Arthur L. Delcher Senior Research Scientist Center for Bioinformatics & Computational Biology University of Maryland College Park, MD 20742 Phone: 301-405-9468 Fax: 301-314-1341 Email: adelcher at umd dot edu Professor Emeritus, Computer Science Department Loyola College in Maryland 4501 N. Charles Street Baltimore, MD 21210-2699 Phone: 410-617-2899/522 Fax: 410-617-2157 Email: adelcher at loyola dot edu

Education

• PhD, Computer Science, Johns Hopkins University, 1989
• MSE, Computer Science, Johns Hopkins University, 1986
• MES, Computer Science, Loyola College in Maryland, 1984
• MA, Mathematics, Johns Hopkins University, 1977
• BA, Mathematics, Loyola College in Maryland, 1973

Research Interests

• Sequence assembly. Currently developing a new assembler at TIGR that will be able to incorporate all available information (such as homology to related organisms) and be able to deal with polymorphism in its output.
• Sequence comparison. The goal is to develop algorithms to compare multiple large genomes efficiently and effectively represent the results.
• Statistical modeling. Create tools to model given sets of sequences for use in gene finding, regulatory region analysis and sequence classification.

Selected Publications

• 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.
• 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.
• 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.
• Versatile and open software for comparing large genomes. S. Kurtz, A. Phillippy, A.L. Delcher, et al. Genome Biol. 5:R12, 2004.
• 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.
• Comparative genome assembly. M. Pop, A. Phillippy, A.L. Delcher, and S.L. Salzberg. Brief. Bioinform. 5:237-248, Sep 2004.
• 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.
• 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.
• 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.
• The dog genome: survey sequencing and comparative analysis. E.F. Kirkness, V. Bafna, et al. Science 301:1898-1903, Sep 26 2003.
• 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.
• The genome sequence of the malaria mosquito Anopheles gambiae. R.A. Holt, G.M. Subramanian, et al. Science 298:129-149, Oct 4 2002.
• 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.
• 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.
• 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 MUMmer system can be downloaded here)
• 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.
• 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]
• A whole-genome assembly of Drosophila. E.W. Myers, G.G. Sutton, A.L. Delcher, et al. Science 287 (2000), 2196–2204.
• The genome sequence of Drosophila melanogaster. M.D. Adams, S.E. Celniker, R.A. Holt, et al. Science 287 (2000), 2185–2195.
• Modeling splice sites with Bayes networks. D. Cai, A. Delcher, B. Kao, and S. Kasif. Bioinformatics 16 (2000), 152–158.
• 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.
• 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, available below.
• 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.  (Contact me for a hardcopy reprint.)  This describes the MUMmer system, available below.
• 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.
• 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.
• 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.
• 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.)
• 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.
• 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

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

Last modified on: 14 September 2006