiology. 7: 98. PMID 17967176 DOI: 10.1186/1471-2180-7-98  0.671
2007 Krause L, McHardy AC, Nattkemper TW, Pühler A, Stoye J, Meyer F. GISMO--gene identification using a support vector machine for ORF classification. Nucleic Acids Research. 35: 540-9. PMID 17175534 DOI: 10.1093/Nar/Gkl1083  0.361
2007 Didier G, Schmidt T, Stoye J, Tsur D. Character sets of strings Journal of Discrete Algorithms. 5: 330-340. DOI: 10.1016/J.Jda.2006.03.021  0.303
2007 Schürmann KB, Stoye J. An incomplex algorithm for fast suffix array construction Software - Practice and Experience. 37: 309-329. DOI: 10.1002/Spe.V37:3  0.317
2006 Sammeth M, Stoye J. Comparing tandem repeats with duplications and excisions of variable degree. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 3: 395-407. PMID 17085848 DOI: 10.1109/Tcbb.2006.46  0.699
2006 Bergeron A, Stoye J. On the similarity of sets of permutations and its applications to genome comparison. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 1340-54. PMID 17037962 DOI: 10.1089/Cmb.2006.13.1340  0.431
2006 Krause L, Diaz NN, Bartels D, Edwards RA, Pühler A, Rohwer F, Meyer F, Stoye J. Finding novel genes in bacterial communities isolated from the environment. Bioinformatics (Oxford, England). 22: e281-9. PMID 16873483 DOI: 10.1093/Bioinformatics/Btl247  0.465
2006 Bergeron A, Mixtacki J, Stoye J. On sorting by translocations. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 567-78. PMID 16597257 DOI: 10.1089/Cmb.2006.13.567  0.41
2006 Rasmussen KR, Stoye J, Myers EW. Efficient q-gram filters for finding all epsilon-matches over a given length. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 296-308. PMID 16597241 DOI: 10.1089/Cmb.2006.13.296  0.424
2006 Sammeth M, Griebel T, Tille F, Stoye J. Panta rhei (QAlign2): an open graphical environment for sequence analysis. Bioinformatics (Oxford, England). 22: 889-90. PMID 16418234 DOI: 10.1093/Bioinformatics/Btl007  0.706
2005 Krause A, Stoye J, Vingron M. Large scale hierarchical clustering of protein sequences. Bmc Bioinformatics. 6: 15. PMID 15663796 DOI: 10.1186/1471-2105-6-15  0.46
2005 Bartels D, Kespohl S, Albaum S, Drüke T, Goesmann A, Herold J, Kaiser O, Pühler A, Pfeiffer F, Raddatz G, Stoye J, Meyer F, Schuster SC. BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. Bioinformatics (Oxford, England). 21: 853-9. PMID 15514001 DOI: 10.1093/Bioinformatics/Bti091  0.451
2005 Bannert C, Stoye J. Protein Annotation by Secondary Structure Based Alignments (PASSTA) Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3695: 79-90. DOI: 10.1007/11560500_8  0.446
2005 Sammeth M, Weniger T, Harmsen D, Stoye J. Alignment of tandem repeats with Excision, Duplication, Substitution and Indels (EDSI) Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3692: 276-290. DOI: 10.1007/11557067_23  0.654
2004 Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB. Correction: Benchmarking tools for the alignment of functional noncoding DNA. Bmc Bioinformatics. 5: 73. PMID 15186509 DOI: 10.1186/1471-2105-5-73  0.327
2004 Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB. Benchmarking tools for the alignment of functional noncoding DNA. Bmc Bioinformatics. 5: 6. PMID 14736341 DOI: 10.1186/1471-2105-5-6  0.496
2004 Gusfield D, Stoye J. Linear time algorithms for finding and representing all the tandem repeats in a string Journal of Computer and System Sciences. 69: 525-546. DOI: 10.1016/J.Jcss.2004.03.004  0.315
2004 Schmidt T, Stoye J. Quadratic time algorithms for finding common intervals in two and more sequences Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3109: 347-358.  0.309
2003 Sammeth M, Morgenstern B, Stoye J. Divide-and-conquer multiple alignment with segment-based constraints. Bioinformatics (Oxford, England). 19: ii189-95. PMID 14534189 DOI: 10.1093/bioinformatics/btg1077  0.676
2003 Sammeth M, Rothgänger J, Esser W, Albert J, Stoye J, Harmsen D. QAlign: quality-based multiple alignments with dynamic phylogenetic analysis. Bioinformatics (Oxford, England). 19: 1592-3. PMID 12912847 DOI: 10.1093/Bioinformatics/Btg197  0.702
2002 Spang R, Rehmsmeier M, Stoye J. A novel approach to remote homology detection: jumping alignments. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 9: 747-60. PMID 12487762 DOI: 10.1089/106652702761034172  0.491
2002 Stoye J, Gusfield D. Simple and flexible detection of contiguous repeats using a suffix tree Theoretical Computer Science. 270: 843-856. DOI: 10.1016/S0304-3975(01)00121-9  0.337
2001 Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R. REPuter: The manifold applications of repeat analysis on a genomic scale Nucleic Acids Research. 29: 4633-4642. PMID 11713313 DOI: 10.1093/Nar/29.22.4633  0.492
2001 Heber S, Stoye J. Algorithms for finding gene clusters Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2149: 252-263. DOI: 10.1007/3-540-44696-6_20  0.34
2000 Reinert K, Stoye J, Will T. An iterative method for faster sum-of-pairs multiple sequence alignment Bioinformatics. 16: 808-814. PMID 11108703  0.333
2000 Krause A, Stoye J, Vingron M. The SYSTERS protein sequence cluster set Nucleic Acids Research. 28: 270-272. PMID 10592244 DOI: 10.1093/Nar/28.1.270  0.357
1998 Stoye J. Multiple sequence alignment with the divide-and-conquer method Gene. 211. PMID 9669886 DOI: 10.1016/S0378-1119(98)00097-3  0.442
1998 Stoye J, Evers D, Meyer F. Rose: Generating sequence families Bioinformatics. 14: 157-163. PMID 9545448 DOI: 10.1093/Bioinformatics/14.2.157  0.48
1998 Dress A, Morgenstern B, Stoye J. The number of standard and of effective multiple alignments Applied Mathematics Letters. 11: 43-49. DOI: 10.1016/S0893-9659(98)00054-8  0.392
1997 Stoye J, Moulton V, Dress AWM. DCA: An efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment Computer Applications in the Biosciences. 13: 625-626. PMID 9475994 DOI: 10.1093/Bioinformatics/13.6.625  0.43
1997 Stoye J, Perrey S, Dress A. Improving the divide-and-conquer approach to sum-of-pairs multiple sequence alignment Applied Mathematics Letters. 10: 67-73. DOI: 10.1016/S0893-9659(97)00013-X  0.431
1997 Brinkmann G, Dress AWM, Perrey SW, Stoye J. Two applications of the divide&conquer principle in the molecular sciences Mathematical Programming. 79: 71-97. DOI: 10.1007/Bf02614312  0.306
1996 Tönges U, Perrey SW, Stoye J, Dress AWM. A general method for fast multiple sequence alignment Gene. 172: 33-41. PMID 8654965 DOI: 10.1016/0378-1119(96)00123-0  0.489
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