Steven Salzberg

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Steven Salzberg
Steven Salzberg.jpg
Steven Salzberg in 2010.
Born 1960 (age 53–54)
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 Pertea
Jonathan Allen
Adam Phillippy
Michael Schatz
Bruce Cole Trapnell[2]
Samuel Angiuoli[3]
David Kelley
Benjamin Langmead[1]
Daehwan Kim
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
ccb.jhu.edu/people/salzberg/

Steven Lloyd Salzberg (born 1960) is an American Biologist and Computer Scientist who since 2011 has been a Professor of Medicine and Biostatistics in the Institute of Genetic Medicine at Johns Hopkins School of Medicine, where he is also Director of the Center for Computational Biology.

Biography[edit]

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]

Prior to 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.

Work[edit]

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[15] 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[16] 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.[17] 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.[18][19]

After the advent of next-generation sequencing in the mid-2000s, Salzberg and his group developed a suite of highly efficient, accurate programs for alignment of these sequences to large genomes. The "Tuxedo" suite, including the Bowtie and TopHat programs, has been downloaded by thousands of scientists and the original papers have over 3000 citations.

Salzberg has also been a vocal advocate 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[20] on science, medicine, and pseudoscience.

References[edit]

  1. ^ a b 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 2836519. PMID 19430453.  edit
  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 3031037. PMID 21148543.  edit
  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 3107244. PMID 21673867.  edit
  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 147303. PMID 9421513.  edit
  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 148804. PMID 10325427.  edit
  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 1821043. PMID 17324286.  edit
  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 2690996. PMID 19261174.  edit
  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 2672628. PMID 19289445.  edit
  10. ^ a b 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. ^ 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.  edit
  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.; 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.  edit
  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. doi:10.1126/science.1071837. PMID 12004073.  edit
  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.  edit
  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.  edit
  19. ^ Salzberg's column at Forbes

External links[edit]