Steven L Salzberg

Summary

Affiliation: Johns Hopkins University
Country: USA

Publications

  1. pmc TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    Daehwan Kim
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
    Genome Biol 14:R36. 2013
  2. pmc A new rhesus macaque assembly and annotation for next-generation sequencing analyses
    Aleksey V Zimin
    Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
    Biol Direct 9:20. 2014
  3. pmc GAGE-B: an evaluation of genome assemblers for bacterial organisms
    Tanja Magoc
    Center for Computational Biology, McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21025, USA
    Bioinformatics 29:1718-25. 2013
  4. 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
  5. 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
  6. pmc TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
    Daehwan Kim
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Genome Biol 12:R72. 2011
  7. pmc GAGE: A critical evaluation of genome assemblies and assembly algorithms
    Steven L Salzberg
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Genome Res 22:557-67. 2012
  8. pmc 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
  9. pmc Repetitive DNA and next-generation sequencing: computational challenges and solutions
    Todd J Treangen
    McKusick Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Nat Rev Genet 13:36-46. 2012
  10. pmc The MaSuRCA genome assembler
    Aleksey V Zimin
    Institute for Physical Sciences and Technology, University of Maryland, College Park, MD 20742, USA, Center for Computational Biology, McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA, Department of Mathematics and Department of Physics, University of Maryland, College Park, MD 20742, USA
    Bioinformatics 29:2669-77. 2013

Detail Information

Publications25

  1. pmc TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    Daehwan Kim
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
    Genome Biol 14:R36. 2013
    ..TopHat2 is available at http://ccb.jhu.edu/software/tophat...
  2. pmc A new rhesus macaque assembly and annotation for next-generation sequencing analyses
    Aleksey V Zimin
    Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
    Biol Direct 9:20. 2014
    ..Annotations for these two assemblies are limited in completeness and accuracy. High quality assembly and annotation files are required for a wide range of studies including expression, genetic and evolutionary analyses...
  3. pmc GAGE-B: an evaluation of genome assemblers for bacterial organisms
    Tanja Magoc
    Center for Computational Biology, McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21025, USA
    Bioinformatics 29:1718-25. 2013
    ..The need to contain costs often results in the creation of only a single sequencing library, which in turn introduces new challenges for genome assembly methods...
  4. 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...
  5. 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...
  6. pmc TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
    Daehwan Kim
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Genome Biol 12:R72. 2011
    ..Using RNA-seq data from breast and prostate cancer cell lines, we detected both previously reported and novel fusions with solid supporting evidence. TopHat-Fusion is available at http://tophat-fusion.sourceforge.net/...
  7. pmc GAGE: A critical evaluation of genome assemblies and assembly algorithms
    Steven L Salzberg
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Genome Res 22:557-67. 2012
    ..To enable others to replicate our results, all of our data and methods are freely available, as are all assemblers used in this study...
  8. pmc 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/...
  9. pmc Repetitive DNA and next-generation sequencing: computational challenges and solutions
    Todd J Treangen
    McKusick Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Nat Rev Genet 13:36-46. 2012
    ..We discuss the computational problems surrounding repeats and describe strategies used by current bioinformatics systems to solve them...
  10. pmc The MaSuRCA genome assembler
    Aleksey V Zimin
    Institute for Physical Sciences and Technology, University of Maryland, College Park, MD 20742, USA, Center for Computational Biology, McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA, Department of Mathematics and Department of Physics, University of Maryland, College Park, MD 20742, USA
    Bioinformatics 29:2669-77. 2013
    ..We call our system the Maryland Super-Read Celera Assembler (abbreviated MaSuRCA and pronounced 'mazurka')...
  11. 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...
  12. 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?..
  13. doi request reprint Using MUMmer to identify similar regions in large sequence sets
    Arthur L Delcher
    The Institute for Genomic Research Rockville, Maryland and Computer Science Department, Loyola College in Maryland, Baltimore, Maryland, USA
    Curr Protoc Bioinformatics . 2003
    ..The system is particularly efficient at comparing highly similar sequences, such as alternative versions of fragment assemblies or closely related strains of the same bacterium...
  14. pmc Fast gapped-read alignment with Bowtie 2
    Ben Langmead
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, USA
    Nat Methods 9:357-9. 2012
    ..Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy...
  15. pmc FLASH: fast length adjustment of short reads to improve genome assemblies
    Tanja Magoc
    McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Bioinformatics 27:2957-63. 2011
    ..The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome...
  16. 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...
  17. 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...
  18. 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...
  19. 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...
  20. pmc 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...
  21. 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...
  22. pmc EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes
    Tanja Magoc
    Center for Computational Biology, McKusick Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
    Evol Bioinform Online 9:127-36. 2013
    ..SOFTWARE: The EDGE-pro tool is implemented as a pipeline of C++ and Perl programs and is freely available as open-source code at http://www.genomics.jhu.edu/software/EDGE/index.shtml...
  23. pmc The genome Assembly Archive: a new public resource
    Steven L Salzberg
    Institute for Genomic Research, Rockville, Maryland, USA
    PLoS Biol 2:E285. 2004
  24. pmc Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation
    David A Rasko
    Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
    Proc Natl Acad Sci U S A 108:5027-32. 2011
    ..This study demonstrates the forensic value of systematic microbiological analysis combined with whole-genome sequencing and comparative genomics...
  25. pmc DIAMUND: direct comparison of genomes to detect mutations
    Steven L Salzberg
    Center for Computational Biology, Johns Hopkins School of Medicine, Baltimore, Maryland, 21205 McKusick Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, 21205
    Hum Mutat 35:283-8. 2014
    ..We demonstrate our results on several example cases, including two family trios in which it correctly found the disease-causing variant while excluding thousands of harmless variants that standard methods had identified. ..