Difference between revisions of "Dr. David W. Ussery Laboratory"
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| − | The '''Dr. David W. Ussery Laboratory''' is where I did [[:Category:Academic Research|scientific research]] from August 2005 - November 2005. | + | The '''Dr. David W. Ussery Laboratory''' is where I did [[:Category:Academic Research|scientific research]] from August 2005 - November 2005. I was also an Amanuensis (aka Teaching Assistant) for the ''Comparative Microbial Genomics'' course (Autumn 2005). |
| − | == Research topics == | + | ==Research topics== |
| − | * [ | + | *[[wikipedia:Comparative_genomics|Comparative genomics]] (microbial) |
| − | * [[Molecular Evolution (academic course)|Melecular evolution]] (microbial) | + | **CBS Archaea: |
| − | * [ | + | ***2010-08-17: '''82''' |
| − | * [[DNA Microarray Analysis (academic course)|DNA microarray analysis]] | + | ***2009-06-10: '''62''' |
| + | ***2007-08-25: '''27''' | ||
| + | **CBS Bacteria: | ||
| + | ***2010-08-17: '''1075''' | ||
| + | ***2009-06-10: '''828''' | ||
| + | ***2007-08-25: '''330 | ||
| + | **CBS Eukaryotes: | ||
| + | ***2010-08-17: '''0''' | ||
| + | ***2009-06-10: '''0''' | ||
| + | ***2007-08-25: '''13''' | ||
| + | *[[Molecular Evolution (academic course)|Melecular evolution]] (microbial) | ||
| + | *[[wikipedia:DNA_microarray|DNA microarray]] | ||
| + | *[[DNA Microarray Analysis (academic course)|DNA microarray analysis]] | ||
| − | == Results == | + | ==Results== |
| − | The research I did in this laboratory yielded a [http:// | + | The research I did in this laboratory yielded a [[Curriculum_Vitae#Publications|paper published]]<ref name=Champ2006>'''P. Christoph Champ''', Tim T. Binnewies, N. Nielsen, Guy Zinman, Kristoffer Kiil, Hang Wu, Jon Bohlin, and David W. Ussery (2006). Genome update: purine strand bias in 280 bacterial chromosomes. [http://mic.sgmjournals.org/future/152.3.shtml ''Microbiology, 152(3):579-583'']. [[http://www.hubmed.org/display.cgi?uids=16514138 HubMed]]</ref> and a Web Server: |
| − | * '''[http://www.cbs.dtu.dk/services/FD/ CBS Fungal Database]''': DNA structural atlases for complete chromosomes and genomes. | + | *'''[http://www.cbs.dtu.dk/services/FD/ CBS Fungal Database]''': DNA structural atlases for complete chromosomes and genomes. |
:: Programmer, Server architect, and administrator; November 2005-December 2005. | :: Programmer, Server architect, and administrator; November 2005-December 2005. | ||
| − | == | + | ==See also== |
| − | * '' | + | *''[[Curriculum Vitae]]'' |
| − | === Further reading === | + | |
| − | * Kellis M, Patterson N, Endrizzi M, Birren B, Lander E (2003). Sequencing and Comparison of yeast species to identify genes and regulatory motifs. ''Nature | + | ==References== |
| − | * Cliften P, Sudarsanam P, Desikan A (2003). Finding functional features in Saccharomyces genomes by phylogenetic footprinting. ''Science | + | <references/> |
| − | * Bofffeli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, Rubin EM (2003). Phylogenetic shadowing of primate sequences to find functional regions of the human genome, ''Science | + | ===Further reading=== |
| − | * Dujon B, ''et al.'' (2004). Genome evolution in yeasts. ''Nature | + | *Kellis M, Patterson N, Endrizzi M, Birren B, Lander E (2003). Sequencing and Comparison of yeast species to identify genes and regulatory motifs. ''Nature, pp. 241-254''. |
| − | * Filipski A, Kumar S (2005). Comparative genomics in eukaryotes. ''The Evolution of the Genome (ed. T.R. Gregory), pp. 521-583. Elsevier, San Diego. | + | *Cliften P, Sudarsanam P, Desikan A (2003). Finding functional features in Saccharomyces genomes by phylogenetic footprinting. ''Science, pp. 71-76''. |
| − | * Gregory TR, DeSalle R (2005). Comparative genomics in prokaryotes. ''The Evolution of the Genome | + | *Bofffeli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, Rubin EM (2003). Phylogenetic shadowing of primate sequences to find functional regions of the human genome, ''Science, 299(5611):1391-1394''. |
| − | * Hardison RC. Comparative genomics. ''PLoS biology | + | *Dujon B, ''et al.'' (2004). Genome evolution in yeasts. ''Nature, 430:35-44''. |
| + | *Filipski A, Kumar S (2005). Comparative genomics in eukaryotes. ''The Evolution of the Genome (ed. T.R. Gregory), pp. 521-583. Elsevier, San Diego''. | ||
| + | *Gregory TR, DeSalle R (2005). Comparative genomics in prokaryotes. ''The Evolution of the Genome (ed. T.R. Gregory), pp. 585-675. Elsevier, San Diego''. | ||
| + | *Hardison RC. Comparative genomics. ''PLoS biology, 1(2):e58''. | ||
| + | |||
| + | ==External links== | ||
| + | *[ftp://ftp.sanger.ac.uk/pub/databases/Pfam/database_files/ Pfam database files] (ftp) | ||
| + | *[http://www.sanger.ac.uk/Software/Pfam/help/rdb_doc.shtml Pfam MySQL database documentation] | ||
| + | *[http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome&cmd=Retrieve&dopt=Overview&list_uids=142 ''Aeropyrum pernix'' K1, complete genome] — example NCBI genome result | ||
[[Category:Academic Research]] | [[Category:Academic Research]] | ||
Latest revision as of 03:37, 27 December 2012
The Dr. David W. Ussery Laboratory is where I did scientific research from August 2005 - November 2005. I was also an Amanuensis (aka Teaching Assistant) for the Comparative Microbial Genomics course (Autumn 2005).
Research topics
- Comparative genomics (microbial)
- CBS Archaea:
- 2010-08-17: 82
- 2009-06-10: 62
- 2007-08-25: 27
- CBS Bacteria:
- 2010-08-17: 1075
- 2009-06-10: 828
- 2007-08-25: 330
- CBS Eukaryotes:
- 2010-08-17: 0
- 2009-06-10: 0
- 2007-08-25: 13
- CBS Archaea:
- Melecular evolution (microbial)
- DNA microarray
- DNA microarray analysis
Results
The research I did in this laboratory yielded a paper published[1] and a Web Server:
- CBS Fungal Database: DNA structural atlases for complete chromosomes and genomes.
- Programmer, Server architect, and administrator; November 2005-December 2005.
See also
References
- ↑ P. Christoph Champ, Tim T. Binnewies, N. Nielsen, Guy Zinman, Kristoffer Kiil, Hang Wu, Jon Bohlin, and David W. Ussery (2006). Genome update: purine strand bias in 280 bacterial chromosomes. Microbiology, 152(3):579-583. [HubMed]
Further reading
- Kellis M, Patterson N, Endrizzi M, Birren B, Lander E (2003). Sequencing and Comparison of yeast species to identify genes and regulatory motifs. Nature, pp. 241-254.
- Cliften P, Sudarsanam P, Desikan A (2003). Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science, pp. 71-76.
- Bofffeli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, Rubin EM (2003). Phylogenetic shadowing of primate sequences to find functional regions of the human genome, Science, 299(5611):1391-1394.
- Dujon B, et al. (2004). Genome evolution in yeasts. Nature, 430:35-44.
- Filipski A, Kumar S (2005). Comparative genomics in eukaryotes. The Evolution of the Genome (ed. T.R. Gregory), pp. 521-583. Elsevier, San Diego.
- Gregory TR, DeSalle R (2005). Comparative genomics in prokaryotes. The Evolution of the Genome (ed. T.R. Gregory), pp. 585-675. Elsevier, San Diego.
- Hardison RC. Comparative genomics. PLoS biology, 1(2):e58.
External links
- Pfam database files (ftp)
- Pfam MySQL database documentation
- Aeropyrum pernix K1, complete genome — example NCBI genome result
