The DOI matches its Crossref record; 61 of the 61 references it cites were found in a registry or an index.
Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis
Open accessAbstract
Xylose is a major constituent of plant lignocellulose, and its fermentation is important for the bioconversion of plant biomass to fuels and chemicals. Pichia stipitis is a well-studied, native xylose-fermenting yeast. The mechanism and regulation of xylose metabolism in P. stipitis have been characterized and genes from P. stipitis have been used to engineer xylose metabolism in Saccharomyces cerevisiae. We have sequenced and assembled the complete genome of P. stipitis. The sequence data have revealed unusual aspects of genome organization, numerous genes for bioconversion, a preliminary insight into regulation of central metabolic pathways and several examples of colocalized genes with related functions. The genome sequence provides insight into how P. stipitis regulates its redox balance while very efficiently fermenting xylose under microaerobic conditions.
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Cites
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
Identification of common molecular subsequences
Smith, T. F., & Waterman, M. S. (1981) · Journal of Molecular Biology · doi:10.1016/0022-2836(81)90087-5 · Cited by 9,940
Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment
Ewing, B., Hillier, L., Wendl, M. C., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.175 · Cited by 6,967
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439
The KEGG resource for deciphering the genome
Kanehisa, M. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh063 · Cited by 5,104
Mauve: Multiple alignment of conserved genomic sequence with rearrangements
Darling, A. C. E., Mau, B., Blattner, F. R., & Perna, N. T. (2004) · Genome Research · doi:10.1101/gr.2289704 · Cited by 4,949
Jacob, H. E. (1988) · Bioelectrochemistry and Bioenergetics · doi:10.1016/0302-4598(88)80052-7 · Cited by 4,792
Repbase Update, a database of eukaryotic repetitive elements
Jurka, J., Kapitonov, V. V., Pavlicek, A., Klonowski, P., Kohany, O., & Walichiewicz, J. (2005) · Cytogenetic and Genome Research · doi:10.1159/000084979 · Cited by 3,370
Consed: A Graphical Tool for Sequence Finishing
Gordon, D., Abajian, C., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.195 · Cited by 3,302
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Evolution of pathogenicity and sexual reproduction in eight Candida genomes
Butler, G., Rasmussen, M. D., Lin, M. F., Santos, M. A. S., Sakthikumar, S., Munro, C. A., Rheinbay, E., Grabherr, M., Forche, A., Reedy, J. L., et al. (2009) · Nature · doi:10.1038/nature08064 · Cited by 1,065
Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus
Fedorova, N. D., Khaldi, N., Joardar, V. S., Maiti, R., Amedeo, P., Anderson, M. J., Crabtree, J., Silva, J. C., Badger, J. H., Albarraq, A., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000046 · Cited by 508
Enzymatic delignification of plant cell wall: from nature to mill
Martínez, Á. T., Ruiz-Dueñas, F. J., Martínez, M. J., del Río, J. C., & Gutiérrez, A. (2009) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2009.05.002 · Cited by 334
Fueling the future with fungal genomics
Grigoriev, I. V., Cullen, D., Goodwin, S. B., Hibbett, D., Jeffries, T. W., Kubicek, C. P., Kuske, C., Magnuson, J. K., Martin, F., Spatafora, J. W., et al. (2011) · Mycology · doi:10.1080/21501203.2011.584577 · Cited by 250
“In addition, reference genomes of mycorrhizae and other soil-inhabiting fungi also will facilitate comprehensive metagenomics studies of soil and the rhizosphere, studies which until now have been mostly limited to bacterial communities (Tringe et al. 2005).”
Self-citationYeast metabolic engineering for hemicellulosic ethanol production
Van Vleet, J., & Jeffries, T. (2009) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2009.06.001 · Cited by 241
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Metadata
- Authors
- Jeffries, T. W., Grigoriev, I. V., Grimwood, J., Laplaza, J. M., Aerts, A., Salamov, A., Schmutz, J., Lindquist, E., Dehal, P., Shapiro, H., Jin, Y.-S., Passoth, V., & Richardson, P. M.
- Venue
- Nature Biotechnology
- Published
- 2007-03
- Volume
- 25
- Issue
- 3
- Pages
- 319-326
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W1970871100
- Cited by
- 494
- References
- 61
- FWCI
- 11.97
- Type
- journal article
- Language
- en
- Open access
- hybrid
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