112 Publications

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[112]
2016 | Journal Article | PUB-ID: 2901460
The BRaliBase Dent – a Tale of Benchmark Design and Interpretation
Löwes B, Chauve C, Ponty Y, Giegerich R (2016)
Briefings in Bioinformatics 18(2): 306-311.
PUB | DOI | WoS | PubMed | Europe PMC
 
[111]
2016 | Journal Article | PUB-ID: 2903044
Integrating Pareto Optimization into Dynamic Programming
Gatter T, Giegerich R, Saule C (2016)
ALGORITHMS 9(1): 12.
PUB | DOI | WoS
 
[110]
2015 | Journal Article | PUB-ID: 2763075
Pareto optimization in algebraic dynamic programming
Saule C, Giegerich R (2015)
Algorithms for Molecular Biology 10: 22.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[109]
2015 | Journal Article | PUB-ID: 2764888
Ambivalent covariance models
Janssen S, Giegerich R (2015)
BMC Bioinformatics 16: 178.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[108]
2015 | Journal Article | PUB-ID: 2733607
Thermodynamic matchers for the construction of the cuckoo RNA family
Reinkensmeier J, Giegerich R (2015)
RNA Biology 12(2): 197-207.
PUB | DOI | WoS | PubMed | Europe PMC
 
[107]
2014 | Journal Article | PUB-ID: 2700599
The RNA shapes studio
Janssen S, Giegerich R (2014)
Bioinformatics 31(3): 423-425.
PUB | DOI | WoS | PubMed | Europe PMC
 
[106]
2014 | Journal Article | PUB-ID: 2905757 PUB | DOI
 
[105]
2014 | Conference Abstract | PUB-ID: 2901695
German Conference on Bioinformatics 2014
Giegerich R, Hofestädt R, Nattkemper TW (2014) .
PUB
 
[104]
2014 | Journal Article | PUB-ID: 2699792
Riboregulation in plant-associated alpha-proteobacteria
Becker A, Overloeper A, Schlueter J-P, Reinkensmeier J, Robledo M, Giegerich R, Narberhaus F, Evguenieva-Hackenberg E (2014)
RNA Biology 11(5): 550-562.
PUB | DOI | WoS | PubMed | Europe PMC
 
[103]
2014 | Journal Article | PUB-ID: 2699802
Genome-wide profiling of Hfq-binding RNAs uncovers extensive post-transcriptional rewiring of major stress response and symbiotic regulons in Sinorhizobium meliloti
Torres-Quesada O, Reinkensmeier J, Schlueter J-P, Robledo M, Peregrina A, Giegerich R, Toro N, Becker A, Jimenez-Zurdo JI (2014)
RNA Biology 11(5): 563-579.
PUB | DOI | WoS | PubMed | Europe PMC
 
[102]
2014 | Journal Article | PUB-ID: 2681698
Yield grammar analysis and product optimization in a domain-specific language for dynamic programming
Sauthoff G, Giegerich R (2014)
Science of Computer Programming 87: 2-22.
PUB | DOI | WoS
 
[101]
2013 | Journal Article | PUB-ID: 2645192
A Silent Exonic SNP in Kdm3a Affects Nucleic Acids Structure but Does Not Regulate Experimental Autoimmune Encephalomyelitis
Gillett A, Bergman P, Parsa R, Bremges A, Giegerich R, Jagodic M (2013)
Plos One 8(12): e81912.
PUB | DOI | WoS | PubMed | Europe PMC
 
[100]
2013 | Conference Paper | PUB-ID: 2901275
Avoiding Ambiguity and Assessing Uniqueness in Minisatellite Alignment
Löwes B, Giegerich R (2013)
In: German Conference on Bioinformatics 2013. Beißbarth T, Kollmar M, Leha A, Morgenstern B, Schultz A-K, Waack S, Wingender E (Eds); OpenAccess Series in Informatics (OASIcs), 34. Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik: 110-124.
PUB | DOI
 
[99]
2013 | Journal Article | PUB-ID: 2607289
Forest alignment with affine gaps and anchors, applied in RNA structure comparison
Schirmer S, Giegerich R (2013)
Theoretical Computer Science 483: 51-67.
PUB | DOI | WoS
 
[98]
2013 | Journal Article | PUB-ID: 2584661
Global mapping of transcription start sites and promoter motifs in the symbiotic a-proteobacterium Sinorhizobium meliloti 1021
Schlueter J-P, Reinkensmeier J, Barnett MJ, Lang C, Krol E, Giegerich R, Long SR, Becker A (2013)
Bmc Genomics 14(1): 156.
PUB | DOI | WoS | PubMed | Europe PMC
 
[97]
2013 | Journal Article | PUB-ID: 2551798
Bellman's GAP -- a Language and Compiler for Dynamic Programming in Sequence Analysis
Sauthoff G, Mohl M, Janssen S, Giegerich R (2013)
Bioinformatics 29(5): 551-560.
PUB | DOI | WoS | PubMed | Europe PMC
 
[96]
2012 | Journal Article | PUB-ID: 2547307
Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package
El-Kalioby M, Abouelhoda M, Krüger J, Giegerich R, Sczyrba A, Wall DP, Tonellato P (2012)
BMC Bioinformatics 13(Suppl 17): S22.
PUB | DOI | WoS | PubMed | Europe PMC
 
[95]
2012 | Book Chapter | PUB-ID: 2439665
Abstract Shape Analysis of RNA
Janssen S, Giegerich R (2012)
In: RNA Bioinformatics t.b.a. Gorodkin J, Weinberg Z (Eds); 1-35.
PUB
 
[94]
2011 | Journal Article | PUB-ID: 2383363
Forest Alignment with Affine Gaps and Anchors
Schirmer S, Giegerich R (2011)
Combinatorial Pattern Matching: 104-117.
PUB | DOI
 
[93]
2011 | Journal Article | PUB-ID: 2410526
Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction
Janssen S, Schudoma C, Steger G, Giegerich R (2011)
BMC Bioinformatics 12(1): 429.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[92]
2011 | Conference Paper | PUB-ID: 2310489
Bellman's GAP: a declarative language for dynamic programming
Sauthoff G, Janssen S, Giegerich R (2011)
In: Proceedings of the 13th international ACM SIGPLAN symposium on Principles and practices of declarative programming. New York, NY, USA: ACM: 29-40.
PUB | DOI
 
[91]
2011 | Journal Article | PUB-ID: 2427226
Conservation and Occurrence of Trans-Encoded sRNAs in the Rhizobiales
Reinkensmeier J, Schlüter J-P, Giegerich R, Becker A (2011)
GENES: 925-956.
PUB | DOI | WoS | PubMed | Europe PMC
 
[90]
2011 | Journal Article | PUB-ID: 2093578
Conveyor: a workflow engine for bioinformatic analyses
Linke B, Giegerich R, Goesmann A (2011)
Bioinformatics 27(7): 903-911.
PUB | DOI | WoS | PubMed | Europe PMC
 
[89]
2011 | Conference Paper | PUB-ID: 2383357
Yield grammar analysis in the Bellman's GAP compiler
Giegerich R, Sauthoff G (2011)
In: Proceedings of the Eleventh Workshop on Language Descriptions, Tools and Applications (ACM).
PUB
 
[88]
2011 | Journal Article | PUB-ID: 2003355
Semantics and Ambiguity of Stochastic RNA Family Models
Giegerich R, Hoener Zu Siederdissen C (2011)
IEEE/ACM Transactions on Computational Biology and Bioinformatics 8(2): 499-516.
PUB | DOI | WoS | PubMed | Europe PMC
 
[87]
2010 | Conference Paper | PUB-ID: 1894008
Prediction of RNA Secondary Structure Including Kissing Hairpin Motifs
Theis C, Janssen S, Giegerich R (2010)
In: Algorithms in Bioinformatics. 10th international workshop (WABI 2010), proceedings. Moulton V, Singh M (Eds); Lecture Notes in Bioinformatics, 6293. Berlin: Springer: 52-64.
PUB | File | DOI
 
[86]
2010 | Journal Article | PUB-ID: 2906810
Fine-tuning structural RNA alignments in the twilight zone
Bremges A, Schirmer S, Giegerich R (2010)
BMC Bioinformatics 11(1): 222.
PUB | DOI
 
[85]
2010 | Journal Article | PUB-ID: 1785497
A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti
Schlüter J-P, Reinkensmeier J, Daschkey S, Evguenieva-Hackenberg E, Janssen S, Jaenicke S, Becker JD, Giegerich R, Becker A (2010)
BMC Genomics 11(1): 245.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[84]
2010 | Journal Article | PUB-ID: 1893946
Faster computation of exact RNA shape probabilities
Janssen S, Giegerich R (2010)
Bioinformatics 26(5): 632-639.
PUB | File | DOI | WoS | PubMed | Europe PMC
 
[83]
2010 | Journal Article | PUB-ID: 1785581
WAMI: a web server for the analysis of minisatellite maps
Abouelhoda M, El-Kalioby M, Giegerich R (2010)
BMC Evolutionary Biology 10(1): 167.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[82]
2010 | Journal Article | PUB-ID: 1785512
Fine-tuning structural RNA alignments in the twilight zone
Bremges A, Schirmer S, Giegerich R (2010)
BMC Bioinformatics 11(1): 222.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[81]
2010 | Journal Article | PUB-ID: 1796697
Analyzing ambiguity of context-free grammars
Brabrand C, Giegerich R, Moller A (2010)
SCIENCE OF COMPUTER PROGRAMMING 75(3): 176-191.
PUB | DOI | WoS
 
[80]
2009 | Journal Article | PUB-ID: 2383411
RNA secondary structure analysis using the RNAshapes package
Reeder J, Giegerich R (2009)
Current Protocols in Bioinformatics.
PUB | DOI | PubMed | Europe PMC
 
[79]
2009 | Conference Paper | PUB-ID: 2383425
GPU Parallization of Algebraic Dynamic Programming
Steffen P, Giegerich R, Giraud M (Unpublished)
In: Proceedings PPAM.
PUB
 
[78]
2009 | Journal Article | PUB-ID: 1634374
mkESA: enhanced suffix array construction tool
Homann R, Fleer D, Giegerich R, Rehmsmeier M (2009)
Bioinformatics 25(8): 1084-1085.
PUB | DOI | WoS | PubMed | Europe PMC
 
[77]
2009 | Journal Article | PUB-ID: 1589458
Significant speedup of database searches with HMMs by search space reduction with PSSM family models
Beckstette M, Homann R, Giegerich R, Kurtz S (2009)
Bioinformatics 25(24): 3251-3258.
PUB | DOI | WoS | PubMed | Europe PMC
 
[76]
2009 | Journal Article | PUB-ID: 2383365
Alignment of minisatellite maps based on run-length encoding scheme
Abouelhoda M, Giegerich R, Behzadi B, Steyaert JM (2009)
Journal of Bioinformatics and Computational Biology 7(02): 287-308.
PUB | DOI | PubMed | Europe PMC
 
[75]
2008 | Conference Abstract | PUB-ID: 1587496
Looking for non-coding RNAs in Corynebacterium glutamicum
Gkogkoglou K, Mentz A, Albersmeier A, Kalinowski J, Giegerich R (2008)
FEBS JOURNAL 275(Suppl. 1): 153.
PUB | WoS
 
[74]
2008 | Conference Paper | PUB-ID: 2383382
Alignment of Minisatellite Maps: A Minimum Spanning Tree based Approach
Abouelhoda MI, Giegerich R, Behzadi B, Steyaert JM (2008)
In: Proceedings of the 6th Asia-Pacific Bioinformatics Conference. Series on Advances in Bioinformatics and Computational Biology, 6. 261-272.
PUB | DOI
 
[73]
2008 | Journal Article | PUB-ID: 1784020
GeneFisher-P: variations of GeneFisher as processes in Bio-jETI
Lamprecht A-L, Margaria T, Steffen B, Sczyrba A, Hartmeier S, Giegerich R (2008)
BMC Bioinformatics 9(Suppl 4): S13.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[72]
2008 | Journal Article | PUB-ID: 1893917
Shape based indexing for faster search of RNA family databases
Janssen S, Reeder J, Giegerich R (2008)
BMC Bioinformatics 9(1): 131.
PUB | Files available | DOI | WoS | PubMed | Europe PMC
 
[71]
2008 | Journal Article | PUB-ID: 1784025
Efficient computation of absent words in genomic sequences
Herold J, Kurtz S, Giegerich R (2008)
BMC Bioinformatics 9(1): 167.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[70]
2008 | Journal Article | PUB-ID: 1783357
KnotInFrame: prediction of –1 ribosomal frameshift events
Theis C, Reeder J, Giegerich R (2008)
Nucleic Acids Research 36(18): 6013-6020.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[69]
2008 | Journal Article | PUB-ID: 1588303
Two interactive bioinformatics courses at the bielefeld university bioinformatics server
Sczyrba A, Konermann S, Giegerich R (2008)
BRIEFINGS IN BIOINFORMATICS 9(3): 243-249.
PUB | DOI | WoS | PubMed | Europe PMC
 
[68]
2008 | Journal Article | PUB-ID: 1588308
The BREW workshop series: a stimulating experience in PhD education
Giegerich R, Brazma A, Jonassen I, Ukkonen E, Vingron M (2008)
Briefings in Bioinformatics 9(3): 250-253.
PUB | DOI | WoS | PubMed | Europe PMC
 
[67]
2007 | Conference Paper | PUB-ID: 1593132
Locomotif: from graphical motif description to RNA motif search
Reeder J, Reeder J, Giegerich R (2007)
Bioinformatics 23(13): I392-I400.
PUB | DOI | WoS | PubMed | Europe PMC
 
[66]
2007 | Conference Paper | PUB-ID: 2383428
Analyzing Ambiguity of Context-Free Grammars
Brabrand C, Giegerich R, Moeller A (2007)
In: Implementation and Application of Automata. 12th International Conference, CIAA 2007, July 16-18, 2007, Revised Selected Papers. Holub J, Žďárek J (Eds); Lecture Notes in Computer Science, 4783. Springer.
PUB | DOI
 
[65]
2007 | Journal Article | PUB-ID: 1587974
pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows
Reeder J, Steffen P, Giegerich R (2007)
NUCLEIC ACIDS RESEARCH 35(Web Server): W320-W324.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[64]
2007 | Conference Paper | PUB-ID: 2383462
Webservices and Workflows on the Bielefeld Bioinformatics Server: Practices and Problems
Hartmeier S, Krüger J, Giegerich R (2007)
In: Proceedings.
PUB
 
[63]
2006 | Journal Article | PUB-ID: 1773864
Fast index based algorithms and software for matching position specific scoring matrices
Beckstette M, Homann R, Giegerich R, Kurtz S (2006)
BMC Bioinformatics 7(1): 389.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[62]
2006 | Journal Article | PUB-ID: 1773871
XML schemas for common bioinformatic data types and their application in workflow systems
Seibel PN, Krüger J, Hartmeier S, Schwarzer K, Löwenthal K, Mersch H, Dandekar T, Giegerich R (2006)
BMC Bioinformatics 7(1): 490.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[61]
2006 | Journal Article | PUB-ID: 1773640
Correction: Versatile and declarative dynamic programming using pair algebras
Steffen P, Giegerich R (2006)
BMC Bioinformatics 7(1): 214.
PUB | PDF | DOI | WoS
 
[60]
2006 | Journal Article | PUB-ID: 1773637
Complete probabilistic analysis of RNA shapes
Voß B, Giegerich R, Rehmsmeier M (2006)
BMC Biology 4(1): 5.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[59]
2006 | Journal Article | PUB-ID: 1597805
Table design in dynamic programming
Steffen P, Giegerich R (2006)
INFORMATION AND COMPUTATION 204(9): 1325-1345.
PUB | DOI | WoS
 
[58]
2006 | Journal Article | PUB-ID: 1600421
RNAshapes: an integrated RNA analysis package based on abstract shapes
Steffen P, Voss B, Rehmsmeier M, Reeder J, Giegerich R (2006)
Bioinformatics 22(4): 500-503.
PUB | DOI | WoS | PubMed | Europe PMC
 
[57]
2006 | Conference Paper | PUB-ID: 1598807
Beyond Mfold: recent advances in RNA bioinformatics
Reeder J, Höchsmann M, Rehmsmeier M, Voss B, Giegerich R (2006)
JOURNAL OF BIOTECHNOLOGY 124(1): 41-55.
PUB | DOI | WoS | PubMed | Europe PMC
 
[56]
2006 | Conference Paper | PUB-ID: 2383518
A graphical programming system for molecular motif search
Reeder J, Giegerich R (2006)
In: Proceedings of the 5th International Conference on Generative Programming and Component Engineering. ACM Press: 131-140.
PUB
 
[55]
2006 | Journal Article | PUB-ID: 1600726
Calculating PSSM probabilities with lazy dynamic programming
Malde K, Giegerich R (2006)
Jornal of Functional Programming 16(01): 75-81.
PUB | DOI | WoS
 
[54]
2006 | Journal Article | PUB-ID: 1946336
Thermodynamic matchers: strengthening the significance of RNA folding energies
Höchsmann T, Höchsmann M, Giegerich R (2006)
Comput Syst Bioinformatics Conf.
PUB | DOI | PubMed | Europe PMC
 
[53]
2006 | Conference Paper | PUB-ID: 2383464
Challenges in the Compilation of a Domain Specific Language for Dynamic Programming
Giegerich R, Steffen P (2006)
In: Proceedings of te 2006 ACM Symposium on Applied Computing.
PUB
 
[52]
2006 | Journal Article | PUB-ID: 1902179 PUB | DOI | WoS | PubMed | Europe PMC
 
[51]
2006 | Journal Article | PUB-ID: 1597065
Surprises in approximating Levenshtein distances
Baake M, Grimm U, Giegerich R (2006)
JOURNAL OF THEORETICAL BIOLOGY 243(2): 279-282.
PUB | DOI | WoS | PubMed | Europe PMC
 
[50]
2005 | Journal Article | PUB-ID: 1773595
Effective ambiguity checking in biosequence analysis
Reeder J, Steffen P, Giegerich R (2005)
BMC Bioinformatics 6(1): 153.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[49]
2005 | Journal Article | PUB-ID: 1773598
Versatile and declarative dynamic programming using pair algebras
Steffen P, Giegerich R (2005)
BMC Bioinformatics 6(1): 224.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[48]
2005 | Journal Article | PUB-ID: 1773613
XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis
Sczyrba A, Beckstette M, Brivanlou AH, Giegerich R, Altmann CR (2005)
BMC Genomics 6(1): 123.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[47]
2005 | Journal Article | PUB-ID: 1602431
Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction
Reeder J, Giegerich R (2005)
BIOINFORMATICS 21(17): 3516-3523.
PUB | DOI | WoS | PubMed | Europe PMC
 
[46]
2004 | Conference (Editor) | PUB-ID: 1918823
Proceedings of the German Conference on Bioinformatics, GCB 2004
Giegerich R, Stoye J (Eds) (2004)
Lecture Notes in Informatics P-53.
PUB
 
[45]
2004 | Journal Article | PUB-ID: 2383529
Genlight: Interactive high-throughput sequence analysis and comparative genomics
Beckstette M, Mailänder JT, Marhöfer RJ, Sczyrba A, Ohlebusch E, Giegerich R, Selzer PM (2004)
Journal of Integrative Bioinformatics 1(1): 0008.
PUB | DOI
 
[44]
2004 | Journal Article | PUB-ID: 1773758 PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[43]
2004 | Journal Article | PUB-ID: 1607394
e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences
Krüger J, Sczyrba A, Kurtz S, Giegerich R (2004)
NUCLEIC ACIDS RESEARCH 32(Web Server): W301-W304.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[42]
2004 | Journal Article | PUB-ID: 1773747
A comprehensive comparison of comparative RNA structure prediction approaches
Gardner PP, Giegerich R (2004)
BMC Bioinformatics 5(1): 140.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[41]
2004 | Journal Article | PUB-ID: 1606393
Abstract shapes of RNA
Giegerich R, Voss B, Rehmsmeier M (2004)
Nucleic Acids Research 32(16): 4843-4851.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[40]
2004 | Journal Article | PUB-ID: 1607656
A discipline of dynamic programming over sequence data
Giegerich R, Meyer C, Steffen P (2004)
SCIENCE OF COMPUTER PROGRAMMING 51(3): 215-263.
PUB | DOI | WoS
 
[39]
2004 | Journal Article | PUB-ID: 1607419
Evaluating the predictability of conformational switching in RNA
Voss B, Meyer C, Giegerich R (2004)
Bioinformatics 20(10): 1573-1582.
PUB | DOI | WoS | PubMed | Europe PMC
 
[38]
2004 | Conference Paper | PUB-ID: 2383561
Identification of 10,500 Xenopus laevis Full Length Clones through EST Clustering and Sequence Analysis
Sczyrba A, Beckstette M, Giegerich R, Altman C (2004)
In: Proceedings of the German Conference on Bioinformatics. Lecture Notes in Informatics: GI.
PUB
 
[37]
2004 | Journal Article | PUB-ID: 1606377
Fast and effective prediction of microRNA/target duplexes
Rehmsmeier M, Steffen P, Höchsmann M, Giegerich R (2004)
RNA-A PUBLICATION OF THE RNA SOCIETY 10(10): 1507-1517.
PUB | DOI | WoS | PubMed | Europe PMC
 
[36]
2004 | Journal Article | PUB-ID: 1600293
Pure multiple RNA secondary structure alignments: A progressive profile approach
Höchsmann M, Voss B, Giegerich R (2004)
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATIOCS 1(1): 53-62.
PUB | DOI | WoS | PubMed | Europe PMC
 
[35]
2004 | Journal Article | PUB-ID: 1606822
GenAlyzer: interactive visualization of sequence similarities between entire genomes
Choudhuri JV, Schleiermacher C, Kurtz S, Giegerich R (2004)
BIOINFORMATICS 20(12): 1964-1965.
PUB | DOI | WoS | PubMed | Europe PMC
 
[34]
2004 | Conference Paper | PUB-ID: 2383543
PoSSuMsearch: Fast and Sensitive Matching of Position Specific Scoring Matrices using Enhanced Suffix Arrays
Beckstette M, Strothmann D, Homann R, Giegerich R, Kurtz S (2004)
In: Proceedings of the German Conference on Bioinformatics. Lecture Notes in Informatics: GI: 53-64.
PUB
 
[33]
2003 | Journal Article | PUB-ID: 1773880
GenDB - an open source genome annotation system for prokaryote genomes
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Pühler A (2003)
Nucleic Acids Research 31(8): 2187-2195.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[32]
2003 | Journal Article | PUB-ID: 1918949
Finden, fast ohne zu suchen: Indexstrukturen in der Bioinformatik
Giegerich R, Stoye J (2003)
Forschung an der Universität Bielefeld 26: 63-68.
PUB
 
[31]
2003 | Journal Article | PUB-ID: 1610397
Efficient implementation of lazy suffix trees
Giegerich R, Kurtz S, Stoye J (2003)
SOFTWARE-PRACTICE & EXPERIENCE 33(11): 1035-1049.
PUB | PDF | DOI | WoS
 
[30]
2003 | Journal Article | PUB-ID: 1773844
RNA-related tools on the Bielefeld Bioinformatics Server
Sczyrba A, Krüger J, Mersch H, Kurtz S, Giegerich R (2003)
Nucleic Acids Research 31(13): 3767-3770.
PUB | Files available | DOI | WoS | PubMed | Europe PMC
 
[29]
2003 | Journal Article | PUB-ID: 1666680
Local similarity in RNA secondary structures.
Höchsmann M, Töller T, Giegerich R, Kurtz S (2003)
Proc IEEE Comput Soc Bioinform Conf 2.
PUB | PubMed | Europe PMC
 
[28]
2003 | Journal Article | PUB-ID: 2383602
Fibonacci-Cayley-numbers and Repetition Pattern in Genomic DNA
Dress A, Giegerich R, Grünewald S, Wagner H (2003)
Annals of Combinatorics: 259-279.
PUB
 
[27]
2002 | Conference Paper | PUB-ID: 1612812
Implementing algebraic dynamic programming in the functional and the imperative programming paradigm
Giegerich R, Steffen P (2002)
In: MATHEMATICS OF PROGRAM CONSTRUCTION. Lecture Notes in Computer Science, 2386. SPRINGER-VERLAG BERLIN: 1-20.
PUB | WoS
 
[26]
2002 | Journal Article | PUB-ID: 1615366
PathFinder: reconstruction and dynamic visualization of metabolic pathways
Goesmann A, Haubrock M, Meyer F, Kalinowski J, Giegerich R (2002)
BIOINFORMATICS 18(1): 124-129.
PUB | DOI | WoS | PubMed | Europe PMC
 
[25]
2002 | Journal Article | PUB-ID: 1614870
Matching and significance evaluation of combined sequence-structure motifs in RNA
Meyer C, Giegerich R (2002)
ZEITSCHRIFT FÜR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS 216(2/2002): 193-216.
PUB | DOI | WoS
 
[24]
2002 | Conference Paper | PUB-ID: 2383608
Algebraic Dynamic Programming
Giegerich R, Meyer C (2002)
In: Algebraic Methodology and Software Technology. Springer: 349-364.
PUB
 
[23]
2001 | Journal Article | PUB-ID: 1773335
REPuter: the manifold applications of repeat analysis on a genomic scale
Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R (2001)
Nucleic Acids Research 29(22): 4633-4642.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[22]
2001 | Journal Article | PUB-ID: 1615572
Minimum conflict: a divide-and-conquer approach to phylogeny estimation
Fuellen G, Wägele JW, Giegerich R (2001)
BIOINFORMATICS 17(12): 1168-1178.
PUB | DOI | WoS | PubMed | Europe PMC
 
[21]
2001 | Journal Article | PUB-ID: 1615460
Best systematist practice transferred to molecular data
Fuellen G, Wägele JW, Giegerich R (2001)
ORGANISMS DIVERSITY & EVOLUTION 1(4): 257-272.
PUB | DOI | WoS
 
[20]
2001 | Conference Paper | PUB-ID: 2383615
Reducing the Conformation Space in RNA Structure Prediction
Evers D, Giegerich R (2001)
In: Proceedings of the German Conference on Bioinformatics. 118-124.
PUB
 
[19]
2000 | Conference Paper | PUB-ID: 1618572
Explaining and controlling ambiguity in dynamic programming
Giegerich R (2000)
In: Combinatorial Pattern Matching. 11th Annual Symposium CPM 2000, Proceedings. Giancarlo R, Sankoff D (Eds); Lecture Notes in Computer Science, 1848. Berlin: Springer: 46-59.
PUB | WoS
 
[18]
2000 | Conference Paper | PUB-ID: 1918988
Computation and Visualization of Degenerate Repeats in Complete Genomes
Kurtz S, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R (2000)
In: Proc. of ISMB 2000. 228-238.
PUB | PubMed | Europe PMC
 
[17]
2000 | Journal Article | PUB-ID: 2383618 PUB
 
[16]
2000 | Journal Article | PUB-ID: 1618574
A systematic approach to dynamic programming in bioinformatics
Giegerich R (2000)
BIOINFORMATICS 16(8): 665-677.
PUB | DOI | WoS | PubMed | Europe PMC
 
[15]
1999 | Conference Paper | PUB-ID: 1620435
Efficient implementation of lazy suffix trees
Giegerich R, Kurtz S, Stoye J (1999)
In: Algorithm Engineering. 3rd International Workshop, WAE’99 London, UK, July 19–21, 1999 Proceedings. LNCS, 1668. 30-42.
PUB | DOI | WoS
 
[14]
1999 | Journal Article | PUB-ID: 1947682
Prediction and visualization of structural switches in RNA
Giegerich R, Haase D, Rehmsmeier M (1999)
Pac Symp Biocomput.
PUB | PubMed | Europe PMC
 
[13]
1999 | Journal Article | PUB-ID: 1623374
RNA movies: visualizing RNA secondary structure spaces
Evers DJ, Giegerich R (1999)
BIOINFORMATICS 15(1): 32-37.
PUB | DOI | WoS | PubMed | Europe PMC
 
[12]
1998 | Conference Paper | PUB-ID: 1883741
ViSeL: An interactive Virtual Laboratory for DNA Sequencing
Lorenz D, Giegerich R (1998)
In: Tagungsband zum Workshop "Multimedia-Systeme" im Rahmen der GI-Jahrestagung 1998. Magdeburg: 53-65.
PUB
 
[11]
1997 | Journal Article | PUB-ID: 1627522 PUB | DOI | WoS
 
[10]
1997 | Conference Paper | PUB-ID: 2383634
International, interdisziplinär und interaaktiv: Der VSNS-Kurs über BioComputing
Fuellen G, Giegerich R (1997)
In: Proceedings: Virtueller Campus. 77-89.
PUB
 
[9]
1996 | Journal Article | PUB-ID: 1639486
Analysis of RNA sequence structure maps by exhaustive enumeration .2. structures of neutral networks and shape space covering
Grüner W, Giegerich R, Strothmann D, Reidys C, Weber J, Hofacker IL, Stadler P, Schuster P (1996)
Monatshefte für Chemie 127(4): 375-389.
PUB | DOI | WoS
 
[8]
1996 | Journal Article | PUB-ID: 1639477
Analysis of RNA sequence structure maps by exhaustive enumeration .1. Neutral networks
Grüner W, Giegerich R, Strothmann D, Reidys C, Weber J, Hofacker IL, Stadler P, Schuster P (1996)
Monatshefte für Chemie 127(4): 355-374.
PUB | DOI | WoS
 
[7]
1996 | Journal Article | PUB-ID: 1947921
GeneFisher--software support for the detection of postulated genes
Giegerich R, Meyer F, Schleiermacher C (1996)
Proc Int Conf Intell Syst Mol Biol 4.
PUB | PubMed | Europe PMC
 
[6]
1995 | Conference Paper | PUB-ID: 1628987
A comparison of imperative and purely functional suffix tree constructions
Giegerich R, Kurtz S (1995)
SCIENCE OF COMPUTER PROGRAMMING 25(2-3): 187-218.
PUB | DOI | WoS
 
[5]
1995 | Conference Paper | PUB-ID: 1639513
A new calculus for semantic matching
Bütow B, Giegerich R, Ohlebusch E, Thesing S (1995)
In: Programming languages: implementations, logics and programs. 7th international symposium ; proceedings. Hermenegildo M, Swierstra SD (Eds); Lecture Notes in Computer Science, 982. Berlin: Springer: 81-96.
PUB | WoS
 
[4]
1992 | Report | PUB-ID: 2383632
Embedding Sequence Analysis in the Functional Programming Paradigm - A Feasability Study
Giegerich R (1992) Report No. 8.
Universität Bielefeld: Technische Fakultät.
PUB
 
[3]
1991 | Journal Article | PUB-ID: 2383627
An Implicit Representation of Infinite Sequences of Terms
Giegerich R, Ohlebusch E (1991)
Bulletin of the EATCS 43: 174-182.
PUB
 
[2]
1990 | Conference Paper | PUB-ID: 1651466
ON THE STRUCTURE OF VERIFIABLE CODE GENERATOR SPECIFICATIONS
Giegerich R (1990)
SIGPLAN NOTICES 25(6): 1-8.
PUB | WoS
 
[1]
1990 | Conference Paper | PUB-ID: 1651134
CODE SELECTION BY INVERSION OF ORDER-SORTED DERIVORS
Giegerich R (1990)
THEORETICAL COMPUTER SCIENCE 73(2): 177-211.
PUB | DOI | WoS
 

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[112]
2016 | Journal Article | PUB-ID: 2901460
The BRaliBase Dent – a Tale of Benchmark Design and Interpretation
Löwes B, Chauve C, Ponty Y, Giegerich R (2016)
Briefings in Bioinformatics 18(2): 306-311.
PUB | DOI | WoS | PubMed | Europe PMC
 
[111]
2016 | Journal Article | PUB-ID: 2903044
Integrating Pareto Optimization into Dynamic Programming
Gatter T, Giegerich R, Saule C (2016)
ALGORITHMS 9(1): 12.
PUB | DOI | WoS
 
[110]
2015 | Journal Article | PUB-ID: 2763075
Pareto optimization in algebraic dynamic programming
Saule C, Giegerich R (2015)
Algorithms for Molecular Biology 10: 22.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[109]
2015 | Journal Article | PUB-ID: 2764888
Ambivalent covariance models
Janssen S, Giegerich R (2015)
BMC Bioinformatics 16: 178.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[108]
2015 | Journal Article | PUB-ID: 2733607
Thermodynamic matchers for the construction of the cuckoo RNA family
Reinkensmeier J, Giegerich R (2015)
RNA Biology 12(2): 197-207.
PUB | DOI | WoS | PubMed | Europe PMC
 
[107]
2014 | Journal Article | PUB-ID: 2700599
The RNA shapes studio
Janssen S, Giegerich R (2014)
Bioinformatics 31(3): 423-425.
PUB | DOI | WoS | PubMed | Europe PMC
 
[106]
2014 | Journal Article | PUB-ID: 2905757 PUB | DOI
 
[105]
2014 | Conference Abstract | PUB-ID: 2901695
German Conference on Bioinformatics 2014
Giegerich R, Hofestädt R, Nattkemper TW (2014) .
PUB
 
[104]
2014 | Journal Article | PUB-ID: 2699792
Riboregulation in plant-associated alpha-proteobacteria
Becker A, Overloeper A, Schlueter J-P, Reinkensmeier J, Robledo M, Giegerich R, Narberhaus F, Evguenieva-Hackenberg E (2014)
RNA Biology 11(5): 550-562.
PUB | DOI | WoS | PubMed | Europe PMC
 
[103]
2014 | Journal Article | PUB-ID: 2699802
Genome-wide profiling of Hfq-binding RNAs uncovers extensive post-transcriptional rewiring of major stress response and symbiotic regulons in Sinorhizobium meliloti
Torres-Quesada O, Reinkensmeier J, Schlueter J-P, Robledo M, Peregrina A, Giegerich R, Toro N, Becker A, Jimenez-Zurdo JI (2014)
RNA Biology 11(5): 563-579.
PUB | DOI | WoS | PubMed | Europe PMC
 
[102]
2014 | Journal Article | PUB-ID: 2681698
Yield grammar analysis and product optimization in a domain-specific language for dynamic programming
Sauthoff G, Giegerich R (2014)
Science of Computer Programming 87: 2-22.
PUB | DOI | WoS
 
[101]
2013 | Journal Article | PUB-ID: 2645192
A Silent Exonic SNP in Kdm3a Affects Nucleic Acids Structure but Does Not Regulate Experimental Autoimmune Encephalomyelitis
Gillett A, Bergman P, Parsa R, Bremges A, Giegerich R, Jagodic M (2013)
Plos One 8(12): e81912.
PUB | DOI | WoS | PubMed | Europe PMC
 
[100]
2013 | Conference Paper | PUB-ID: 2901275
Avoiding Ambiguity and Assessing Uniqueness in Minisatellite Alignment
Löwes B, Giegerich R (2013)
In: German Conference on Bioinformatics 2013. Beißbarth T, Kollmar M, Leha A, Morgenstern B, Schultz A-K, Waack S, Wingender E (Eds); OpenAccess Series in Informatics (OASIcs), 34. Dagstuhl, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik: 110-124.
PUB | DOI
 
[99]
2013 | Journal Article | PUB-ID: 2607289
Forest alignment with affine gaps and anchors, applied in RNA structure comparison
Schirmer S, Giegerich R (2013)
Theoretical Computer Science 483: 51-67.
PUB | DOI | WoS
 
[98]
2013 | Journal Article | PUB-ID: 2584661
Global mapping of transcription start sites and promoter motifs in the symbiotic a-proteobacterium Sinorhizobium meliloti 1021
Schlueter J-P, Reinkensmeier J, Barnett MJ, Lang C, Krol E, Giegerich R, Long SR, Becker A (2013)
Bmc Genomics 14(1): 156.
PUB | DOI | WoS | PubMed | Europe PMC
 
[97]
2013 | Journal Article | PUB-ID: 2551798
Bellman's GAP -- a Language and Compiler for Dynamic Programming in Sequence Analysis
Sauthoff G, Mohl M, Janssen S, Giegerich R (2013)
Bioinformatics 29(5): 551-560.
PUB | DOI | WoS | PubMed | Europe PMC
 
[96]
2012 | Journal Article | PUB-ID: 2547307
Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package
El-Kalioby M, Abouelhoda M, Krüger J, Giegerich R, Sczyrba A, Wall DP, Tonellato P (2012)
BMC Bioinformatics 13(Suppl 17): S22.
PUB | DOI | WoS | PubMed | Europe PMC
 
[95]
2012 | Book Chapter | PUB-ID: 2439665
Abstract Shape Analysis of RNA
Janssen S, Giegerich R (2012)
In: RNA Bioinformatics t.b.a. Gorodkin J, Weinberg Z (Eds); 1-35.
PUB
 
[94]
2011 | Journal Article | PUB-ID: 2383363
Forest Alignment with Affine Gaps and Anchors
Schirmer S, Giegerich R (2011)
Combinatorial Pattern Matching: 104-117.
PUB | DOI
 
[93]
2011 | Journal Article | PUB-ID: 2410526
Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction
Janssen S, Schudoma C, Steger G, Giegerich R (2011)
BMC Bioinformatics 12(1): 429.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[92]
2011 | Conference Paper | PUB-ID: 2310489
Bellman's GAP: a declarative language for dynamic programming
Sauthoff G, Janssen S, Giegerich R (2011)
In: Proceedings of the 13th international ACM SIGPLAN symposium on Principles and practices of declarative programming. New York, NY, USA: ACM: 29-40.
PUB | DOI
 
[91]
2011 | Journal Article | PUB-ID: 2427226
Conservation and Occurrence of Trans-Encoded sRNAs in the Rhizobiales
Reinkensmeier J, Schlüter J-P, Giegerich R, Becker A (2011)
GENES: 925-956.
PUB | DOI | WoS | PubMed | Europe PMC
 
[90]
2011 | Journal Article | PUB-ID: 2093578
Conveyor: a workflow engine for bioinformatic analyses
Linke B, Giegerich R, Goesmann A (2011)
Bioinformatics 27(7): 903-911.
PUB | DOI | WoS | PubMed | Europe PMC
 
[89]
2011 | Conference Paper | PUB-ID: 2383357
Yield grammar analysis in the Bellman's GAP compiler
Giegerich R, Sauthoff G (2011)
In: Proceedings of the Eleventh Workshop on Language Descriptions, Tools and Applications (ACM).
PUB
 
[88]
2011 | Journal Article | PUB-ID: 2003355
Semantics and Ambiguity of Stochastic RNA Family Models
Giegerich R, Hoener Zu Siederdissen C (2011)
IEEE/ACM Transactions on Computational Biology and Bioinformatics 8(2): 499-516.
PUB | DOI | WoS | PubMed | Europe PMC
 
[87]
2010 | Conference Paper | PUB-ID: 1894008
Prediction of RNA Secondary Structure Including Kissing Hairpin Motifs
Theis C, Janssen S, Giegerich R (2010)
In: Algorithms in Bioinformatics. 10th international workshop (WABI 2010), proceedings. Moulton V, Singh M (Eds); Lecture Notes in Bioinformatics, 6293. Berlin: Springer: 52-64.
PUB | File | DOI
 
[86]
2010 | Journal Article | PUB-ID: 2906810
Fine-tuning structural RNA alignments in the twilight zone
Bremges A, Schirmer S, Giegerich R (2010)
BMC Bioinformatics 11(1): 222.
PUB | DOI
 
[85]
2010 | Journal Article | PUB-ID: 1785497
A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti
Schlüter J-P, Reinkensmeier J, Daschkey S, Evguenieva-Hackenberg E, Janssen S, Jaenicke S, Becker JD, Giegerich R, Becker A (2010)
BMC Genomics 11(1): 245.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[84]
2010 | Journal Article | PUB-ID: 1893946
Faster computation of exact RNA shape probabilities
Janssen S, Giegerich R (2010)
Bioinformatics 26(5): 632-639.
PUB | File | DOI | WoS | PubMed | Europe PMC
 
[83]
2010 | Journal Article | PUB-ID: 1785581
WAMI: a web server for the analysis of minisatellite maps
Abouelhoda M, El-Kalioby M, Giegerich R (2010)
BMC Evolutionary Biology 10(1): 167.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[82]
2010 | Journal Article | PUB-ID: 1785512
Fine-tuning structural RNA alignments in the twilight zone
Bremges A, Schirmer S, Giegerich R (2010)
BMC Bioinformatics 11(1): 222.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[81]
2010 | Journal Article | PUB-ID: 1796697
Analyzing ambiguity of context-free grammars
Brabrand C, Giegerich R, Moller A (2010)
SCIENCE OF COMPUTER PROGRAMMING 75(3): 176-191.
PUB | DOI | WoS
 
[80]
2009 | Journal Article | PUB-ID: 2383411
RNA secondary structure analysis using the RNAshapes package
Reeder J, Giegerich R (2009)
Current Protocols in Bioinformatics.
PUB | DOI | PubMed | Europe PMC
 
[79]
2009 | Conference Paper | PUB-ID: 2383425
GPU Parallization of Algebraic Dynamic Programming
Steffen P, Giegerich R, Giraud M (Unpublished)
In: Proceedings PPAM.
PUB
 
[78]
2009 | Journal Article | PUB-ID: 1634374
mkESA: enhanced suffix array construction tool
Homann R, Fleer D, Giegerich R, Rehmsmeier M (2009)
Bioinformatics 25(8): 1084-1085.
PUB | DOI | WoS | PubMed | Europe PMC
 
[77]
2009 | Journal Article | PUB-ID: 1589458
Significant speedup of database searches with HMMs by search space reduction with PSSM family models
Beckstette M, Homann R, Giegerich R, Kurtz S (2009)
Bioinformatics 25(24): 3251-3258.
PUB | DOI | WoS | PubMed | Europe PMC
 
[76]
2009 | Journal Article | PUB-ID: 2383365
Alignment of minisatellite maps based on run-length encoding scheme
Abouelhoda M, Giegerich R, Behzadi B, Steyaert JM (2009)
Journal of Bioinformatics and Computational Biology 7(02): 287-308.
PUB | DOI | PubMed | Europe PMC
 
[75]
2008 | Conference Abstract | PUB-ID: 1587496
Looking for non-coding RNAs in Corynebacterium glutamicum
Gkogkoglou K, Mentz A, Albersmeier A, Kalinowski J, Giegerich R (2008)
FEBS JOURNAL 275(Suppl. 1): 153.
PUB | WoS
 
[74]
2008 | Conference Paper | PUB-ID: 2383382
Alignment of Minisatellite Maps: A Minimum Spanning Tree based Approach
Abouelhoda MI, Giegerich R, Behzadi B, Steyaert JM (2008)
In: Proceedings of the 6th Asia-Pacific Bioinformatics Conference. Series on Advances in Bioinformatics and Computational Biology, 6. 261-272.
PUB | DOI
 
[73]
2008 | Journal Article | PUB-ID: 1784020
GeneFisher-P: variations of GeneFisher as processes in Bio-jETI
Lamprecht A-L, Margaria T, Steffen B, Sczyrba A, Hartmeier S, Giegerich R (2008)
BMC Bioinformatics 9(Suppl 4): S13.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[72]
2008 | Journal Article | PUB-ID: 1893917
Shape based indexing for faster search of RNA family databases
Janssen S, Reeder J, Giegerich R (2008)
BMC Bioinformatics 9(1): 131.
PUB | Files available | DOI | WoS | PubMed | Europe PMC
 
[71]
2008 | Journal Article | PUB-ID: 1784025
Efficient computation of absent words in genomic sequences
Herold J, Kurtz S, Giegerich R (2008)
BMC Bioinformatics 9(1): 167.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[70]
2008 | Journal Article | PUB-ID: 1783357
KnotInFrame: prediction of –1 ribosomal frameshift events
Theis C, Reeder J, Giegerich R (2008)
Nucleic Acids Research 36(18): 6013-6020.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[69]
2008 | Journal Article | PUB-ID: 1588303
Two interactive bioinformatics courses at the bielefeld university bioinformatics server
Sczyrba A, Konermann S, Giegerich R (2008)
BRIEFINGS IN BIOINFORMATICS 9(3): 243-249.
PUB | DOI | WoS | PubMed | Europe PMC
 
[68]
2008 | Journal Article | PUB-ID: 1588308
The BREW workshop series: a stimulating experience in PhD education
Giegerich R, Brazma A, Jonassen I, Ukkonen E, Vingron M (2008)
Briefings in Bioinformatics 9(3): 250-253.
PUB | DOI | WoS | PubMed | Europe PMC
 
[67]
2007 | Conference Paper | PUB-ID: 1593132
Locomotif: from graphical motif description to RNA motif search
Reeder J, Reeder J, Giegerich R (2007)
Bioinformatics 23(13): I392-I400.
PUB | DOI | WoS | PubMed | Europe PMC
 
[66]
2007 | Conference Paper | PUB-ID: 2383428
Analyzing Ambiguity of Context-Free Grammars
Brabrand C, Giegerich R, Moeller A (2007)
In: Implementation and Application of Automata. 12th International Conference, CIAA 2007, July 16-18, 2007, Revised Selected Papers. Holub J, Žďárek J (Eds); Lecture Notes in Computer Science, 4783. Springer.
PUB | DOI
 
[65]
2007 | Journal Article | PUB-ID: 1587974
pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows
Reeder J, Steffen P, Giegerich R (2007)
NUCLEIC ACIDS RESEARCH 35(Web Server): W320-W324.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[64]
2007 | Conference Paper | PUB-ID: 2383462
Webservices and Workflows on the Bielefeld Bioinformatics Server: Practices and Problems
Hartmeier S, Krüger J, Giegerich R (2007)
In: Proceedings.
PUB
 
[63]
2006 | Journal Article | PUB-ID: 1773864
Fast index based algorithms and software for matching position specific scoring matrices
Beckstette M, Homann R, Giegerich R, Kurtz S (2006)
BMC Bioinformatics 7(1): 389.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[62]
2006 | Journal Article | PUB-ID: 1773871
XML schemas for common bioinformatic data types and their application in workflow systems
Seibel PN, Krüger J, Hartmeier S, Schwarzer K, Löwenthal K, Mersch H, Dandekar T, Giegerich R (2006)
BMC Bioinformatics 7(1): 490.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[61]
2006 | Journal Article | PUB-ID: 1773640
Correction: Versatile and declarative dynamic programming using pair algebras
Steffen P, Giegerich R (2006)
BMC Bioinformatics 7(1): 214.
PUB | PDF | DOI | WoS
 
[60]
2006 | Journal Article | PUB-ID: 1773637
Complete probabilistic analysis of RNA shapes
Voß B, Giegerich R, Rehmsmeier M (2006)
BMC Biology 4(1): 5.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[59]
2006 | Journal Article | PUB-ID: 1597805
Table design in dynamic programming
Steffen P, Giegerich R (2006)
INFORMATION AND COMPUTATION 204(9): 1325-1345.
PUB | DOI | WoS
 
[58]
2006 | Journal Article | PUB-ID: 1600421
RNAshapes: an integrated RNA analysis package based on abstract shapes
Steffen P, Voss B, Rehmsmeier M, Reeder J, Giegerich R (2006)
Bioinformatics 22(4): 500-503.
PUB | DOI | WoS | PubMed | Europe PMC
 
[57]
2006 | Conference Paper | PUB-ID: 1598807
Beyond Mfold: recent advances in RNA bioinformatics
Reeder J, Höchsmann M, Rehmsmeier M, Voss B, Giegerich R (2006)
JOURNAL OF BIOTECHNOLOGY 124(1): 41-55.
PUB | DOI | WoS | PubMed | Europe PMC
 
[56]
2006 | Conference Paper | PUB-ID: 2383518
A graphical programming system for molecular motif search
Reeder J, Giegerich R (2006)
In: Proceedings of the 5th International Conference on Generative Programming and Component Engineering. ACM Press: 131-140.
PUB
 
[55]
2006 | Journal Article | PUB-ID: 1600726
Calculating PSSM probabilities with lazy dynamic programming
Malde K, Giegerich R (2006)
Jornal of Functional Programming 16(01): 75-81.
PUB | DOI | WoS
 
[54]
2006 | Journal Article | PUB-ID: 1946336
Thermodynamic matchers: strengthening the significance of RNA folding energies
Höchsmann T, Höchsmann M, Giegerich R (2006)
Comput Syst Bioinformatics Conf.
PUB | DOI | PubMed | Europe PMC
 
[53]
2006 | Conference Paper | PUB-ID: 2383464
Challenges in the Compilation of a Domain Specific Language for Dynamic Programming
Giegerich R, Steffen P (2006)
In: Proceedings of te 2006 ACM Symposium on Applied Computing.
PUB
 
[52]
2006 | Journal Article | PUB-ID: 1902179 PUB | DOI | WoS | PubMed | Europe PMC
 
[51]
2006 | Journal Article | PUB-ID: 1597065
Surprises in approximating Levenshtein distances
Baake M, Grimm U, Giegerich R (2006)
JOURNAL OF THEORETICAL BIOLOGY 243(2): 279-282.
PUB | DOI | WoS | PubMed | Europe PMC
 
[50]
2005 | Journal Article | PUB-ID: 1773595
Effective ambiguity checking in biosequence analysis
Reeder J, Steffen P, Giegerich R (2005)
BMC Bioinformatics 6(1): 153.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[49]
2005 | Journal Article | PUB-ID: 1773598
Versatile and declarative dynamic programming using pair algebras
Steffen P, Giegerich R (2005)
BMC Bioinformatics 6(1): 224.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[48]
2005 | Journal Article | PUB-ID: 1773613
XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis
Sczyrba A, Beckstette M, Brivanlou AH, Giegerich R, Altmann CR (2005)
BMC Genomics 6(1): 123.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[47]
2005 | Journal Article | PUB-ID: 1602431
Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction
Reeder J, Giegerich R (2005)
BIOINFORMATICS 21(17): 3516-3523.
PUB | DOI | WoS | PubMed | Europe PMC
 
[46]
2004 | Conference (Editor) | PUB-ID: 1918823
Proceedings of the German Conference on Bioinformatics, GCB 2004
Giegerich R, Stoye J (Eds) (2004)
Lecture Notes in Informatics P-53.
PUB
 
[45]
2004 | Journal Article | PUB-ID: 2383529
Genlight: Interactive high-throughput sequence analysis and comparative genomics
Beckstette M, Mailänder JT, Marhöfer RJ, Sczyrba A, Ohlebusch E, Giegerich R, Selzer PM (2004)
Journal of Integrative Bioinformatics 1(1): 0008.
PUB | DOI
 
[44]
2004 | Journal Article | PUB-ID: 1773758 PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[43]
2004 | Journal Article | PUB-ID: 1607394
e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences
Krüger J, Sczyrba A, Kurtz S, Giegerich R (2004)
NUCLEIC ACIDS RESEARCH 32(Web Server): W301-W304.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[42]
2004 | Journal Article | PUB-ID: 1773747
A comprehensive comparison of comparative RNA structure prediction approaches
Gardner PP, Giegerich R (2004)
BMC Bioinformatics 5(1): 140.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[41]
2004 | Journal Article | PUB-ID: 1606393
Abstract shapes of RNA
Giegerich R, Voss B, Rehmsmeier M (2004)
Nucleic Acids Research 32(16): 4843-4851.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[40]
2004 | Journal Article | PUB-ID: 1607656
A discipline of dynamic programming over sequence data
Giegerich R, Meyer C, Steffen P (2004)
SCIENCE OF COMPUTER PROGRAMMING 51(3): 215-263.
PUB | DOI | WoS
 
[39]
2004 | Journal Article | PUB-ID: 1607419
Evaluating the predictability of conformational switching in RNA
Voss B, Meyer C, Giegerich R (2004)
Bioinformatics 20(10): 1573-1582.
PUB | DOI | WoS | PubMed | Europe PMC
 
[38]
2004 | Conference Paper | PUB-ID: 2383561
Identification of 10,500 Xenopus laevis Full Length Clones through EST Clustering and Sequence Analysis
Sczyrba A, Beckstette M, Giegerich R, Altman C (2004)
In: Proceedings of the German Conference on Bioinformatics. Lecture Notes in Informatics: GI.
PUB
 
[37]
2004 | Journal Article | PUB-ID: 1606377
Fast and effective prediction of microRNA/target duplexes
Rehmsmeier M, Steffen P, Höchsmann M, Giegerich R (2004)
RNA-A PUBLICATION OF THE RNA SOCIETY 10(10): 1507-1517.
PUB | DOI | WoS | PubMed | Europe PMC
 
[36]
2004 | Journal Article | PUB-ID: 1600293
Pure multiple RNA secondary structure alignments: A progressive profile approach
Höchsmann M, Voss B, Giegerich R (2004)
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATIOCS 1(1): 53-62.
PUB | DOI | WoS | PubMed | Europe PMC
 
[35]
2004 | Journal Article | PUB-ID: 1606822
GenAlyzer: interactive visualization of sequence similarities between entire genomes
Choudhuri JV, Schleiermacher C, Kurtz S, Giegerich R (2004)
BIOINFORMATICS 20(12): 1964-1965.
PUB | DOI | WoS | PubMed | Europe PMC
 
[34]
2004 | Conference Paper | PUB-ID: 2383543
PoSSuMsearch: Fast and Sensitive Matching of Position Specific Scoring Matrices using Enhanced Suffix Arrays
Beckstette M, Strothmann D, Homann R, Giegerich R, Kurtz S (2004)
In: Proceedings of the German Conference on Bioinformatics. Lecture Notes in Informatics: GI: 53-64.
PUB
 
[33]
2003 | Journal Article | PUB-ID: 1773880
GenDB - an open source genome annotation system for prokaryote genomes
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Pühler A (2003)
Nucleic Acids Research 31(8): 2187-2195.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[32]
2003 | Journal Article | PUB-ID: 1918949
Finden, fast ohne zu suchen: Indexstrukturen in der Bioinformatik
Giegerich R, Stoye J (2003)
Forschung an der Universität Bielefeld 26: 63-68.
PUB
 
[31]
2003 | Journal Article | PUB-ID: 1610397
Efficient implementation of lazy suffix trees
Giegerich R, Kurtz S, Stoye J (2003)
SOFTWARE-PRACTICE & EXPERIENCE 33(11): 1035-1049.
PUB | PDF | DOI | WoS
 
[30]
2003 | Journal Article | PUB-ID: 1773844
RNA-related tools on the Bielefeld Bioinformatics Server
Sczyrba A, Krüger J, Mersch H, Kurtz S, Giegerich R (2003)
Nucleic Acids Research 31(13): 3767-3770.
PUB | Files available | DOI | WoS | PubMed | Europe PMC
 
[29]
2003 | Journal Article | PUB-ID: 1666680
Local similarity in RNA secondary structures.
Höchsmann M, Töller T, Giegerich R, Kurtz S (2003)
Proc IEEE Comput Soc Bioinform Conf 2.
PUB | PubMed | Europe PMC
 
[28]
2003 | Journal Article | PUB-ID: 2383602
Fibonacci-Cayley-numbers and Repetition Pattern in Genomic DNA
Dress A, Giegerich R, Grünewald S, Wagner H (2003)
Annals of Combinatorics: 259-279.
PUB
 
[27]
2002 | Conference Paper | PUB-ID: 1612812
Implementing algebraic dynamic programming in the functional and the imperative programming paradigm
Giegerich R, Steffen P (2002)
In: MATHEMATICS OF PROGRAM CONSTRUCTION. Lecture Notes in Computer Science, 2386. SPRINGER-VERLAG BERLIN: 1-20.
PUB | WoS
 
[26]
2002 | Journal Article | PUB-ID: 1615366
PathFinder: reconstruction and dynamic visualization of metabolic pathways
Goesmann A, Haubrock M, Meyer F, Kalinowski J, Giegerich R (2002)
BIOINFORMATICS 18(1): 124-129.
PUB | DOI | WoS | PubMed | Europe PMC
 
[25]
2002 | Journal Article | PUB-ID: 1614870
Matching and significance evaluation of combined sequence-structure motifs in RNA
Meyer C, Giegerich R (2002)
ZEITSCHRIFT FÜR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS 216(2/2002): 193-216.
PUB | DOI | WoS
 
[24]
2002 | Conference Paper | PUB-ID: 2383608
Algebraic Dynamic Programming
Giegerich R, Meyer C (2002)
In: Algebraic Methodology and Software Technology. Springer: 349-364.
PUB
 
[23]
2001 | Journal Article | PUB-ID: 1773335
REPuter: the manifold applications of repeat analysis on a genomic scale
Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R (2001)
Nucleic Acids Research 29(22): 4633-4642.
PUB | PDF | DOI | WoS | PubMed | Europe PMC
 
[22]
2001 | Journal Article | PUB-ID: 1615572
Minimum conflict: a divide-and-conquer approach to phylogeny estimation
Fuellen G, Wägele JW, Giegerich R (2001)
BIOINFORMATICS 17(12): 1168-1178.
PUB | DOI | WoS | PubMed | Europe PMC
 
[21]
2001 | Journal Article | PUB-ID: 1615460
Best systematist practice transferred to molecular data
Fuellen G, Wägele JW, Giegerich R (2001)
ORGANISMS DIVERSITY & EVOLUTION 1(4): 257-272.
PUB | DOI | WoS
 
[20]
2001 | Conference Paper | PUB-ID: 2383615
Reducing the Conformation Space in RNA Structure Prediction
Evers D, Giegerich R (2001)
In: Proceedings of the German Conference on Bioinformatics. 118-124.
PUB
 
[19]
2000 | Conference Paper | PUB-ID: 1618572
Explaining and controlling ambiguity in dynamic programming
Giegerich R (2000)
In: Combinatorial Pattern Matching. 11th Annual Symposium CPM 2000, Proceedings. Giancarlo R, Sankoff D (Eds); Lecture Notes in Computer Science, 1848. Berlin: Springer: 46-59.
PUB | WoS
 
[18]
2000 | Conference Paper | PUB-ID: 1918988
Computation and Visualization of Degenerate Repeats in Complete Genomes
Kurtz S, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R (2000)
In: Proc. of ISMB 2000. 228-238.
PUB | PubMed | Europe PMC
 
[17]
2000 | Journal Article | PUB-ID: 2383618 PUB
 
[16]
2000 | Journal Article | PUB-ID: 1618574
A systematic approach to dynamic programming in bioinformatics
Giegerich R (2000)
BIOINFORMATICS 16(8): 665-677.
PUB | DOI | WoS | PubMed | Europe PMC
 
[15]
1999 | Conference Paper | PUB-ID: 1620435
Efficient implementation of lazy suffix trees
Giegerich R, Kurtz S, Stoye J (1999)
In: Algorithm Engineering. 3rd International Workshop, WAE’99 London, UK, July 19–21, 1999 Proceedings. LNCS, 1668. 30-42.
PUB | DOI | WoS
 
[14]
1999 | Journal Article | PUB-ID: 1947682
Prediction and visualization of structural switches in RNA
Giegerich R, Haase D, Rehmsmeier M (1999)
Pac Symp Biocomput.
PUB | PubMed | Europe PMC
 
[13]
1999 | Journal Article | PUB-ID: 1623374
RNA movies: visualizing RNA secondary structure spaces
Evers DJ, Giegerich R (1999)
BIOINFORMATICS 15(1): 32-37.
PUB | DOI | WoS | PubMed | Europe PMC
 
[12]
1998 | Conference Paper | PUB-ID: 1883741
ViSeL: An interactive Virtual Laboratory for DNA Sequencing
Lorenz D, Giegerich R (1998)
In: Tagungsband zum Workshop "Multimedia-Systeme" im Rahmen der GI-Jahrestagung 1998. Magdeburg: 53-65.
PUB
 
[11]
1997 | Journal Article | PUB-ID: 1627522 PUB | DOI | WoS
 
[10]
1997 | Conference Paper | PUB-ID: 2383634
International, interdisziplinär und interaaktiv: Der VSNS-Kurs über BioComputing
Fuellen G, Giegerich R (1997)
In: Proceedings: Virtueller Campus. 77-89.
PUB
 
[9]
1996 | Journal Article | PUB-ID: 1639486
Analysis of RNA sequence structure maps by exhaustive enumeration .2. structures of neutral networks and shape space covering
Grüner W, Giegerich R, Strothmann D, Reidys C, Weber J, Hofacker IL, Stadler P, Schuster P (1996)
Monatshefte für Chemie 127(4): 375-389.
PUB | DOI | WoS
 
[8]
1996 | Journal Article | PUB-ID: 1639477
Analysis of RNA sequence structure maps by exhaustive enumeration .1. Neutral networks
Grüner W, Giegerich R, Strothmann D, Reidys C, Weber J, Hofacker IL, Stadler P, Schuster P (1996)
Monatshefte für Chemie 127(4): 355-374.
PUB | DOI | WoS
 
[7]
1996 | Journal Article | PUB-ID: 1947921
GeneFisher--software support for the detection of postulated genes
Giegerich R, Meyer F, Schleiermacher C (1996)
Proc Int Conf Intell Syst Mol Biol 4.
PUB | PubMed | Europe PMC
 
[6]
1995 | Conference Paper | PUB-ID: 1628987
A comparison of imperative and purely functional suffix tree constructions
Giegerich R, Kurtz S (1995)
SCIENCE OF COMPUTER PROGRAMMING 25(2-3): 187-218.
PUB | DOI | WoS
 
[5]
1995 | Conference Paper | PUB-ID: 1639513
A new calculus for semantic matching
Bütow B, Giegerich R, Ohlebusch E, Thesing S (1995)
In: Programming languages: implementations, logics and programs. 7th international symposium ; proceedings. Hermenegildo M, Swierstra SD (Eds); Lecture Notes in Computer Science, 982. Berlin: Springer: 81-96.
PUB | WoS
 
[4]
1992 | Report | PUB-ID: 2383632
Embedding Sequence Analysis in the Functional Programming Paradigm - A Feasability Study
Giegerich R (1992) Report No. 8.
Universität Bielefeld: Technische Fakultät.
PUB
 
[3]
1991 | Journal Article | PUB-ID: 2383627
An Implicit Representation of Infinite Sequences of Terms
Giegerich R, Ohlebusch E (1991)
Bulletin of the EATCS 43: 174-182.
PUB
 
[2]
1990 | Conference Paper | PUB-ID: 1651466
ON THE STRUCTURE OF VERIFIABLE CODE GENERATOR SPECIFICATIONS
Giegerich R (1990)
SIGPLAN NOTICES 25(6): 1-8.
PUB | WoS
 
[1]
1990 | Conference Paper | PUB-ID: 1651134
CODE SELECTION BY INVERSION OF ORDER-SORTED DERIVORS
Giegerich R (1990)
THEORETICAL COMPUTER SCIENCE 73(2): 177-211.
PUB | DOI | WoS
 

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