:: Publications sorted by year ::

2014
2013
2012
  • El-Kalioby, Mohamed and Abouelhoda, Mohamed and Krüger, Jan and Giegerich, Robert and Sczyrba, Alexander and Wall, Dennis P and Tonellato, Peter: Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package. in BMCBI, 13 Suppl 17, Pages:S22, 2012
  • Garcia, Sarahi L and McMahon, Katherine D and Martinez-Garcia, Manuel and Srivastava, Abhishek and Sczyrba, Alexander and Stepanauskas, Ramunas and Grossart, Hans-Peter and Woyke, Tanja and Warnecke, Falk: Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton. in ISME J, 7(1) , Pages:137-147, 2012
  • Giegerich, Robert and Voss, Björn: RNA Secondary Structure Analysis Using Abstract Shapes in Handbook of RNA Biochemistry, Pages:1-22, Editors: Hartmann, Roland K and Bindereif, Alberecht and Schön, Astrid and Westhoff, Eric, Wiley-VCH, 2012
  • Janssen, Stefan and Giegerich, Robert: RNA structure analysis and motif search with abstract shapes in RNA Sequence, Structure and Function: Compoutational and Bioinformatic Methods, Editors: Gorodkin, Jan and Ruzzo, Walter L., Springer, 2012
  • Schirmer, Stefanie and Giegerich, Robert: Forest Alignment with Affine Gaps and Anchors, applied in RNA Structure Comparison in Theoretical Computer Science, Pages:1-25, 2012
2011
  • Giegerich, Robert and Sauthoff, Georg: Yield grammar analysis in the Bellman's GAP compiler in Proceedings of the Eleventh Workshop on Language Descriptions, Tools and Applications (ACM) , 2011
  • Hess, Matthias and Sczyrba, Alexander and Egan, Rob and Kim, Tae-Wan and Chokhawala, Harshal and Schroth, Gary and Luo, Shujun and Clark, Douglas S and Chen, Feng and Zhang, Tao and Mackie, Roderick I and Pennacchio, Len A and Tringe, Susannah G and Visel, Axel and Woyke, Tanja and Wang, Zhong and Rubin, Edward M: Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. in Science, 331(6016) , Pages:463-467, 2011
  • Janssen, Stefan and Schudoma, Christian and Steger, Gerhard and Giegerich, Robert: Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction in BMC Bioinformatics, 12(1) , Pages:429, 2011
  • Kim, Tae-Wan and Chokhawala, Harshal A and Hess, Matthias and Dana, Craig M and Baer, Zachary and Sczyrba, Alexander and Rubin, Edward M and Blanch, Harvey W and Clark, Douglas S: High-Throughput In-Vitro Glycoside Hydrolase (HIGH) Screening for Enzyme Discovery. in Angew. Chem. Int. Ed. Engl., 50(47) , Pages:11215-11218, 2011
  • Linke, B. and Giegerich, R. and Goesmann, A.: Conveyor: a workflow engine for bioinformatic analyses in Bioinformatics, 27(7) , Pages:903-911, 2011
  • Reinkensmeier, Jan and Schlüter, Jan-Philip and Giegerich, Robert and Becker, Anke: Conservation and Occurrence of Trans-Encoded sRNAs in the Rhizobiales in GENES, Pages:925-956, 2011
  • Robert Giegerich and Christian Höner zu Siederdissen: Semantics and Ambiguity of Stochastic RNA Family Models in IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(2) , Pages:499-516, 2011
  • Sales, Christopher M and Mahendra, Shaily and Grostern, Ariel and Parales, Rebecca E and Goodwin, Lynne A and Woyke, Tanja and Nolan, Matt and Lapidus, Alla and Chertkov, Olga and Ovchinnikova, Galina and Sczyrba, Alexander and Alvarez-Cohen, Lisa: Genome sequence of the 1,4-dioxane-degrading Pseudonocardia dioxanivorans strain CB1190. in J. Bacteriol., 193(17) , Pages:4549-4550, 2011
  • Sauthoff, Georg and Janssen, Stefan and Giegerich, Robert: Bellman's GAP: a declarative language for dynamic programming in Proceedings of the 13th international ACM SIGPLAN symposium on Principles and practices of declarative programming, Pages:29-40 (ACM) , 2011
  • Schirmer, Stefanie and Giegerich, Robert: Forest Alignment with Affine Gaps and Anchors in Combinatorial Pattern Matching, Pages:104-117 (Springer) , 2011
  • Swan, Brandon K and Martinez-Garcia, Manuel and Preston, Christina M and Sczyrba, Alexander and Woyke, Tanja and Lamy, Dominique and Reinthaler, Thomas and Poulton, Nicole J and Masland, E Dashiell P and Gomez, Monica Lluesma and Sieracki, Michael E and DeLong, Edward F and Herndl, Gerhard J and Stepanauskas, Ramunas: Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. in Science, 333(6047) , Pages:1296-1300, 2011
  • Woyke, Tanja and Sczyrba, Alexander and Lee, Janey and Rinke, Christian and Tighe, Damon and Clingenpeel, Scott and Malmstrom, Rex and Stepanauskas, Ramunas and Cheng, Jan-Fang: Decontamination of MDA Reagents for Single Cell Whole Genome Amplification in PLoS ONE, 6(10) , Pages:e26161, 2011
2010
2009
  • Abouelhoda, M. I. and Giegerich, R. and Behzadi, B. and Steyaert, J. M.: Alignment of minisatellite maps based on run-length encoding scheme in J Bioinform Comput Biol, 7(2) , Pages:287-308, 2009
  • Beckstette, M and Homann, R and Giegerich, R and Kurtz, S: Significant speedup of databae searches with HMMs by search space reduction with PSSM family models in Bioinformatics, 2009
  • Homann, Robert and Fleer, David and Giegerich, Robert and Rehmsmeier , Marc: mkESA: enhanced suffix array construction tool in Bioinformatics, 25(8) , Pages:1084-1085, 2009
  • Reeder, J and Giegerich, R: RNA secondary structure analysis using the RNAshapes package in Curr Protoc Bioinformatics, 2009
2008
2007
  • Claus Brabrand and Robert Giegerich and Anders Møller: Analyzing Ambiguity of Context-Free Grammars in Proc. 12th International Conference on Implementation and Application of Automata, CIAA~'07, 2007
  • Hartmeier, S. and Krüger, J. and Giegerich, R.: Webservices and Workflows on the Bielefeld Bioinformatics Server: Practices and Problems in NETTAB 2007 Proceedings, 2007
  • Kaiser, A. and Krüger, J. and Evers, D.J.: RNA Movies 2 : sequential animation of RNA secondary structures in Nucl. Acids. Res., 2007
  • Reeder, Janina and Reeder, Jens and Giegerich, Robert: Locomotif: from graphical motif description to RNA motif search. in Bioinformatics, 23(13) , Pages:i392, 2007
  • Reeder, Jens and Steffen, Peter and Giegerich, Robert: pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows. in Nucleic Acids Res, 35(Web Server issue) , Pages:W320-4., 2007
2006
2005
2004
  • Giegerich, R. and Stoye, J.: German Conference on Bioinformatics (GI-Edition) , 2004
  • B. Voss and C. Meyer and R. Giegerich: Evaluating the Predictability of Conformational Switching in RNA in Bioinformatics, 20, Pages:1573-1582, 2004
  • Beckstette, M. and Mailänder, J.T. and Marhöfer, R.J. and Sczyrba, A. and Ohlebusch, E. and Giegerich, R. and Selzer, P.M.: Genlight: Interactive high-throughput sequence analysis and comparative genomics in Journal of Integrative Bioinformatics, 0008, 2004
  • Beckstette, M. and Sczyrba, A. and Selzer, P.M.: Genlight: Interactive high-throughput sequence analysis and comparative genomics in Proceedings of the German Conference on Bioinformatics, Pages:179-186 (GI Lecture Notes in Informatics) , 2004
  • Beckstette, M. and Strothmann, D. and Homann, R. and Giegerich, R. and Kurtz, S.: PoSSuMsearch: Fast and Sensitive Matching of Position Specific Scoring Matrices using Enhanced Suffix Arrays in Proceedings of the German Conference on Bioinformatics, Pages:53-64 (GI Lecture Notes in Informatics) , 2004
  • Choudhuri, J. and Schleiermacher, C. and Kurtz, S. and Giegerich, R.: Genalyzer: Interactive Visualization of Sequence Similarities Between Entire Genomes in Bioinformatics, 20, Pages:1964-1965, 2004
  • Gardner, P.P. and Giegerich, R.: A comprehensive comparison of comparative RNA structure prediction approaches in BMC Bioinformatics, 5(140) , 2004
  • Giegerich, R. and Meyer, C. and Wagner, H.: A Combinator Based Approach to the Combinatorics of Recursive Structures, 2004(submitted)
  • Giegerich, Robert and Meyer, Carsten and Steffen, Peter: A discipline of dynamic programming over sequence data. in Science of Computer Programming, 51(3) , Pages:215-263, 2004
  • Giegerich, Robert and Voß, Björn and Rehmsmeier, Marc: Abstract shapes of RNA in Nucleic Acids Research, 32(16) , Pages:4843, 2004
  • Henning Hermjakob and Luisa Montecchi-Palazzi and Gary Bader and Jérôme Wojcik and Lukasz Salwinski and Arnaud Ceol and Susan Moore and Sandra Orchard and Ugis Sarkans and Christian von Mering and Bernd Roechert and Sylvain Poux and Eva Jung and Henning Mersch and Paul Kersey and Michael Lappe and Yixue Lix and Rong Zeng and Debashis Rana and Macha Nikolski and Holger Husi and Christine Brun and K. Shanker and Seth G.N. Grant and Chris Sander and Peer Bork and Weimin Zhu and Akhilesh Pandey and Alvis Brazma and Bernard Jacq and Marc Vidal and David Sherman and Pierre Legrain and Gianni Cesareni and Ioannis Xenarios and David Eisenberg and Boris Steipe and Chris Hogue and Rolf Apweiler: The HUPO PSI Molecular Interaction Format - A community standard for the representation of protein interaction data in Nature Biotechnology, 22(2) , Pages:177 183, 2004
  • Höchsmann, M. and Voss, B. and Giegerich, R.: Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach in IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1(1) , Pages:53-62, 2004
  • Krüger, Jan and Sczyrba, Alexander and Kurtz, Stefan and Giegerich, Robert: e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences in Nucl. Acids. Res., 32(suppl 2) , Pages:W301-304, 2004
  • Mersch, Henning: BiBiWS - Ein Framework für die Entwicklung asynchroner WebServices auf dem BiBiServ, Bielefeld University, 2004
  • Reeder, Jens and Giegerich, Robert: Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. in BMC Bioinformatics, 5, Pages:104, 2004
  • Rehmsmeier, M. and Steffen, P. and Höchsmann, M. and Giegerich, R.: Fast and effective prediction of microRNA/target duplexes in RNA, 10, Pages:1507-1517, 2004
  • Sczyrba, A. and Beckstette, M. and Giegerich, R. and Altman, C.: Identification of 10,500 Xenopus laevis Full Length Clones through EST Clustering and Sequence Analysis in Proceedings of the German Conference on Bioinformatics (GI Lecture Notes in Informatics) , 2004
  • Taher, L. and Rinner, O. and Garg, S. and Sczyrba, A. and Morgenstern, B.: AGenDA: gene prediction by cross-species sequence comparison in Nucl. Acids. Res., 32(suppl_2) , Pages:W305-308, 2004
2003
  • Abouelhoda, M. I. and Ohlebusch, E.: A Local Chaining Algorithm and its Applications in Comparative Genomics in Proceedings of the 3rd Workshop on Algorithms in Bioinformatics, LNCS (Springer Verlag) , 2003
  • Abouelhoda, M. I. and Ohlebusch, E.: Multiple Genome Alignment: Chaining Algorithms Revisited in Proceedings of the 14th Annual Symposium on Combinatorial Pattern Matching, LNCS, Pages:1-16 (Springer Verlag) , 2003
  • Beckstette, M. and Mailaender, J. and Giegerich, R. and Selzer, P.M.: G-enlight: Interactive high-throughput sequence analysis and (differential) comparative genomics in Poster abstracts of the 9th Pacific Symposium on Biocomputing, Lihue, USA, 2003, 2003
  • Dondrup, M. and Goesmann, A. and Bartels, D. and Kalinowski, J. and Krause, L. and Linke, B. and Rupp, O. and Sczyrba, A. and Pühler, A. and Meyer, F.: EMMA: a platform for consistent storage and efficient analysis of microarray data in Journal of Biotechnology, 106(2-3) , Pages:135-146, 2003
  • Dress, A. and Giegerich, R. and Grünewald, S. and Wagner,H.: Fibonacci-Cayley-numbers and Repetition Patterns in Genomic DNA in Annals of Combinatorics, Pages:259-279, 2003
  • Giegerich, Robert and Kurtz, Stefan and Stoye, Jens: Efficient implementation of lazy suffix trees in Software Practice and Experience, 33(11) , Pages:1035-1049, 2003
  • Henning Mersch and Georg Fuellen: paper2sequences: Retrieval of sequences listed in a publication in Applied Bioinformatics, 2(2) , Pages:113-116, 2003
  • Höchsmann,M. and Töller, T. and Giegerich, R. and Kurtz, S.: Local Similarity in RNA Secondary Structures in Proceedings of the IEEE Computational Systems Bioinformatics Conference (CSB 2003), Pages:159-168, 2003
  • Marian, C.O. and Bordoli, S.J. and Goltz, M. and Santarella, R.A. and Jackson, L.P. and Danilevskaya, O. and Beckstette, M. and Meeley, R. and Bass, H.W.: The Maize Single myb histone 1 Gene, Smh1, Belongs to a Novel Gene Family and Encodes a Protein That Binds Telomere DNA Repeats in Vitro in Plant Physiology, 133, Pages:1336-1335, 2003
  • Meyer, F. and Goesmann, A. and McHardy, A. and Bartels, D. and Bekel, T. and Clausen, J. and Kalinowski, J. and Linke, B. and Rupp, O. and Giegerich, R. and Pühler, A.: GenDB - An open source genome annotation system for prokaryote genomes in Nucleic Acids Res., 31(8) , Pages:2187-2195, 2003
  • Morgenstern, B. and Goel, S. and Sczyrba, A. and Dress, A.: AltAVisT : A WWW tool for comparison of alternative multiple alignments in Bioinformatics, 19(3) , Pages:425-426, 2003
  • Sczyrba, A. and Krüger, J. and Mersch, H. and Kurtz, S. and Giegerich, R.: RNA-related tools on the Bielefeld Bioinformatics Server in Nucleic Acids Research, 31(13) , Pages:3767-3770, 2003
  • Taher, L. and Rinner, O. and Garg, S. and Sczyrba, A. and Brudno, M. and Batzoglou, S. and Morgenstern, B.: AGenDA: homology-based gene prediction in Bioinformatics, 19(12) , Pages:1575-1577, 2003
2002
  • Abouelhoda, M.I. and Kurtz, S. and Ohlebusch, E.: The Enhanced Suffix Array and its Applications to Genome Analysis in Proceedings of the Second Workshop on Algorithms in Bioinformatics, LNCS 2452 , Pages:449-463 (Springer Verlag) , 2002
  • Abouelhoda, M.I. and Ohlebusch, E. and Kurtz, S.: Optimal Exact String Matching Based on Suffix Arrays in Proceedings of the Ninth International Symposium on String Processing and Information Retrieval, LNCS, Pages:31-43 (Springer-Verlag) , 2002
  • Ferch, M. and Zhang, J. and Höchsmann,M.: Learning cooperative assembly with the graph representation of a state-action space in IEEE/RSJ International Conference on Intelligent Robots and Systems, 2002
  • Giegerich, R. and Meyer, C.: Algebraic Dynamic Programming in Algebraic Methodology And Software Technology, 9th International Conference, AMAST 2002, Pages:349-364 (Springer) , 2002
  • Giegerich, R. and Meyer, C. and Steffen, P.: Towards a discipline of dynamic programming in Informatik bewegt, Pages:3-44 (Bonner Köllen Verlag) , 2002
  • Giegerich, R. and Steffen, P.: Implementing Algebraic Dynamic Programming in the Functional and the Imperative Programming Paradigm in Mathematics of Program Construction, Pages:1-20 (LNCS 2386) , 2002
  • Goesmann, A. and Haubrock, M. and Meyer, F. and Kalinowski, J. and Giegerich, R.: PathFinder: Reconstruction and dynamic visualization of metabolic pathways in Bioinformatics, 18, Pages:124-129, 2002
  • Meyer, C. and Giegerich, R.: Matching and Significance Evaluation of Sequence-Structure Patterns in RNA in J. Physical Chemistry, 216, Pages:1-24, 2002
  • Rössler, B. and Zhang, J. and Höchsmann,M.: Visual Guided Grasping and Generalization using Self-Valuing Learning in IEEE/RSJ International Conference on Intelligent Robots and Systems, 2002
  • Taher, L. and Rinner, O. and Garg, S. and Sczyrba, A. and Brudno, M. and Batzouglou, S. and Morgenstern, B.: AGenDA: A WWW server for gene recognition by comparative sequence analysis in European Conference on Computational Biology 2002, Poster Abstracts, 2002
2001
  • Altmann, C.R. and Bell, E. and Sczyrba, A. and Pun, J. and Bekiranov, S. and Gaasterland, T. and Brivanlou, A.H.: Microarray-Based Analysis of Early Development in Xenopus laevis in Dev Biol, 236(1) , Pages:64-75, 2001
  • Evers, D. and Giegerich, R.: Reducing the Conformation Space in RNA Structure Prediction in German Conference on Bioinformatics, Pages:118-124, 2001
  • Fuellen, G. and Wägele, J.W. and Giegerich, R.: Minimum Conflict - A Divide-And-Conquer Approach to Phylogeny Estimation in Bioinformatics, 17, Pages:1168-1178, 2001
  • Fuellen, G. and Wägele, J.W. and Giegerich, R.: Best Systematist Practice Tranferred to Molecular Data in Organisms, Diversity and Evolution, 1, Pages:257-272, 2001
  • Fuellen, G. and Wägele, J.W. and Giegerich, R.: Minimum Conflict - A Divide-And-Conquer Approach to Phylogeny Estimation in Bioinformatics, 17, Pages:1168-1178, 2001
  • Futamura, N. and Aluru, S. and Kurtz, S.: Parallel Suffix Sorting in Proc. of the Ninth International Conference on Advanced Computing and Communications, Bhubaneshwar, India (Tata McGraw-Hill) , 2001
  • Gopal, S. and Schroeder, M. and Pieper, U. and Sczyrba, A. and Aytekin-Kurban, G. and Bekiranov, S. and Fajardo, J.E. and Eswar, N. and Sanchez, R. and Sali, A. and Gaasterland, T.: Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome in Nat Genet, 27(3) , Pages:337-340, 2001
  • Gräf, S. and Steger, G. and Strothmann, D. and Kurtz, S.: HyPaLib: a Database of RNAs and RNA Structural Elements defined by Hybrid Patterns in Nucleic Acids Res., 29(1) , Pages:196-198, 2001
  • Kurtz, S. and Choudhuri, J.V. and Ohlebusch, E. and Schleiermacher, C. and Stoye, J. and Giegerich, R.: REPuter: the Manifold Applications of Repeat Analysis on a Genomic Scale in Nucleic Acids Res., 29(22) , Pages:4633-4642, 2001
  • Marco Balke and Thomas Dettbarn and Robert Homann and Sebastian Jaenicke and Tim Köhler and Henning Mersch and Holger Weiss: Eine asynchrone Implementierung eines Microprozessors auf einem FPGA, Technische Fakultät, Technical Report TR2001-04, 2001
2000
  • Balkenhol, B. and Kurtz, S.: Universal Data Compression Based on the Burrows and Wheeler Transformation: Theory and Practice in IEEE Trans. on Computers, 49(1) , Pages:1043-1046, 2000
  • Evers, D. and Giegerich, R.: Systematic Dynamic Programming in Bioinformatics in Intelligent Systems for Molecular Biology (Tutorial Notes) (AAAI Press, Menlo Park, CA, USA) , 2000
  • Gaasterland, T. and Sczyrba, A. and Thomas, E. and Kurban, G.: MAGPIE/EGRET annotation of the 2.9-Mb Drosophila melanogaster Adh region in Genome Res, 10(4) , Pages:502-510, 2000
  • Giegerich, R.: A Systematic Approach to Dynamic Programming in Bioinformatics in Bioinformatics, 16, Pages:665-677, 2000
  • Giegerich, R.: Explaining and Controlling Ambiguity in Dynamic Programming in Proc. Combinatorial Pattern Matching, Pages:46-59 (Springer) , 2000
  • Giegerich, Robert and Evers, Dirk: Bioinformatik: Jäger, Sammler und Forscher im Daten-Dschungel der Molekularbiologie in BIOforum, 1-2, Pages:30-32, 2000
  • Kurtz, S. and Balkenhol, B.: Space Efficient Linear Time Computation of the Burrows and Wheeler Transformation in Numbers, Information and Complexity, Pages:375-383, 2000
  • Kurtz, S. and Ohlebusch, E. and Schleiermacher, C. and Stoye, J. and Giegerich, R.: Computation and Visualization of Degenerate Repeats in Complete Genomes in Proc. of the International Conference on Intelligent Systems for Molecular Biology, Pages:228-238 (AAAI Press) , 2000
  • Strothmann, D. and Kurtz, S. and Gräf, S. and Steger, G.: The Syntax and Semantics of a Language for Describing Complex Patterns in Biological Sequences, Technische Fakultät, Universität Bielefeld, Report 2000-06, 2000
1999
  • Giegerich, R. and Wingender, E.: German Conference on Bioinformatics (GBF Braunschweig) , 1999
  • Balkenhol, B. and Kurtz, S. and Shtarkov, Y.M.: Modification of the Burrows and Wheeler Data Compression Algorithm in Proceedings of the IEEE Data Compression Conference, Snowbird, Utah, Pages:188-197 (IEEE Computer Society Press) , 1999
  • Bütow, B. and Giegerich, R. and Ohlebusch, E. and Thesing, S.: Semantic Matching for Left-Linear Convergent Rewrite Systems in The Journal of Functional and Logic Programming, 1999(10) , 1999
  • Evers, D. and Giegerich, R.: RNA Movies: Visualizing RNA Secondary Structure Spaces in Bioinformatics, 15(1) , Pages:32-37, 1999
  • Evers, D. and Giegerich, R. and Kurtz, S.: A General Pattern Matching Language for Specific Motifs in RNA Secondary Structure in Proc. of the 4th European Conference on Theory and Mathematics in Biology and Medicine, 1999
  • Giegerich, R.: Towards a Discipline of Dynamic Programming in Bioinformatics. Parts 1 and 2: Sequence Comparison and RNA Folding, Technische Fakultät, Universität Bielefeld, Report 99-05, 1999
  • Giegerich, R. and Hinze, R. and Kurtz, S.: Straight to the Heart of Computer Science via Functional Programming in Proceedings of the Workshop on Functional and Declarative Programming in Education, Pages:1-5 (Technical Report Rice COMP TR99-346, Department of Computer Science, Rice University, Editor: Matthias Felleisen) , 1999
  • Giegerich, R. and Kurtz, S. and Stoye, J.: Efficient Implementation of Lazy Suffix Trees in Proc. of the Third Workshop on Algorithmic Engineering (WAE99), Pages:30-42 (Lecture Notes in Computer Science 1668) , 1999
  • Giegerich, R. and Kurtz, S. and Weiller, G.F.: An Algebraic Dynamic Programming Approach to the Analysis of Recombinant DNA Sequences in Proceedings of Workshop on Algorithmic Ascpects of Advanced Programming Languages (WAAAPL), Paris, September 1999, Pages:77-88, 1999
  • Giegerich, Robert and Haase, Dirk and Rehmsmeier, Marc: Prediction and Visualization of Structural Switches in RNA in Proc. 1999 Pacific Symposium on Biocomputing, Pages:126-137 (World Scientific) , 1999
  • Kurtz, S.: Reducing the Space Requirement of Suffix Trees in Software-Practice and Experience, 29(13) , Pages:1149-1171, 1999
  • Kurtz, S.: Manual: A C-Library for the Efficient Construction and Application of Suffix Trees, 1999
  • Kurtz, S. and Schleiermacher, C.: REPuter: Fast Computation of Maximal Repeats in Complete Genomes in Bioinformatics, 15(5) , Pages:426-427, 1999
1998
  • Balkenhol, B. and Kurtz, S.: Universal Data Compression Based on the Burrows and Wheeler Transformation: Theory and Practice, Sonderforschungsbereich: Diskrete Strukturen in der Mathematik, Universität Bielefeld, 98-069, Technical Report, 1998
  • Evers, D. and Giegerich, R.: Bioinformatik - Jäger, Sammler und Forscher im Datendschungel der Molekularbiologie, 1998
  • Giegerich, R.: A Declarative Approach to the Development of Dynamic Programming Algorithms, Applied to RNA Folding, Technische Fakultät, Universität Bielefeld, Report 98-02, 1998
  • Giegerich, Robert and Lorenz, Dieter: ViSeL - An Interactive Course in DNA Sequencing in Proceedings Workshop on Multimedia Systeme in Wissenschaft und Technik, 1998
  • Kurtz, S.: Reducing the Space Requirement of Suffix Trees, Technische Fakultät, Universität Bielefeld, Report 98-03, 1998
  • Sczyrba, A.: Methods for Automatic Annotation of Biological Sequences, Bielefeld University, 1998
1997
  • Fuellen, G. and Giegerich, R.: International, interdisziplinär und interaktiv: Der VSNS-Kurs über BioComputing in Proceedings: Virtueller Campus, Pages:77-89 (Waxmann) , 1997
  • Giegerich, R. and Hischke, F. and Kurtz, S. and Ohlebusch, E.: A General Technique to Improve Filter Algorithms for Approximate String Matching in Proc. of Fourth South American Workshop on String Processing, Valparaiso, Chile, Pages:38-52, 1997
  • Giegerich, R. and Hofestädt, R. and Lipinski, W. and Schomburg, D. and Werner, T.: Curricularempfehlung zur Bioinformatik (1997), 1997
  • Giegerich, R. and Kurtz, S.: From Ukkonen to McCreight and Weiner: A Unifying View of Linear-Time Suffix Tree Construction in Algorithmica, 19, Pages:331-353, 1997
  • Hermjakob, H. and Giegerich, R. and Arnold, W.: RIFLE: Rapid Identification of Microorganisms by Fragment Length Evaluation in Proc. Intelligent Systems for Molecular Biology, Pages:131-137 (AAAI Press, Menlo Park, CA, USA) , 1997
  • Kurtz, S. and Myers, G.: Estimating the Probability of Approximate Matches in Proc. of the Annual Symposium on Combinatorial Pattern Matching (CPM'97), Pages:52-64, 1997
1996
  • Bueschking, C. and Giegerich, R.: Sequenzanalyse mit verteilten Ressourcen - ein WWW-basierter Kurs in it + ti, 38(5) , Pages:39 - 46, 1996
  • De La Vega, F. and Giegerich, R. and Fuellen, G.: Distance Education through the Internet: The GNA-VSNS Biocomputing Course in Proceedings of Pacific Symposium on Bioccomputing, Pages:203-215, 1996
  • Giegerich, R. and Hischke, F. and Kurtz, S. and Ohlebusch, E.: Static and Dynamic Filtering Methods for Approximate String Matching, Technische Fakultät, Universität Bielefeld, Report 96-01, 1996
  • Giegerich, R. and Meyer, F. and Schleiermacher, C.: GeneFisher - Software Support for the Detection of Postulated Genes in Proc. Intelligent Systems for Molecular Biology, Pages:68-77 (AAAI Press, Menlo Park, CA, USA) , 1996
  • Grüner, W. and Giegerich, R. and Strothmann, D. and Reidys, C. and Weber, J. and Hofacker, I.L. and Stadler, P.F. and Schuster, P.: Analysis of RNA Sequence Structure Maps by Exhaustive Enumeration I. Neutral Networks in Chemical Monthly, 127, Pages:355-374, 1996
  • Grüner, W. and Giegerich, R. and Strothmann, D. and Reidys, C. and Weber, J. and Hofacker, I.L. and Stadler, P.F. and Schuster, P.: Analysis of RNA Sequence Structure Maps by Exhaustive Enumeration II. Structure of Neutral Networks and Shape Space Covering in Chemical Monthly, 127, Pages:375-389, 1996
  • Kurtz, S.: Approximate String Searching under Weighted Edit Distance in Proc. of Third South American Workshop on String Processing, Pages:156-170, 1996
1995
  • Bütow, B. and Giegerich, R. and Ohlebusch, E. and Thesing, S.: A New Strategy for Semantic Matching in Programming Languages: Implementations, Logics and Programs, Pages:81-96 (Springer) , 1995
  • Giegerich, R. and Kurtz, S.: A Comparison of Imperative and Purely Functional Suffix Tree Constructions in Science of Computer Programming, 25(2-3) , Pages:187-218, 1995
  • Grüner, W. and Giegerich, R. and Strothmann, D.: Algorithmic Representation of Large RNA Folding Landscapes in Bioinformatics: From Nucleic Acids and Proteins to Cell Metabolism; GBF Monographs Volume 18, 1995
  • Kurtz, S.: Fundamental Algorithms for a Declarative Pattern Matching System, Technische Fakultät, Universität Bielefeld, available as Report 95-03, 1995
1994
  • Giegerich, R.: Algorithmen auf Sequenzen, 1994
  • Giegerich, R.: Personal Communication, 1994
  • Giegerich, R. and Kurtz, S.: A Comparison of Imperative and Purely Functional Suffix Tree Constructions, Technische Fakultät, Universität Bielefeld, Report No. 14, 1994
  • Giegerich, R. and Kurtz, S.: Suffix Trees in the Functional Programming Paradigm in Proceedings of the European Symposium on Programming (ESOP'94), Pages:225-240 (Springer) , 1994
1993
  • Brehme, B. and Giegerich, R.: So zählt Miranda, 1993
  • Giegerich, R. and Kurtz, S.: Suffix Trees in the Functional Programming Paradigm, Technische Fakultät, Universität Bielefeld, Report Nr. 12, 1993
1992
  • Giegerich, R. and Graham, S.L.: Workshop on Code Generation - Concepts, Tools and Techniques (Springer) , 1992
  • Cruse, H. and Giegerich, R. and Hinze, J. and Schepper, W.: Der Studiengang Naturwissenschaftliche Informatik an der Universität Bielefeld, Technische Fakultät, Universität Bielefeld, Interner Bericht, 1992
  • Giegerich, R.: Considerate Code Selection, Pages:51-65, 1992
  • Giegerich, R.: Embedding Sequence Analysis in the Functional Programming Paradigm - A Feasibility Study, Technische Fakultät, Universität Bielefeld, Report Nr. 8, 1992
  • Kurtz, S.: Narrowing and Basic Forward Closures, Technische Fakultät, Universität Bielefeld, Report Nr. 5, 1992
  • Kurtz, S.: Narrowing and Basic Forward Closures in Proceedings of the Sixth International Workshop on Unification, Schloß Dagstuhl, Pages:68-71 (Technical Report #93-004, Computer Science Department, Boston University) , 1992
1991
  • Giegerich, R. and Ohlebusch, E.: An Implicit Representation of Infinite Sequences of Terms in Bulletin of the EATCS, 43, Pages:174-182, 1991
1990
  • Giegerich, R.: Code Selection by Inversion of Order-Sorted Derivors in Theoretical Computer Science, 73, Pages:177-211, 1990
  • Giegerich, R.: On the Structure of Verifiable Code Generator Specifications in Proc. SIGPLAN `90 Conference on Programming Language Design and Implementation, Pages:1-8 (SIGPLAN NOTICES 25(6)) , 1990
  • Kurtz, S.: Bottom-up Narrowing with Basic Rule Closures in Second German Workshop on Term Rewriting: Theory and Applications, Forschungsbericht Nr. 336, Fachbereich Informatik, Universität Dortmund, Pages:47-49, 1990
1989
  • Kurtz, S.: Eine compilierte deterministische Narrowingstrategie für spezielle Regelsysteme, Fachbereich Informatik, Universität Dortmund, 1989
1988
  • Giegerich, R.: Composition and Evaluation of Attribute Coupled Grammars in Acta Informatica, 25, Pages:355-423, 1988
  • Giegerich, R. and Schmal, K.: Code Selection Techniques: Pattern Matching, Tree Parsing and Inversion of Derivors in Proc. European Symposium on Programming 1988, Pages:247-268 (Springer) , 1988
1987
  • Ganzinger, H. and Giegerich, R.: A Note on Termination of Combinations of Heterogeneous Term Rewriting Systems in Bulletin of the EATCS, 31, Pages:22-28, 1987
1985
  • Giegerich, R.: Logic Specification of Code Generation Techniques in Workshop on Programs as Data Objects, Pages:96-111 (Springer) , 1985
1984
  • Ganzinger, H. and Giegerich, R.: Attribute Coupled Grammars in Proc. of the ACM Symposium on Compiler Construction, Pages:157-170 (SIGPLAN NOTICES 19(6)) , 1984
1983
  • Giegerich, R.: A Formal Framework for the Derivation of Machine-Specific Optimizers in ACM Transactions on Programming Languages and Systems, 5(3) , Pages:478-498, 1983
1982
  • Giegerich, R.: A Formal Model of Instruction Set Semantics in 7.~Fachtagung Programmiersprachen und Programmentwicklung, Pages:177-190 (Springer Informatik Fachberichte 53) , 1982
  • Giegerich, R. and Ganzinger, H. and Möncke, U. and Wilhelm, R.: A Truly Generative Semantics-Directed Compiler Generator in Proceedings of the ACM Symposium on Compiler Construction, Boston, Pages:172-184 (SIGPLAN Notices 17(6)) , 1982
  • Giegerich, R. and Möncke, U. and Wilhelm, R.: Invariance of Approximate Semantics with Respect to Program Transformations in Proceedings of GI-11.~Jahrestagung, M"unchen, Pages:1-10 (Springer) , 1982
1981
  • Giegerich, R.: Automatische Erzeugung von Maschinencode-Optimierern, Institut für Informatik, TU München, 1981
1978
  • Giegerich, R. and Wilhelm, R.: Attribute Evaluation in State of the Art and Future Trends in Compilation (INRIA, Paris) , 1978
  • Giegerich, R. and Wilhelm, R.: Counter-one-pass Features in One-pass Compilation: A Formalization Using Attribute Grammars in Information Processing Letters, 7(6) , Pages:279-284, 1978
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