Steven Salzberg

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. He is a member of the Institute of Genetic Medicine at Johns Hopkins School of Medicine, where he is also Director of the Center for Computational Biology.

Steven Salzberg
Steven Salzberg in at the Intelligent Systems for Molecular Biology (ISMB) conference in 2018
Born
Steven Lloyd Salzberg

1960 (age 60–61)
Alma materYale University
Harvard University
Known forGLIMMER[1]
MUMmer[2]
AMOS assembler[3]
Bowtie[4]
TopHat[5]
Spouse(s)Claudia Pasche[6]
AwardsBen Franklin Award (2013)
Scientific career
InstitutionsUniversity of Maryland, College Park
The Institute for Genomic Research
Johns Hopkins University
ThesisLearning with nested generalized exemplars (1989)
Doctoral advisorWilliam Aaron Woods[7]
Doctoral students
Other notable studentsOlga Troyanskaya[8]
Websitesalzberg-lab.org

Education

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. After several years in a startup company, he enrolled at Harvard University, where he was earned a Ph.D. in Computer Science in 1989.[9]

Career and research

Before joining Johns Hopkins School of Medicine in 2011, he was the Director of the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park, where he was also the Horvitz Professor of Computer Science. From 1998–2005, he was the head of the Bioinformatics department at The Institute for Genomic Research, one of the world's largest genome sequencing centers, and prior to that he was a computer science professor at Johns Hopkins University.[6][10]

In 2013, Salzberg won the Benjamin Franklin award[11] in bioinformatics.

In 2014, 2015, 2016, and 2017, 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.

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.[12] The Bloomberg Distinguished Professorships were established in 2013 by a gift from Michael Bloomberg.[13] 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.

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[14] 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 is one of the initiators of the open source AMOS project. He was a participant in the human genome project[15] 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.[16] 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 started the Influenza Genome Sequencing Project in 2003, a project to sequence and make available the genomes of thousands of influenza virus isolates.[17][18]

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 in favor of the teaching of evolution in schools, and has authored editorials and appeared in print media on this topic. He writes a widely read column at Forbes magazine[19] on science, medicine, and pseudoscience. His work at Forbes won the 2012 Robert P. Balles Prize in Critical Thinking.[20] In 2018, he was elected a Fellow of the American Academy of Arts and Sciences.

The subject was a charter member of the The Cambridge Working Group in 2014 that signaled alarm in the scientific community over the creation of highly transmissible and contagious viruses and the likelihood of an accidental lab release.[21] His doctoral students and postdoctoral researchers include Cole Trapnell, Ben Langmead,[7] and Olga Troyanskaya.

References
  1. Salzberg, S. L.; Delcher, A. L.; Kasif, S.; White, O. (1998). "Microbial gene identification using interpolated Markov models". Nucleic Acids Research. 26 (2): 544–548. doi:10.1093/nar/26.2.544. PMC 147303. PMID 9421513.
  2. Delcher, A. L.; Kasif, S.; Fleischmann, R. D.; Peterson, J.; White, O.; Salzberg, S. L. (1999). "Alignment of whole genomes". Nucleic Acids Research. 27 (11): 2369–2376. doi:10.1093/nar/27.11.2369. PMC 148804. PMID 10325427.
  3. Sommer, D. D.; Delcher, A. L.; Salzberg, S. L.; Pop, M. (2007). "Minimus: A fast, lightweight genome assembler". BMC Bioinformatics. 8: 64. doi:10.1186/1471-2105-8-64. PMC 1821043. PMID 17324286.
  4. Langmead, B.; Trapnell, C.; Pop, M.; Salzberg, S. L. (2009). "Ultrafast and memory-efficient alignment of short DNA sequences to the human genome". Genome Biology. 10 (3): R25. doi:10.1186/gb-2009-10-3-r25. PMC 2690996. PMID 19261174.
  5. Trapnell, C.; Pachter, L.; Salzberg, S. L. (2009). "TopHat: Discovering splice junctions with RNA-Seq". Bioinformatics. 25 (9): 1105–1111. doi:10.1093/bioinformatics/btp120. PMC 2672628. PMID 19289445.
  6. ccb.jhu.edu Brief biosketch
  7. Steven Salzberg at the Mathematics Genealogy Project
  8. Mullins, J.; Morrison Mckay, B. (2011). "International Society for Computational Biology Honors Michael Ashburner and Olga Troyanskaya with Top Bioinformatics/Computational Biology Awards for 2011". PLOS Computational Biology. 7 (6): e1002081. Bibcode:2011PLSCB...7E2081M. doi:10.1371/journal.pcbi.1002081. PMC 3107244.
  9. Salzberg, Steven Lloyd (1989). Learning with nested generalized exemplars (PhD thesis). Harvard University. ProQuest 303755625.
  10. Editorial on evolution and the flu, Philadelphia Inquirer
  11. "Steven Salzberg on Microbial Genomes, Open Access, Flu Shots and Gene Patents".
  12. "With Bloomberg Distinguished Professorships, Johns Hopkins aims to foster cross-specialty collaboration 2014". 2014-02-17.
  13. "Michael R. Bloomberg Commits $350 Million to Johns Hopkins for Transformational Academic Initiative 2013".
  14. Delcher, A.; Harmon, D.; Kasif, S.; White, O.; Salzberg, S. (1999). "Improved microbial gene identification with GLIMMER". Nucleic Acids Research. 27 (23): 4636–4641. doi:10.1093/nar/27.23.4636. PMC 148753. PMID 10556321.
  15. Venter, J. C.; 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.; et al. (2001). "The Sequence of the Human Genome". Science. 291 (5507): 1304–1351. Bibcode:2001Sci...291.1304V. doi:10.1126/science.1058040. PMID 11181995.
  16. 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. (2002). "Comparative Genome Sequencing for Discovery of Novel Polymorphisms in Bacillus anthracis". Science. 296 (5575): 2028–2033. Bibcode:2002Sci...296.2028R. doi:10.1126/science.1071837. PMID 12004073. S2CID 15470665.
  17. Ghedin, E.; Sengamalay, N. A.; Shumway, M.; Zaborsky, J.; Feldblyum, T.; Subbu, V.; Spiro, D. J.; Sitz, J.; Koo, H.; Bolotov, P.; Dernovoy, D.; Tatusova, T.; Bao, Y.; St George, K.; Taylor, J.; Lipman, D. J.; Fraser, C. M.; Taubenberger, J. K.; Salzberg, S. L. (2005). "Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution". Nature. 437 (7062): 1162–1166. Bibcode:2005Natur.437.1162G. doi:10.1038/nature04239. PMID 16208317.
  18. Holmes, E. C.; Ghedin, E.; Miller, N.; Taylor, J.; Bao, Y.; St George, K.; Grenfell, B. T.; Salzberg, S. L.; Fraser, C. M.; Lipman, D. J.; Taubenberger, J. K. (2005). "Whole-Genome Analysis of Human Influenza A Virus Reveals Multiple Persistent Lineages and Reassortment among Recent H3N2 Viruses". PLOS Biology. 3 (9): e300. doi:10.1371/journal.pbio.0030300. PMC 1180517. PMID 16026181.
  19. Salzberg's column at Forbes
  20. "Skeptic Authors Steven Salzberg and Joe Nickell to Receive Balles Prize in Critical Thinking".
  21. 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.
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