Steven L Salzberg

Summary

Affiliation: University of Maryland
Country: USA

Publications

  1. pmc Between a chicken and a grape: estimating the number of human genes
    Mihaela Pertea
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Genome Biol 11:206. 2010
  2. pmc Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    Ben Langmead
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA
    Genome Biol 10:R25. 2009
  3. pmc Gene-boosted assembly of a novel bacterial genome from very short reads
    Steven L Salzberg
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
    PLoS Comput Biol 4:e1000186. 2008
  4. 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
  5. 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
  6. pmc Genome analysis linking recent European and African influenza (H5N1) viruses
    Steven L Salzberg
    University of Maryland Center for Bioinformatics and Computational Biology, College Park, Maryland 20742, USA
    Emerg Infect Dis 13:713-8. 2007
  7. pmc Do-it-yourself genetic testing
    Steven L Salzberg
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Genome Biol 11:404. 2010
  8. 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
  9. ncbi request reprint JIGSAW: integration of multiple sources of evidence for gene prediction
    Jonathan E Allen
    Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies, College Park, MD 20742, USA
    Bioinformatics 21:3596-603. 2005
  10. 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

Collaborators

Detail Information

Publications91

  1. pmc Between a chicken and a grape: estimating the number of human genes
    Mihaela Pertea
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Genome Biol 11:206. 2010
    ..Many people expected the question 'How many genes in the human genome?' to be resolved with the publication of the genome sequence in 2001, but estimates continue to fluctuate...
  2. pmc Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    Ben Langmead
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA
    Genome Biol 10:R25. 2009
    ..Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source (http://bowtie.cbcb.umd.edu)...
  3. pmc Gene-boosted assembly of a novel bacterial genome from very short reads
    Steven L Salzberg
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
    PLoS Comput Biol 4:e1000186. 2008
    ....
  4. 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...
  5. 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...
  6. pmc Genome analysis linking recent European and African influenza (H5N1) viruses
    Steven L Salzberg
    University of Maryland Center for Bioinformatics and Computational Biology, College Park, Maryland 20742, USA
    Emerg Infect Dis 13:713-8. 2007
    ..One isolate provides evidence that 2 of these sublineages have recently reassorted...
  7. pmc Do-it-yourself genetic testing
    Steven L Salzberg
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Genome Biol 11:404. 2010
    ..ABSTRACT : We developed a computational screen that tests an individual's genome for mutations in the BRCA genes, despite the fact that both are currently protected by patents...
  8. 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...
  9. ncbi request reprint JIGSAW: integration of multiple sources of evidence for gene prediction
    Jonathan E Allen
    Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies, College Park, MD 20742, USA
    Bioinformatics 21:3596-603. 2005
    ..Genome annotation pipelines collect a variety of types of evidence about gene structure and synthesize the results, which can then be refined further through manual, expert curation of gene models...
  10. 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
    ....
  11. ncbi request reprint Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes
    Malcolm J Gardner
    Institute for Genomic Research TIGR, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 309:134-7. 2005
    ..Several biosynthetic pathways are incomplete or absent, suggesting substantial metabolic dependence on the host cell. One protein family that may generate parasite antigenic diversity is not telomere-associated...
  12. 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...
  13. pmc Comparative genomics of the neglected human malaria parasite Plasmodium vivax
    Jane M Carlton
    The Institute for Genomic Research J Craig Venter Institute, 9704 Medical Research Drive, Rockville, Maryland 20850, USA
    Nature 455:757-63. 2008
    ..Completion of the P. vivax genome provides the scientific community with a valuable resource that can be used to advance investigation into this neglected species...
  14. 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...
  15. pmc Genome sequence of Aedes aegypti, a major arbovirus vector
    Vishvanath Nene
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 316:1718-23. 2007
    ..An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species...
  16. 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
    ....
  17. pmc Comprehensive DNA signature discovery and validation
    Adam M Phillippy
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
    PLoS Comput Biol 3:e98. 2007
    ..The Insignia system is freely accessible via a Web interface and has been released as open source software at: http://insignia.cbcb.umd.edu...
  18. 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...
  19. pmc Hierarchical scaffolding with Bambus
    Mihai Pop
    The Institute for Genomic Research TIGR, Rockville, Maryland 20850, USA
    Genome Res 14:149-59. 2004
    ..Bambus is available as an open-source package from our Web site...
  20. pmc Computational gene prediction using multiple sources of evidence
    Jonathan E Allen
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Res 14:142-8. 2004
    ..Our results show that combining gene prediction evidence consistently outperforms even the best individual gene finder and, in some cases, can produce dramatic improvements in sensitivity and specificity...
  21. 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...
  22. ncbi request reprint The genome sequence of the malaria mosquito Anopheles gambiae
    Robert A Holt
    Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
    Science 298:129-49. 2002
    ..An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect...
  23. ncbi request reprint Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus
    William C Nierman
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Nature 438:1151-6. 2005
    ..The Af293 genome sequence provides an unparalleled resource for the future understanding of this remarkable fungus...
  24. 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...
  25. pmc Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
    Brian J Haas
    J Craig Venter Institute, The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Biol 9:R7. 2008
    ..Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation...
  26. pmc JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions
    Jonathan E Allen
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Genome Biol 7:S9.1-13. 2006
    ....
  27. pmc Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    Cole Trapnell
    Department of Computer Science, University of Maryland, College Park, Maryland, USA
    Nat Biotechnol 28:511-5. 2010
    ..These results suggest that Cufflinks can illuminate the substantial regulatory flexibility and complexity in even this well-studied model of muscle development and that it can improve transcriptome-based genome annotation...
  28. pmc Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species
    C Robin Buell
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Res 15:1284-91. 2005
    ....
  29. 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...
  30. pmc The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans
    Brendan J Loftus
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 307:1321-4. 2005
    ..neoformans encodes unique genes that may contribute to its unusual virulence properties, and comparison of two phenotypically distinct strains reveals variation in gene content in addition to sequence polymorphisms between the genomes...
  31. pmc Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake
    Carleton L Kingsford
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Genome Biol 8:R22. 2007
    ..Previous computational methods to predict Rho-independent terminators have been slow or limited in the organisms they consider...
  32. ncbi request reprint Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14
    Malcolm J Gardner
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 419:531-4. 2002
    ..We report here the nucleotide sequences of chromosomes 10, 11 and 14, and a re-analysis of the chromosome 2 sequence. These chromosomes represent about 35% of the 23-megabase P. falciparum genome...
  33. ncbi request reprint Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii
    Jane M Carlton
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 419:512-9. 2002
    ..This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease...
  34. 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...
  35. 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...
  36. pmc Insignia: a DNA signature search web server for diagnostic assay development
    Adam M Phillippy
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
    Nucleic Acids Res 37:W229-34. 2009
    ..The Insignia website (http://insignia.cbcb.umd.edu) is free and open to all users and there is no login requirement. In addition, the source code for the computational pipeline is freely available...
  37. pmc OperonDB: a comprehensive database of predicted operons in microbial genomes
    Mihaela Pertea
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Nucleic Acids Res 37:D479-82. 2009
    ..The new database is updated regularly as additional genomes become available in public archives. OperonDB can be accessed at: http://operondb.cbcb.umd.edu...
  38. pmc An empirical analysis of training protocols for probabilistic gene finders
    William H Majoros
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    BMC Bioinformatics 5:206. 2004
    ....
  39. ncbi request reprint The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria
    Timothy D Read
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 423:81-6. 2003
    ..The complete sequence of B. anthracis is a step towards a better understanding of anthrax pathogenesis...
  40. 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
    ....
  41. pmc Detection and correction of false segmental duplications caused by genome mis-assembly
    David R Kelley
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA
    Genome Biol 11:R28. 2010
    ..For each genome, we corrected mis-assemblies, improved estimates of the amount of duplicated sequence, and recovered polymorphisms between the sequenced chromosomes...
  42. pmc Genome assembly has a major impact on gene content: a comparison of annotation in two Bos taurus assemblies
    Liliana Florea
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
    PLoS ONE 6:e21400. 2011
    ..As a side benefit, our analyses helped us identify many specific loci for improvement in the Bos taurus genome assembly...
  43. doi request reprint Using GlimmerM to find genes in eukaryotic genomes
    Mihaela Pertea
    The Institute for Genomic Research, Rockville, Maryland, USA
    Curr Protoc Bioinformatics . 2002
    ..A unique feature of the system compared to other eukaryotic gene finders is a module that allows users to provide their own data and train GlimmerM for any organism...
  44. 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...
  45. pmc What are decision trees?
    Carl Kingsford
    Department of Computer Science, Institute for Advanced Computer Studies and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA
    Nat Biotechnol 26:1011-3. 2008
    ..Decision trees have been applied to problems such as assigning protein function and predicting splice sites. How do these classifiers work, what types of problems can they solve and what are their advantages over alternatives?..
  46. pmc A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana
    Mihaela Pertea
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    BMC Bioinformatics 8:159. 2007
    ..However exonic splicing enhancers have been shown to enhance the utilization of nearby splice sites...
  47. pmc The complete genome sequence of Bacillus anthracis Ames "Ancestor"
    Jacques Ravel
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    J Bacteriol 191:445-6. 2009
    ..This study describes the complete genome sequence of that original isolate, derived from a sample kept in cold storage since 1981...
  48. ncbi request reprint The age of the Arabidopsis thaliana genome duplication
    Maria D Ermolaeva
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Plant Mol Biol 51:859-66. 2003
    ..In each case, our estimate places the age of the genome duplication as significantly younger than previously reported...
  49. pmc Computational discovery of internal micro-exons
    Natalia Volfovsky
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    Genome Res 13:1216-21. 2003
    ..The algorithm also aids in the discovery of micro-exon-skipping events and cross-species micro-exon conservation...
  50. 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...
  51. pmc Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
    Arthur Brady
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
    Nat Methods 6:673-6. 2009
    ..We also describe how combining Phymm with sequence alignment algorithms improves accuracy...
  52. ncbi request reprint Genome sequence of the human malaria parasite Plasmodium falciparum
    Malcolm J Gardner
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 419:498-511. 2002
    ..The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria...
  53. pmc TopHat: discovering splice junctions with RNA-Seq
    Cole Trapnell
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Bioinformatics 25:1105-11. 2009
    ..TopHat is an efficient read-mapping algorithm designed to align reads from an RNA-Seq experiment to a reference genome without relying on known splice sites...
  54. 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...
  55. pmc Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath)
    Naomi Ward
    The Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Biol 2:e303. 2004
    ..We have gained evidence for greater metabolic flexibility than was previously known, and for genetic components that may have biotechnological potential...
  56. pmc Quake: quality-aware detection and correction of sequencing errors
    David R Kelley
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, and Department of Computer Science, University of Maryland, College Park, MD 20742, USA
    Genome Biol 11:R116. 2010
    ..Quake can be used for any size project, including more than one billion human reads, and is freely available as open source software from http://www.cbcb.umd.edu/software/quake...
  57. pmc Full-length messenger RNA sequences greatly improve genome annotation
    Brian J Haas
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Genome Biol 3:RESEARCH0029. 2002
    ..We have mapped these transcripts to their exact chromosomal locations and, using alignment programs, have created gene models that provide a reference set for this organism...
  58. pmc Genome sequence of the Wolbachia endosymbiont of Culex quinquefasciatus JHB
    Steven L Salzberg
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, 20742, USA
    J Bacteriol 191:1725. 2009
    ..Here we describe the genome sequence of a Wolbachia strain that was discovered in the whole-genome sequencing data for the mosquito Culex quinquefasciatus strain JHB...
  59. pmc Thousands of missed genes found in bacterial genomes and their analysis with COMBREX
    Derrick E Wood
    Department of Computer Science, University of Maryland, College Park, MD 20742, USA
    Biol Direct 7:37. 2012
    ..Annotation methods vary considerably and may fail to identify some genes. Here we draw attention to a large number of likely genes missing from annotations using common tools such as Glimmer and BLAST...
  60. ncbi request reprint Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis
    Timothy D Read
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
    Science 296:2028-33. 2002
    ..These results demonstrate that genome-based analysis of microbial pathogens will provide a powerful new tool for investigation of infectious disease outbreaks...
  61. pmc Hawkeye: an interactive visual analytics tool for genome assemblies
    Michael C Schatz
    Center for Bioinformatics and Computational Biology, Biomolecular Sciences Building, University of Maryland, College Park, Maryland 20742, USA
    Genome Biol 8:R34. 2007
    ..Hawkeye is freely available and released as part of the open source AMOS project http://amos.sourceforge.net/hawkeye...
  62. pmc How to map billions of short reads onto genomes
    Cole Trapnell
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
    Nat Biotechnol 27:455-7. 2009
    ..Mapping the vast quantities of short sequence fragments produced by next-generation sequencing platforms is a challenge. What programs are available and how do they work?..
  63. 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...
  64. pmc Improving pan-genome annotation using whole genome multiple alignment
    Samuel V Angiuoli
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    BMC Bioinformatics 12:272. 2011
    ..Genome annotations can contain inconsistencies and errors that hinder comparative analysis even within a single species. Tools are needed to compare and improve annotation quality across sets of closely related genomes...
  65. pmc GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders
    William H Majoros
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 31:3601-4. 2003
    ..Cases have been found where each of the genefinders outperforms each of the others, demonstrating the collective value of this ensemble of genefinders. These programs are all accessible through webservers at http://www.tigr.org/software...
  66. pmc The value of complete microbial genome sequencing (you get what you pay for)
    Claire M Fraser
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    J Bacteriol 184:6403-5; discusion 6405. 2002
  67. 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...
  68. pmc Automated correction of genome sequence errors
    Pawel Gajer
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 32:562-9. 2004
    ..It also greatly improves our ability to discover single nucleotide polymorphisms (SNPs) between closely related strains and isolates of the same species...
  69. ncbi request reprint Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution
    Elodie Ghedin
    The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, Maryland 20850, USA
    Nature 437:1162-6. 2005
    ..All data from this project are being deposited, without delay, in public archives...
  70. pmc Detection of lineage-specific evolutionary changes among primate species
    Mihaela Pertea
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
    BMC Bioinformatics 12:274. 2011
    ..Because the primate genomes are highly similar to one another, methods developed for analysis of more divergent species do not always detect signs of evolutionary selection...
  71. ncbi request reprint Physiogenomic resources for rat models of heart, lung and blood disorders
    Renae L Malek
    TREX, The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nat Genet 38:234-9. 2006
    ..We performed a variety of data-mining manipulations on the profiles and used complementary physiological data from the PhysGen resource to demonstrate how TREX can be used by the cardiovascular community for hypothesis generation...
  72. pmc Genome re-annotation: a wiki solution?
    Steven L Salzberg
    Center for Bioinformatics and Computational Biology and Department of Computer Science, 3125 Biomolecular Sciences Building, University of Maryland, College Park, MD 20742, USA
    Genome Biol 8:102. 2007
    ..Unfortunately, annotation is rarely if ever updated and resources to support routine reannotation are scarce. Wiki software, which would allow many scientists to edit each genome's annotation, offers one possible solution...
  73. pmc Mugsy: fast multiple alignment of closely related whole genomes
    Samuel V Angiuoli
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
    Bioinformatics 27:334-42. 2011
    ..This increasing volume of data requires tools that can quickly compare multiple whole-genome sequences, millions of base pairs in length, to aid in the study of populations, pan-genomes, and genome evolution...
  74. pmc Efficient oligonucleotide probe selection for pan-genomic tiling arrays
    Adam M Phillippy
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    BMC Bioinformatics 10:293. 2009
    ..Prior microarrays have included only a single strain per array or the conserved sequences of gene families. These arrays omit potentially important genes and sequence variants from the pan-genome...
  75. pmc Clustering metagenomic sequences with interpolated Markov models
    David R Kelley
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, College Park, MD 20742, USA
    BMC Bioinformatics 11:544. 2010
    ..Many effective approaches to this task rely on sequenced genomes in public databases, but these genomes are a highly biased sample that is not necessarily representative of environments interesting to many metagenomics projects...
  76. pmc 2009 Swine-origin influenza A (H1N1) resembles previous influenza isolates
    Carl Kingsford
    Center for Bioinformatics and Computational Biology, Institute for Advance Computer Studies, University of Maryland, College Park, Maryland, United States of America
    PLoS ONE 4:e6402. 2009
    ..The viruses were genetically characterized as a novel influenza A (H1N1) strain originating in swine, and within a very short time the S-OIV strain spread across the globe via human-to-human contact...
  77. pmc The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts
    Ian T Paulsen
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 99:13148-53. 2002
    ..A limited repertoire of genes homologous to known bacterial virulence factors were identified...
  78. ncbi request reprint Computational gene finding in plants
    Mihaela Pertea
    Institute for Genome Research, Rockville, MD 20850, USA
    Plant Mol Biol 48:39-48. 2002
    ..This paper reviews some of the most widely used algorithms for gene finding in plants, including technical descriptions of how they work and recent measurements of their success on the genomes of Arabidopsis thaliana and rice...
  79. pmc The genome Assembly Archive: a new public resource
    Steven L Salzberg
    Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Biol 2:E285. 2004
  80. 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...
  81. ncbi request reprint Genomics: Yeast rises again
    Steven L Salzberg
    Nature 423:233-4. 2003
  82. 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
    ....
  83. pmc Bioinformatics challenges of new sequencing technology
    Mihai Pop
    Center for Bioinformatics and Computational Biology, University of Maryland, MD 20742, USA
    Trends Genet 24:142-9. 2008
    ....
  84. ncbi request reprint Beware of mis-assembled genomes
    Steven L Salzberg
    Bioinformatics 21:4320-1. 2005
  85. pmc Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura
    Benjamin P Berman
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Genome Biol 5:R61. 2004
    ..Nine of these clusters overlapped known enhancers. Here, we report the results of in vivo functional analysis of 27 remaining clusters...
  86. 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...
  87. 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...
  88. pmc Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses
    Edward C Holmes
    Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
    PLoS Biol 3:e300. 2005
    ....
  89. ncbi request reprint Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster
    Evgeny M Zdobnov
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Science 298:149-59. 2002
    ....
  90. ncbi request reprint Contamination in the draft of the human genome masquerades as lateral gene transfer
    Eske Willerslev
    DNA Seq 13:75-6. 2002
  91. pmc It is time to end the patenting of software
    John Quackenbush
    Bioinformatics 22:1416-7. 2006