Steven Salzberg Explained

Steven Salzberg
Birth Name:Steven Lloyd Salzberg
Workplaces:University of Maryland, College Park
The Institute for Genomic Research
Johns Hopkins University
Alma Mater:Yale University
Harvard University
Thesis Title:Learning with nested generalized exemplars
Thesis Url:http://search.proquest.com/docview/303755625
Thesis Year:1989
Doctoral Advisor:William Aaron Woods
Notable Students:Olga Troyanskaya[1]
Known For:GLIMMER[2]
MUMmer[3]
AMOS assembler[4]
Bowtie[5]
TopHat[6]
Awards:Ben Franklin Award (2013)
Spouse:Claudia Pasche

Steven Lloyd Salzberg (born 1960) is an American computational biologist and computer scientist who is a Bloomberg Distinguished Professor of Biomedical Engineering, Computer Science, and Biostatistics at Johns Hopkins University, where he is also Director of the Center for Computational Biology.

Early life and education

Salzberg was born in 1960 as one of four children to Herman Salzberg, a Distinguished Professor Emeritus of Psychology, and Adele Salzberg, a retired school teacher.[7] Salzberg did his undergraduate studies at Yale University where he received his Bachelor of Arts degree in English in 1980. In 1981 he returned to Yale, and he received his Master of Science and Master of Philosophy degrees in Computer Science in 1982 and 1984, respectively. After several years in a startup company, he enrolled at Harvard University, where he earned a Ph.D. in Computer Science in 1989.[8]

Career

After obtaining his undergraduate degree, he worked for a local power company in South Carolina, where he gained programming experience using IBM mainframe.[9] He also learned COBOL and IBM Assembler. He then joined a Boston-based AI startup upon completion of his masters degree in Computer Science.

After earning his Ph.D., Salzberg joined Johns Hopkins University as an assistant professor in the Department of Computer Science, and was promoted to associate professor in 1997. From 1998 to 2005, he was the head of the Bioinformatics department at The Institute for Genomic Research, one of the world's largest genome sequencing centers. Salzberg then joined the Department of Computer Science at the University of Maryland, College Park, where he was the Horvitz Professor of Computer Science as well as the Director of the Center for Bioinformatics and Computational Biology. In 2011, Salzberg returned to Johns Hopkins University as a professor in the Department of Medicine. From 2014, he was a professor in the Department of Biomedical Engineering in the School of Medicine; the Department of Computer Science in the Whiting School of Engineering; and in the Department of Biostatistics in the Bloomberg School of Public Health.[10] [11] [12]

In 2013, Salzberg won the Benjamin Franklin award[13] in bioinformatics.

In March 2015, he was named a Bloomberg Distinguished Professor at Johns Hopkins University for his accomplishments as an interdisciplinary researcher and excellence in teaching the next generation of scholars.[14] The Bloomberg Distinguished Professorships were established in 2013 by a gift from Michael Bloomberg.[15] Salzberg holds joint appointments in the Johns Hopkins Whiting School of Engineering, Johns Hopkins School of Medicine, and the Johns Hopkins Bloomberg School of Public Health.

Research

Salzberg has been a prominent scientist in the field of bioinformatics and computational biology since the 1990s. He has made many contributions to gene finding algorithms, notably the GLIMMER[16] program for bacterial gene finding as well as several related programs for finding genes in animals, plants, and other organisms. He has also been a leader in genome assembly research and has led the assembly of dozens of genomes, both large and small. He was a participant in the human genome project[17] as well as many other genome projects, including the malaria genome (Plasmodium falciparum) and the genome of the model plant Arabidopsis thaliana. In 2001–2002, he and his colleagues sequenced the anthrax that was used in the 2001 anthrax attacks. They published their results in the journal Science in 2002.[18] These findings helped the FBI track the source of the attacks to a single vial at Ft. Detrick in Frederick, Maryland.

Salzberg together with David Lipman and Lone Simonsen started the Influenza Genome Sequencing Project in 2003, a project to sequence and make available the genomes of thousands of influenza virus isolates.[19] [20]

Soon after the advent of next-generation sequencing (NGS) in the mid-2000s, Salzberg's research lab and his collaborators developed a suite of highly efficient, accurate programs for alignment of NGS sequences to large genomes and for assembly of sequences from RNA-Seq experiments. These include the "Tuxedo" suite, comprising the Bowtie, TopHat, and Cufflinks programs, which have been cited tens of thousands of times in the years since their publication.

Salzberg has also been a vocal advocate against pseudoscience and has authored editorials and appeared in print media on this topic. Since 2010, he has written a column at Forbes magazine[21] on science, medicine, and pseudoscience, where he has published hundreds of articles that have received tens of millions of views. His work at Forbes won the 2012 Robert P. Balles Prize in Critical Thinking.[22]

Salzberg was a charter member of the Cambridge Working Group in 2014, which was created to express alarm in the scientific community over the creation of highly transmissible and contagious viruses (also called Gain-of-function research) and the likelihood of an accidental lab release.[23]

Publications

Salzberg has authored or co-authored over 300 scientific publications.[24] He has more than 300,000 citations in Google Scholar and an h-index of 159.[25] In 2014 and every year since (through at least 2022), Salzberg was selected for inclusion in HighlyCited.com, a ranking compiled by the Institute for Scientific Information of scientists who are among the top 1% most cited for their subject field during the previous ten years. He was also chosen for this list when it was first created in 2001. This list of highly cited researchers continues under Clarivate, and Salzberg was also included in the list in 2018, 2019, 2020, 2021, 2022, and 2023.[26]

Highly cited articles (more than 10,000 citations)

Awards

External links

Notes and References

  1. Mullins . J. . Morrison Mckay . B. . 10.1371/journal.pcbi.1002081 . International Society for Computational Biology Honors Michael Ashburner and Olga Troyanskaya with Top Bioinformatics/Computational Biology Awards for 2011 . . 7 . 6 . e1002081 . 2011 . 3107244. 2011PLSCB...7E2081M . free .
  2. Salzberg . S. L. . Delcher . A. L. . Kasif . S. . White . O. . Microbial gene identification using interpolated Markov models . Nucleic Acids Research . 26 . 2 . 544–548 . 1998 . 9421513 . 147303 . 10.1093/nar/26.2.544.
  3. 10.1093/nar/27.11.2369 . Delcher . A. L. . Kasif . S. . Fleischmann . R. D. . Peterson . J. . White . O. . Salzberg . S. L. . Alignment of whole genomes . Nucleic Acids Research . 27 . 11 . 2369–2376 . 1999 . 10325427 . 148804.
  4. Sommer . D. D. . Delcher . A. L. . Salzberg . S. L. . Pop . M. . Minimus: A fast, lightweight genome assembler . 10.1186/1471-2105-8-64 . BMC Bioinformatics . 8 . 64 . 2007 . 17324286 . 1821043 . free .
  5. Langmead . B. . Trapnell . C. . Pop . M. . Salzberg . S. L. . Ultrafast and memory-efficient alignment of short DNA sequences to the human genome . 10.1186/gb-2009-10-3-r25 . Genome Biology . 10 . 3 . R25 . 2009 . 19261174 . 2690996 . free .
  6. Trapnell . C. . Pachter . L. . Lior Pachter. Salzberg . S. L. . 10.1093/bioinformatics/btp120 . TopHat: Discovering splice junctions with RNA-Seq . Bioinformatics . 25 . 9 . 1105–1111 . 2009 . 19289445 . 2672628 .
  7. Web site: 2015-02-21. Steven Salzberg: brief biography. 2021-06-03. Salzberg Lab. en.
  8. PhD . Steven Lloyd. Salzberg . Learning with nested generalized exemplars . Harvard University . 1989 . Steven Salzberg. .
  9. Web site: Fogg . Christina . Kovats . Diane . Shamir . Ron . October 29, 2021 . 2020 ISCB accomplishments by a Senior Scientist Award: Steven Salzberg . 2023-07-26 . Oxford Academic.
  10. http://ccb.jhu.edu/people/salzberg/biosketch.html ccb.jhu.edu
  11. http://ccb.jhu.edu/people/salzberg/docs/Phila-Inquirer-Editorial.htm Editorial on evolution and the flu, Philadelphia Inquirer
  12. Web site: Bloomberg Distinguished Professorships Steven Salzberg. Johns Hopkins Office of Research. 9 September 2016 .
  13. Web site: Steven Salzberg on Microbial Genomes, Open Access, Flu Shots and Gene Patents.
  14. Web site: With Bloomberg Distinguished Professorships, Johns Hopkins aims to foster cross-specialty collaboration 2014. 2014-02-17.
  15. Web site: Michael R. Bloomberg Commits $350 Million to Johns Hopkins for Transformational Academic Initiative 2013.
  16. Delcher . A. . Harmon . D. . Kasif . S. . White . O. . Salzberg . S. . Improved microbial gene identification with GLIMMER . Nucleic Acids Research . 27 . 23 . 4636–4641 . 1999 . 10556321 . 148753 . 10.1093/nar/27.23.4636.
  17. Venter . J. C. . Craig Venter. Adams . M. . Myers . E. . Li . P. . Mural . R. . Sutton . G. . Smith . H. . Yandell . M. . Evans . C. . Holt . R. A. . Gocayne . J. D. . Amanatides . P. . Ballew . R. M. . Huson . D. H. . Wortman . J. R. . Zhang . Q. . Kodira . C. D. . Zheng . X. H. . Chen . L. . Skupski . M. . Subramanian . G. . Thomas . P. D. . Zhang . J. . Gabor Miklos . G. L. . Nelson . C. . Broder . S. . Clark . A. G. . Nadeau . J. . McKusick . V. A. . Zinder . N. . The Sequence of the Human Genome . 10.1126/science.1058040 . Science . 291 . 5507 . 1304–1351 . 2001 . 11181995. 2001Sci...291.1304V . 29 . free .
  18. Read . T. D. . Salzberg . S. . Pop . M. . Shumway . M. . Umayam . L. . Jiang . L. . Holtzapple . E. . Busch . J. . Smith . K. . Schupp . J. M. . Solomon . D. . Keim . P. . Fraser . C. M. . Comparative Genome Sequencing for Discovery of Novel Polymorphisms in Bacillus anthracis . 10.1126/science.1071837 . Science . 296 . 5575 . 2028–2033 . 2002 . 12004073 . 2002Sci...296.2028R. 15470665 . free .
  19. Ghedin . E. . Sengamalay . N. A. . Shumway . M. . Zaborsky . J. . Feldblyum . T. . Subbu . V. . Spiro . D. J. . Sitz . J. . Koo . H. . Bolotov . 10.1038/nature04239 . P. . Dernovoy . D. . Tatusova . T. . Bao . Y. . St George . K. . Taylor . J. . Lipman . D. J. . Fraser . C. M. . Taubenberger . J. K. . Salzberg . S. L. . Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution . Nature . 437 . 7062 . 1162–1166 . 2005 . 16208317. 2005Natur.437.1162G . free .
  20. Holmes . E. C. . Ghedin . E. . Miller . N. . Taylor . J. . Bao . Y. . St George . K. . Grenfell . B. T. . Salzberg . S. L. . Fraser . C. M. . Lipman . 10.1371/journal.pbio.0030300 . D. J. . Taubenberger . J. K. . Whole-Genome Analysis of Human Influenza A Virus Reveals Multiple Persistent Lineages and Reassortment among Recent H3N2 Viruses . PLOS Biology . 3 . 9 . e300 . 2005 . 16026181 . 1180517 . free .
  21. https://www.forbes.com/sites/stevensalzberg/ Salzberg's column at Forbes
  22. Web site: Skeptic Authors Steven Salzberg and Joe Nickell to Receive Balles Prize in Critical Thinking. 14 June 2013 .
  23. Baker, Nicholson. (4 January 2021). "The Lab-Leak Hypothesis For decades, scientists have been hot-wiring viruses in hopes of preventing a pandemic, not causing one. But what if …?". New York magazine Retrieved 18 January 2021.
  24. Web site: Steven Salzberg, Ph.D., Professor of Biomedical Engineering. 2021-06-03. Johns Hopkins Medicine. en.
  25. Web site: Steven Salzberg. 2021-06-03. scholar.google.com.
  26. Web site: Highly Cited Researchers. 2021-06-03. publons.com.
  27. Web site: Steven Salzberg, Ph.D., Professor of Biomedical Engineering. 2021-05-04. Johns Hopkins Medicine. en.

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