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421 Publikationen

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).
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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).
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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).
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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).
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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).
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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).
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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).
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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).
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2009 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 1918945
Stoye, J.: Computational Short Read Metagenomics. Presented at the JOBIM 2009, Nantes, France (2009).
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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).
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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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2008 | Bielefelder E-Dissertation | PUB-ID: 2306324 OA
Baumbach, J.: CoryneRegNet : a reference database and analysis platform for corynebacterial gene regulatory networks. Bielefeld University, Bielefeld (Germany) (2008).
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2008 | Bielefelder E-Dissertation | PUB-ID: 2302950 OA
Zakotnik, J.: The double cut and join operation and its applications to genome rearrangements. Bielefeld University, Bielefeld (Germany) (2008).
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2659345
Oliveira, M.T., Barau, J.G., Junqueira, A.C.M., Feijão, P., Rosa, A.C. da, Abreu, C.F., Azeredo-Espin, A.M.L., Lessinger, A.C.: Structure and evolution of the mitochondrial genomes of Haematobia irritans and Stomoxys calcitrans: The Muscidae (Diptera: Calyptratae) perspective. Molecular Phylogenetics and Evolution. 48, 850-857 (2008).
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2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2308903
Cicalese, F., Laber, E.S.: Function Evaluation Via Linear Programming in the Priced Information Model. Proc. ICALP 2008. p. 173-185. (2008).
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2008 | Report | Veröffentlicht | PUB-ID: 2308927 OA
Cicalese, F., Milanivc, M.: On Parsimony Haplotyping. Forschungsberichte der Technischen Fakultät, Abteilung Informationstechnik / Universität Bielefeld. Universität Bielefeld, Technische Fakultät, Bielefeld (2008).
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2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2308974
Fritzilas, E., Rios-Solis, Y.A., Rahmann, S.: Structural Identifiability in Low-Rank Matrix Factorization. In: Hu, X. and Wang, J. (eds.) Computing and Combinatorics 14th Annual International Conference, COCOON 2008 Dalian, China, June 27-29, 2008 Proceedings. Lecture Notes in Computer Science, 5092. p. 140-148. Springer, Berlin u.a. (2008).
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2008 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2499103
Milanivc, M., Monnot, J.: The Complexity of the Exact Weighted Independent Set Problem. Combinatorial optimization and theoretical computer science: interfaces and perspectives : 30th anniversary of the LAMSADE. p. 393-432. (2008).
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2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2499108
Mixtacki, J.: Genome Halving under DCJ Revisited. In: Hu, X. and Wang, J. (eds.) Computing and Combinatorics. 14th Annual International Conference, COCOON 2008 Dalian, China, June 27-29, 2008 Proceedings. Lecture Notes in Computer Science, 5092. p. 276-286. (2008).
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2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919198
Quitzau, J.A.A., Stoye, J.: Detecting Repeat Families in Incompletely Sequenced Genomes. Proc. of WABI 2008. LNBI. 5251, p. 342-353. (2008).
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2498846
Boyar, J., Medvedev, P.: The relative worst order ratio applied to seat reservation. ACM Transactions on Algorithms. 4, 1-22 (2008).
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2008 | Report | Veröffentlicht | PUB-ID: 2499065
Cicalese, F., Milanic, M.: Computing with Priced Information: game trees and the value dependent cost model. Technische Fakultät, Universität Bielefeld (2008).
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2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2499072
Herms, I., Rahmann, S.: Computing Alignment Seed Sensitivity with Probabilistic Arithmetic Automata. In: Crandall, K.A. and Lagergren, J. (eds.) Algorithms in Bioinformatics: 8th International Workshop, WABI 2008, Karlsruhe, Germany, September 15-19, 2008. Proceedings. Lecture Notes in Computer Science, 5251. p. 318-329. Springer, Berlin u.a. (2008).
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2008 | Report | Veröffentlicht | PUB-ID: 2308930 OA
Cicalese, F., Milanivc, M.: Computing with Priced Information: game trees and the value dependent cost model. Forschungsberichte der Technischen Fakultät, Abteilung Informationstechnik / Universität Bielefeld. Universität Bielefeld, Technische Fakultät, Bielefeld (2008).
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2499098
Lozin, V.V., Milanic, M.: A polynomial algorithm to find an independent set of maximum weight in a fork-free graph. J. Discr. Alg. 6, 595-604 (2008).
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2008 | Sammelwerksbeitrag | Veröffentlicht | PUB-ID: 2499120
Rahmann, S., Klau, G.W.: Integer Linear Programming Techniques for Discovering Approximate Gene Clusters. In: Mǎndoiu, I.I. and Zelikovsky, A. (eds.) Bioinformatics Algorithms: Techniques and Applications. p. 203-222. Wiley Interscience (2008).
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2008 | Report | PUB-ID: 1970459 OA
Quitzau, J.A.A., Stoye, J.: A space efficient representation for sparse de Bruijn subgraphs. Forschungsberichte der Technischen Fakultät, Abteilung Informationstechnik / Universität Bielefeld. Technische Fakultät der Universität Bielefeld, Bielefeld (2008).
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2008 | Report | PUB-ID: 1970461 OA
Ejaz, T., Rahmann, S., Stoye, J.: Online Abelian Pattern Matching. Forschungsberichte der Technischen Fakultät, Abteilung Informationstechnik / Universität Bielefeld. Technische Fakultät der Universität Bielefeld, Bielefeld (2008).
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1636699
Neuweger, H., Albaum, S., 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. 24, 2726-2732 (2008).
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2008 | Bielefelder E-Dissertation | PUB-ID: 2305571 OA
Bannert, C.: Flexible protein annotation with sequence- and secondary structure information. Bielefeld University, Bielefeld (Germany) (2008).
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2008 | Lexikoneintrag | Veröffentlicht | PUB-ID: 1918834
Stoye, J.: Suffix Tree Construction in RAM (1997; Farach-Colton). In: Kao, M.-Y. (ed.) Encyclopedia of Algorithms. p. 925-928. Springer Verlag (2008).
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2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919192
Böcker, S., Jahn, K., Mixtacki, J., Stoye, J.: Computation of Median Gene Clusters. Proc. of RECOMB 2008. LNBI. 4955, p. 331-345. (2008).
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2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919200
Bergeron, A., Mixtacki, J., Stoye, J.: On Computing the Breakpoint Reuse Rate in Rearrangement Scenarios. Proc. of Recomb-CG 2008. LNBI. 5267, p. 226-240. (2008).
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2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2018405
Loyek, C., Woermann, F.G., Nattkemper, T.W.: Detection of Focal Cortical Dysplasia in MRI Using Textural Features. Proceedings of BVM 2008. p. 432-436. Springer Verlag, Berlin, Heidelberg (2008).
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1636280 OA
Timm, W., Scherbart, A., Boecker, S., Kohlbacher, O., Nattkemper, T.W.: Peak intensity prediction in MALDI-TOF mass spectrometry: A machine learning study to support quantitative proteomics. BMC Bioinformatics. 9, 443 (2008).
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1592257
Schoen, C., Blom, J., Claus, H., Schramm-Glueck, A., Brandt, P., Mueller, T., Goesmann, A., Joseph, B., Konietzny, S., Kurzai, O., Schmitt, C., Friedrich, T., Linke, B., Vogel, U., Frosch, M.: Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 105, 3473-3478 (2008).
PUB | DOI | WoS | PubMed | Europe PMC | GenBank
 
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1587304
Hazelhurst, S., Hide, W., Lipták, Z., Nogueira, R., Starfield, R.: An overview of the wcd EST clustering tool. BIOINFORMATICS. 24, 1542-1546 (2008).
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1592737
Boecker, S., Lipták, Z., Martin, M., Pervukhin, A., Sudek, H.: DECOMP - from interpreting mass spectrometry peaks to solving the money changing problem. BIOINFORMATICS. 24, 591-593 (2008).
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1587078
Schürmann, K.-B., Stoye, J.: Counting suffix arrays and strings. THEORETICAL COMPUTER SCIENCE. 395, 220-234 (2008).
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1586009
Krause, L., Diaz, N.N., Edwards, R.A., Gartemann, K.-H., Krömeke, H., Neuweger, H., Pühler, A., Runte, K.J., 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 (2008).
PUB | DOI | WoS | PubMed | Europe PMC
 
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1587052
Martin, C., Diaz, N.N., Ontrup, J., Nattkemper, T.W.: Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification. Bioinformatics. 24, 1568-1574 (2008).
PUB | DOI | WoS | PubMed | Europe PMC
 
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1586785 OA
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-W437 (2008).
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1585939
Tauch, A., Schneider, J., Szczepanowski, R., Tilker, A., Viehöver, P., Gartemann, K.-H., Arnold, W., Blom, J., Brinkrolf, K., Brune, I., Goetker, S., Weisshaar, B., Goesmann, A., Droege, M., Pühler, A.: Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids. Journal of Biotechnology. 136, 22-30 (2008).
PUB | DOI | WoS | PubMed | Europe PMC
 
2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1783364 OA
Krause, L., Diaz, N.N., Goesmann, A., Kelley, S., Nattkemper, T.W., Rohwer, F., Edwards, R.A., Stoye, J.: Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Research. 36, 2230-2239 (2008).
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1919195
Bergeron, A., Mixtacki, J., Stoye, J.: HP Distance via Double Cut and Join Distance. Combinatorial Pattern Matching. 19th Annual Symposium, CPM 2008, Pisa, Italy, June 18-20, 2008 Proceedings. Lecture Notes in Computer Science, 5029. p. 56-68. (2008).
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2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2018409
Martin, C., Nattkemper, T.W.: A Tree Index to Support Clustering Based Exploratory Data Analysis. Bioinformatics Research and Development : Second International Conference, BIRD 2008 Vienna, Austria, July 7-9, 2008 Proceedings. Communications in Computer and Information Science. 13, p. 1-15. Springer, Berlin, Heidelberg (2008).
PUB | DOI
 
2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2018435
Scherbart, A., Timm, W., Böcker, S., Nattkemper, T.W.: Improved Mass Spectrometry Peak Intensity Prediction by Adaptive Feature Weighting. International Conference on Neural Information Processing. Auckland, New Zealand (2008).
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2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2018381
Albaum, S., Neuweger, H., Lange, S., Mertens, D., Runte, K., Kalinowski, J., Nattkemper, T.W., Goesmann, A.: ProSE - "Software as a Service" for Quantitative Proteomics (Poster abstract). HUPO 7th Annual World Congress. (2008).
PUB
 
2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2018398
Herold, J., Friedenberger, M., Bode, M., Rajpoot, N., Schubert, W., Nattkemper, T.W.: Flexible Synapse Detection in Fluorescence Micrographs by Modeling Human Expert Grading. Proc. of 2008 IEEE International Symposium on Biomedical Imaging. (2008).
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