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Publications AG Genominformatik (old format, until 2011)

2011
[1]W. Gerlach and J. Stoye. Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic Acids Res., 39(14):e91, May 2011. [ bib ]
[2]J. Blom, T. Jakobi, D. Doppmeier, S. Jaenicke, J. Kalinowski, J. Stoye, and A. Goesmann. Exact and complete short read alignment to microbial genomes using GPU programming. Bioinformatics, 27(10):1351-1358, 2011. [ bib ]
[3]K. Brankatschk, J. Blom, A. Goesmann, T. H. M. Smits, and B. Duffy. The genome of a european fresh vegetable food safety outbreak strain Salmonella enterica subsp. enterica serovar weltevreden. J. Bacteriol., 193(8):JB-00123, 2011. [ bib ]
[4]F. Cicalese, P. Erdős, and Zsuzsanna Lipták. Efficient reconstruction of RC-equivalent strings. In Proc. WOCA, volume 6460 of Lecture Notes in Computer Science, pages 349-362, 2011. [ bib ]
[5]M. Dias Vieira Braga, E. Willing, and J. Stoye. Double cut and join with insertions and deletions. J.Comp.Biol., 18(9):1167-1184, 2011. [ bib ]
[6]P. L. Erdős, L. Soukup, and J. Stoye. Balanced vertices in trees and a simpler algorithm to compute the genomic distance. Appl. Math. Lett., 24(1):82-86, 2011. [ bib ]
[7]M. Hackl, T. Jakobi, J. Blom, D. Doppmeier, K. Brinkrolf, R. Szczepanowski, S. H. Bernhart, C. Höner zu Siederdissen, J. H. Bort, M. Wieser, R. Kunert, S. Jeffs, I. L. Hofacker, A. Goesmann, A. Pühler, N. Borth, and J. Grillari. Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: identification, annotation and profiling of microRNAs as targets for cellular engineering. J. Biotechnol., 153:62-75, 2011. [ bib ]
[8]S. Heber, R. Mayr, and J. Stoye. Common intervals of multiple permutations. Algorithmica, 60(2):1351-1358, 2011. [ bib ]
[9]F. Hufsky, L. Kuchenbecker, K. Jahn, J. Stoye, and S. Böcker. Swiftly computing center strings. BMC Bioinformatics, 12:106, 2011. [ bib ]
[10]B. Joseph, R.F. Schwarz, B. Linke, J. Blom, A. Becker, H. Claus, A. Goesmann, M. Frosch, T. Müller, U. Vogel, and C. Schoen. Virulence evolution of the human pathogen Neisseria meningitidis by recombination in the core and accessory genome. PloS one, 6(4):e18441, 2011. [ bib ]
[11]J. Kováč, R. Warren, M. Dias Vieira Braga, and J. Stoye. Restricted dcj model: Rearrangement problems with chromosome reincorporation. J. Comp.Biol., 18:1231-1241, 2011. [ bib ]
[12]I. Margaret, A. Becker, J. Blom, I. Bonilla, A. Goesmann, M. Göttfert, J. Lloret, V. Mittard-Runte, C. Rückert, J.E. Ruiz-Sainz, Vinardell J.M., and Weidner S. Symbiotic properties and first analyses of the genomic sequence of the fast growing model strain Sinorhizobium fredii HH103 nodulating soybean. J. Biotechnol., 155(1):11-9, 2011. [ bib ]
[13]R. Powney, T. H. M. Smits, T. Sawbridge, B. Frey, J. Blom, J. E. Frey, K. M. Plummer, S. V. Beer, J. Luck, B. Duffy, and B. Rodoni. Genome sequence of an Erwinia amylovora strain with pathogenicity restricted to Rubus plants. J. Bacteriol., 193(3):785, 2011. [ bib ]
[14]C. Rückert, J. Blom, X.H. Chen, O. Reva, and R. Borriss. Genome sequence of B. amyloliquefaciens type strain DSM7T reveals differences to plant-associated B. amyloliquefaciens FZB42. J. Biotechnol., 155:78-85, 2011. [ bib ]
[15]S. Schneiker-Bekel, D. Wibberg, T. Bekel, J. Blom, B. Linke, H. Neuweger, M. Stiens, F.J. Vorhölter, S. Weidner, A. Goesmann, A. Pühler, and A. Schlüter. The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome. J. Biotechnol., 155(1):20-33, 2011. [ bib ]
[16]C. Schoen, J. Weber-Lehmann, J. Blom, B. Joseph, A. Goesmann, A. Strittmatter, and M. Frosch. Whole-genome sequence of the transformable Neisseria meningitidis serogroup A strain WUE2594. J. Bacteriol., 193(8):2064-5, 2011. [ bib ]
[17]P. Schwientek, R. Szczepanowski, C. Rückert, J. Stoye, and A. Pühler. Sequencing of high G+C microbial genomes using the ultrafast pyrosequencing technology. J. Biotechnol., 155(1):68-77, 2011. [ bib ]
[18]D. Wibberg, J. Blom, S. Jaenicke, F. Kollin, O. Rupp, B. Scharf, S. Schneiker-Bekel, R. Sczcepanowski, A. Goesmann, J.C. Setubal, R. Schmitt, A. Pühler, and A. Schlüter. Complete genome sequencing of Agrobacterium sp H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid. J. Biotechnol., 155(1):50-62, 2011. [ bib ]
[19]R. Wittler, J. Maňuch, M. Patterson, and J. Stoye. Consistency of sequence-based gene clusters. J. Comp.Biol., 18(9):1023-1039, 2011. [ bib ]
[20]S. Wolfsheimer, I. Herms, S. Rahmann, and A. K. Hartmann. Accurate statistics for local sequence alignment with position-dependent scoring by rare-event sampling. BMC Bioinformatics, 12(47):1471-2105, 2011. [ bib ]
2010
[21]A. Bergeron, P. Medvedev, and J. Stoye. Rearrangement models and single-cut operations. J. Comp. Biol., 17(9):1213-1225, 2010. [ bib ]
[22]S. Besenbacher, B. Schwikowski, and J. Stoye. Indexing and searching a mass spectrometry database. In Algorithms and Applications: Essays Dedicated to Esko Ukkonen on the Occasion of His 60th Birthday, volume 6060 of LNCS, pages 62-76. 2010. [ bib ]
[23]G. Blin, D. Faye, and J. Stoye. Finding nested common intervals efficiently. J. Comp. Biol., 17(9):1183-1194, 2010. [ bib ]
[24]A. Bunkowski. Software tool for coupling chromatographic total ion current dependencies of GC/MSD and MCC/IMS. Int. J. Ion Mobil. Spectrom., 13(3-4):169-175, 2010. [ bib ]
[25]A. Bunkowski, S. Maddula, A. N. Davies, M. Westhoff, P. Litterst, B. Bödeker, and J. I. Baumbach. One-year time series of investigations of analytes within human breath using ion mobility spectrometry. Int. J. Ion Mobil. Spectrom., 13(3-4):141-148, 2010. [ bib ]
[26]P. Burcsi, F. Cicalese, G. Fici, and Zs. Lipták. On table arrangements, scrabble freaks, and jumbled pattern matching. In Proc. FUN, pages 89-101, 2010. [ bib ]
[27]F. Cicalese, P. L. Erdős, and Zs. Lipták. Efficient reconstruction of RC-equivalent strings. In Proc. IWOCA 2010, 2010. [ bib ]
[28]M. Dias Vieira Braga and J. Stoye. The solution space of sorting by DCJ. J. Comp. Biol., 17(9):1145-1165, 2010. [ bib ]
[29]M. Dias Vieira Braga, E. Willing, and J. Stoye. Genomic distance with DCJ and indels. In Proc. WABI, LNBI, pages 90-101, 2010. [ bib ]
[30]P. L. Erdős, L. Soukup, and J. Stoye. Balanced vertices in trees and a simpler algorithm to compute the genomic distance. Appl. Math. Lett., 24(1):82-86, 2010. [ bib ]
[31]P. L. Erdős, L. Soukup, and J. Stoye. Balanced vertices in trees and a simpler algorithm to compute the genomic distace. Technical report, arXiv:1004.2735v1 [cs.DM], 2010. [ bib ]
[32]F. Hufsky, L. Kuchenbecker, K. Jahn, J. Stoye, and S. Böcker. Swiftly computing center strings. In Proc. WABI, volume 6293 of LNBI, pages 325-336, 2010. [ bib ]
[33]P. Husemann and J. Stoye. Phylogenetic comparative assembly. Algorithms Mol. Biol., 5(1):3, 2010. [ bib ]
[34]P. Husemann and J. Stoye. r2cat: synteny plots and comparative assembly. Bioinformatics, 26(4):570-571, 2010. [ bib ]
[35]P. Husemann and J. Stoye. Repeat-aware comparative genome assembly. In Proc. GCB, volume P-173 of LNI, pages 61-70, 2010. [ bib ]
[36]K. Jahn. Efficient computation of approximate gene clusters based on reference occurrences. In Proc. RECOMB-CG, volume 6398 of LNBI, pages 264-277, 2010. [ bib ]
[37]B. Joseph, S. Schneiker-Bekel, A. Schramm-Gluck, J. Blom, H. Claus, B. Linke, R. F. Schwarz, A. Becker, A. Goesmann, M. Frosch, and C. Schön. Comparative genome biology of a serogroup B carriage and disease strain supports a polygenic nature of meningococcal virulence. J. Bacteriol., 192(20):5363, 2010. [ bib ]
[38]J. Kováč, M. Dias Vieira Braga, and J. Stoye. The problem of chomosome reincorporation in DCJ sorting and halving. In RECOMB-CG 2010, volume 6398 of LNBI, pages 13-24, 2010. [ bib ]
[39]J. Schneider, F. J Vorhölter, E. Trost, J. Blom, Y.R. Musa, H. Neuweger, K. Niehaus, S. Schatschneider, A. Tauch, and A. Goesmann. CARMEN - comparative analysis and in silico reconstruction of organism-specific metabolic networks. Genet. Mol. Res., 9(1):1660-1672, 2010. [ bib ]
[40]P. Schwientek, P. Ellinghaus, S. Steppan, D. D'Urso, M. Seewald, A. Kassner, R. Cebulla, S. Schulte-Eistrup, M. Morshuis, D. Röfe, A. El Banayosy, R. Körfer, and H. Milting. Global gene expression analysis in nonfailing and failing myocardium pre- and postpulsatile and nonpulsatile ventricular assist device support. Physiological Genomics, 42(3):397-405, 2010. [ bib ]
[41]T. H. M. Smits, F. Rezzonico, T. Kamber, J. Blom, A. Goesmann, J. E. Frey, and B. Duffy. Complete genome sequence of the fire blight pathogen Erwinia amylovora CFBP 1430 and comparison to other Erwinia spp. Mol. Plant-Microbe In., 23(4):384-393, 2010. [ bib ]
[42]E. Trost, S. Götktker, J. Schneider, S. Schneiker-Bekel, R. Szczepanowski, A. Tilker, P. Viehoever, W. Arnold, T. Bekel, J. Blom, K. H. Gartemann, B. Linke, A. Goesmann, A. Pühler, S. K. Shukla, and A. Tauch. Complete genome sequence and lifestyle of black-pigmented Corynebacterium aurimucosum ATCC 700975 (formerly C. nigricans CN-1) isolated from a vaginal swab of a woman with spontaneous abortion. BMC Genomics, 11(1):91, 2010. [ bib ]
[43]E. Trost, L. Ott, J. Schneider, J. Schröder, S. Jaenicke, A. Goesmann, P. Husemann, J. Stoye, F. A. Dorella, F. S.Rocha, S. de Castro Soares, V. D'Afonseca, A. Miyoshi, J. Ruiz, Ar. Silva, V. Azevedo, A. Burkovski, N. Guiso, O. F Join-Lambert, S. Kayal, and A. Tauch. 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(1):728, 2010. [ bib ]
[44]T. Wittkop, D. Emig, S. J. Lange, S. Rahmann, M. Albrecht, J. H. Morris, S. Böcker, J. Stoye, and J. Baumbach. Partitioning biological data with transitivity clustering. Nature Methods, 7(6):419-420, 2010. [ bib ]
[45]R. Wittler and J. Stoye. Consistency of sequence-based gene clusters. In Proc. RECOMB-CG, volume 6398 of LNBI, pages 252-263. Springer Verlag, 2010. [ bib ]
2009
[46]R. Ahlswede, F. Cicalese, C. Deppe, and U. Vaccaro. Two batch search with lie cost. IEEE. Trans. Inf. Theory, 55(4):1433-1439, 2009. [ bib ]
[47]T. Bekel, K. Henckel, H. Küster, V. M. Runte, H. Neuweger, D. Paarmann, O. Rupp, M. Zakrzewski, A. Puehler, J. Stoye, and A. Goesmann. 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. J. Biotechnol., 140(1-2):3-12, 2009. [ bib ]
[48]A. Bergeron, J. Mixtacki, and J. Stoye. A new linear time algorithm to compute the genomic distance via the double cut and join distance. Theor. Comput. Sci, 410(51):5300-5316, 2009. [ bib ]
[49]G. Blin and J. Stoye. Finding nested common intervals efficiently. In Proc. Recomb-CG 2009, volume 5817 of LNBI, pages 59-69, 2009. [ bib ]
[50]A. Bunkowski, B. Bodeker, S. Bader, M. Westhoff, P. Litterst, and J. I. Baumbach. MCC/IMS signals in human breath related to sarcoidosis-results of a feasibility study using an automated peak finding procedure. J. Breath Res., 3(4):046001 (10pp), 2009. [ bib ]
[51]S. Böcker, M. C. Letzel, Zs. Lipták, and A. Pervukhin. SIRIUS: decomposing isotope patterns for metabolite identification. Bioinformatics, 25(2):218-224, 2009. [ bib ]
[52]S. Böcker, K. Jahn, J. Mixtacki, and J. Stoye. Computation of median gene clusters. J. Comp. Biol., 16(8):1085-1099, 2009. [ bib ]
[53]F. Cicalese, G. Fici, and Zs. Lipták. Searching for jumbled patterns in strings. In Proc. of the Prague Stringology Conference 2009, pages 105-117, 2009. [ bib ]
[54]F. Cicalese, E. S. Laber, and M. Molinaro. On the complexity of searching in trees: Average-case minimization. CoRR, abs/0904.3503, 2009. [ bib ]
[55]F. Cicalese, F. Manne, and Q. Xin. Faster deterministic communication in radio networks. Algorithmica, 54(2):226-242, 2009. [ bib ]
[56]F. Cicalese and M. Milanič. Competitive evaluation of threshold functions in the priced information model. Annals of Operations Research, pages 1-22, 2009. [ bib ]
[57]M. Dias Vieira Braga and J. Stoye. Counting all DCJ sorting scenarios. In The Problem of Chromosome Reincorporation in DCJ Sorting and Halving, volume 5817 of LNBI, pages 36-47, 2009. [ bib ]
[58]J.C. Engelmann, S. Rahmann, M. Wolf, J. Schultz, E. Fritzilas, S. Kneitz, T. Dandekar, and T. Müller. Modeling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species. Mol. Ecol. Resour., 9(1):83-93, 2009. [ bib ]
[59]B. Escoffier, M. Milanič, and V. Th. Paschos. Simple and fast reoptimizations for the Steiner tree problem. Algorithmic Operations Research, 4(2):86-94, 2009. [ bib ]
[60]W. Gerlach, S. Jünemann, F. Tille, A. Goesmann, and J. Stoye. WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics, 10(1):430, 2009. [ bib ]
[61]N. Hoffmann and J. Stoye. ChromA: Signal based retention time alignment for chromatography-mass spectrometry data. Bioinformatics, 25(16):2080-2081, 2009. [ bib ]
[62]P. Husemann and J. Stoye. Phylogenetic comparative assembly. In Proc. WABI 2009, volume 5724 of LNBI, pages 145-156, 2009. [ bib ]
[63]K. Jahn and J. Stoye. Approximative Gencluster und ihre Anwendung in der komparativen Genomik. Informatik-Spektrum, 32(4):288-300, 2009. [ bib ]
[64]M. Kaminski, V. V. Lozin, and M. Milanič. Recent developments on graphs of bounded clique-width. Discrete Appl. Math., 157:2747-2761, 2009. [ bib ]
[65]M. Kaminski, P. Medvedev, and M. Milanič. On the plane-width of graphs. Electronic Notes in Discrete Mathematics, 34:633-637, 2009. [ bib ]
[66]P. Medvedev and J. Stoye. Rearrangement models and single-cut operations. In Proc. Recomb-CG 2009, LNBI, pages 84-97, 2009. [ bib ]
[67]J. Stoye and R. Wittler. A unified approach for reconstructing ancient gene clusters. IEEE/ACM Trans. Comput. Biol. Bioinf., 6(3):387-400, 2009. [ bib ]
[68]M. Zeschnigk, M. Martin, G. Betzl, A. Kalbe, C. Sirsch, K. Buiting, S. Gross, E. Fritzilas, B. Frey, S. Rahmann, and B. Horsthemke. Massive parallel bisulfite sequencing of CG-rich DNA fragments reveals that methylation of many X-chromosomal CpG islands in female blood DNA is incomplete. Hum. Mol. Genet., 18(8):1439-1448, 2009. [ bib ]
2008
[69]R. Ahlswede, F. Cicalese, and C. Deppe. Searching with lies under error cost constraints. Discrete Appl. Math., 156(9):1444-1460, 2008. [ bib ]
[70]V. E. Alekseev, V. V. Lozin, D. Malyshev, and M. Milanič. The maximum independent set problem in planar graphs. In Proc. MFCS 2008, pages 96-107, 2008. [ bib ]
[71]J. A. Amgarten Quitzau and J. Stoye. A space efficient representation for sparse de Bruijn subgraphs. Report 2008-02, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2008. [ bib ]
[72]J. A. Amgarten Quitzau and J. Stoye. Detecting repeat families in incompletely sequenced genomes. In Proc. WABI, volume 5251 of LNBI, pages 342-353, 2008. [ bib ]
[73]S. Böcker, K. Jahn, J. Mixtacki, and J. Stoye. Computation of median gene clusters. In Proc. RECOMB 2008, volume 4955 of Lecture Notes in Computer Science, pages 331-345, 2008. [ bib ]
[74]J. Baumbach and L. Apeltsin. Linking cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics, 9(1):184, 2008. [ bib ]
[75]J. Baumbach, T. Wittkop, J. Weile, T. Kohl, and S. Rahmann. MoRAine - A web server for fast computational transcription factor binding motif re-annotation. J. Int. Bioinf., 5(2), 2008. [ bib ]
[76]A. Bergeron, J. Mixtacki, and J. Stoye. On computing the breakpoint reuse rate in rearrangement scenarios. In Proc. Recomb-CG 2008, volume 5267 of LNBI, pages 226-240, 2008. [ bib ]
[77]A. Bergeron, J. Mixtacki, and J. Stoye. HP distance via double cut and join. In Proc. CPM 2008, volume 5029 of LNCS, pages 56-68, 2008. [ bib ]
[78]J. Boyar and P. Medvedev. The relative worst order ratio applied to seat reservation. ACM Trans. Algorithms, 4(4):1-22, 2008. [ bib ]
[79]S. Böcker, Zs. Lipták, M. Martin, A. Pervukhin, and H. Sudek. Decomp - from interpreting mass spectrometry peaks to solving the money changing problem. Bioinformatics, 24(4):591-593, 2008. [ bib ]
[80]S. A. de Carvalho Jr. and S. Rahmann. Modeling and optimizing oligonucleotide microarray layout. In Bioinformatics Algorithms: Techniques and Applications, Wiley Book Series on Bioinformatics. 2008. [ bib ]
[81]F. Cicalese and E. S. Laber. Function evaluation via linear programming in the priced information model. In Proc. ICALP 2008, pages 173-185, 2008. [ bib ]
[82]F. Cicalese and M. Milanič. On parsimony haplotyping. Technical report 2008-04, Technische Fakultät, Universität Bielefeld, 2008. [ bib ]
[83]F. Cicalese and M. Milanič. Computing with priced information: game trees and the value dependent cost model. Technical report 2008-03, Technische Fakultät, Universität Bielefeld, 2008. [ bib ]
[84]F. Cicalese and M. Milanič. Computing with priced information: when the value makes the price. In Proc. ISAAC 2008, pages 378-389, 2008. [ bib ]
[85]T. Ejaz, S. Rahmann, and J. Stoye. Online abelian pattern matching. Report 2008-01, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2008. [ bib ]
[86]E. Fritzilas, Y.A. Rios-Solis, and S. Rahmann. Structural identifiability in low-rank matrix factorization. In Proc. COCOON 2008, pages 140-148, 2008. [ bib ]
[87]S. Hazelhurst, W. Hide, Zs. Lipták, R. Nogueira, and R. Starfield. An overview of the WCD EST clustering tool. Bioinformatics, 24(13):1542-1546, 2008. [ bib ]
[88]I. Herms and S. Rahmann. Computing alignment seed sensitivity with probabilistic arithmetic automata. In Proc. WABI 2008, pages 318-329, 2008. [ bib ]
[89]T. Kohl, J. Baumbach, B. Jungwirth, A. Pühler, and A. Tauch. The GlxR regulon of the amino acid producer Corynebacterium glutamicum: in silico and in vitro detection of DNA binding sites of a global transcription regulator. J. Biotechnol., 135(4):340-350, 2008. [ bib ]
[90]L. Krause, N. Diaz, A. Goesmann, S. Kelley, T. Nattkemper, F. Rohwer, R. Edwards, and J. Stoye. Phylogenetic classification of short environmental DNA Fragments. Nucleic Acids Res., 36(7):2230-2239, 2008. [ bib ]
[91]L. Krause, N. N. Diaz, R. A. Edwards, K.-H. Gartemann, H. Krömeke, H. Neuweger, A. Pühler, K. Runte, A. Schlüter, J. Stoye, R. Szczepanowski, A. Tauch, and A. Goesmann. Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor. J. Biotechnol., 136(1-2):91-101, 2008. [ bib ]
[92]V. V. Lozin and M. Milanič. On finding augmenting graphs. Discrete Appl. Math., 156:2517-2529, 2008. [ bib ]
[93]V. V. Lozin and M. Milanič. A polynomial algorithm to find an independent set of maximum weight in a fork-free graph. J. Discr. Alg., 6(4):595-604, 2008. [ bib ]
[94]M. Milanič and J. Monnot. The complexity of the exact weighted independent set problem. In Combinatorial optimization and theoretical computer science: interfaces and perspectives : 30th anniversary of the LAMSADE, pages 393-432. 2008. [ bib ]
[95]J. Mixtacki. Genome halving under DCJ revisited. In Proc. COCOON 2008, pages 276-286, 2008. [ bib ]
[96]H. Neuweger, S.P. Albaum, M. Dondrup, M. Persicke, T. Watt, K. Niehaus, J. Stoye, and A. Goesmann. MeltDB: A software platform for the analysis and integration of metabolomics experiment data. Bioinformatics, 24(23):2726-2732, 2008. [ bib ]
[97]S. Oehm, D. Gilbert, A. Tauch, J. Stoye, and A. Goesmann. Comparative Pathway Analyzer-a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. Nucl. Acids Res., 36:W433-437, 2008. [ bib ]
[98]P.Medvedev and M. Brudno. Ab initio whole genome shotgun assembly with mated short reads. In Proc. RECOMB 2008, pages 50-64, 2008. [ bib ]
[99]S. Rahmann and G. W. Klau. Integer linear programming techniques for discovering approximate gene clusters. In Bioinformatics Algorithms: Techniques and Applications. 2008. [ bib ]
[100]C. Schoen, J. Blom, H. Claus, A. Schramm-Gluck, P. Brandt, T. Muller, A. Goesmann, B. Joseph, S. Konietzny, and O. Kurzai. Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis. Proc. Nat. Acad. Sci., USA, 105:3473-3478, 2008. [ bib ]
[101]K.-B. Schürmann and J. Stoye. Counting suffix arrays and strings. Theor. Comp. Sci., 395(2-3):220-234, 2008. [ bib ]
[102]J. Stoye. Suffix tree construction in RAM (1997; Farach-Colton). In M. Y. Kao (ed.): Encyclopedia of Algorithms, pages 925-928. 2008. [ bib ]
[103]A. Tauch, J. Schneider, R. Szczepanowski, A. Tilker, P. Viehoever, K.H. Gartemann, W. Arnold, J. Blom, K. Brinkrolf, and I. Brune. Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids. J. Biotechnol., 2008. [ bib ]
2007
[104]E. Baake and I. Herms. Single-crossover dynamics: Finite versus infinite populations. Bull. Math. Biol., 2007. [ bib ]
[105]N. Bansal, M. Cieliebak, and Zs. Lipták. Finding submasses in weighted strings with fast fourier transform. Discrete Applied Mathmatics, 155:707-718, 2007. [ bib ]
[106]J. Baumbach. CoryneRegNet 4.0 - a reference database for corynebacterial gene regulatory networks. BMC Bioinformatics, 8(1):429, 2007. [ bib ]
[107]J. Baumbach, A. Bunkowski, S. Lange, T. Oberwahrenbrock, N. Kleinbölting, and S. Rahmann. An integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath. Bioinformatics Journal of Integrative Bioinformatics, 4(3):75, 2007. [ bib ]
[108]J. Baumbach, A. Bunkowski, S. Lange, T. Oberwahrenbrock, N. Kleinbölting, S. Rahmann, and J.I. Baumbach. IMS2 - an integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath. Journal of Integrative Bioinformatics, 4(3):75, 2007. [ bib ]
[109]J. Baumbach, T. Wittkop, S. Rahmann, K. Brinkrolf, and A. Tauch. CoryneRegNet 3.0 - an interactive bioinformatics platform for the analysis of gene regulatory networks in corynebacteria and escherichia coli. J. Biotechnol., 129:279-289, 2007. [ bib ]
[110]S. Böcker and H.-M. Kaltenbach. Mass spectra alignments and their significance. J. Discrete Algorithms, 5(4):714-728, 2007. [ bib ]
[111]S. Böcker, M.C. Letzel, Zs. Lipták, and A. Pervukhin. Identifying metabolites with integer decomposition techniques, using only their mass spectrometric isotope patterns. Technical Report Technical report no. 2007-01, Technical Faculty, Bielefeld University, 2007. [ bib ]
[112]S. Böcker and Zs. Lipták. A fast and simple algorithm for the Money Changing Problem. Algorithmica, 48(4):413-432, 2007. [ bib ]
[113]S.A. de Carvalho Jr. and S. Rahmann. Improving the design of GeneChip arrays by combining placement and embedding. In Computational Systems Bioformatics Conference, pages 417-427, 2007. [ bib ]
[114]F. Cicalese and J. A. Amgarten Quitzau. 2-stage fault tolerant interval group testing. In Proceedings of the 18th International Symposium on Algorithms and Computation, volume 4835, pages 858-868, 2007. [ bib ]
[115]F. Cicalese and J. A. Amgarten Quitzau. 2-stage fault tolerant interval group testing. Technical Report 2007-2, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2007. [ bib ]
[116]F. Cicalese, P. Damaschke, L. Tansini, and S. Werth. Overlaps help: Improved bounds for group testing with interval queries. Discrete Applied Mathematics, 155(3):288-299, 2007. [ bib ]
[117]F. Cicalese and C. Deppe. Perfect minimally adaptive q-ary search with unreliable tests. Journal of Statistical Planning and Inference, 137:162-175, 2007. [ bib ]
[118]G. Didier, T. Schmidt, J. Stoye, and D. Tsur. Character sets of strings. J. Discr. Alg., 5(2):330-340, 2007. [ bib ]
[119]B. Escoffier, M. Milanič, and V.Th. Paschos. Simple and fast reoptimizations for the Steiner tree problem. DIMACS technical report 2007-01, DIMACS, Center for Discrete Mathematics and Theoretical Computer Science, NJ, 2007. [ bib ]
[120]D. Gerlach, M. Wolf, T. Dandekar, T. Müller, A. Pokorny, and S. Rahmann. Deep metazoan phylogeny. In Silico Biology, 7:Article 15, 2007. [ bib ]
[121]C. Höner zu Siederdissen, S. Ragg, and S. Rahmann. Discovering biomarkers for myocardial infarction from SELDI-TOF spectra. In Advances in Data Analysis - Proceedings of the 30th Annual Conference of the Gesellschaft für Klassifikation e.V., Studies in Classification, Data Analysis, and Knowledge Organization, pages 569-576, 2007. [ bib ]
[122]H.-M. Kaltenbach, A. Wilke, and S. Böcker. SAMPI: Protein identification with mass spectra alignments. BMC Bioinformatics, 8:102, 2007. [ bib ]
[123]M. Kaminski, V.V. Lozin, and M. Milanič. Recent developments on graphs of bounded clique-width. RUTCOR research report 06-2007, Rutgers Center for Operations Research, Rutgers University, NJ, 2007. [ bib ]
[124]G. W. Klau, S. Rahmann, A. Schliep, M. Vingron, and K. Reinert. Integer linear programming approaches for non-unique probe selection. Discrete Applied Mathematics, 155(6-7):840-856, 2007. [ bib ]
[125]L. Krause, A. C. McHardy, T. W. Nattkemper, A. Pühler, J. Stoye, and F. Meyer. GISMO - gene identification using a support vector machine for ORF classification. Nucleic Acids Res., 35(2):540-549, 2007. [ bib ]
[126]V.V. Lozin and M. Milanič. Maximum independent sets in graphs of low degree. In Proc. 18th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 2007), pages 874-880, 2007. [ bib ]
[127]V.V Lozin and M. Milanič. Tree-width and optimization in bounded degree graphs. In Proc. 33rd International Workshop on Graph-Theoretic Concepts in Computer Science (WG 2007), volume 4769 of LNCS, pages 45-54, 2007. [ bib ]
[128]C. Meisinger-Henschel, M. Schmidt, S. Lukassen, B. Linke, L. Krause, S. Konietzny, A. Goesmann, P. Howley, P. Chaplin, M. Suter, and J. Hausmann. The genomic sequence of chorioallantois vaccinia virus ankara, the ancestor of modified vaccinia virus ankara. J Gen Viro, 88(12):3249-3259, 2007. [ bib ]
[129]H. Neuweger, J. Baumbach, S. Albaum, T. Bekel, M. Dondrup, A. Hueser, J. Kalinowski, S. Oehm, A. Puehler, S. Rahmann, J. Weile, and A. Goesmann. CoryneCenter - an online resource for the integrated analysis of corynebacterial genome and transcriptome data. BMC Syst Biol, 1(1):55, 2007. [ bib ]
[130]S. Rahmann, T. Wittkop, J. Baumbach, M. Martin, A. Truss, and S. Böcker. Exact and heuristic algorithms for weighted cluster editing. Comput Syst Bioinformatics Conf, 6(1):391-401, 2007. [ bib ]
[131]A. Scherbart, W. Timm, S. Böcker, and T. W. Nattkemper. Neural network approach for mass spectrometry prediction by peptide prototyping. In ICANN'07, 2007. [ bib ]
[132]A. Scherbart, W. Timm, S. Böcker, and T. W. Nattkemper. Som-based peptide prototyping for mass spectrometry peak intensity prediction. In WSOM'07, 2007. [ bib ]
[133]T. Schmidt and J. Stoye. Gecko and GhostFam - rigorous and efficient gene cluster detection in prokaryotic genomes. In Methods in Molecular Biology, volume 2, chapter 12, pages 165-182. 2007. [ bib ]
[134]S. Schneiker-Bekel, O. Perlova, O. Kaiser, K. Gerth, A. Alici, M. Altmeyer, D. Bartels, T. Bekel, S. Beyer, E. Bode, C. Bolten H. Bode, J. Choudhuri, S. Doss, Y. Elnakady, B. Frank, L. Gaigalat, A. Goesmann, C. Groeger, F. Gross, L. Jelsbak, L. Jelsbak, J. Kalinowski, C. Kegler, T. Knauber, S. Konietzny, M. Kopp, L. Krause, D. Krug, B. Linke, T. Mahmud, R. Martinez-Arias, A. McHardy, M. Merai, F. Meyer, S. Mormann, J. Munoz-Dorado, J. Perez, S. Pradella, S. Rachid, G. Raddatz, F. Rosenau, and F. Sasse C. Rückert, M. Scharfe, S. Schuster, G. Suen, A. Treuner-Lange, G. Velicer, F. Vorhölte, K. Weissman, R. Welch, S. Wenzel, D. Whitworth, S. Wilhelm, C. Wittmann, H. Blocker, A. Pühler, and Rolf Müller. Complete genome sequence of the myxobacterium Sorangium cellulosum. Nat. Biotechnol., 25(11):1281-1289, 2007. [ bib ]
[135]K.-B. Schürmann and J. Stoye. An incomplex algorithm for fast suffix array construction. Softw. Pract. Exper., 37(3):309-329, 2007. [ bib ]
[136]A. Mellmann and. T. Weniger, C. Berssenbrügge, J. Rothgänger, M. Sammeth, J. Stoye, and D. Harmsen. 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, 2007. [ bib ]
[137]N. Välimäki, W. Gerlach, K. Dixit, and V. Mäkinen. Compressed suffix tree - a basis for genome-scale sequence analysis. Bioinformatics, 23:629-630, 2007. [ bib ]
[138]N. Välimäki, W. Gerlach, K. Dixit, and V. Mäkinen. Engineering a compressed suffix tree implementation. In Proceedings of 6th Workshop on Experimental Algorithms (WEA'07), LNCS 4525, pages 217-228, 2007. [ bib ]
[139]T. Wittkop, J. Baumbach, FP. Lobo, and S. Rahmann. Large scale clustering of protein sequences with FORCE - a layout based heuristic for weighted cluster editing. BMC Bioinformatics, 8(1):396, 2007. [ bib ]
2006
[140]J. Baumbach, K. Brinkrolf, L. Czaja, S. Rahmann, and A. Tauch. CoryneRegNet: An ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. BMC Genomics, 7(1):24, 2006. [ bib ]
[141]J. Baumbach, K. Brinkrolf, T. Wittkop, A. Tauch, and S. Rahmann. CoryneRegNet 2: An integrative bioinformatics approach for reconstruction and comparison of transcriptional regulatory networks in prokaryotes. Journal of Integrative Bioinformatics, 3(2):24, 2006. [ bib ]
[142]A. Bergeron, J. Mixtacki, and J. Stoye. On sorting by translocations. J. Comp. Biol., 13(2):567-578, 2006. [ bib ]
[143]A. Bergeron, J. Mixtacki, and J. Stoye. A unifying view of genome rearrangements. In Proc. WABI, volume 4175 of LNBI, pages 163-173, 2006. [ bib ]
[144]A. Bergeron and J. Stoye. On the similarity of sets of permutations and its applications to genome comparison. J. Comp. Biol., 13(7):1345-1354, 2006. [ bib ]
[145]S. Böcker. Sequencing from compomers: The puzzle. Theor. Comput. Syst., 39(3):455-471, 2006. [ bib ]
[146]S. Böcker, M. Letzel, Zs. Lipták, and A. Pervukhin. Decomposing metabolomic isotope patterns. In Proc. WABI, volume 4175 of LNCS, pages 12-23, 2006. [ bib ]
[147]S. Böcker and V. Mäkinen. Combinatorial approaches for mass spectra recalibration. In Computational Proteomics, number 05471 in Dagstuhl Seminar Proceedings, 2006. [ bib ]
[148]S.A. de Carvalho Jr. and S. Rahmann. Improving the layout of oligonucleotide microarrays: Pivot Partitioning. In Proc. 6th Workshop of Algorithms in Bioinformatics, volume 4175 of LNBI, pages 321-332, 2006. [ bib ]
[149]S.A. de Carvalho Jr. and S. Rahmann. Microarray layout as a quadratic assignment problem. In Proc. German Conference on Bioinformatics, volume P-83 of Lecture Notes in Informatics, pages 11-20, 2006. [ bib ]
[150]C. Chauve, Y. Diekmann, S. Heber, J. Mixtacki, S. Rahmann, and J. Stoye. On common intervals with errors. Technical Report 2006-02, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2006. [ bib ]
[151]F. Cicalese and C. Deppe. Q-ary Ulam-Rényi game with constrained lies. In General Theory of Information Transfer and Combinatorics, volume 4123 of LNCS, pages 663-679, 2006. [ bib ]
[152]F. Cicalese, L. Gargano, and U. Vaccaro. A note on approximation of uniform distributions from variable-to-fixed length codes. IEEE Transactions on Information Theory, 52(8):3772-3777, 2006. [ bib ]
[153]F. Cicalese and E. Laber. On the competitive ratio of evaluating priced functions. In Proc. 17th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 2006), pages 944-953, 2006. [ bib ]
[154]F. Cicalese, F. Manne, and Q. Xin. Faster centralized communication in radio networks. In Proc. 17th International Symposium on Algorithms and Computation (ISAAC 2006), volume 4288 of LNCS, pages 339-348, 2006. [ bib ]
[155]K. Dixit, W. Gerlach, V. Mäkinen, and N. Välimäki. Engineering a compressed suffix tree implementation. Technical Report C-2006-37, Department of Computer Science, University of Helsinki, 2006. [ bib ]
[156]C. Höner zu Siederdissen, S. Ragg, and S. Rahmann. Discovering biomarkers for myocardial infarction from SELDI-TOF spectra. In Proc. 30th Annual Conference of the German Classification Society. 2006. [ bib ]
[157]H.-M. Kaltenbach, S. Böcker, and S. Rahmann. Markov additive chains and applications to fragment statistics for peptide mass fingerprinting. In Proc. RECOMB Satellite Conference on Systems Biology and Computational Proteomics, LNBI, 2006. [ bib ]
[158]L. Krause, N. N. Diaz, D. Bartels, R. A. Edwards, A. Pühler, F. Rohwer, F. Meyer, and J. Stoye. Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22(14):e281-e289, 2006. [ bib ]
[159]J. Köhler, J. Baumbach, J. Taubert, M. Specht, Andre Skusa, Alexander Rueegg, Chris Rawlings, Paul Verrier, and Stephan Philippi. Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics, 22(11):1383-1390, 2006. [ bib ]
[160]S. Rahmann. Subsequence combinatorics and applications to microarray production, DNA sequencing and chaining algorithms. In Combinatorial Pattern Matching (CPM), volume 4009 of LNCS, pages 153-164, 2006. [ bib ]
[161]S. Rahmann and G. W. Klau. Integer linear programs for discovering approximate gene clusters. In Proc. 6th Workshop on Algorithms in Bioinformatics (WABI), volume 4175 of LNBI, pages 298-309, 2006. [ bib ]
[162]S. Rahmann, T. Müller, T. Dandekar, and M. Wolf. Efficient and robust analysis of large phylogenetic datasets. In Advanced Data Mining Techonolgies in Bioinformatics, chapter VI, pages 104-117. 2006. [ bib ]
[163]K. Rasmussen, J. Stoye, and E. W. Myers. Efficient q-gram filters for finding all epsilon-matches over a given length. J. Comp. Biol., 13(2):296-308, 2006. [ bib ]
[164]M. Sammeth, T. Griebel, F. Tille, and J. Stoye. Panta rhei (QAlign2): an open graphical environment for sequence analysis. Bioinformatics, 22(7):889-890, 2006. [ bib ]
[165]M. Sammeth and J. Stoye. Comparing tandem repeats with duplications and excisions of variable degree. IEEE/ACM Trans. Comput. Biol. Bioinf., 3(4):395-407, 2006. [ bib ]
[166]A. Schliep and S. Rahmann. Decoding non-unique oligonucleotide hybridization experiments of targets related by a phylogenetic tree. Bioinformatics, 22(14; ISMB'06):e424-e430, 2006. [ bib ]
[167]J. Stoye. Index structures in biological sequence analysis: From simplicity to complexity and back. In Proc. JOBIM 2006, page 3, 2006. Invited Abstract. [ bib ]
[168]W. Timm, S. Böcker, T. Twellmann, and T. W. Nattkemper. Peak intensity prediction for PMF mass spectra using support vector regression. In Proc. of International FLINS Conference on Applied Artificial Intelligence (FLINS 2006), pages 565-572, 2006. [ bib ]
2005
[169]R. Ahlswede, F. Cicalese, and C. Deppe. Searching with lies under error transition cost constraints. Electronic Notes in Discrete Mathematics, 21:173-179, 2005. [ bib ]
[170]W. R. Atchley, J. Zhao, A. D. Fernandes, and T. Drüke. Solving the protein sequence metric problem. Proc. Natl. Acad. Sci. USA, 102(18), 2005. [ bib ]
[171]S. Böcker and H.-M. Kaltenbach. Mass spectra alignments and their significance. In Proc. Combinatorial Pattern Matching, volume 3537 of LNBI, pages 429-441, 2005. [ bib ]
[172]C. Bannert and J. Stoye. Protein annotation by secondary structure based alignments (PASSTA). In Proc. CompLife 2005, volume 3695 of LNBI, pages 79-90, 2005. [ bib ]
[173]D. Bartels, S. Kespohl, S. Albaum, T. Drüke, A. Goesmann, J. Herold, O. Kaiser, A. Pühler, F. Pfeiffer, G. Raddatz, J. Stoye, F. Meyer, and S. Schuster. BACCardi - a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. Bioinformatics, 21(7):853-859, 2005. [ bib ]
[174]A. Bergeron, J. Mixtacki, and J. Stoye. On sorting by translocations. In Proc. RECOMB 2005, pages 615-629, 2005. [ bib ]
[175]A. Bergeron, J. Mixtacki, and J. Stoye. The inversion distance problem. In Mathematics of Evolution and Phylogeny, chapter 10, pages 262-290. 2005. [ bib ]
[176]S. Böcker and H.-M. Kaltenbach. Mass spectra alignments and their significance. In Proc. of Combinatorial Pattern Matching Symposium (CPM 2005), volume 3537 of LNCS, pages 429-441, 2005. [ bib ]
[177]S. Böcker and Zs. Lipták. The money changing problem revisited: Computing the Frobenius number in time O(k a1). In Proc. 11th Annual International Conference on Computing and Combinatorics (COCOON 2005), volume 3595 of LNCS, pages 965-974, 2005. [ bib ]
[178]S. Böcker and Zs. Lipták. Efficient mass decomposition. In Symposium on Applied Computing (SAC 2005), pages 151-157, 2005. [ bib ]
[179]S. Böcker and V. Mäkinen. Maximum line-pair stabbing problem and its variations. In Proc. 21st European Workshop on Computational Geometry (EWCG 2005), pages 183-186, 2005. [ bib ]
[180]S. Böcker and J. Stoye. Informatische Methoden zur Protein-Identifikation. LaborPraxis, 29(10):24-26, 2005. [ bib ]
[181]S. de Carvalho Jr. and S. Rahmann. Searching for the shortest common supersequence. Technical Report 2005-03, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2005. [ bib ]
[182]F. Cicalese, P. Damaschke, L. Tansini, and S. Werth. Overlaps help: Improved bounds for group testing with interval queries. Technical Report 2005-1, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2005. [ bib ]
[183]F. Cicalese, P. Damaschke, L. Tansini, and S. Werth. Overlaps help: Improved bounds for group testing with interval queries. In Proc. 11th Annual International Conference on Computing and Combinatorics (COCOON 2005), pages 935-944, 2005. [ bib ]
[184]F. Cicalese, P. Damaschke, and U. Vaccaro. Optimal group testing strategies with interval queries and their application to splice site detection. In Proc. 5th International Conference on Computational Science (ICCS 2005), volume 3515 of LNCS, pages 1029-1037, 2005. [ bib ]
[185]F. Cicalese and C. Deppe. Q-ary Ulam-Rényi game with constrained lies. Electronic Notes in Discrete Mathematics, 21:255-261, 2005. [ bib ]
[186]F. Cicalese and E. S. Laber. An optimal algorithm for querying priced information: Monotone boolean functions and game trees. In Proc. 13th Annual European Symposium on Algorithms (ESA 2005), volume 3669 of LNCS, pages 664-676, 2005. [ bib ]
[187]F. Cicalese and E. S. Laber. A new strategy for querying priced information. In Proc. 37th Annual ACM Symposium on Theory of Computing (STOC 2005), pages 674-683, 2005. [ bib ]
[188]M. Ehrich, S. Böcker, and D. van den Boom. Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS. Nucleic Acids Res., 33(4):e38, 2005. [ bib ]
[189]K. Fredriksson, V. Mäkinen, and G. Navarro. Flexible music retrieval in sublinear time. In Proceedings of Prague Stringology Conference (PSC 2005), pages 174-188, 2005. [ bib ]
[190]R. González, S. Grabowski, V. Mäkinen, and G. Navarro. Practical implementation of rank and select queries. In Poster Proc. of Workshop on Efficient and Experimental Algorithms (WEA 2005), 2005. [ bib ]
[191]J. Grossmann, F.F. Roos, M. Cieliebak, Zs. Lipták, L.K. Mathis, M. Müller, W. Gruissem, and S. Baginsky. Audens: a tool for automated peptide de novo sequencing. Journal of Proteome Research, 10:1768-1774, 2005. [ bib ]
[192]J. Grossmann, F. F. Roos, M. Cieliebak, R. Jacob, Zs. Lipták, L. K. Mathis, M. Müller, P. Widmayer, W. Gruissem, and S. Baginsky. AUDENS: A tool for automated peptide de novo sequencing. J. Proteome Res., 10:1768-1774, 2005. [ bib ]
[193]H.-M. Kaltenbach, H. Sudek, S. Böcker, and S. Rahmann. Statistics of cleavage fragments in random weighted strings. Technical Report 2005-06, Abteilung Informationstechnik, Technische Fakultät, Universität Bielefeld, 2005. [ bib ]
[194]H.-M. Kaltenbach, H. Sudek, S. Böcker, and S. Rahmann. Statistics of cleavage fragments in random weighted strings. Technical Report 2005-06, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2005. [ bib ]
[195]A. Krause, J. Stoye, and M. Vingron. Large scale hierarchical clustering of protein sequences. BMC Bioinformatics, 6(15), 2005. [ bib ]
[196]Zs. Lipták. Strings in Proteomics and Transcriptomics. Algorithmic and Combinatorial Questions in Mass Spectrometry and EST Clustering. PhD thesis, Universität Bielefeld, 2005. [ bib ]
[197]V. Mäkinen. Peak alignment using restricted edit distances. In Proc. 6th International Symposium on Computational Biology and Genome Informatics (CBGI 2005), 2005. [ bib ]
[198]V. Mäkinen and G. Navarro. Succinct suffix arrays based on run-length encoding. In Proc. 16th Annual Symposium on Combinatorial Pattern Matching (CPM 2005), volume 3537 of LNCS, pages 45-56, 2005. [ bib ]
[199]M. J. Palakal, S. Rahmann, and B. Liao. Editorial message: special track on bioinformatics. In Proc. ACM Symposium on Applied Computing (SAC), page 99. 2005. [ bib ]
[200]S. Röpcke, S. Grossmann, S. Rahmann, and M. Vingron. T-Reg Comparator: an analysis tool for the comparison of position weight matrices. Nucleic Acids Research, 33(Web server issue):W438-W441, 2005. [ bib ]
[201]S. Rahmann. Algorithmen für das Design von DNA-Microarrays. In Ausgezeichnete Informatikdissertationen 2004, volume D-5 of Lecture Notes in Informatics, pages 145-154. 2005. [ bib ]
[202]K. R. Rasmussen, J. Stoye, and E. W. Myers. Efficient q-gram filters for finding all ε-matches over a given length. In Proc. RECOMB 2005, volume 3500 of LNBI, pages 189-203, 2005. [ bib ]
[203]M. Sammeth and J. Stoye. Alignment of tandem repeats with excision, duplication, substitution and indels (EDSI). Report 2005-05, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2005. [ bib ]
[204]M. Sammeth, T. Weniger, D. Harmsen, and J. Stoye. Alignment of tandem repeats with excision, duplication, substitution and indels (EDSI). In Proc. WABI 2005, volume 3692 of LNBI, pages 276-290, 2005. [ bib ]
[205]K.-B. Schürmann and J. Stoye. An incomplex algorithm for fast suffix array construction. In Proc. ALENEX/ANALCO 2005, pages 77-85, 2005. [ bib ]
[206]K.-B. Schürmann and J. Stoye. Counting suffix arrays and strings. Report 2005-04, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2005. [ bib ]
[207]K.-B. Schürmann and J. Stoye. Counting suffix arrays and strings. In Proc. SPIRE 2005, volume 3772 of LNCS, pages 55-66, 2005. [ bib ]
2004
[208]N. Bansal, M. Cieliebak, and Zs. Lipták. Efficient algorithms for finding submasses in weighted strings. In Proc. of Combinatorial Pattern Matching Symposium (CPM 2004), volume 3109 of LNCS, pages 194-204, 2004. [ bib ]
[209]A. Bergeron, J. Mixtacki, and J. Stoye. Reversal distance without hurdles and fortresses. In Proc. CPM 2004, volume 3109 of LNCS, pages 388-399, 2004. [ bib ]
[210]S. Böcker. Sequencing from compomers is NP-hard. Technical Report 2004-01, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2004. [ bib ]
[211]S. Böcker. Weighted sequencing from compomers: DNA de-novo sequencing from mass spectrometry data in the presence of false negative peaks. In Proc. GCB 2004, volume P-53 of LNI, pages 13-23, 2004. [ bib ]
[212]S. Böcker. Sequencing from compomers: The puzzle. In Proc. FUN with Algorithms 2004 (FUN 2004), pages 132-146, 2004. [ bib ]
[213]S. Böcker. Unrooted supertrees: Limitations, traps, and phylogenetic patchworks. In Phylogenetic supertrees: Combining information to reveal the Tree of Life, volume 4 of Computational Biology Book Series, chapter 15, pages 331-351. 2004. [ bib ]
[214]S. Böcker. Sequencing from compomers: Using mass spectrometry for DNA de-novo sequencing of 200+ nt. J. Comput. Biol., 11(6):1110-1134, 2004. [ bib ]
[215]S. Böcker and Zs. Lipták. The money changing problem revisited: Computing the Frobenius number in time O(k a1). Technical Report 2004-2, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2004. [ bib ]
[216]M. Cieliebak, T. Erlebach, Zs. Lipták, J. Stoye, and Emo Welzl. Algorithmic complexity of protein identification: Combinatorics of weighted strings. Discrete Appl. Math., 137(1):27-46, 2004. [ bib ]
[217]C. Dieterich, S. Rahmann, and M. Vingron. Functional inference from non-random distributions of conserved predicted transcription factor binding sites. Bioinformatics, 20(Suppl.1):i109-i115, 2004. [ bib ]
[218]P. Ferragina, G. Manzini, V. Mäkinen, and G. Navarro. Compressed representations of sequences and full-text indexes. Technical Report 2004-5, Technische Fakultät, Universität Bielefeld, 2004. [ bib ]
[219]S. Grabowski, V. Mäkinen, and G. Navarro. First huffman, then burrows-wheeler: A simple alphabet-independent fm-index (abstract). In Proc. of String Processing and Information Retrieval (SPIRE 2004), volume 3246 of LNCS, pages 210-211, 2004. [ bib ]
[220]D. Gusfield and J. Stoye. Linear time algorithms for finding and representing all the tandem repeats in a string. J. Comput. Syst. Sci., 69:525-546, 2004. [ bib ]
[221]S. Inenaga, T. Kivioja, and V. Mäkinen. Finding missing patterns. In Proc. of Workshop on Algorithms in Bioinformatics (WABI 2004), volume 3240 of LNCS, pages 463-474, 2004. [ bib ]
[222]G. W. Klau, S. Rahmann, A. Schliep, M. Vingron, and K. Reinert. Optimal robust non-unique probe selection using integer linear programming. Bioinformatics, 20(Suppl.1):i186-i193, 2004. [ bib ]
[223]M. Lefmann, C. Honisch, S. Böcker, N. Storm, F. von Wintzingerode, C. Schloetelburg, A. Moter, D. van den Boom, and U. B. Goebel. A novel mass spectrometry based tool for genotypic identification of mycobacteria. J. Clin. Microbiol., 42(1):339-346, 2004. [ bib ]
[224]T. Müller, S. Rahmann, T. Dandekar, and M. Wolf. Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta). BMC Evolutionary Biology, 4:Article 20, 2004. [ bib ]
[225]M. Michael, C. Dieterich, and J. Stoye. Suboptimal local alignments across multiple scoring schemes. In Proc. WABI 2004, volume 3240 of LNBI, pages 99-110, 2004. [ bib ]
[226]V. Mäkinen, G. Navarro, and K. Sadakane. Advantages of backward searching - efficient secondary memory and distributed implementation of compressed suffix arrays. In Proc. of International Symposium on Algorithms and Computation (ISAAC 2004), volume 3341 of LNCS, pages 681-692, 2004. [ bib ]
[227]H.-H. Niller, D. Salamon, S. Rahmann, K. Ilg, A. Koroknai, F. Banati, F. Schwarzmann, H. Wolf, and J. Minarovits. A 30 kb region of the Epstein-Barr virus genome is colinear with the rearranged human immunoglobulin gene loci: implications for a “ping-pong evolution” model for persisting viruses and their hosts. A review. Acta Microbiol. Immunol. Hung., 51(4):469-484, 2004. [ bib ]
[228]D. A. Pollard, C. M. Bergman, J. Stoye, S. E. Celniker, and M. B. Eisen. Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics, 5(6), 2004. [ bib ]
[229]S. Rahmann and C. Gräfe. Mean and variance of the Gibbs free energy of oligonucleotides in the nearest neighbor model under varying conditions. Bioinformatics, 20(17):2928-2933, 2004. [ bib ]
[230]S. Rahmann and T. Müller. The embedding problem for evolutionary Markov processes. In Proceedings of the Karlsruher Stochastik-Tage. 2004. [ bib ]
[231]S. Rahmann, T. Müller, and M. Vingron. Non-unique probe selection by matrix condition optimization. In Currents in Computational Molecular Biology 2004. 2004. [ bib ]
[232]T. Schmidt and J. Stoye. Quadratic time algorithms for finding common intervals in two and more sequences. In Proc. CPM 2004, volume 3109 of LNCS, pages 347-358, 2004. [ bib ]
[233]B. Schuster-Böckler, J. Schultz, and S. Rahmann. HMM Logos for visualization of protein families. BMC Bioinformatics, 5:Article 7, 2004. [ bib ]
[234]P. Stanssens, M. Zabeau, G. Meersseman, G. Remes, Y. Gansemans, N. Storm, R. Hartmer, C. Honisch, C. P. Rodi, S. Böcker, and D. van den Boom. High-throughput MALDI-TOF discovery of genomic sequence polymorphisms. Genome Res., 14:126-133, 2004. [ bib ]
[235]P. Stanssens, M. Zabeau, G. Meersseman, G. Remes, Y. Gansemans, N. Storm, R. Hartmer, C. Honisch, C. P. Rodi, S. Böcker, and D. van den Boom. High-throughput MALDI-TOF discovery of genomic sequence polymorphisms. Genome Res., 14:126-133, 2004. [ bib ]
[236]J. Zimmermann, Zs. Lipták, and S. Hazelhurst. A method for evaluating the quality of string dissimilarity measures and clustering algorithms for est clustering. In Proc. BIBE, pages 301-309, 2004. [ bib ]
[237]R. Giegerich and J. Stoye, editors. Proc. German Conference on Bioinformatics (GCB 2004), number P-53 in LNI, 2004. [ bib ]
2003
[238]C. Bannert. Systematic investigation of jumping alignments. Report 2003-05, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2003. [ bib ]
[239]C. Bannert and J. Stoye. Evaluation of the jumping alignment algorithm with artificial and biological data. In Proc. GCB 2003, pages 21-25, 2003. [ bib ]
[240]A. Bergeron and J. Stoye. On the similarity of sets of permutations and its applications to genome comparison. Report 2003-01, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2003. [ bib ]
[241]A. Bergeron and J. Stoye. On the similarity of sets of permutations and its applications to genome comparison. In Proc.COCOON 2003, volume 2697 of LNCS, pages 68-79, 2003. [ bib ]
[242]S. Böcker. SNP and mutation discovery using base-specific cleavage and MALDI-TOF mass spectrometry. Bioinformatics, 19(Suppl. 1):i44-i53, 2003. [ bib ]
[243]S. Böcker. SNP and mutation discovery using base-specific cleavage and MALDI-TOF mass spectrometry. Technical Report 2003-02, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2003. [ bib ]
[244]S. Böcker. Sequencing from compomers: Using mass spectrometry for DNA de-novo sequencing of 200+ nt. Technical Report 2003-04, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2003. [ bib ]
[245]S. Böcker. Sequencing from compomers in the presence of false negative peaks. Technical Report 2003-07, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2003. [ bib ]
[246]S. Böcker. Sequencing from compomers: Using mass spectrometry for DNA de-novo sequencing of 200+ nt. Extended abstract. In Proc. WABI, volume 2812 of LNCS, pages 476-497, 2003. [ bib ]
[247]R. Giegerich, S. Kurtz, and J. Stoye. Efficient implementation of lazy suffix trees. Softw. Pract. Exper., 33(11):1035-1049, 2003. [ bib ]
[248]R. Giegerich and J. Stoye. Finden, fast ohne zu suchen: Indexstrukturen in der Bioinformatik. Forschung an der Universität Bielefeld, 26:63-68, 2003. [ bib ]
[249]R. Hartmer, N. Storm, S. Böcker, C. P. Rodi, F. Hillenkamp, C. Jurinke, and D. van den Boom. RNAse T1 mediated base-specific cleavage and MALDI-TOF MS for high-throughput comparative sequence analysis. Nucl. Acids. Res., 31(9):e47, 2003. [ bib ]
[250]S. Hazelhurst, Zs. Lipták, and J. Zimmerman. A comparative study of biological distances for est clustering. Technical Report TR-Wits-CS-2003-3, School of Computer Science, University of the Witwatersrand, 2003. [ bib ]
[251]S. Heber and J. Stoye. The european conference on computational biology. Drug Discovery Today, 8(3):113-114, 2003. [ bib ]
[252]M. Sammeth, B. Morgenstern, and J. Stoye. Divide-and-conquer multiple alignment with segment-based constraints. Bioinformatics, 19(Suppl. 2):ii189-ii195, 2003. [ bib ]
[253]M. Sammeth, J. Rothgänger, W. Esser, J. Albert, J. Stoye, and D. Harmsen. QAlign: quality-based multiple alignments with dynamic phylogenetic analysis. Bioinformatics, 19(12):1592-1593, 2003. [ bib ]
[254]K.-B. Schürmann and J. Stoye. Suffix tree construction and storage with limited main memory. Report 2003-06, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2003. [ bib ]
2002
[255]A. Bergeron, S. Heber, and J. Stoye. Common intervals and sorting by reversals: A marriage of necessity. Bioinformatics, 18(Suppl. 2):S54-S63, 2002. [ bib ]
[256]M. Cieliebak, Zs.  , E. Welzl, T. Erlebach, and J. Stoye. Algorithmic complexity of protein identification: Searching in weighted strings. In Proc. 2nd IFIP International Conference on Theoretical Computer Science (TCS 2002) Foundations of Information Technology in the Era of Network and Mobile Computing, pages 143-156, 2002. [ bib ]
[257]S. Heber, J. Stoye, M. Frohme, J. Hoheisel, and M. Vingron. Resampling methods in physical mapping. In Classification, Automation, and New Media: Proc. 24th Annual Conference of the GfKl, 2000, volume 20 of Studies in Classification, Data Analysis, and Knowledge Organization, pages 437-444, 2002. [ bib ]
[258]R. Spang, M. Rehmsmeier, and J. Stoye. A novel approach to remote homology detection: Jumping alignments. J. Comp. Biol., 9(5):747-760, 2002. [ bib ]
[259]J. Stoye and D. Gusfield. Simple and flexible detection of contiguous repeats using a suffix tree. Theor. Comput. Sci., 270(1-2):843-856, 2002. [ bib ]
[260]M. Cieliebak, T. Erlebach, Zs. Lipták, J. Stoye, and E. Welzl. Algorithmic complexity of protein identification: Combinatorics of weighted strings. Technical Report 361, ETH Zürich, Dept. of Computer Science, 2001. [ bib ]
2001
[261]S. Heber and J. Stoye. Finding all common intervals of k permutations. In Proc. 12th Annual Symposium on Combinatorial Pattern Matching (CPM 2001), volume 2089 of LNCS, pages 207-218, 2001. [ bib ]
[262]S. Heber and J. Stoye. Algorithms for finding gene clusters. In Proc. WABI, volume 2149 of LNCS, pages 252-263, 2001. [ bib ]
[263]S. Kurtz, J. V. Choudhuri, E. Ohlebusch, C. Schleiermacher, J. Stoye, and R. Giegerich. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res., 29(22):4643-4653, 2001. [ bib ]
2000
[264]G. S. Brodal, R. B. Lyngsø, C. N. S. Pedersen, and J. Stoye. Finding maximal pairs with bounded gap. J. Discr. Alg., 1:77-104, 2000. [ bib ]
[265]S. Heber, J. Stoye, M. Frohme, J. Hoheisel, and M. Vingron. Contig selection in physical mapping. J. Comp. Biol., 7(3/4):395-408, 2000. [ bib ]
[266]S. Heber, J. Stoye, J. Hoheisel, and M. Vingron. Contig selection in physical mapping. In Proc. Fourth Annual International Conference on Computational Molecular Biology (RECOMB 2000), pages 155-164, 2000. [ bib ]
[267]A. Krause, J. Stoye, and M. Vingron. The SYSTERS protein sequence cluster set. Nucleic Acids Res., 28(1):270-272, 2000. [ bib ]
[268]S. Kurtz, E. Ohlebusch, C. Schleiermacher, J. Stoye, and R. Giegerich. Computation and visualization of degenerate repeats in complete genomes. In Proc. Eighth International Conference on Intelligent Systems for Molecular Biology (ISMB 2000), pages 228-238, 2000. [ bib ]
[269]Zs. Lipták and A. Nickelsen. Broadcasting in complete networks with dynamic edge faults. In Proc. 4th International Conference on Principles of Distributed Systems (OPODIS 2000), pages 123-142, 2000. [ bib ]
[270]K. Reinert, J. Stoye, and T. Will. An iterative method for faster sum-of-pairs multiple sequence alignment. Bioinformatics, 16(9):808-814, 2000. [ bib ]
[271]R. Spang, M. Rehmsmeier, and J. Stoye. Sequence database search using jumping alignments. In Proc. Eighth International Conference on Intelligent Systems for Molecular Biology (ISMB 2000), pages 367-375, 2000. [ bib ]
[272]J. Stoye. Affix trees. Report 2000-04, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 2000. [ bib ]
[273]E. Bornberg-Bauer, U. Rost, J. Stoye, and M. Vingron, editors. Proc. German Conference on Bioinformatics (GCB 2000), 2000. [ bib ]
1999
[274]G. S. Brodal, R. B. Lyngsø, C. N. S. Pedersen, and J. Stoye. Finding maximal pairs with bounded gap. Report RS-99-12, BRICS, 1999. [ bib ]
[275]G. S. Brodal, R. B. Lyngsø, C. N. S. Pedersen, and J. Stoye. Finding maximal pairs with bounded gap. In Proc. 10th Annual Symposium on Combinatorial Pattern Matching (CPM 1999), volume 1645 of LNCS, pages 134-149, 1999. [ bib ]
[276]R. Giegerich, S. Kurtz, and J. Stoye. Efficient implementation of lazy suffix trees. In Proc. 3rd Workshop on Algorithm Engineering (WAE 1999), volume 1668 of LNCS, pages 30-42, 1999. [ bib ]
[277]B. Morgenstern, J. Stoye, and A. Dress. Consistent equivalence relations: A set-theoretical framework for multiple sequence alignment. Materialien/Preprints 133, Universität Bielefeld, Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse, 1999. [ bib ]
[278]K. Reinert, J. Stoye, and T. Will. Combining divide-and-conquer, the A*-algorithm, and successive realignment approaches to speed up multiple sequence alignment. In Proc. German Conference on Bioinformatics (GCB 1999), pages 17-24, 1999. [ bib ]
1998
[279]A. Dress, B. Morgenstern, and J. Stoye. The number of standard and of effective multiple alignments. Appl. Math. Lett., 11(4):43-49, 1998. [ bib ]
[280]D. Gusfield and J. Stoye. Linear time algorithms for finding and representing all the tandem repeats in a string. Report CSE-98-4, Department of Computer Science, University of California, Davis, 1998. [ bib ]
[281]M. Hildebrand and J. Stoye. Die Bedeutung der Zusammenarbeit der Disziplinen in der Anwendung - erläutert anhand von Beispielen. Der Mathematikunterricht, 44(6):34-53, 1998. [ bib ]
[282]J. Stoye. Multiple sequence alignment with the divide-and-conquer method. Gene, 211(2):GC45-GC56, 1998. [ bib ]
[283]J. Stoye, D. Evers, and F. Meyer. Rose: Generating sequence families. Bioinformatics, 14(2):157-163, 1998. [ bib ]
[284]J. Stoye and D. Gusfield. Simple and flexible detection of contiguous repeats using a suffix tree. Report CSE-98-2, Department of Computer Science, University of California, Davis, 1998. [ bib ]
[285]J. Stoye and D. Gusfield. Simple and flexible detection of contiguous repeats using a suffix tree. In Proc. 9th Annual Symposium on Combinatorial Pattern Matching (CPM 1998), volume 1448 of LNCS, pages 140-152, 1998. [ bib ]
1997
[286]G. Brinkmann, A. W. M. Dress, S. W. Perrey, and J. Stoye. Two applications of the divide & conquer principle in the molecular sciences. Research Report 151, University of Canterbury, Christchurch, New Zealand. Department of Mathematics and Statistics, 1997. [ bib ]
[287]G. Brinkmann, A. W. M. Dress, S. W. Perrey, and J. Stoye. Two applications of the divide & conquer principle in the molecular sciences. Materialien/Preprints 109, Universität Bielefeld, Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse, 1997. [ bib ]
[288]G. Brinkmann, A. W. M. Dress, S. W. Perrey, and J. Stoye. Two applications of the divide&conquer principle in the molecular sciences. Math. Program., 79:71-97, 1997. [ bib ]
[289]A. Dress, B. Morgenstern, and J. Stoye. On the number of standard and of effective multiple alignments. Materialien/Preprints 112, Universität Bielefeld, Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse, 1997. [ bib ]
[290]S. W. Perrey, J. Stoye, and V. Moulton. FDCA: Fast and accurate approximation to sum-of-pairs score optimal multiple sequence alignment. Materialien/Preprints 114, Universität Bielefeld, Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse, 1997. [ bib ]
[291]S. W. Perrey, J. Stoye, V. Moulton, and A. W. M. Dress. On simultaneous versus iterative multiple sequence alignment. Materialien/Preprints 111, Universität Bielefeld, Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse, 1997. [ bib ]
[292]J. Stoye. Divide-and-conquer multiple sequence alignment. Dissertation Thesis. Report 97-02, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 1997. [ bib ]
[293]J. Stoye, D. Evers, and F. Meyer. Generating benchmarks for multiple sequence alignments and phylogenetic reconstructions. In Proc. Fifth International Conference on Intelligent Systems for Molecular Biology (ISMB 1997), pages 303-306, 1997. [ bib ]
[294]J. Stoye, D. Evers, and F. Meyer. Rose: Generating sequence families. Report 97-04, Technische Fakultät der Universität Bielefeld, Abteilung Informationstechnik, 1997. [ bib ]
[295]J. Stoye, V. Moulton, and A. W. M. Dress. DCA: An efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment. CABIOS, 13(6):625-626, 1997. [ bib ]
[296]J. Stoye, S. W. Perrey, and A. W. M. Dress. Improving the divide-and-conquer approach to sum-of-pairs multiple sequence alignment. Appl. Math. Lett., 10(2):67-73, 1997. [ bib ]
1996
[297]S. W. Perrey and J. Stoye. Fast approximation to the NP-hard problem of multiple sequence alignment. Information and Mathematical Sciences Reports, Series B: 96/06, Massey University, New Zealand, 1996. [ bib ]
[298]J. Stoye, A. W. M. Dress, and S. W. Perrey. Improving the divide-and-conquer approach to sum-of-pairs multiple sequence alignment. Materialien/Preprints 102, Universität Bielefeld, Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse, 1996. [ bib ]
[299]U. Tönges, S. W. Perrey, J. Stoye, and A. W. M. Dress. A general method for fast multiple sequence alignment. Gene, 172(1):GC33-GC41, 1996. [ bib ]
[300]U. Tönges, S. W. Perrey, J. Stoye, and A. W. M. Dress. A general method for fast multiple sequence alignment. Materialien/Preprints XCIX, Universität Bielefeld, Forschungsschwerpunkt Mathematisierung - Strukturbildungsprozesse, 1996. [ bib ]
publications_oldformat.txt · Last modified: 2016/01/19 12:37 (external edit)