Steven Salzberg

Steven Salzberg

Steven Salzberg in 2010.
Born 1960 (age 55–56)
Institutions University of Maryland, College Park
The Institute for Genomic Research
Johns Hopkins University
Alma mater Yale University
Harvard University
Thesis Learning with nested generalized exemplars (1989)
Doctoral advisor William Aaron Woods[1]
Doctoral students

Sreerama Murthy
John Sheppard
Mihaela (Ela) Pertea
Jonathan Allen
Adam Phillippy
Michael Schatz
Bruce Cole Trapnell

[2]
Samuel Angiuoli[3]
David Kelley
Benjamin Langmead[1]
Daehwan Kim
Derrick Wood
Other notable students Olga Troyanskaya[4]
Known for GLIMMER[5]
MUMmer[6]
AMOS assembler[7]
Bowtie[8]
TopHat[9]
Cufflinks[10]
Notable awards Benjamin Franklin Award (Bioinformatics) (2013)
Spouse Claudia Salzberg (née Pasche)[11]
Website
salzberg-lab.org

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.

Biography

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 awarded a Ph.D. in Computer Science in 1989.[12]

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.[11][13]

In 2013, Salzberg won the Benjamin Franklin award[14] in bioinformatics.

In 2014 and again in 2015, 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 and year of publication—between 2002 and 2012. 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.[15] The Bloomberg Distinguished Professorships were established in 2013 by a gift from Michael Bloomberg.[16] 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.

Work

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[17] 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[18] 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.[19] 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.[20][21]

After the advent of next-generation sequencing in the mid-2000s, Salzberg's research lab and their collaborators developed a suite of highly efficient, accurate programs for alignment of these sequences to large genomes. The "Tuxedo" suite, including the Bowtie, TopHat, and Cufflinks programs, has been downloaded by thousands of scientists and the original papers have over 20,000 citations.

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[22] on science, medicine, and pseudoscience. His work at Forbes won the 2012 Robert P. Balles Prize in Critical Thinking.[23]

References

  1. 1 2 Steven Salzberg at the Mathematics Genealogy Project
  2. ↑ Trapnell, C.; Salzberg, S. L. (2009). "How to map billions of short reads onto genomes". Nature Biotechnology. 27 (5): 455–457. doi:10.1038/nbt0509-455. PMC 2836519Freely accessible. PMID 19430453.
  3. ↑ Angiuoli, S. V.; Salzberg, S. L. (2010). "Mugsy: Fast multiple alignment of closely related whole genomes". Bioinformatics. 27 (3): 334–342. doi:10.1093/bioinformatics/btq665. PMC 3031037Freely accessible. PMID 21148543.
  4. ↑ 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. doi:10.1371/journal.pcbi.1002081. PMC 3107244Freely accessible.
  5. ↑ 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 147303Freely accessible. PMID 9421513.
  6. ↑ 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 148804Freely accessible. PMID 10325427.
  7. ↑ 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 1821043Freely accessible. PMID 17324286.
  8. ↑ 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 2690996Freely accessible. PMID 19261174.
  9. ↑ 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 2672628Freely accessible. PMID 19289445.
  10. 1 2 ccb.jhu.edu Brief biosketch
  11. ↑ Salzberg, Steven Lloyd (1989). Learning with nested generalized exemplars (PhD thesis). Harvard University.
  12. ↑ Editorial on evolution and the flu, Philadelphia Inquirer
  13. ↑ "Steven Salzberg on Microbial Genomes, Open Access, Flu Shots and Gene Patents".
  14. ↑ "With Bloomberg Distinguished Professorships, Johns Hopkins aims to foster cross-specialty collaboration 2014".
  15. ↑ "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. (1999). "Improved microbial gene identification with GLIMMER". Nucleic Acids Research. 27 (23): 4636–4641. doi:10.1093/nar/27.23.4636. PMC 148753Freely accessible. PMID 10556321.
  17. ↑ 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.; Zinder, N. (2001). "The Sequence of the Human Genome". Science. 291 (5507): 1304–1351. Bibcode:2001Sci...291.1304V. doi:10.1126/science.1058040. PMID 11181995.
  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. (2002). "Comparative Genome Sequencing for Discovery of Novel Polymorphisms in Bacillus anthracis". Science. 296 (5575): 2028–2033. doi:10.1126/science.1071837. PMID 12004073.
  19. ↑ 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.
  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, 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 1180517Freely accessible. PMID 16026181.
  21. ↑ Salzberg's column at Forbes
  22. ↑ "Skeptic Authors Steven Salzberg and Joe Nickell to Receive Balles Prize in Critical Thinking".
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