1. M.I. Abouelhoda, S. Kurtz, and E. Ohlebusch. The Enhanced Suffix Array and its Applications to Genome Analysis.In Proceedings of the Second Workshop on Algorithms in Bioinformatics, pages 449-463. Lecture Notes in Computer Science 2452, Springer-Verlag, 2002.

2. M.I. Abouelhoda, S. Kurtz, and E. Ohlebusch. Replacing Suffix Treeswith Enhanced Suffix Arrays. Journal of Discrete Algorithms, 2:53-86, 2004.

3. M.I. Abouelhoda and E. Ohlebush. A Local Chaining Algorithm and its Applications in Comparative Genomics. In Proc. 3rd Worksh. Algorithms in Bioinformatics (WABI 2003), number 2812 in Lecture Notes in Bioinformatics, pages 1-16. Springer-Verlag, 2003.

4. M. Beckstette, D. Strothmann, R. Homann, R. Giegerich, and S. Kurtz. PoSSuMsearch: Fast and Sensitive Matching of Position Specific Scoring Matrices using Enhanced Suffix Arrays. In Giegerich, R. and Stoye, J., editor, Proc. of the German Conference on Bioinformatics, GI-Edition, Lecture Notes in Informatics, volume P-53, pages 53-64, 2004.

5. V. Brendel, S. Kurtz, and V. Walbot. Comparative Genomics of Arabidopsis and Maize: Prospects and Limitations. Genome Biology, 3(3):reviews1005.1-1005.6, 2002.

6. P.G. Buckley, C. Jarbo, U. Menzel, T. Mathiesen, C. Scott, S.G. Gregory, C.F. Langford, and J.P. Dumanski. Comprehensive DNA Copy Number Profiling of Meningioma Using a Chromosome 1 Tiling Path Microarray identifies Novel Candidate Tumor Surpressor Loci. Cancer Res., 65(7):2653-2661, 2005.

7. J.V. Choudhuri, C. Schleiermacher, S. Kurtz, and R. Giegerich. Genalyzer: Interactive Visualization of Sequence Similarities Between Entire Genomes. Bioinformatics, 20:1964-1965, 2004.

8. E. Coward, S.A. Haas, and M. Vingron. SpliceNest: Visualization of Gene Structure and Alternative Splicing Based on EST Clusters. Trends Genet., 18(1):53-55, 2002.

9. Q. Dong, C.J. Lawrence, S.D. Schlueter, M.D. Wilkerson, S. Kurtz, C. Lushbough, and V. Brendel. Comparative Plant Genomics Resources at PlantGDB. Plant Physiology, Plant Database Focus Issue, 2005.

10. Q. Dong, L. Roy, M. Freeling, V. Walbot, and V. Brendel. ZmDB, an integrated Database for Maize Genome Research. Nucleic Acids Res., 31:244-247, 2003.

11. J. Fernandes, Q. Dong, B. Schneider, D.J. Morrow, G.-L. Nan, V. Brendel, and V. Walbot. Genome-wide mutagenesis of Zea mays L. using RescueMu transposons. Genome Biology, 5(10):R82, 2004.

12. J.P. Fitch, S.N. Gardner, T.A. Kuczmarski, S. Kurtz, R. Myers, L.L. Ott, T.R. Slezak, E.A. Vitalis, A.T. Zemla, and P.M. McCready. Rapid Development of Nucleic Acid Diagnostics. Proceedings of the IEEE, 90(11):1708-1721, 2002.

13. S.N. Gardner, T.A. Kuczmarski, E.A. Vitalis, and T.R. Slezak. Limitations of TaqMan PCR for Detecting Viral Pathogens I llustrated by Hepatitis A, B, C, and E Viruses and Human Immunodeficiency Virus. J. of Clinical Microbiology, 41(6):2417-2427, 2003.

14. S. Gräf, D. Strothmann, S. Kurtz, and G. Steger. HyPaLib: a Database of RNAs and RNA Structural Elements defined by Hybrid Patterns. Nucleic Acids
Res., 29(1):196-198, 2001.

15. M. Höhl, S. Kurtz, and E. Ohlebusch. Efficient Multiple Genome Alignment. Bioinformatics, 18(Suppl. 1):S312-S320, 2002.

16. R.J.M. Hulzink, H. Weerdesteyn, A.F. Croes, M.M.A. Gerats, T. van Herpen, and J. van Helden. In Silico Identification of Putative Regulatory Sequence Elements in the 5'-Untranslated Region of Genes That Are Expressed during Male Gametogenesis Gene Co-regulation. Plant Physiol., 132:75-83, 2003.

17. J. Krüger, A. Sczyrba, S. Kurtz, and R. Giegerich. e2g: An Interactive Web-Based Server for Efficiently Mapping large EST and cDNA Sets to Genomic Sequences. Nucleic Acids Res., 32:W301-W304, 2004.

18. S. Kurtz. A Time and Space Efficient Algorithm for the Substring Matching Problem, 2002.

19. S. Kurtz, J.V. Choudhuri, E. Ohlebusch, C. Schleiermacher, J. Stoye, and R. Giegerich. REPuter: The Manifold Applications of Repeat Analysis on a Genomic Scale.Nucleic Acids Res., 29(22):4633-4642, 2001.

20. U. Manber and E.W. Myers. Suffix Arrays: A New Method for On-Line String Searches. SIAM Journal on Computing, 22(5):935-948, 1993.

21. G. Myers. A Fast Bit-Vector Algorithm for Approximate String Matching Based on Dynamic Programming. Journal of the ACM, 46:395-415, 1999.

22. S. Rahmann. Rapid Large-Scale Selection of Oligonucleotides for Microarrays.In Proceedings of the First IEEE Computer Society Bioinformatics Conference (CSB 2002), pages 54-63. IEEE-Press, 2002.

23. A. Sczyrba, M. Beckstette, A.H. Brivanlou, R. Giegerich, and C.R. Altmann. Xendb: Full length cDNA prediction and cross species mapping in xenopus laevis. BMC Genomics, 2005.

24. N. Simonis, S.J. Wodak, G.N. Cohen, and J van Helden. Combining Pattern Discovery and Discriminant Analysis to Predict Gene Co-regulation. Bioinformatics, 20:2370-2379, 2004.

25. T. Slezak, T. Kuczmarski, L. Ott, C. Torres, D. Medeiros, J. Smith, B. Truitt, N. Mulakken, M. Lam, E. Vitalis, A. Zemla, C.E. Zhou, and S. Gardner. Comparative Genomics Tools Applied to Bioterrorism Defense. Briefings in Bioinformatics, 4(2):133-149, 2003.

26. E. Ukkonen. Algorithms for Approximate String Matching. Information and Control, 64:100-118, 1985.

27. J. van Helden, A.F. Rios, and J. Collado-Vides. Discovering Regulatory Elements in Non-Coding Sequences by Analysis of Spaced Dyads. Nucleic Acids Res., 28(8):1808-1818, 2000.

28. N. Volfovsky, B.J. Haas, and S.L. Salzberg. A Clustering Method for Repeat Analysis in DNA Sequences. Genome Biology, 2(8):research0027.1-0027.11, 2001.

29. Z. Zhang, S. Schwartz, L. Wagner, and W. Miller. A Greedy Algorithm for Aligning DNA Sequences. J. Comp. Biol., 7(1/2):203-214, 2000.