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136 Publikationen

2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2901460
Löwes, B., Chauve, C., Ponty, Y., Giegerich, R.: The BRaliBase Dent – a Tale of Benchmark Design and Interpretation. Briefings in Bioinformatics. 18, 306-311 (2017).
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2903044
Gatter, T., Giegerich, R., Saule, C.: Integrating Pareto Optimization into Dynamic Programming. ALGORITHMS. 9, : 12 (2016).
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2015 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2917100
Nuss, A.M., Heroven, A.K., Waldmann, B., Reinkensmeier, J., Jarek, M., Beckstette, M., Dersch, P.: Transcriptomic Profiling of Yersinia pseudotuberculosis Reveals Reprogramming of the Crp Regulon by Temperature and Uncovers Crp as a Master Regulator of Small RNAs. PLOS GENETICS. 11, : 26 (2015).
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2905757
Giegerich, R., Touzet, H.: Modeling Dynamic Programming Problems over Sequences and Trees with Inverse Coupled Rewrite Systems. Algorithms. 7, 62-144 (2014).
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2014 | Bielefelder E-Dissertation | PUB-ID: 2682131 OA
Janssen, S.: Kisses, ambivalent models and more: Contributions to the analysis of RNA secondary structure. Universitätsbibliothek, Bielefeld (2014).
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2699802
Torres-Quesada, O., Reinkensmeier, J., Schlueter, J.-P., Robledo, M., Peregrina, A., Giegerich, R., Toro, N., Becker, A., Jimenez-Zurdo, J.I.: Genome-wide profiling of Hfq-binding RNAs uncovers extensive post-transcriptional rewiring of major stress response and symbiotic regulons in Sinorhizobium meliloti. RNA Biology. 11, 563-579 (2014).
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2681698
Sauthoff, G., Giegerich, R.: Yield grammar analysis and product optimization in a domain-specific language for dynamic programming. Science of Computer Programming. 87, 2-22 (2014).
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2699792
Becker, A., Overloeper, A., Schlueter, J.-P., Reinkensmeier, J., Robledo, M., Giegerich, R., Narberhaus, F., Evguenieva-Hackenberg, E.: Riboregulation in plant-associated alpha-proteobacteria. RNA Biology. 11, 550-562 (2014).
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2584661
Schlueter, J.-P., Reinkensmeier, J., Barnett, M.J., Lang, C., Krol, E., Giegerich, R., Long, S.R., Becker, A.: Global mapping of transcription start sites and promoter motifs in the symbiotic a-proteobacterium Sinorhizobium meliloti 1021. Bmc Genomics. 14, 156 (2013).
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2645192
Gillett, A., Bergman, P., Parsa, R., Bremges, A., Giegerich, R., Jagodic, M.: A Silent Exonic SNP in Kdm3a Affects Nucleic Acids Structure but Does Not Regulate Experimental Autoimmune Encephalomyelitis. Plos One. 8, e81912 (2013).
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2013 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2901275
Löwes, B., Giegerich, R.: Avoiding Ambiguity and Assessing Uniqueness in Minisatellite Alignment. In: Beißbarth, T., Kollmar, M., Leha, A., Morgenstern, B., Schultz, A.-K., Waack, S., and Wingender, E. (eds.) German Conference on Bioinformatics 2013. OpenAccess Series in Informatics (OASIcs). 34, p. 110-124. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, Dagstuhl, Germany (2013).
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2607289
Schirmer, S., Giegerich, R.: Forest alignment with affine gaps and anchors, applied in RNA structure comparison. Theoretical Computer Science. 483, 51-67 (2013).
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2012 | Sammelwerksbeitrag | PUB-ID: 2439665
Janssen, S., Giegerich, R.: Abstract Shape Analysis of RNA. In: Gorodkin, J. and Weinberg, Z. (eds.) RNA Bioinformatics t.b.a. p. 1-35. (2012).
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2410526 OA
Janssen, S., Schudoma, C., Steger, G., Giegerich, R.: Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction. BMC Bioinformatics. 12, 429 (2011).
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2427226
Reinkensmeier, J., Schlüter, J.-P., Giegerich, R., Becker, A.: Conservation and Occurrence of Trans-Encoded sRNAs in the Rhizobiales. GENES. 925-956 (2011).
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2011 | Bielefelder E-Dissertation | PUB-ID: 2302459 OA
Abdul-Hak, S.: Analytische und empirische Untersuchungen über abstrakte Shapes von RNA-Sekundärstrukturen. Bielefeld University, Bielefeld (Germany) (2011).
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2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2383357
Giegerich, R., Sauthoff, G.: Yield grammar analysis in the Bellman's GAP compiler. Proceedings of the Eleventh Workshop on Language Descriptions, Tools and Applications (ACM). (2011).
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2383363
Schirmer, S., Giegerich, R.: Forest Alignment with Affine Gaps and Anchors. Combinatorial Pattern Matching. 104-117 (2011).
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2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2310489
Sauthoff, G., Janssen, S., Giegerich, R.: Bellman's GAP: a declarative language for dynamic programming. Proceedings of the 13th international ACM SIGPLAN symposium on Principles and practices of declarative programming. p. 29-40. ACM, New York, NY, USA (2011).
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2011 | Bielefelder E-Dissertation | PUB-ID: 2474238 OA
Schirmer, S.: Comparing forests. Bielefeld University, Bielefeld (2011).
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2003355
Giegerich, R., Hoener Zu Siederdissen, C.: Semantics and Ambiguity of Stochastic RNA Family Models. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8, 499-516 (2011).
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2093578
Linke, B., Giegerich, R., Goesmann, A.: Conveyor: a workflow engine for bioinformatic analyses. Bioinformatics. 27, 903-911 (2011).
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2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1893988 OA
Grond, F., Janssen, S., Schirmer, S., Hermann, T.: Browsing RNA Structures by Interactive Sonification. In: Bresin, R., Hermann, T., and Hunt, A. (eds.) Proceedings of the 3rd Interactive Sonification Workshop. p. 11-16. KTH School of Computer Science and Communication (CSC), KTH, Stockholm, Sweden (2010).
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2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2906810
Bremges, A., Schirmer, S., Giegerich, R.: Fine-tuning structural RNA alignments in the twilight zone. BMC Bioinformatics. 11, : 222 (2010).
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2010 | Bielefelder E-Dissertation | PUB-ID: 2304195 OA
Sauthoff, G.: Bellman's GAP : a 2nd generation language and system for algebraic dynamic programming. Bielefeld University, Bielefeld (Germany) (2010).
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2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1796697
Brabrand, C., Giegerich, R., Moller, A.: Analyzing ambiguity of context-free grammars. SCIENCE OF COMPUTER PROGRAMMING. 75, 176-191 (2010).
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2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1894008 OA
Theis, C., Janssen, S., Giegerich, R.: Prediction of RNA Secondary Structure Including Kissing Hairpin Motifs. In: Moulton, V. and Singh, M. (eds.) Algorithms in Bioinformatics. 10th international workshop (WABI 2010), proceedings. Lecture Notes in Bioinformatics. 6293, p. 52-64. Springer, Berlin (2010).
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2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1893946 OA
Janssen, S., Giegerich, R.: Faster computation of exact RNA shape probabilities. Bioinformatics. 26, 632-639 (2010).
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2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1785497 OA
Schlüter, J.-P., Reinkensmeier, J., Daschkey, S., Evguenieva-Hackenberg, E., Janssen, S., Jaenicke, S., Becker, J.D., Giegerich, R., Becker, A.: A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti. BMC Genomics. 11, : 245 (2010).
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2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1785512 OA
Bremges, A., Schirmer, S., Giegerich, R.: Fine-tuning structural RNA alignments in the twilight zone. BMC Bioinformatics. 11, 222 (2010).
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2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1785581 OA
Abouelhoda, M., El-Kalioby, M., Giegerich, R.: WAMI: a web server for the analysis of minisatellite maps. BMC Evolutionary Biology. 10, 167 (2010).
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2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2383365
Abouelhoda, M., Giegerich, R., Behzadi, B., Steyaert, J.M.: Alignment of minisatellite maps based on run-length encoding scheme. Journal of Bioinformatics and Computational Biology. 7, 287-308 (2009).
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2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2383411
Reeder, J., Giegerich, R.: RNA secondary structure analysis using the RNAshapes package. Current Protocols in Bioinformatics. (2009).
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2009 | Konferenzbeitrag | Entwurf | PUB-ID: 2383425
Steffen, P., Giegerich, R., Giraud, M.: GPU Parallization of Algebraic Dynamic Programming. Proceedings PPAM. (Unpublished).
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2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1589458
Beckstette, M., Homann, R., Giegerich, R., Kurtz, S.: Significant speedup of database searches with HMMs by search space reduction with PSSM family models. Bioinformatics. 25, 3251-3258 (2009).
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2009 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1634374
Homann, R., Fleer, D., Giegerich, R., Rehmsmeier, M.: mkESA: enhanced suffix array construction tool. Bioinformatics. 25, 1084-1085 (2009).
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2008 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2383382
Abouelhoda, M.I., Giegerich, R., Behzadi, B., Steyaert, J.M.: Alignment of Minisatellite Maps: A Minimum Spanning Tree based Approach. Proceedings of the 6th Asia-Pacific Bioinformatics Conference. Series on Advances in Bioinformatics and Computational Biology, 6. p. 261-272. (2008).
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2008 | Bielefelder E-Dissertation | PUB-ID: 2305281 OA
Fiedler, T.: The jPREdictor and its application to motif discovery, motif clustering and the prediction of Polycomb/Trithorax response elements. Bielefeld University, Bielefeld (Germany) (2008).
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1784020 OA
Lamprecht, A.-L., Margaria, T., Steffen, B., Sczyrba, A., Hartmeier, S., Giegerich, R.: GeneFisher-P: variations of GeneFisher as processes in Bio-jETI. BMC Bioinformatics. 9, S13 (2008).
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1784025 OA
Herold, J., Kurtz, S., Giegerich, R.: Efficient computation of absent words in genomic sequences. BMC Bioinformatics. 9, 167 (2008).
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2008 | Kurzbeitrag Konferenz / Poster | Veröffentlicht | PUB-ID: 1587496
Gkogkoglou, K., Mentz, A., Albersmeier, A., Kalinowski, J., Giegerich, R.: Looking for non-coding RNAs in Corynebacterium glutamicum. FEBS JOURNAL. 275, 153 (2008).
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1588303
Sczyrba, A., Konermann, S., Giegerich, R.: Two interactive bioinformatics courses at the bielefeld university bioinformatics server. BRIEFINGS IN BIOINFORMATICS. 9, 243-249 (2008).
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1588308
Giegerich, R., Brazma, A., Jonassen, I., Ukkonen, E., Vingron, M.: The BREW workshop series: a stimulating experience in PhD education. Briefings in Bioinformatics. 9, 250-253 (2008).
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1783357 OA
Theis, C., Reeder, J., Giegerich, R.: KnotInFrame: prediction of –1 ribosomal frameshift events. Nucleic Acids Research. 36, 6013-6020 (2008).
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1893917 OA
Janssen, S., Reeder, J., Giegerich, R.: Shape based indexing for faster search of RNA family databases. BMC Bioinformatics. 9, 131 (2008).
PUB | Dateien verfügbar | DOI | WoS | PubMed | Europe PMC
 
2007 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2383428
Brabrand, C., Giegerich, R., Moeller, A.: Analyzing Ambiguity of Context-Free Grammars. In: Holub, J. and Žďárek, J. (eds.) Implementation and Application of Automata. 12th International Conference, CIAA 2007, July 16-18, 2007, Revised Selected Papers. Lecture Notes in Computer Science, 4783. Springer (2007).
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2007 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2383462
Hartmeier, S., Krüger, J., Giegerich, R.: Webservices and Workflows on the Bielefeld Bioinformatics Server: Practices and Problems. Proceedings. (2007).
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2007 | Bielefelder E-Dissertation | PUB-ID: 2305575 OA
Beckstette, M.: Index-based algorithms for motif search and their integration in a system for differential genome analysis. Bielefeld University, Bielefeld (Germany) (2007).
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2007 | Bielefelder Masterarbeit | PUB-ID: 2306578 OA
Sauthoff, G.: Java-Backend für den ADP-Compiler. Bielefeld University, Bielefeld (Germany) (2007).
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2007 | Bielefelder E-Dissertation | PUB-ID: 2306594 OA
Reeder, J.: Algorithms for RNA secondary structure analysis : prediction of pseudoknots and the consensus shapes approach. Bielefeld University, Bielefeld (Germany) (2007).
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