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Steven Salzberg, M.Phil., M.S., Ph.D.

Professor of Biomedical Engineering

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  • Professor
  • Director, Center for Computational Biology
  • Member, McKusick-Nathans Institute of Genetic Medicine
  • Professor of Biomedical Engineering
  • Professor of Medicine

Centers & Institutes

  • McKusick-Nathans Institute of Genetic Medicine

Research Interests

Genomics; Bioinformatics; Gene finding; Genome assembly; Genome technology


Steven Salzberg is a Professor of Medicine and the Director of the Center for Computational Biology in the McKusick-Nathans Institute of Genetic Medicine at Johns Hopkins University. He holds joint appointments as Professor in the Departments of Biostatistics and Computer Science. From 2005-2011, he was the Director of the Center for Bioinformatics and Computational Biology (CBCB) and the Horvitz Professor of Computer Science at the University of Maryland, College Park. From 1997-2005 he was Senior Director of Bioinformatics at The Institute for Genomic Research (TIGR) in Rockville, Maryland, one of the world's leading DNA sequencing centers at the time. 

Dr. Salzberg received his B.A. degree in English and M.S. and M.Phil. degrees in Computer Science from Yale University, and his Ph.D. in Computer Science from Harvard University. He joined the Computer Science Department at Johns Hopkins as an Assistant Professor in 1989.

Dr. Salzberg has authored or co-authored over 200 publications in leading scientific journals, and his h-index is 102. He is a Fellow of the American Association for the Advancement of Science (AAAS), a Fellow of the International Society for Computational Biology (ISCB), and a former member of the Board of Scientific Counselors of the National Center for Biotechnology Information at NIH. He was the 2013 recipient of the Benjamin Franklin Award for Open Access in the Life Sciences.


  • English
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    • Ph.D., Harvard University, 1989
    • M.Phil., Yale University, 1984
    • M.S., Yale Univeristy, 1982
    • B.A., Yale University, 1980
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    Research Summary

    Dr. Salzberg's interest in the human genome project motivated him to develop one of the first computational gene-finding systems for the human genome in the early 1990s. His initial collaborations with TIGR  at that time led to the development of the Glimmer gene finder, which has been used in the analysis of thousands of bacterial, archaeal, and viral genomes, including  Borrelia burgdorferi (the Lyme disease bacterium), Treponema pallidum  (the syphilis bacterium), Mycobacterium tuberculosis, Vibrio cholerae, Bacillus anthracis(anthrax), and many others. He and his research team developed a eukaryotic gene finder for Plasmodium falciparum, the malaria parasite, and later adapted it for the human genome, the model plant Arabidopsis thalianaOryza sativa  (rice), Cryptococcus neoformans, Brugia malayi, and other species. Salzberg's lab has a major focus on next-generation sequence alignment and on large-scale genome assembly. They have assembled hundreds of genomes, large and small, and have developed a variety of assembly software systems, including the open-source  AMOS assembly package. In recent years they have developed several pioneering, highly efficient systems for alignment of next-generation sequencing reads, including the Bowtie, Tophat, and Cufflinks systems, which are now used by thousands of labs around the world. All of the group's software is free and open source, and their systems have been downloaded hundreds of thousands of times. In addition to his software systems, Salzberg has contributed analyses to many genome sequencing projects, including the human genome, multiple plant and animal genomes, and many bacteria. He was a co-founder of the Influenza Genome Sequencing Project, the first large-scale genomics study of human and avian influenza viruses.


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    • Biomedical Engineering
    • Medicine - General Internal Medicine

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    Phone:    410-614-6112

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