S L Salzberg

Summary

Affiliation: The Institute for Genomic Research
Country: USA

Publications

  1. ncbi request reprint A decision tree system for finding genes in DNA
    S Salzberg
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    J Comput Biol 5:667-80. 1998
  2. 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
  3. 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
  4. 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
  5. 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
  6. pmc Microbial gene identification using interpolated Markov models
    S L Salzberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 26:544-8. 1998
  7. pmc The genome Assembly Archive: a new public resource
    Steven L Salzberg
    Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Biol 2:E285. 2004
  8. 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
  9. 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
  10. ncbi request reprint Microbial genes in the human genome: lateral transfer or gene loss?
    S L Salzberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 292:1903-6. 2001

Detail Information

Publications82

  1. ncbi request reprint A decision tree system for finding genes in DNA
    S Salzberg
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    J Comput Biol 5:667-80. 1998
    ..This paper describes the MORGAN system, including its decision tree routines and the algorithms for site recognition, and its performance on a benchmark database of vertebrate DNA...
  2. 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...
  3. 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...
  4. 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
    ....
  5. 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...
  6. pmc Microbial gene identification using interpolated Markov models
    S L Salzberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 26:544-8. 1998
    ..As a result, GLIMMER is more flexible and more powerful than fixed-order Markov methods, which have previously been the primary content-based technique for finding genes in microbial DNA...
  7. pmc The genome Assembly Archive: a new public resource
    Steven L Salzberg
    Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Biol 2:E285. 2004
  8. 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...
  9. 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
    ....
  10. ncbi request reprint Microbial genes in the human genome: lateral transfer or gene loss?
    S L Salzberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 292:1903-6. 2001
    ..Gene loss combined with sample size effects and evolutionary rate variation provide an alternative, more biologically plausible explanation...
  11. ncbi request reprint Skewed oligomers and origins of replication
    S L Salzberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Gene 217:57-67. 1998
    ..Possible explanations for the phenomenon of skewed oligomers are discussed. Explanations are presented for why some bacterial genomes contain hundreds of highly skewed oligomers, whereas others contain only a handful...
  12. ncbi request reprint Interpolated Markov models for eukaryotic gene finding
    S L Salzberg
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Genomics 59:24-31. 1999
    ..With the rapid progress in sequencing the genome of P. falciparum, the availability of this new gene finder will greatly facilitate the annotation process...
  13. ncbi request reprint Complete genome sequence of a virulent isolate of Streptococcus pneumoniae
    H Tettelin
    The Institute for Genomic Research (TIGR, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 293:498-506. 2001
    ..Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae that could contribute to differences in virulence and antigenicity...
  14. pmc GeneSplicer: a new computational method for splice site prediction
    M Pertea
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 29:1185-90. 2001
    ..In each case GeneSplicer performed comparably to the best alternative, in terms of both accuracy and computational efficiency...
  15. pmc A clustering method for repeat analysis in DNA sequences
    N Volfovsky
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Genome Biol 2:RESEARCH0027. 2001
    ..The method uses suffix trees to organize and search the input sequences; this data structure has been used previously for efficient computation of exact and degenerate repeats...
  16. pmc Evidence for symmetric chromosomal inversions around the replication origin in bacteria
    J A Eisen
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Genome Biol 1:RESEARCH0011. 2000
    ..Until recently, however, comparisons were mainly possible only between distantly related species. Complete genome sequences are now becoming available from multiple sets of closely related strains or species...
  17. ncbi request reprint Efficient implementation of a generalized pair hidden Markov model for comparative gene finding
    W H Majoros
    Bioinformatics Department, The Institute for Genomic Research, Rockville, MD, USA
    Bioinformatics 21:1782-8. 2005
    ....
  18. ncbi request reprint Prediction of transcription terminators in bacterial genomes
    M D Ermolaeva
    The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
    J Mol Biol 301:27-33. 2000
    ..A set of 131 experimentally determined E. coli terminators was used to evaluate the sensitivity of the method, which ranges from 89 % to 98 %, with corresponding false positive rates of 2 % and 18 %...
  19. ncbi request reprint Optimized multiplex PCR: efficiently closing a whole-genome shotgun sequencing project
    H Tettelin
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Genomics 62:500-7. 1999
    ..The pipette optimized multiplex PCR method has been employed in the final phases of closing the Streptococcus pneumoniae genome sequence, with excellent results...
  20. pmc Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains
    R D Fleischmann
    The Institute for Genomic Research, Rockville, Maryland 20850, USA
    J Bacteriol 184:5479-90. 2002
    ..Together, these results demonstrate that polymorphisms among M. tuberculosis strains are more extensive than initially anticipated, and genetic variation may have an important role in disease pathogenesis and immunity...
  21. pmc Prediction of operons in microbial genomes
    M D Ermolaeva
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 29:1216-21. 2001
    ..98) to belong to the same operon. The sensitivity of our method is 30-50% for the Escherichia coli genome. The predicted gene pairs are available from our World Wide Web site http://www.tigr.org/tigr-scripts/operons/operons.cgi...
  22. ncbi request reprint TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders
    W H Majoros
    Bioinformatics Department, The Institute for Genomic Research, Rockville, MD 20850, USA
    Bioinformatics 20:2878-9. 2004
    ..Both programs have been used at TIGR for the annotation of the Aspergillus fumigatus and Toxoplasma gondii genomes...
  23. ncbi request reprint DNA uptake signal sequences in naturally transformable bacteria
    H O Smith
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Res Microbiol 150:603-16. 1999
    ..Neisseria meningitidis contains 1891 copies of the USS sequence 5'-GCCGTCTGAA. The USSs are often found in the base paired stem of transcription terminators...
  24. pmc Rice bioinformatics. analysis of rice sequence data and leveraging the data to other plant species
    Q Yuan
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Plant Physiol 125:1166-74. 2001
    ..In addition, we have used data from The Institute of Genomic Research Gene Indices and the Arabidopsis and Rice Genome Projects to identify putative orthologues and paralogues among these nine genomes...
  25. pmc Complete genome sequence of Caulobacter crescentus
    W C Nierman
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Proc Natl Acad Sci U S A 98:4136-41. 2001
    ....
  26. pmc Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae
    T D Read
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 31:2134-47. 2003
    ..pneumoniae. This crucial addition to the set of completed Chlamydiaceae genome sequences is enabling dissection of the roles played by niche-specific genes in these important bacterial pathogens...
  27. pmc The perils of gene patents
    S L Salzberg
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    Clin Pharmacol Ther 91:969-71. 2012
    ..Second, I explain how gene patents interfere with scientific progress, slowing down the development of new cures and treatments for genetic diseases...
  28. 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
    ....
  29. 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...
  30. 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
    ....
  31. ncbi request reprint The genome of the African trypanosome Trypanosoma brucei
    Matthew Berriman
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Science 309:416-22. 2005
    ..brucei and the greatest in L. major. Horizontal transfer of genes of bacterial origin has contributed to some of the metabolic differences in these parasites, and a number of novel potential drug targets have been identified...
  32. 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
    ....
  33. 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...
  34. ncbi request reprint Beware of mis-assembled genomes
    Steven L Salzberg
    Bioinformatics 21:4320-1. 2005
  35. 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...
  36. 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...
  37. 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...
  38. 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...
  39. 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
    ....
  40. 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...
  41. 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...
  42. 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
    ....
  43. 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...
  44. 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
    ....
  45. 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...
  46. 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...
  47. 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...
  48. 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...
  49. 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...
  50. 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...
  51. 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...
  52. 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...
  53. 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...
  54. pmc It is time to end the patenting of software
    John Quackenbush
    Bioinformatics 22:1416-7. 2006
  55. 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
    ....
  56. 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...
  57. 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
  58. 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...
  59. 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...
  60. pmc 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...
  61. 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
    ....
  62. 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...
  63. 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...
  64. ncbi request reprint Contamination in the draft of the human genome masquerades as lateral gene transfer
    Eske Willerslev
    DNA Seq 13:75-6. 2002
  65. 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
    ....
  66. 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...
  67. 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...
  68. ncbi request reprint Genomics: Yeast rises again
    Steven L Salzberg
    Nature 423:233-4. 2003
  69. 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...
  70. 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...
  71. 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...
  72. 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...
  73. 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...
  74. 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...
  75. 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...
  76. 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...
  77. 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...
  78. 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...
  79. 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...
  80. 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...
  81. 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...
  82. 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...