Sean Eddy

Sean Roberts Eddy is Professor of Molecular & Cellular Biology and of Applied Mathematics at Harvard University. Previously he was based at the Janelia Research Campus from 2006 to 2015^[5][7][8] in Virginia. His research interests are in bioinformatics, computational biology and biological sequence analysis.^{[9][10][11][12]} As of 2016^[update] projects include the use of Hidden Markov models^[13][14] in HMMER, Infernal^[15] Pfam and Rfam.^{[16][17][18][19]}

Sean Eddy
Sean Eddy
Born	Sean Roberts Eddy
Alma mater	California Institute of Technology (BS) University of Colorado (PhD)
Known for	HMMER[1] Infernal[2] Pfam[3] Rfam[4]
Awards	Ben Franklin award (2007)
Scientific career
Fields	Computational Genome Analysis[5]
Institutions	Harvard University Howard Hughes Medical Institute (HHMI) Janelia Farm Research Campus Washington University in St. Louis California Institute of Technology University of Colorado Laboratory of Molecular Biology (LMB)
Thesis	Introns in the T-even bacteriophages (1991)
Doctoral advisor	Larry Gold[6]
Other academic advisors	John Sulston Richard Durbin
Website	cryptogenomicon.org www.hhmi.org/scientists/sean-r-eddy

Education

Eddy graduated June, 1982 from Marion Center Area High School, Marion Center, Pennsylvania. He then completed a Bachelor of Science in Biology at California Institute of Technology in 1986,^[20] followed by a Doctor of Philosophy in molecular biology at the University of Colorado under the supervision of Larry Gold in 1991 studying the T4 phage.^[6][21][22]

Career

From 1992 to 1995 he was a postdoctoral research fellow at the Medical Research Council (MRC) Laboratory of Molecular Biology (LMB) in Cambridge UK working with John Sulston and Richard Durbin. From 1995 to 2007 he worked at Washington University School of Medicine and has been working for the Howard Hughes Medical Institute since 2000.

Awards and honours

In 2007, Sean was the winner of the Benjamin Franklin Award in Bioinformatics for contributions to Open Access in the Life Sciences.^[23]

In 2022, Eddy was elected as a Fellow of the International Society for Computational Biology.^[24]

References

1. Finn, R. D.; Clements, J.; Eddy, S. R. (2011). "HMMER web server: Interactive sequence similarity searching". Nucleic Acids Research. 39 (Web Server issue): W29–W37. doi:10.1093/nar/gkr367. PMC 3125773. PMID 21593126.
2. Nawrocki, E. P.; Kolbe, D. L.; Eddy, S. R. (2009). "Infernal 1.0: Inference of RNA alignments". Bioinformatics. 25 (10): 1335–1337. doi:10.1093/bioinformatics/btp157. PMC 2732312. PMID 19307242.
3. Bateman, A.; Coin, L.; Durbin, R.; Finn, R. D.; Hollich, V.; Griffiths-Jones, S.; Khanna, A.; Marshall, M.; Moxon, S.; Sonnhammer, E. L.; Studholme, D. J.; Yeats, C.; Eddy, S. R. (2004). "The Pfam protein families database". Nucleic Acids Research. 32 (Database issue): 138D–1141. doi:10.1093/nar/gkh121. ISSN 0305-1048. PMC 308855. PMID 14681378.
4. Gardner, P. P.; Daub, J.; Tate, J.; Moore, B. L.; Osuch, I. H.; Griffiths-Jones, S.; Finn, R. D.; Nawrocki, E. P.; Kolbe, D. L.; Eddy, S. R.; Bateman, A. (2010). "Rfam: Wikipedia, clans and the "decimal" release". Nucleic Acids Research. 39 (Database issue): D141–D145. doi:10.1093/nar/gkq1129. PMC 3013711. PMID 21062808.
5. Sean Eddy publications indexed by Google Scholar
6. Eddy, Sean Roberts (1991). Introns in the T-even bacteriophages (PhD thesis). University of Colorado. OCLC 28253022. ProQuest 303935681.
7. Anon (2012). "HHMI Scientist Bio: Sean R. Eddy, Ph.D." Archived from the original on 2012-06-16.
8. Kaplan, Karen (2011). "A roll of the dice: Sean Eddy has his dream job". Nature. 479 (7373): 433–435. doi:10.1038/nj7373-433a. PMID 22106470.
9. Durbin, Richard M.; Eddy, Sean R.; Krogh, Anders; Mitchison, Graeme (1998), Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids (1st ed.), Cambridge, New York: Cambridge University Press, ISBN 0-521-62971-3, OCLC 593254083
10. Rivas, E.; Lang, R.; Eddy, S. R. (2011). "A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more". RNA. 18 (2): 193–212. doi:10.1261/rna.030049.111. PMC 3264907. PMID 22194308.
11. Lander, E. S.; Linton, M.; Birren, B.; Nusbaum, C.; Zody, C.; Baldwin, J.; Devon, K.; Dewar, K.; Doyle, M.; Fitzhugh, W.; Funke, R.; Gage, D.; Harris, K.; Heaford, A.; Howland, J.; Kann, L.; Lehoczky, J.; Levine, R.; McEwan, P.; McKernan, K.; Meldrim, J.; Mesirov, J. P.; Miranda, C.; Morris, W.; Naylor, J.; Raymond, C.; Rosetti, M.; Santos, R.; Sheridan, A.; et al. (Feb 2001). "Initial sequencing and analysis of the human genome" (PDF). Nature. 409 (6822): 860–921. Bibcode:2001Natur.409..860L. doi:10.1038/35057062. ISSN 0028-0836. PMID 11237011.
12. "Sean Eddy's homepage". selab.janelia.org. Archived from the original on 2010-12-04.
13. Eddy, S. R. (2004). "What is a hidden Markov model?". Nature Biotechnology. 22 (10): 1315–1316. doi:10.1038/nbt1004-1315. PMID 15470472.
14. Eddy, S. (1998). "Profile hidden Markov models". Bioinformatics. 14 (9): 755–763. doi:10.1093/bioinformatics/14.9.755. PMID 9918945.
15. "Sean Eddy's blog". cryptogenomicon.org.
16. Eddy, S. R. (2012). "The C-value paradox, junk DNA and ENCODE". Current Biology. 22 (21): R898–R899. doi:10.1016/j.cub.2012.10.002. PMID 23137679.
17. Sean Eddy's publications indexed by the Scopus bibliographic database. (subscription required)
18. Reading Genomes Bit by Bit - Sean Eddy on YouTube, GenomeTV
19. Sean Eddy Keynote OBF BOSC on YouTube, 2013-07-20
20. "Sean Eddy CV" (PDF). selab.janelia.org. Archived from the original (PDF) on 2012-03-09.
21. Eddy, S. R.; Gold, L. (1991). "The phage T4 nrdB intron: A deletion mutant of a version found in the wild". Genes & Development. 5 (6): 1032–1041. doi:10.1101/gad.5.6.1032. PMID 2044951.
22. Tuerk, C.; Eddy, S.; Parma, D.; Gold, L. (1990). "Autogenous translational operator recognized by bacteriophage T4 DNA polymerase". Journal of Molecular Biology. 213 (4): 749–761. doi:10.1016/S0022-2836(05)80261-X. PMID 2359122.
23. Anon (2007). "BioMed Central Blog: Sean Eddy wins open access award". blogs.openaccesscentral.com. Archived from the original on 2011-06-07.
24. "April 28, 2022: ISCB Congratulates and Introduces the 2022 Class of Fellows!". www.iscb.org. Retrieved 17 June 2022.