Steven Salzberg

Summary

Affiliation: University of Maryland
Country: USA

Publications

  1. ncbi Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths
    Jacob Enk
    McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L9, Canada
    Genome Biol 12:R51. 2011
  2. ncbi 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
  3. ncbi Searching for SNPs with cloud computing
    Ben Langmead
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, USA
    Genome Biol 10:R134. 2009
  4. ncbi 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
  5. ncbi 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
  6. ncbi 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
  7. ncbi 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
  8. ncbi 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
  9. ncbi Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification
    Xiangyu Deng
    National Center for Food Safety and Technology, Illinois Institute of Technology, Summit, Illinois 60501, USA
    BMC Genomics 11:500. 2010
  10. ncbi 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

Research Grants

  1. Bioinformatics Software for Analyzing Microbial Genomes
    Steven Salzberg; Fiscal Year: 2006
  2. Computational Gene Modeling and Genome Sequence Assembly
    Steven Salzberg; Fiscal Year: 2005
  3. Bioinformatics Software for Analyzing Microbial Genomes
    Steven L Salzberg; Fiscal Year: 2010
  4. Computational Gene Modeling and Genome Sequence Assembly
    Steven L Salzberg; Fiscal Year: 2010
  5. COMPUTATIONAL MODELING OF GENES AND GENE STRUCTURE
    Steven Salzberg; Fiscal Year: 2001
  6. Computational Gene Modeling and Genome Sequence Assembly
    Steven Salzberg; Fiscal Year: 2002
  7. Computational Gene Modeling and Genome Sequence Assembly
    Steven Salzberg; Fiscal Year: 2009

Detail Information

Publications87

  1. ncbi Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths
    Jacob Enk
    McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L9, Canada
    Genome Biol 12:R51. 2011
    ..Here, we take an interspecific approach to clarifying mammoth phylogeny by targeting Columbian mammoth remains for mitogenomic sequencing...
  2. ncbi 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...
  3. ncbi Searching for SNPs with cloud computing
    Ben Langmead
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, USA
    Genome Biol 10:R134. 2009
    ..Crossbow is available from http://bowtie-bio.sourceforge.net/crossbow/...
  4. ncbi 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...
  5. ncbi 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
    ..We relate these findings to our current plans for future research...
  6. ncbi 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...
  7. ncbi 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...
  8. ncbi 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...
  9. ncbi Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification
    Xiangyu Deng
    National Center for Food Safety and Technology, Illinois Institute of Technology, Summit, Illinois 60501, USA
    BMC Genomics 11:500. 2010
    ..Two of these lineages predominantly cause human sporadic and epidemic infections, whereas the third lineage has never been implicated in human disease outbreaks despite its overall conservation of many known virulence factors...
  10. ncbi 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...
  11. ncbi 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...
  12. ncbi 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...
  13. ncbi 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...
  14. ncbi 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...
  15. ncbi 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...
  16. ncbi 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...
  17. ncbi 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...
  18. ncbi 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...
  19. ncbi 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...
  20. ncbi 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...
  21. ncbi 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...
  22. ncbi 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...
  23. ncbi 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...
  24. ncbi 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...
  25. ncbi 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...
  26. ncbi 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...
  27. ncbi 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?..
  28. ncbi 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...
  29. ncbi 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...
  30. ncbi 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...
  31. ncbi 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)...
  32. ncbi 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...
  33. ncbi 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?..
  34. ncbi 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...
  35. ncbi 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...
  36. ncbi 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
    ....
  37. ncbi 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...
  38. ncbi 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...
  39. ncbi 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
    ....
  40. ncbi 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...
  41. ncbi Re-assembly of the genome of Francisella tularensis subsp. holarctica OSU18
    Daniela Puiu
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
    PLoS ONE 3:e3427. 2008
    ..This assembly will provide a more accurate basis for future comparative studies of this pathogen...
  42. ncbi 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...
  43. ncbi 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...
  44. ncbi 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
    ....
  45. ncbi 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...
  46. ncbi 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...
  47. ncbi 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
    ....
  48. ncbi 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...
  49. ncbi 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...
  50. ncbi 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...
  51. ncbi 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...
  52. ncbi 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...
  53. ncbi 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...
  54. ncbi 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...
  55. ncbi 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...
  56. ncbi 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...
  57. ncbi Genomics: Yeast rises again
    Steven L Salzberg
    Nature 423:233-4. 2003
  58. ncbi 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...
  59. ncbi 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
  60. ncbi 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
    ....
  61. ncbi 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...
  62. ncbi 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...
  63. ncbi Contamination in the draft of the human genome masquerades as lateral gene transfer
    Eske Willerslev
    DNA Seq 13:75-6. 2002
  64. ncbi 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...
  65. ncbi 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
    ....
  66. ncbi 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...
  67. ncbi 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...
  68. ncbi 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...
  69. ncbi 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...
  70. ncbi 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...
  71. ncbi 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. ncbi 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...
  73. ncbi Beware of mis-assembled genomes
    Steven L Salzberg
    Bioinformatics 21:4320-1. 2005
  74. ncbi 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...
  75. ncbi 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
    ....
  76. ncbi 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...
  77. ncbi 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
    ....
  78. ncbi 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...
  79. ncbi 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...
  80. ncbi 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...
  81. ncbi 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...
  82. ncbi 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
    ....
  83. ncbi 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...
  84. ncbi The genome Assembly Archive: a new public resource
    Steven L Salzberg
    Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Biol 2:E285. 2004
  85. ncbi It is time to end the patenting of software
    John Quackenbush
    Bioinformatics 22:1416-7. 2006
  86. ncbi 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...
  87. ncbi 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...

Research Grants22

  1. Bioinformatics Software for Analyzing Microbial Genomes
    Steven Salzberg; Fiscal Year: 2006
    ..Both the software and the operon database will be freely available to the scientific community. ..
  2. Computational Gene Modeling and Genome Sequence Assembly
    Steven Salzberg; Fiscal Year: 2005
    ..For all of the software development projects, the source code will be made freely available to investigators in the scientific research community worldwide. ..
  3. Bioinformatics Software for Analyzing Microbial Genomes
    Steven L Salzberg; Fiscal Year: 2010
    ....
  4. Computational Gene Modeling and Genome Sequence Assembly
    Steven L Salzberg; Fiscal Year: 2010
    ..For all of the software development projects, we will continue our practice of making all our source code freely available to investigators in the scientific research community worldwide. ..
  5. COMPUTATIONAL MODELING OF GENES AND GENE STRUCTURE
    Steven Salzberg; Fiscal Year: 2001
    ..The approach to developing these bioinformatics tools will be interdisciplinary, building on the PI's experience in computer science and his NIH-supported training in genomics. ..
  6. Computational Gene Modeling and Genome Sequence Assembly
    Steven Salzberg; Fiscal Year: 2002
    ..For all of the software development projects, the source code will be made freely available to investigators in the scientific research community worldwide. ..
  7. Computational Gene Modeling and Genome Sequence Assembly
    Steven Salzberg; Fiscal Year: 2009
    ..For all of the software development projects, we will continue our practice of making all our source code freely available to investigators in the scientific research community worldwide. ..