Research Topics
| Arthur L DelcherSummaryAffiliation: University of Maryland Country: USA Publications
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Detail Information
Publications
Identifying bacterial genes and endosymbiont DNA with GlimmerArthur 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...- Minimus: a fast, lightweight genome assemblerDaniel 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... - Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99ASteven 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... - Assembly of large genomes using second-generation sequencingMichael 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... - A whole-genome assembly of the domestic cow, Bos taurusAleksey 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... - Gene prediction with Glimmer for metagenomic sequences augmented by classification and clusteringDavid 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... - Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila speciesSteven 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... - High-throughput sequence alignment using Graphics Processing UnitsMichael C Schatz
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
BMC Bioinformatics 8:474. 2007.... - A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genesCarl 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... 
A preprocessor for shotgun assembly of large genomesMichael 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...- Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalisJane 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... - Evolution of genes and genomes on the Drosophila phylogenyAndrew 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... - Using MUMmer to identify similar regions in large sequence setsArthur 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... - 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.... - Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryoteJonathan 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... - Fast algorithms for large-scale genome alignment and comparisonArthur 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... - The dog genome: survey sequencing and comparative analysisEwen 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... - Versatile and open software for comparing large genomesStefan 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... - PROBEmer: A web-based software tool for selecting optimal DNA oligosScott 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... - DAGchainer: a tool for mining segmental genome duplications and syntenyBrian 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... - A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genomeRichard J Mural
Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
Science 296:1661-71. 2002.... - Comparative genome assemblyMihai 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... - Efficient decoding algorithms for generalized hidden Markov model gene findersWilliam 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... - Serendipitous discovery of Wolbachia genomes in multiple Drosophila speciesSteven L Salzberg
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Genome Biol 6:R23. 2005.... - Comparative genomics of trypanosomatid parasitic protozoaNajib 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... - Improving the Arabidopsis genome annotation using maximal transcript alignment assembliesBrian 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... - Whole-genome shotgun assembly and comparison of human genome assembliesSorin 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... - Draft genome of the filarial nematode parasite Brugia malayiElodie 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... - The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas diseaseNajib M El-Sayed
Department of Parasite Genomics, Institute for Genomic Research, Rockville, MD 20850, USA
Science 309:409-15. 2005....