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Detection of genomic variation by selection of a 9 mb DNA region and high throughput sequencing.

Nikolaev SI, Iseli C, Sharp AJ, Robyr D, Rougemont J, Gehrig C, Farinelli L, Antonarakis SE.

PLoS One. 2009 Aug 17;4(8):e6659. doi: 10.1371/journal.pone.0006659.


Genomics enabled approaches in strain engineering.

Warner JR, Patnaik R, Gill RT.

Curr Opin Microbiol. 2009 Jun;12(3):223-30. doi: 10.1016/j.mib.2009.04.005. Epub 2009 May 19. Review.


Probabilistic base calling of Solexa sequencing data.

Rougemont J, Amzallag A, Iseli C, Farinelli L, Xenarios I, Naef F.

BMC Bioinformatics. 2008 Oct 13;9:431. doi: 10.1186/1471-2105-9-431.


A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.

Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB.

Nat Biotechnol. 2008 Oct;26(10):1155-60. doi: 10.1038/nbt1492.


Next-generation DNA sequencing.

Shendure J, Ji H.

Nat Biotechnol. 2008 Oct;26(10):1135-45. doi: 10.1038/nbt1486.


What would you do if you could sequence everything?

Kahvejian A, Quackenbush J, Thompson JF.

Nat Biotechnol. 2008 Oct;26(10):1125-33. doi: 10.1038/nbt1494.


Applications of next-generation sequencing technologies in functional genomics.

Morozova O, Marra MA.

Genomics. 2008 Nov;92(5):255-64. doi: 10.1016/j.ygeno.2008.07.001. Epub 2008 Aug 24. Review.


The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism.

Nookaew I, Jewett MC, Meechai A, Thammarongtham C, Laoteng K, Cheevadhanarak S, Nielsen J, Bhumiratana S.

BMC Syst Biol. 2008 Aug 7;2:71. doi: 10.1186/1752-0509-2-71.


High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies.

Srivatsan A, Han Y, Peng J, Tehranchi AK, Gibbs R, Wang JD, Chen R.

PLoS Genet. 2008 Aug 1;4(8):e1000139. doi: 10.1371/journal.pgen.1000139.


De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.

Hernandez D, François P, Farinelli L, Osterås M, Schrenzel J.

Genome Res. 2008 May;18(5):802-9. doi: 10.1101/gr.072033.107. Epub 2008 Mar 10.


YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae.

Monteiro PT, Mendes ND, Teixeira MC, d'Orey S, Tenreiro S, Mira NP, Pais H, Francisco AP, Carvalho AM, Lourenço AB, Sá-Correia I, Oliveira AL, Freitas AT.

Nucleic Acids Res. 2008 Jan;36(Database issue):D132-6. Epub 2007 Nov 21.


Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae.

Nielsen J, Jewett MC.

FEMS Yeast Res. 2008 Feb;8(1):122-31. Epub 2007 Aug 29. Review.


Production of plant sesquiterpenes in Saccharomyces cerevisiae: effect of ERG9 repression on sesquiterpene biosynthesis.

Asadollahi MA, Maury J, Møller K, Nielsen KF, Schalk M, Clark A, Nielsen J.

Biotechnol Bioeng. 2008 Feb 15;99(3):666-77.


Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains.

Schacherer J, Ruderfer DM, Gresham D, Dolinski K, Botstein D, Kruglyak L.

PLoS One. 2007 Mar 28;2(3):e322.


Expanding the metabolic engineering toolbox: more options to engineer cells.

Tyo KE, Alper HS, Stephanopoulos GN.

Trends Biotechnol. 2007 Mar;25(3):132-7. Epub 2007 Jan 24. Review.


From genomes to systems: the path with yeast.

Oliver SG.

Philos Trans R Soc Lond B Biol Sci. 2006 Mar 29;361(1467):477-82. Review.


The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae.

Teixeira MC, Monteiro P, Jain P, Tenreiro S, Fernandes AR, Mira NP, Alenquer M, Freitas AT, Oliveira AL, Sá-Correia I.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D446-51.


Microbial isoprenoid production: an example of green chemistry through metabolic engineering.

Maury J, Asadollahi MA, Møller K, Clark A, Nielsen J.

Adv Biochem Eng Biotechnol. 2005;100:19-51. Review.


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