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50 Publikationen

2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2919006
Rubert, D., Hoshino, E.A., Dias Vieira Braga, M., Stoye, J. & Martinez, F.H.V. (2018). Computing the family-free DCJ similarity. BMC Bioinformatics, 19(Suppl. 6): 152. BioMed Central. doi:10.1186/s12859-018-2130-5.
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2910493
Romano, P., Hofestädt, R., Lange, M. & D'Elia, D. (2017). The joint NETTAB/Integrative Bioinformatics 2015 Meeting: aims, topics and outcomes. BMC BIOINFORMATICS, 18: 101. Biomed Central Ltd. doi:10.1186/s12859-017-1532-0.
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2907670
Feijão, P. & Soares de Araujo, F.E. (2016). Fast ancestral gene order reconstruction of genomes with unequal gene content. BMC Bioinformatics, 17(S14): 413. Gehalten auf der 14th Annual Research in Computational Molecular Biology (RECOMB) Comparative Genomics Satellite Workshop, Springer Nature. doi:10.1186/s12859-016-1261-9.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2775617
Stadermann, K.B., Weisshaar, B. & Holtgräwe, D. (2015). SMRT sequencing only de novo assembly of the sugar beet (Beta vulgaris) chloroplast genome. BMC Bioinformatics, 16: 295. Springer Science + Business Media. doi:10.1186/s12859-015-0726-6.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2764888
Janssen, S. & Giegerich, R. (2015). Ambivalent covariance models. BMC Bioinformatics, 16: 178. Springer Science + Business Media. doi:10.1186/s12859-015-0569-1.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2900856
Feijão, P., Martinez, F. & Thévenin, A. (2015). On the distribution of cycles and paths in multichromosomal breakpoint graphs and the expected value of rearrangement distance. BMC Bioinformatics, 16(Suppl 19): S1. Springer Science + Business Media. doi:10.1186/1471-2105-16-s19-s1.
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2783101
Feijão, P. (2015). Reconstruction of ancestral gene orders using intermediate genomes. BMC Bioinformatics, 16(Suppl 14): S3. Springer Science + Business Media. doi:10.1186/1471-2105-16-S14-S3.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2575011
Ander, C., Schulz-Trieglaff, O.B., Stoye, J. & Cox, A.J. (2013). metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences. BMC Bioinformatics, 14(Suppl 5: Proc. of RECOMB-Seq 2013), S2. Springer Science + Business Media. doi:10.1186/1471-2105-14-S5-S2.
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2611633
Jahn, K., Winter, S., Stoye, J. & Böcker, S. (2013). Statistics for approximate gene clusters. BMC Bioinformatics, 14(Suppl 15: Proc. of RECOMB-CG 2013), S14. Springer Science + Business Media. doi:10.1186/1471-2105-14-S15-S14.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2512642
Dörr, D., Thévenin, A. & Stoye, J. (2012). Gene family assignment-free comparative genomics. BMC Bioinformatics, 13(Suppl 19: Proc. of RECOMB-CG 2012), S3. Springer Science + Business Media. doi:10.1186/1471-2105-13-S19-S3.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2517239
Hoffmann, N., Keck, M., Neuweger, H., Wilhelm, M., Högy, P., Niehaus, K. & Stoye, J. (2012). Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets. BMC Bioinformatics, 13(1), 21. Springer Science + Business Media. doi:10.1186/1471-2105-13-21.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2553300
Manuch, J., Patterson, M., Wittler, R., Chauve, C. & Tannier, E. (2012). Linearization of ancestral multichromosomal genomes. BMC Bioinformatics, 13(Proc. of RECOMB-CG 2012). Springer Science + Business Media. doi:10.1186/1471-2105-13-S19-S11.
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2012 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2547307
El-Kalioby, M., Abouelhoda, M., Krüger, J., Giegerich, R., Sczyrba, A., Wall, D.P. & Tonellato, P. (2012). Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package. BMC Bioinformatics, 13(Suppl 17), S22. Springer Science + Business Media. doi:10.1186/1471-2105-13-S17-S22.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2410526
Janssen, S., Schudoma, C., Steger, G. & Giegerich, R. (2011). Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction. BMC Bioinformatics, 12(1), 429. Springer Science + Business Media. doi:10.1186/1471-2105-12-429.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2300082
Loyek, C., Khan, M., Rajpoot, N. & Nattkemper, T.W. (2011). BIOIMAX - A Web 2.0 approach for easy exploratory and collaborative access to multivariate bioimage data. BMC Bioinformatics, 12(1), 297. Springer Science + Business Media. doi:10.1186/1471-2105-12-297.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2603576
Thomas, P.E., Klinger, R., Furlong, L.I., Hofmann-Apitius, M. & Friedrich, C.M. (2011). Challenges in the association of human single nucleotide polymorphism mentions with unique database identifiers. BMC Bioinformatics, 12(Suppl 4), S4. Springer Science + Business Media. doi:10.1186/1471-2105-12-S4-S4.
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2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2329973
Wittler, R. & Chauve, C. (2011). Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes (BMC Bioinformatics), 12(Suppl. 9), S21. Gehalten auf der RECOMB-CG 2011, BMC. doi:10.1186/1471-2105-12-S9-S21.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2425310
Wolfsheimer, S., Herms, I., Rahmann, S. & Hartmann, A.K. (2011). Accurate statistics for local sequence alignment with position-dependent scoring by rare-event sampling. BMC Bioinformatics, 12(1), 47-2105. Springer Science + Business Media. doi:10.1186/1471-2105-12-47.
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2091779
Hufsky, F., Kuchenbecker, L., Jahn, K., Stoye, J. & Böcker, S. (2011). Swiftly Computing Center Strings. BMC Bioinformatics, 12(1), 106. Springer Science + Business Media. doi:10.1186/1471-2105-12-106.
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2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2906810
Bremges, A., Schirmer, S. & Giegerich, R. (2010). Fine-tuning structural RNA alignments in the twilight zone. BMC Bioinformatics, 11(1): 222. Springer Nature. doi:10.1186/1471-2105-11-222.
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2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2316624
Gurtowski, J., Cancio, A., Shah, H., Levovitz, C., George, A., Homann, R. & Sachidanandam, R. (2010). Geoseq: a tool for dissecting deep-sequencing datasets. BMC Bioinformatics, 11(1), 506. Springer Science + Business Media. doi:10.1186/1471-2105-11-506.
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2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1785512
Bremges, A., Schirmer, S. & Giegerich, R. (2010). Fine-tuning structural RNA alignments in the twilight zone. BMC Bioinformatics, 11(1), 222. Springer Science + Business Media. doi:10.1186/1471-2105-11-222.
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2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2603504
Corinna, K., Klinger, R. & Hofmann-Apitius, M. (2009). Identification of Histone Modifications in Biomedical Text for Supporting Epigenomic Research. BMC Bioinformatics, 10(Suppl 1), S28. Springer Science + Business Media. doi:10.1186/1471-2105-10-S1-S28.
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2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1783187
Blom, J., Albaum, S., Doppmeier, D., Pühler, A., Vorhölter, F.-J., Zakrzewski, M. & Goesmann, A. (2009). EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics, 10(1): 154. Springer Science + Business Media. doi:10.1186/1471-2105-10-154.
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2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1635314
Diaz, N.N., Krause, L., Goesmann, A., Niehaus, K. & Nattkemper, T.W. (2009). TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics, 10(1), 56. Springer Science + Business Media. doi:10.1186/1471-2105-10-56.
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2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1635321
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. (2009). EMMA 2-A MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics, 10(1): 50. Springer Science + Business Media. doi:10.1186/1471-2105-10-50.
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2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1589098
Gerlach, W., Jünemann, S., Tille, F., Goesmann, A. & Stoye, J. (2009). WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics, 10(1), 430. Springer Science + Business Media. doi:10.1186/1471-2105-10-430.
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1784020
Lamprecht, A.-L., Margaria, T., Steffen, B., Sczyrba, A., Hartmeier, S. & Giegerich, R. (2008). GeneFisher-P: variations of GeneFisher as processes in Bio-jETI. BMC Bioinformatics, 9(Suppl 4), S13. doi:10.1186/1471-2105-9-S4-S13.
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1784025
Herold, J., Kurtz, S. & Giegerich, R. (2008). Efficient computation of absent words in genomic sequences. BMC Bioinformatics, 9(1), 167. doi:10.1186/1471-2105-9-167.
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1783280
Tscherepanow, M., Jensen, N. & Kummert, F. (2008). An incremental approach to automated protein localisation. BMC Bioinformatics, 9(1), 445. doi:10.1186/1471-2105-9-445.
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1636280
Timm, W., Scherbart, A., Boecker, S., Kohlbacher, O. & Nattkemper, T.W. (2008). Peak intensity prediction in MALDI-TOF mass spectrometry: A machine learning study to support quantitative proteomics. BMC Bioinformatics, 9(1), 443. BIOMED CENTRAL LTD. doi:10.1186/1471-2105-9-443.
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1585611
Wei, N., Flaschel, E., Friehs, K. & Nattkemper, T.W. (2008). A machine vision system for automated non-invasive assessment of cell viability via dark field microscopy, wavelet feature selection and classification. BMC Bioinformatics, 9(1), 449. BIOMED CENTRAL LTD. doi:10.1186/1471-2105-9-449.
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1893917
Janssen, S., Reeder, J. & Giegerich, R. (2008). Shape based indexing for faster search of RNA family databases. BMC Bioinformatics, 9(1), 131. Biomed Central. doi:10.1186/1471-2105-9-131.
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2007 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2499132
Baumbach, J. (2007). CoryneRegNet 4.0 – A reference database for corynebacterial gene regulatory networks. BMC Bioinformatics, 8(1), 429. doi:10.1186/1471-2105-8-429.
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2007 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1783712
Kaltenbach, H.-M., Wilke, A. & Böcker, S. (2007). SAMPI: protein identification with mass spectra alignments. BMC Bioinformatics, 8(1), 102. doi:10.1186/1471-2105-8-102.
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2007 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1783743
Baumbach, J. (2007). CoryneRegNet 4.0: a reference database for corynebacterial gene regulatory networks. BMC Bioinformatics, 8(1), 429. doi:10.1186/1471-2105-8-429.
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2007 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1784011
Wittkop, T., Baumbach, J., Lobo, F.P. & Rahmann, S. (2007). Large scale clustering of protein sequences with FORCE - a layout based heuristic for weighted cluster editing. BMC Bioinformatics, 8(1), 396. doi:10.1186/1471-2105-8-396.
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2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773701
Köhler, J., Munn, K., Rüegg, A., Skusa, A. & Smith, B. (2006). Quality control for terms and definitions in ontologies and taxonomies. BMC Bioinformatics, 7(1), 212. doi:10.1186/1471-2105-7-212.
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2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773864
Beckstette, M., Homann, R., Giegerich, R. & Kurtz, S. (2006). Fast index based algorithms and software for matching position specific scoring matrices. BMC Bioinformatics, 7(1), 389. doi:10.1186/1471-2105-7-389.
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2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773871
Seibel, P.N., Krüger, J., Hartmeier, S., Schwarzer, K., Löwenthal, K., Mersch, H., Dandekar, T. & Giegerich, R. (2006). XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinformatics, 7(1), 490. doi:10.1186/1471-2105-7-490.
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2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773640
Steffen, P. & Giegerich, R. (2006). Correction: Versatile and declarative dynamic programming using pair algebras. BMC Bioinformatics, 7(1), 214. doi:10.1186/1471-2105-7-214.
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2006 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1599756
Spitzer, M., Lorkowski, S., Cullen, P., Sczyrba, A. & Fuellen, G. (2006). IsoSVM - Distinguishing isoforms and paralogs on the protein level. BMC Bioinformatics, 7(1), 110. BIOMED CENTRAL LTD. doi:10.1186/1471-2105-7-110.
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2005 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1775168
Krause, A., Stoye, J. & Vingron, M. (2005). Large scale hierarchical clustering of protein sequences. BMC Bioinformatics, 6(1), 15. doi:10.1186/1471-2105-6-15.
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2005 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773595
Reeder, J., Steffen, P. & Giegerich, R. (2005). Effective ambiguity checking in biosequence analysis. BMC Bioinformatics, 6(1), 153. doi:10.1186/1471-2105-6-153.
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2005 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773598
Steffen, P. & Giegerich, R. (2005). Versatile and declarative dynamic programming using pair algebras. BMC Bioinformatics, 6(1), 224. doi:10.1186/1471-2105-6-224.
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2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773554
Pollard, D.A., Bergman, C.M., Stoye, J., Celniker, S.E. & Eisen, M.B. (2004). Correction: Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics, 5(1), 73. doi:10.1186/1471-2105-5-73.
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2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773758
Reeder, J. & Giegerich, R. (2004). Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics, 5(1), 104. doi:10.1186/1471-2105-5-104.
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2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773312
Pollard, D.A., Bergman, C.M., Stoye, J., Celniker, S.E. & Eisen, M.B. (2004). Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics, 5(1), 6. doi:10.1186/1471-2105-5-6.
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2004 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773747
Gardner, P.P. & Giegerich, R. (2004). A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics, 5(1), 140. doi:10.1186/1471-2105-5-140.
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2003 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1773767
Brudno, M., Chapman, M., Göttgens, B., Batzoglou, S. & Morgenstern, B. (2003). Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics, 4(1), 66. doi:10.1186/1471-2105-4-66.
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