Sean Eddy

Sean Eddy
Sean Eddy
	Sean Eddy
Born	Sean Roberts Eddy
Alma mater	California Institute of Technology (BS); University of Colorado (PhD);
Known for	HMMER; Infernal; Pfam; Rfam;
Awards	Ben Franklin award (2007)
	Scientific career
Fields	Computational Genome Analysis
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
Other academic advisors	John Sulston; Richard Durbin
Website	cryptogenomicon.org; www.hhmi.org/scientists/sean-r-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^[1]^[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]

^ ^a ^b Sean Eddy publications indexed by Google Scholar
^ Cite error: The named reference eddyphd was invoked but never defined (see the help page).
^ 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.
^ 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.
^ 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.
^ 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.
^ Anon (2012). "HHMI Scientist Bio: Sean R. Eddy, Ph.D." Archived from the original on 2012-06-16.
^ 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.
^ 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
^ 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.
^ 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.
^ "Sean Eddy's homepage". selab.janelia.org. Archived from the original on 2010-12-04.
^ Eddy, S. R. (2004). "What is a hidden Markov model?". Nature Biotechnology. 22 (10): 1315–1316. doi:10.1038/nbt1004-1315. PMID 15470472.
^ Eddy, S. (1998). "Profile hidden Markov models". Bioinformatics. 14 (9): 755–763. doi:10.1093/bioinformatics/14.9.755. PMID 9918945.
^ "Sean Eddy's blog". cryptogenomicon.org.
^ 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.
^ Sean Eddy's publications indexed by the Scopus bibliographic database. (subscription required)
^ Reading Genomes Bit by Bit - Sean Eddy on YouTube, GenomeTV
^ Sean Eddy Keynote OBF BOSC on YouTube, 2013-07-20

[googlescholar-1] Sean Eddy publications indexed by Google Scholar

[eddyphd-2] Cite error: The named reference eddyphd was invoked but never defined (see the help page).

[3] 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.

[4] 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.

[5] 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.

[6] 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.

[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.

[encode-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.

[scopus-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

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