Skip Navigation
Find a Doctor


Photo of Dr. Steven Salzberg

Steven Salzberg, M.Phil.

Professor of Biomedical Engineering



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

Centers & Institutes


Contact for Research Inquiries

Phone: 410-614-6112

Research Interests

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


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. more

    Additional Information

  • Education +
    • B.A., Yale University (Connecticut) (1980)
    • M.S., Yale University (Connecticut) (1982)
    • M.Phil., Yale University (Connecticut) (1984)
    • Ph.D., Harvard University (Massachusetts) (1989)
  • Research & Publications +

    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 thaliana, Oryza 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.


    Selected Publications View all on PubMed


    • S.L. Salzberg and T. Warnow (editors). Algorithms in Bioinformatics: 9th International Workshop, WABI 2009. ISBN: 978-3-642-04240-9. Berlin: Springer-Verlag, 2009.
    • S.L. Salzberg, D. Searls, and S. Kasif (editors). Computational Methods in Molecular Biology. Amsterdam: Elsevier Science B.V., 1998.
    • S.L. Salzberg. Learning with Nested Generalized Exemplars. Norwell, MA: Kluwer Academic Publishers, 1990.


    Additional Articles:

  • Academic Affiliations & Courses +

    Courses and Syllabi

    Bioinformatics for Metagenomics (CMSC 828G)
    University of Maryland

    Computational Gene Finding and Genome Assembly (CMSC 828N/H)
    University of Maryland

    Computational Biology (CS 600.439)
    Johns Hopkins University

    Artificial Intelligence (CS 600.435)
    Johns Hopkins University

    Expert Systems (CS 600.350)
    Johns Hopkins University

    Machine Learning (CS 600.661)
    Johns Hopkins University

    Natural Language Processing (CS 600.665)
    Johns Hopkins University

  • Activities & Honors +


    • “The Hottest Research of 1999-2000”, Institute for Scientific Information.
    • Chosen for
    • Member, International Advisory Committee
    • Editorial Board, Artificial Intelligence Review, 1995 - 2002
    • Career Award, NIH, 1996 - 1998
    • Editorial Board, Pattern Analysis and Applications, 1997 - 2000
    • Editorial Board, Gene, 1999 - 2003
    • Associate Editor, Bioinformatics, 2001 - 2006
    • Associate Editor, Journal of Computational Biology, 2002
    • Editorial Board, Applied Bioinformatics, 2002 - 2006
    • Editorial Board, BMC Genomics, 2003
    • Editorial Board, BMC Bioinformatics, 2003
    • Editorial Board, BMC Biology, 2003
    • Board of Scientific Counselors, National Center for Biotechnology Information, 2003 - 2008
    • Fellow, American Association for the Advancement of Science, 2004
    • Editorial Board, Evolutionary Bioinformatics, 2005
    • Editorial Board, PLoS ONE, 2006
    • Hot 100 authors, BioMed Central, 2007
    • Member, Biodata Management and Analysis Study Section, 2007 - 2011
    • Board of Reviewers, PLoS Currents Influenza, 2008 - 2012
    • Editorial Board, Biology Direct, 2008
    • Member, Faculty of 1000, 2008
    • Editorial Advisory Board, Genome Biology, 2009
    • Editorial Board, Genome Research, 2009
    • Co-winner of Genome Biology Award, 2009
    • Fellow, International Society for Computational Biology, 2013
    • Winner, Robert G. Balles Prize in Critical Thinking, 2013
    • Winner, Benjamin Franklin Award for Open Access in the Life Sciences, 2013
  • Videos & Media +

    Recent News Articles & Media Coverage

Is This You? Edit Profile

© The Johns Hopkins University, The Johns Hopkins Hospital, and Johns Hopkins Health System. All rights reserved.