Arthur L Delcher

Summary

Affiliation: University of Maryland
Country: USA

Publications

  1. pmc Identifying bacterial genes and endosymbiont DNA with Glimmer
    Arthur L Delcher
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Bioinformatics 23:673-9. 2007
  2. pmc Minimus: a fast, lightweight genome assembler
    Daniel D Sommer
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    BMC Bioinformatics 8:64. 2007
  3. pmc Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
    Steven L Salzberg
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    BMC Genomics 9:204. 2008
  4. pmc Assembly of large genomes using second-generation sequencing
    Michael C Schatz
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA
    Genome Res 20:1165-73. 2010
  5. pmc A whole-genome assembly of the domestic cow, Bos taurus
    Aleksey V Zimin
    Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA
    Genome Biol 10:R42. 2009
  6. pmc Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering
    David R Kelley
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, Department of Computer Science, 3115 Biomolecular Sciences Building 296, University of Maryland, College Park, MD 20742, USA
    Nucleic Acids Res 40:e9. 2012
  7. pmc Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species
    Steven L Salzberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Genome Biol 6:402. 2005
  8. pmc High-throughput sequence alignment using Graphics Processing Units
    Michael C Schatz
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
    BMC Bioinformatics 8:474. 2007
  9. pmc A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genes
    Carl Kingsford
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, USA
    Mol Biol Evol 24:2091-8. 2007
  10. ncbi request reprint A preprocessor for shotgun assembly of large genomes
    Michael Roberts
    Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742 2431, USA
    J Comput Biol 11:734-52. 2004

Detail Information

Publications29

  1. pmc Identifying bacterial genes and endosymbiont DNA with Glimmer
    Arthur L Delcher
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Bioinformatics 23:673-9. 2007
    ..This module was developed in response to the discovery that eukaryotic genome sequencing projects sometimes inadvertently capture the DNA of intracellular bacteria living in the host...
  2. pmc Minimus: a fast, lightweight genome assembler
    Daniel D Sommer
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    BMC Bioinformatics 8:64. 2007
    ..Many of the most common uses of assemblers, however, are best served by a simpler type of assembler that requires fewer software components, uses less memory, and is far easier to install and run...
  3. pmc Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
    Steven L Salzberg
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    BMC Genomics 9:204. 2008
    ..We report here on the complete genome sequence of strain PXO99A and its comparison to two previously sequenced strains, KACC10331 and MAFF311018, which are highly similar to one another...
  4. pmc Assembly of large genomes using second-generation sequencing
    Michael C Schatz
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA
    Genome Res 20:1165-73. 2010
    ..We also review the genomes that have been assembled recently from short reads and make recommendations for sequencing strategies that will yield a high-quality assembly...
  5. pmc A whole-genome assembly of the domestic cow, Bos taurus
    Aleksey V Zimin
    Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA
    Genome Biol 10:R42. 2009
    ..The genome of the domestic cow, Bos taurus, was sequenced using a mixture of hierarchical and whole-genome shotgun sequencing methods...
  6. pmc Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering
    David R Kelley
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, Department of Computer Science, 3115 Biomolecular Sciences Building 296, University of Maryland, College Park, MD 20742, USA
    Nucleic Acids Res 40:e9. 2012
    ..In a comparison among multiple gene finding methods, Glimmer-MG makes the most sensitive and precise predictions on simulated and real metagenomes for all read lengths and error rates tested...
  7. pmc Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species
    Steven L Salzberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Genome Biol 6:402. 2005
    ..A correction to Serendipitous discovery of Wolbachia genomes in multiple Drosophila species by SL Salzberg, JC Dunning Hotopp, AL Delcher, M Pop, DR Smith, MB Eisen and WC Nelson. Genome Biology 2005, 6:R23...
  8. pmc High-throughput sequence alignment using Graphics Processing Units
    Michael C Schatz
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
    BMC Bioinformatics 8:474. 2007
    ....
  9. pmc A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genes
    Carl Kingsford
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, USA
    Mol Biol Evol 24:2091-8. 2007
    ..This suggests a dynamic picture of continual overlap creation and elimination...
  10. ncbi request reprint A preprocessor for shotgun assembly of large genomes
    Michael Roberts
    Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742 2431, USA
    J Comput Biol 11:734-52. 2004
    ..We tested the UMD Overlapper on Celera's Drosophila reads. When we replaced Celera's overlap procedures in the front end of their assembler, it was able to produce a significantly improved genome...
  11. pmc Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis
    Jane M Carlton
    Institute for Genomic Research, 9712 Medical Research Drive, Rockville, MD 20850, USA
    Science 315:207-12. 2007
    ..The genome sequence predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria...
  12. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...
  13. doi request reprint Using MUMmer to identify similar regions in large sequence sets
    Arthur L Delcher
    The Institute for Genomic Research Rockville, Maryland and Computer Science Department, Loyola College in Maryland, Baltimore, Maryland, USA
    Curr Protoc Bioinformatics . 2003
    ..The system is particularly efficient at comparing highly similar sequences, such as alternative versions of fragment assemblies or closely related strains of the same bacterium...
  14. pmc The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
    Ray Ming
    Hawaii Agriculture Research Center, Aiea, Hawaii 96701, USA
    Nature 452:991-6. 2008
    ....
  15. pmc Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote
    Jonathan A Eisen
    The Institute for Genomic Research, Rockville, Maryland, United States of America
    PLoS Biol 4:e286. 2006
    ..thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance...
  16. pmc Fast algorithms for large-scale genome alignment and comparison
    Arthur L Delcher
    Department of Computer Science, Loyola College in Maryland, Baltimore, MD 21210, USA
    Nucleic Acids Res 30:2478-83. 2002
    ..The system code is being made freely available by the authors...
  17. ncbi request reprint The dog genome: survey sequencing and comparative analysis
    Ewen F Kirkness
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Science 301:1898-903. 2003
    ..A variety of polymorphic elements are identified that will be valuable for mapping the genetic basis of diseases and traits in the dog...
  18. pmc Versatile and open software for comparing large genomes
    Stefan Kurtz
    Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
    Genome Biol 5:R12. 2004
    ..This allows other developers to contribute to the code base and freely redistribute the code. The MUMmer sources are available at http://www.tigr.org/software/mummer...
  19. pmc PROBEmer: A web-based software tool for selecting optimal DNA oligos
    Scott J Emrich
    Interdepartmental Bioinformatics and Computational Biology, Iowa State University, Rockville, MD, USA
    Nucleic Acids Res 31:3746-50. 2003
    ..In this paper, we describe how to use PROBEmer, the computational methods it employs, and experimental results for oligos identified by this software tool...
  20. ncbi request reprint DAGchainer: a tool for mining segmental genome duplications and synteny
    Brian J Haas
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Bioinformatics 20:3643-6. 2004
    ..Automated mining of the Arabidopsis genome for segmental duplications illustrates the use of DAGchainer...
  21. ncbi request reprint A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome
    Richard J Mural
    Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
    Science 296:1661-71. 2002
    ....
  22. ncbi request reprint Comparative genome assembly
    Mihai Pop
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Brief Bioinform 5:237-48. 2004
    ..The software is available as part of the open-source AMOS project...
  23. pmc Efficient decoding algorithms for generalized hidden Markov model gene finders
    William H Majoros
    Bioinformatics Department, The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD, USA
    BMC Bioinformatics 6:16. 2005
    ..Unfortunately, the task of implementing an efficient GHMM-based gene finder is already a nontrivial one, and it can be expected that this task will only grow more onerous as our models increase in complexity...
  24. pmc Serendipitous discovery of Wolbachia genomes in multiple Drosophila species
    Steven L Salzberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Genome Biol 6:R23. 2005
    ....
  25. ncbi request reprint Comparative genomics of trypanosomatid parasitic protozoa
    Najib M El-Sayed
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 309:404-9. 2005
    ..Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont...
  26. pmc Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
    Brian J Haas
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 31:5654-66. 2003
    ..The algorithm of the Program to Assemble Spliced Alignments (PASA) tool is described, as well as the results of automated updates to Arabidopsis gene annotations...
  27. pmc Whole-genome shotgun assembly and comparison of human genome assemblies
    Sorin Istrail
    Applied Biosystems, 45 West Gude Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 101:1916-21. 2004
    ..The Celera results provide more order and orientation, and the consortium sequence provides better coverage of exact and nearly exact repeats...
  28. pmc Draft genome of the filarial nematode parasite Brugia malayi
    Elodie Ghedin
    Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
    Science 317:1756-60. 2007
    ..malayi to niches in its human and vector hosts and insights into the molecular basis of a mutualistic relationship with its Wolbachia endosymbiont. These findings offer a foundation for rational drug design...
  29. ncbi request reprint The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease
    Najib M El-Sayed
    Department of Parasite Genomics, Institute for Genomic Research, Rockville, MD 20850, USA
    Science 309:409-15. 2005
    ....