Arthur L. Delcher

Visiting Senior Research Scientist
Center for Bioinformatics & Computational Biology
Surge Building Room 3107
University of Maryland
College Park, MD 20742
Phone: 301-405-9468   Fax: 301-314-1341

Email: adelcher AT umiacs.umd.edu



Professor Emeritus
Computer Science Department
Loyola College in Maryland
4501 N. Charles Street
Baltimore, MD 21210-2699

Education

  1. PhD, Computer Science, Johns Hopkins University, 1989
  2. MSE, Computer Science, Johns Hopkins University, 1986
  3. MES, Computer Science, Loyola College in Maryland, 1984
  4. MA, Mathematics, Johns Hopkins University, 1977
  5. BA, Mathematics, Loyola College in Maryland, 1973

Research Interests

  1. DNA Sequence Assembly. Working to develop new algorithms to incorporate all available information (such as homology to related organisms) and be able to deal with polymorphism in its output. Results will be part of the AMOS development effort.
  2. Sequence Comparison. The goal is to develop algorithms to compare multiple large genomes efficiently and effectively represent the results.
  3. Statistical Modeling of Sequence Data. Create tools to model sets of sequences for use in gene finding (e.g., in Glimmer), regulatory region analysis and sequence classification.

Selected Publications

  1. Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. S.L. Salzberg, J.C. Dunning Hotopp, A.L. Delcher, et al. Genome Biol. 6:R23, Feb 2005.
  2. Efficient decoding algorithms for generalized hidden Markov model gene finders. W.H. Majoros, M. Pertea, A.L. Delcher, and S.L. Salzberg. BMC Bioinformatics 6:16, Jan 24 2005.
  3. DAGchainer: a tool for mining segmental genome duplications and synteny. B.J. Haas, A.L. Delcher, J.R. Wortman, and S.L. Salzberg. Bioinformatics 20:3643-3646, Dec 12 2004.
  4. Versatile and open software for comparing large genomes. S. Kurtz, A. Phillippy, A.L. Delcher, et al. Genome Biol. 5:R12, 2004.
  5. Human, mouse, and rat genome large-scale rearrangements: stability versus speciation. S. Zhao, J. Shetty, L. Hou, A.L. Delcher, et al. Fraser. Genome Res. 14:1851-1860, Oct 2004.
  6. Comparative genome assembly. M. Pop, A. Phillippy, A.L. Delcher, and S.L. Salzberg. Brief. Bioinform. 5:237-248, Sep 2004.
  7. A preprocessor for shotgun assembly of large genomes. M. Roberts, B.R. Hunt, J.A. Yorke, R.A. Bolanos, and A.L. Delcher. J. Comput. Biol. 11:734-752, 2004.
  8. Whole-genome shotgun assembly and comparison of human genome assemblies. S. Istrail, L. Florea, A.L. Halpern, et al. Proc. Natl. Acad. Sci. 101(7):1916--21, Feb 2004.
  9. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. B.J. Haas, A.L. Delcher, et al. Nucleic Acids Res. 31:5654-5666, Oct 1 2003.
  10. The dog genome: survey sequencing and comparative analysis. E.F. Kirkness, V. Bafna, et al. Science 301:1898-1903, Sep 26 2003.
  11. PROBEmer: a web-based software tool for selecting optimal DNA oligos. S.J. Emrich, M. Lowe, and A.L. Delcher. Nucleic Acids Res. 31:3746-3750, Jul 1 2003.
  12. The genome sequence of the malaria mosquito Anopheles gambiae. R.A. Holt, G.M. Subramanian, et al. Science 298:129-149, Oct 4 2002.
  13. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. R.D. Fleischmann, D. Alland, J.A. Eisen, et al. J. Bacteriology 184(19):5479--90, Oct 2002.
  14. A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome.  R.J. Mural et al. (176 authors).  Science 296 (2002), 1661-1671.
  15. Fast algorithms for large-scale genome alignment and comparison. (Abstract) (Full text PDF) A.L. Delcher. A. Phillippy, J. Carlton, and S.L. Salzberg. Nucleic Acids Research 30:11 (2002), 2478-2483.  (This is the MUMmer 2 paper; the latest MUMmer system is available here.)
  16. Design of a compartmentalized shotgun assembler for the human genome. D.H. Huson, K. Reinert, S.A. Kravitz et al. Bioinformatics 17 (2001), 132S-139S.
  17. The sequence of the human genome.  (free at the Science website) J. Craig Venter et al. (274 authors), Science 291 (2001), 1304-1351.  Get the figures showing genome-scale duplications in PDF format here: [Page 1] [Page 2]
  18. A whole-genome assembly of Drosophila. E.W. Myers, G.G. Sutton, A.L. Delcher, et al. Science 287 (2000), 2196-2204.
  19. The genome sequence of Drosophila melanogaster. M.D. Adams, S.E. Celniker, R.A. Holt, et al. Science 287 (2000), 2185-2195.
  20. Modeling splice sites with Bayes networks. D. Cai, A. Delcher, B. Kao, and S. Kasif. Bioinformatics 16 (2000), 152-158.
  21. Improved microbial gene identification with GLIMMER.  A.L. Delcher, D. Harmon, S. Kasif, O. White, and S.L. Salzberg.  Nucleic Acids Research, 27:23 (1999), 4636-4641.
  22. Interpolated Markov models for eukaryotic gene finding.  S.L. Salzberg, M. Pertea, A.L. Delcher, M.J. Gardner, and H. Tettelin.  Genomics, 59 (1999), 24-31.  This describes the GlimmerM gene finder.
  23. Alignment of Whole Genomes.  A.L. Delcher, S. Kasif, R.D. Fleischmann, J. Peterson, O. White, and S.L. Salzberg.  Nucleic Acids Research, 27:11 (1999), 2369-2376.  Note that Figure 6 is supposed to be in color, and was mistakenly printed as black and white.  Click here for the color figure (PDF).  Reproduced with permission from NAR Online at http://www.oup.co.uk/nar.  This describes the first MUMmer system.
  24. Microbial gene identification using interpolated Markov models. S.L. Salzberg, A.L. Delcher, S. Kasif, and O. White. Nucleic Acids Research, 26:2 (1998), 544-548. Reproduced with permission from NAR Online at http://www.oup.co.uk/nar. Also in gzipped Postscript format (214K).  This paper describes the Glimmer system (version 1.0), available here.
  25. A Decision Tree System for Finding Genes in DNA. (preprint only). S.L. Salzberg, A.L. Delcher, K. Fasman, and J. Henderson. Journal of Computational Biology 5:4 (1998), 667-680. The MORGAN code has been superseded by GlimmerM.
  26. Optimal parallel evaluation of tree-structured computations by raking.  S.R. Kosaraju and A.L. Delcher. VLSI Algorithms and Architectures: Proceedings of 1988 Aegean Workshop on Computing, 101-110, Springer-Verlag, 1998, LNCS No. 319.
  27. Best-Case Results for Nearest-Neighbor Learning.  S.L. Salzberg, A.L. Delcher, D. Heath, and S. Kasif. IEEE Transactions on Pattern Analysis and Machine Intelligence17:6, June 1995, 599-608. (Earlier version, "Learning with a Helpful Teacher," appeared in the IJCAI-91 proceedings.)
  28. Large-scale assembly of DNA strings and space-efficient construction of suffix trees.  S.R. Kosaraju and A.L. Delcher. Proceedings of the 27th ACM Symposium on the Theory of Computing, May 1995.
  29. An NC algorithm for evaluating monotone planar circuits. A.L. Delcher and S.R. Kosaraju. SIAM Journal on Computing, 24(2):369--375, April 1995.

Software

  1. Glimmer, a system that uses interpolated Markov models to find genes in microbial DNA.
  2. MUMmer, a system for aligning whole genomes, chromosomes, and other very long DNA sequences
  3. PROBEmer, a system for finding maximally discriminatory PCR and hybridization target probes. Principally developed by Scott Emrich while at Loyola College.

 

Last update 27 June 2005