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419 Publikationen

2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919211
Hufsky, F., Kuchenbecker, L., Jahn, K., Stoye, J., Böcker, S.: Swiftly Computing Center Strings. Proc. of WABI 2010. LNBI. 6293, p. 325-336. (2010).
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919216
Kovac, J., Dias Vieira Braga, M., Stoye, J.: The Problem of Chromosome Reincorporation in DCJ Sorting and Halving. Proc. of Recomb-CG 2010. LNBI. 6398, p. 13-24. (2010).
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2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1794419
Herold, J., Zhou, L., Abouna, S., Pelengaris, S., Epstein, D., Khan, M., Nattkemper, T.W.: Integrating semantic annotation and information visualization for the analysis of multichannel fluorescence micrographs from pancreatic tissue. Computerized Medical Imaging and Graphics. 34, 446-452 (2010).
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898025
Dias Vieira Braga, M., Stoye, J.: The Solution Space of Sorting by DCJ. Journal of Computational Biology. 17, 1145-1165 (2010).
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919215
Dias Vieira Braga, M., Willing, E., Stoye, J.: Genomic Distance with DCJ and Indels. Proc. of WABI 2010. LNBI. 6293, p. 90-101. (2010).
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2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1929860
Schwientek, P., Ellinghaus, P., Steppan, S., D'Urso, D., Seewald, M., Kassner, A., Cebulla, R., Schulte-Eistrup, S., Morshuis, M., Roefe, D., El Banayosy, A., Koerfer, R., Milting, H.: Global gene expression analysis in nonfailing and failing myocardium pre- and postpulsatile and nonpulsatile ventricular assist device support. PHYSIOLOGICAL GENOMICS. 42, 397-405 (2010).
PUB | DOI | WoS | PubMed | Europe PMC
 
2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1930110
Joseph, B., Schneiker-Bekel, S., Schramm-Glueck, A., Blom, J., Claus, H., Linke, B., Schwarz, R.F., Becker, A., Goesmann, A., Frosch, M., Schoen, C.: Comparative Genome Biology of a Serogroup B Carriage and Disease Strain Supports a Polygenic Nature of Meningococcal Virulence. JOURNAL OF BACTERIOLOGY. 192, 5363-5377 (2010).
PUB | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1589663
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 (2009).
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2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2427059
Escoffier, B., Milanič, M., Paschos, V.T.: Simple and fast reoptimizations for the Steiner tree problem. Algorithmic Operations Research. 4, 86-94 (2009).
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2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2308924
Cicalese, F., Milanic, M.: Competitive evaluation of threshold functions in the priced information model. Annals of Operations Research. 188, 111-132 (2009).
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2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2426437
Bunkowski, A., Bödeker, B., Bader, S., Westhoff, M., Litterst, P., Baumbach, J.I.: MCC/IMS signals in human breath related to sarcoidosis-results of a feasibility study using an automated peak finding procedure. Journal of Breath Research. 3, 046001 (2009).
PUB | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2426487
Böcker, S., Lipták, Z., Pervukhin, A., Letzel, M.C.: SIRIUS: decomposing isotope patterns for metabolite identification. Bioinformatics. 25, 218-224 (2009).
PUB | DOI | WoS | PubMed | Europe PMC
 
2009 | Preprint | Veröffentlicht | PUB-ID: 2426653
Cicalese, F., Jacobs, T., Laber, E.S., Molinaro, M.: On the Complexity of Searching in Trees: Average-case Minimization. (2009).
PUB | arXiv
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2426660
Cicalese, F., Manne, F., Xin, Q.: Faster Deterministic Communication in Radio Networks. Algorithmica. 54, 226-242 (2009).
PUB | DOI | WoS
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2427118
Engelmann, J.A., Rahmann, S., Wolf, M., Schultz, J., Fritzilas, E., Kneitz, S., Dandekar, T., Müller, T.: Modeling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species. Molecular Ecology Resources. 9, 83-93 (2009).
PUB | DOI | WoS | PubMed | Europe PMC
 
2009 | Bielefelder E-Dissertation | PUB-ID: 2305073 OA
Oehm, S.: Comparing organisms on the level of metabolism. Bielefeld University, Bielefeld (Germany) (2009).
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2009 | Bielefelder E-Dissertation | PUB-ID: 2301318 OA
Neuweger, H.: MeltDB : a software platform for the analysis and integration of metabolomics experiment data. Bielefeld University, Bielefeld (Germany) (2009).
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2009 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2659405
Feijão, P., Meidanis, J.: SCJ: A Variant of Breakpoint Distance for Which Sorting, Genome Median and Genome Halving Problems Are Easy. In: Salzberg, S.L. and Warnow, T. (eds.) Algorithms in Bioinformatics. Lecture Notes in Computer Science. 5724, p. 85-96. (2009).
PUB | DOI
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2427161
Kamiński, M., Lozin, V.V., Milanič, M.: Recent developments on graphs of bounded clique-width. Discrete Appl. Math. 157, 2747-2761 (2009).
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2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2427173
Kamiński, M., Medvedev, P., Milanič, M.: On the plane-width of graphs. Electronic Notes in Discrete Mathematics. 34, 633-637 (2009).
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2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919206
Dias Vieira Braga, M., Stoye, J.: Counting All DCJ Sorting Scenarios. Proc. of Recomb-CG 2009. LNBI. 5817, p. 36-47. (2009).
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2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2426605
Cicalese, F., Fici, G., Lipták, Z.: Searching for Jumbled Patterns in Strings. Proc. of the Prague Stringology Conference 2009. p. 105-117. (2009).
PUB
 
2009 | Bielefelder E-Dissertation | PUB-ID: 2303240 OA
Gagie, T.: New algorithms and lower bounds for sequential-access data compression. Bielefeld University, Bielefeld (Germany) (2009).
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2009 | Bielefelder E-Dissertation | PUB-ID: 2302608 OA
Herms, I.: Probabilistic arithmetic automata : applications of a stochastic computational framework in biological sequence analysis. Bielefeld University, Bielefeld (Germany) (2009).
PUB | PDF
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2406118
Välimäki, N., Mäkinen, V., Gerlach, W., Dixit, K.: Engineering a compressed suffix tree implementation. Journal of Experimental Algorithmics (JEA). 14, 4.2-2:4.23 (2009).
PUB | DOI
 
2009 | Bielefelder E-Dissertation | PUB-ID: 2304745 OA
Fritzilas, E.: Combinatorial aspects of low-rank matrix factorization and two applications in bioinformatics. Bielefeld University, Bielefeld (Germany) (2009).
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2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919207
Blin, G., Stoye, J.: Finding Nested Common Intervals Efficiently. Proc. of Recomb-CG 2009. LNBI. 5817, p. 59-69. (2009).
PUB | DOI | WoS | PubMed | Europe PMC
 
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2018390
Herold, J., Abouna, S., Zhou, L., Pelengaris, S., Epstein, D.B.A., Khan, M., Nattkemper, T.W.: A way towards analyzing high-content bioimage data by means of semantic annotation and visual data mining. SPIE Medical Imaging. (2009).
PUB | DOI
 
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2018422
Ontrup, J., Ehnert, N., Bergmann, M., Nattkemper, T.W.: BIIGLE - Web 2.0 enabled labelling and exploring of images from the Arctic deep-sea observatory HAUSGARTEN. OCEANS 2009 - Europe. Bremen (2009).
PUB | DOI
 
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2018427
Qureshi, H., Rajpoot, N., Nattkemper, T.W., Hans, V.: A Robust Adaptive Wavelet-based Method for Classification of Meningioma Histology Images. MICCAI«2009 Workshop on Optical Tissue Image Analysis in Microscopy, Histology, and Endoscopy. (2009).
PUB
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1783187 OA
Blom, J., Albaum, S., Doppmeier, D., Pühler, A., Vorhölter, F.-J., Zakrzewski, M., Goesmann, A.: EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics. 10, : 154 (2009).
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1636062
Ontrup, J., Ritter, H., Scholz, S., Wagner, R.: Detecting, Assessing, and Monitoring Relevant Topics in Virtual Information Environments. IEEE Transactions on Knowledge and Data Engineering. 21, 415-427 (2009).
PUB | DOI | WoS
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898137
Jahn, K., Stoye, J.: Approximative Gencluster und ihre Anwendung in der komparativen Genomik. Informatik-Spektrum. 32, 288-300 (2009).
PUB | DOI
 
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1893884
Husemann, P., Stoye, J.: Phylogenetic Comparative Assembly. Proc. of WABI 2009. LNBI. 5724, p. 145-156. (2009).
PUB | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1635314 OA
Diaz, N.N., Krause, L., Goesmann, A., Niehaus, K., Nattkemper, T.W.: TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics. 10, 56 (2009).
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1635321 OA
Dondrup, M., Albaum, S., Griebel, T., Henckel, K., Jünemann, S., Kahlke, T., Kleindt, C.K., Kuester, H., Linke, B., Mertens, D., Mittard-Runte, V., Neuweger, H., Runte, K.J., Tauch, A., Tille, F., Pühler, A., Goesmann, A.: EMMA 2-A MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics. 10, : 50 (2009).
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1591507
Stoye, J., Wittler, R.: A Unified Approach for Reconstructing Ancient Gene Clusters. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 6, 387-400 (2009).
PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1589098 OA
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 (2009).
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1589531
Albaum, S., Neuweger, H., Fraenzel, B., Lange, S., Mertens, D., Troetschel, C., Wolters, D., Kalinowski, J., Nattkemper, T.W., Goesmann, A.: Qupe-a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments. Bioinformatics. 25, 3128-3134 (2009).
PUB | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1590204
Brudno, M., Medvedev, P., Stoye, J., De La Vega, F.M.: A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG). BIOINFORMATICS. 25, 2863-2864 (2009).
PUB | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1588783
Purser, A., Bergmann, M., Ontrup, J., Nattkemper, T.W.: Use of machine-learning algorithms for the automated detection of cold-water coral habitats: a pilot study. Marine Ecology Progress Series. 397, 241-251 (2009).
PUB | DOI | WoS
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1898105
Böcker, S., Jahn, K., Mixtacki, J., Stoye, J.: Computation of Median Gene Clusters. Journal of Computational Biology. 16, 1085-1099 (2009).
PUB | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1591319
Hoffmann, N., Stoye, J.: ChromA: signal-based retention time alignment for chromatography-mass spectrometry data. Bioinformatics. 25, 2080-2081 (2009).
PUB | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1588760 OA
Dias Vieira Braga, M., Gautier, C., Sagot, M.-F.: An asymmetric approach to preserve common intervals while sorting by reversals. Algorithms for Molecular Biology. 4, 16 (2009).
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919209
Medvedev, P., Stoye, J.: 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. 5817, p. 84-97. Springer, Berlin, Heidelberg (2009).
PUB | DOI
 
2009 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2018440
Schoening, T., Ehnert, N., Ontrup, J., Nattkemper, T.W.: BIIGLE Tools - A Web 2.0 Approach for Visual Bioimage Database Mining. IV 09 - Intl. Conference on Information Visualization. (2009).
PUB | DOI
 
2009 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 1918945
Stoye, J.: Computational Short Read Metagenomics. Presented at the JOBIM 2009, Nantes, France (2009).
PUB
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1634447
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 (2009).
PUB | DOI | WoS | PubMed | Europe PMC
 
2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1634615
Zeschnigk, M., Martin, M., Betzl, G., Kalbe, A., Sirsch, C., Buiting, K., Gross, S., Fritzilas, E., Frey, B., Rahmann, S., Horsthemke, B.: Massive parallel bisulfite sequencing of CG-rich DNA fragments reveals that methylation of many X-chromosomal CpG islands in female blood DNA is incomplete. HUMAN MOLECULAR GENETICS. 18, 1439-1448 (2009).
PUB | DOI | WoS | PubMed | Europe PMC
 
2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2427252
Alekseev, V.E., Lozin, V.V., Malyshev, D., Milanič, M.: The Maximum Independent Set Problem in Planar Graphs. Proc. MFCS 2008. p. 96-107. (2008).
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