next up previous contents
Next: About this document ... Up: Thesis Title Page Previous: Conclusions

Bibliography

Altschul et al., 1990
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990).
Basic local alignment search tool.
J. Mol. Biol., 215, 403-410.

Altschul et al., 1997
Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997).
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs.
Nucl. Acids Res., 25, 3389-3402.
Available at http://www.ncbi.nlm.nih.gov/BLAST/.

Amiri, 1994
Amiri, K. (1994).
Fibrillarin-like proteins occur in the domain Archaea.
J Bacteriol, 176, 2124-7.

Bachellerie & Cavaille, 1997
Bachellerie, J. & Cavaille, J. (1997).
Guiding ribose methylation of rRNA.
Trends Biochem Sci, 22, 257-61.

Bachellerie & Cavaille, 1998
Bachellerie, J. & Cavaille, J. (1998).
Small nucleolar RNAs guide the ribose methylations of eukaryotic rRNAs.
In H. Grosjean & R. Benne (Eds.), Modification and Editing of RNA (pp. 255-272). ASM Press.

Bachellerie et al., 1995
Bachellerie, J.-P., Michot, B., Nicoloso, M., Balakin, A., Ni, J., & Fournier, M. J. (1995).
Antisense snoRNAs: A family of nucleolar RNAs with long complementarities to rRNA.
Trends Biochem. Sci., 20, 261-264.

Bakin & Ofengand, 1995
Bakin, A. & Ofengand, J. (1995).
Mapping of the 13 pseudouridine residues in Saccharomyces cerevisiae small subunit ribosomal RNA to nucleotide resolution.
Nucl. Acids Res., 23, 3290-3294.

Balakin et al., 1996
Balakin, A., Smith, L., & Fournier, M. (1996).
The RNA world of the nucleolus: two major families of small RNAs defined by different box elements with related functions.
Cell, 86, 823-34.

Barrett et al., 1997
Barrett, C., Hughey, R., & Karplus, K. (1997).
Scoring hidden Markov models.
Comput. Applic. Biosci., 13, 191-199.

Baudin et al., 1993
Baudin, A., Ozier-Kalogeropoulos, O., Denouel, A., Lacroute, F., & Cullin, C. (1993).
A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae.
Nucleic Acids Res, 21, 3329-30.

Beltrame & Tollervey, 1995
Beltrame, M. & Tollervey, D. (1995).
Base pairing between U3 and the pre-ribosomal RNA is required for 18S rRNA synthesis.
EMBO J, 14, 4350-6.

Bennetzen & Hall, 1982
Bennetzen, J. & Hall, B. (1982).
Codon selection in yeast.
J Biol Chem, 257, 3026-31.

Benson et al., 1999
Benson, D., Boguski, M., Lipman, D., Ostell, J., Ouellette, B., Rapp, B., & Wheeler, D. (1999).
Genbank.
Nucleic Acids Res, 27, 12-7.

Billoud et al., 1996
Billoud, B., Kontic, M., & Viari, A. (1996).
Palingol: a declarative programming language to describe nucleic acids' secondary structures and to scan sequence database.
Nucleic Acids Res, 24, 1395-403.

Blattner et al., 1997
Blattner, F. R., Plunkett, G., Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., Gregor, J., Davis, N. W., Kirkpatrick, H. A., Goeden, M. A., Rose, D. J., Mau, B., & Shao, Y. (1997).
The complete genome sequence of Escherichia coli K-12.
Science, 277, 1453-1462.

Boguski et al., 1993
Boguski, M., Lowe, T., & Tolstoshev, C. (1993).
dbEST - database for expressed sequence tags.
Nature Genet., 4, 332-333.

Brannan et al., 1990
Brannan, C. I., Dees, E. C., Ingram, R. S., & Tilghman, S. H. (1990).
The product of the H19 gene may function as an RNA.
Mol. Cell. Biol., 10, 28-36.

Brockdorff et al., 1992
Brockdorff, N., Ashworth, A., Kay, G. F., McCabe, V. M., Norris, D. P., Cooper, P. J., Swift, S., & Rastan, S. (1992).
The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus.
Cell, 71, 515-526.

Brown et al., 1992
Brown, C. J., Hendrich, B. D., Rupert, J. L., Lafreniere, R. G., Xing, Y., Lawrence, J., & Willard, H. F. (1992).
The human Xist gene: Analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus.
Cell, 71, 527-542.

Brown, 1999
Brown, J. (1999).
The Ribonuclease P database.
Nucleic Acids Res, 27, 314.
Available at http://www.mbio.ncsu.edu/RNaseP/home.html.

Bult et al., 1996
Bult, C. J., White, O., Olsen, G. J., Zhou, L., Fleischmann, R. D., Sutton, G. G., Borodovsky, M., Klenk, H.-P., Fraser, C. M., Smith, H. O., Woese, C. R., Venter, J. C., et al. (1996).
Complete genome sequence of the methanogenic Archaeon, Methanococcus jannaschii.
Science, 273, 1058-1073.
Current annotation at http://www.tigr.org/tdb/.

Burge & Karlin, 1997
Burge, C. & Karlin, S. (1997).
Prediction of complete gene structures in human genomic DNA.
J Mol Biol, 268, 78-94.

Caffarelli et al., 1998
Caffarelli, E., Losito, M., Giorgi, C., Fatica, A., & Bozzoni, I. (1998).
In vivo identification of nuclear factors interacting with the conserved elements of box C/D small nucleolar RNAs.
Mol Cell Biol, 18, 1023-8.

Cavaille & Bachellerie, 1998
Cavaille, J. & Bachellerie, J. (1998).
SnoRNA-guided ribose methylation of rRNA: structural features of the guide RNA duplex influencing the extent of the reaction.
Nucleic Acids Res, 26, 1576-87.

Cavaille et al., 1996
Cavaille, J., Nicoloso, M., & Bachellerie, J. (1996).
Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides.
Nature, 383, 732-5.

C. elegans Sequencing Consortium, 1998
C. elegans Sequencing Consortium (1998).
Genome sequence of the nematode C. elegans: a platform for investigating biology.
Science, 282, 2012-8.

Chamberlain et al., 1998
Chamberlain, J., Lee, Y., Lane, W., & Engelke, D. (1998).
Purification and characterization of the nuclear RNAse P holoenzyme complex reveals extensive subunit overlap with RNAse MRP.
Genes Dev, 12, 1678-90.

Chanfreau et al., 1998a
Chanfreau, G., Legrain, P., & Jacquier, A. (1998a).
Yeast RNAse III as a key processing enzyme in small nucleolar RNAs metabolism.
J Mol Biol, 284, 975-88.

Chanfreau et al., 1998b
Chanfreau, G., Rotondo, G., Legrain, P., & Jacquier, A. (1998b).
Processing of a dicistronic small nucleolar RNA precursor by the RNA endonuclease Rnt1.
EMBO J, 17, 3726-37.

Crick, 1966
Crick, F. (1966).
Codon-anticodon pairing: the wobble hypothesis.
J Mol Biol, 19, 548-55.

Dandekar & Hentze, 1995
Dandekar, T. & Hentze, M. W. (1995).
Finding the hairpin in the haystack: Searching for RNA motifs.
Trends Genet., 11, 45-50.

Daniels & Deininger, 1985
Daniels, G. R. & Deininger, P. L. (1985).
Repeat sequence families derived from mammalian tRNA genes.
Nature, 317, 819-822.

Deininger, 1989
Deininger, P. L. (1989).
SINEs: Short interspersed repeated DNA elements in higher eucaryotes.
In D. E. Berg & M. M. Howe (Eds.), Mobile DNA. American Society for Microbiology.

Dong et al., 1996
Dong, H., Nilsson, L., & Kurland, C. (1996).
Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates.
J Mol Biol, 260, 649-63.

Dunbar & Baserga, 1998
Dunbar, D. & Baserga, S. (1998).
The U14 snoRNA is required for 2'-O-methylation of the pre-18S rRNA in Xenopus oocytes.
RNA, 4, 195-204.

Dunbar et al., 1999
Dunbar, D., Wormsley, S., Lowe, T., & Baserga, S. (1999).
Fibrillarin-associated box C/D snoRNAs in Trypanosoma brucei: sequence conservation and implications for 2'-O-ribose methylation of rRNA.
Submitted.

Durbin et al., 1998
Durbin, R., Eddy, S. R., Krogh, A., & Mitchison, G. J. (1998).
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids.
Cambridge UK: Cambridge University Press.

Eddy, 1996
Eddy, S. R. (1996).
Hidden Markov models.
Curr. Opin. Struct. Biol., 6, 361-365.

Eddy & Durbin, 1994
Eddy, S. R. & Durbin, R. (1994).
RNA sequence analysis using covariance models.
Nucl. Acids Res., 22, 2079-2088.
COVE software available at http://www.genetics.wustl.edu/eddy/software/.

El-Mabrouk & Lisacek, 1996
El-Mabrouk, N. & Lisacek, F. (1996).
Very fast identification of RNA motifs in genomics DNA. application to tRNA search in the yeast genome.
J. Mol. Biol., (pp. 46-55).

Fichant & Burks, 1991
Fichant, G. A. & Burks, C. (1991).
Identifying potential tRNA genes in genomic DNA sequences.
J. Mol. Biol., 220, 659-671.

Fleischmann et al., 1995
Fleischmann, R., Adams, M., White, O., Clayton, R., Kirkness, E., Kerlavage, A., Bult, C., et al. (1995).
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.
Science, 269, 496-512.
Current annotation at http://www.tigr.org/tdb/.

Fraser et al., 1995
Fraser, C., Gocayne, J., White, O., Adams, M., Clayton, R., Fleischmann, R., Bult, C., Kerlavage, A., Sutton, G., Kelley, J., Fritchman, J., Weidman, J., Small, K., Sandusky, M., Fuhrmann, J., Nguyen, D., Utterback, T., Saudek, D., Phillips, C., Merrick, J., Tomb, J.-F., Dougherty, D., Bott, K., Hu, P.-C., Lucier, T., Peterson, S., Smith, H., Hutchison, C., & Venter, J. (1995).
The minimal gene complement of Mycoplasma genitalium.
Science, 270, 397-403.
Current annotation at http://www.tigr.org/tdb/.

Gannot et al., 1997
Gannot, P., Bortolin, M.-L., & Kiss, T. (1997).
Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs.
Cell, 89, 799-809.

Gautheret et al., 1990
Gautheret, D., Major, F., & Cedergren, R. (1990).
Pattern searching/alignment with RNA primary and secondary structures: An effective descriptor for tRNA.
Comput. Applic. Biosci., 6, 325-331.

Gautier et al., 1997
Gautier, T., Berges, T., Tollervey, D., & Hurt, E. (1997).
Nucleolar KKE/D repeat proteins Nop56p and Nop58p interact with Nop1p and are required for ribosome biogenesis.
Mol Cell Biol, 17, 7088-98.

Gish, 1998
Gish, W. (1998).
WU-BLAST.
Available from http://blast.wustl.edu/.

Goffeau et al., 1996
Goffeau, A., Barrell, B. G., Bussey, H., Davis, R. W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J. D., Jacq, C., Johnston, M., Louis, E. J., Mewes, H. W., Murakami, Y., Philippsen, P., Tettelin, H., & Oliver, S. G. (1996).
Life with 6000 genes.
Science, 274, 546-567.

Grate, 1995
Grate, L. (1995).
Automatic RNA secondary structure determination with stochastic context-free grammars.
In C. Rawlings & others (Eds.), Proc. Third Int. Conf. on Intelligent Systems in Molecular Biology (pp. 136-144). Menlo Park, California: AAAI Press.

Green & Vold, 1993
Green, C. & Vold, B. (1993).
Staphylococcus aureus has clustered tRNA genes.
J Bacteriol, 175, 5091-6.

Greenwood et al., 1996
Greenwood, S., Schnare, M., & Gray, M. (1996).
Molecular characterization of U3 small nucleolar RNA from the early diverging protist, Euglena gracilis.
Curr Genet, 30, 338-46.

Gribskov, 1994
Gribskov, M. (1994).
Profile analysis.
In A. Griffin & H. Griffin (Eds.), Methods in Molecular Biology: Computer Analysis of Sequence Data Part II (pp. 247-267). Totowa NJ: Humana Press.

Gribskov et al., 1990
Gribskov, M., Luthy, R., & Eisenberg, D. (1990).
Profile analysis.
Meth. Enzymol., 183, 146-159.

Gutell, 1994
Gutell, R. (1994).
Collection of small subunit (16S- and 16S-like) ribosomal RNA structures: 1994.
Nucl. Acids Res., 22, 3502-3507.

Gutell et al., 1993
Gutell, R., Gray, M., & Schnare, M. (1993).
A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993.
Nucleic Acids Res, 21, 3055-74.

Gutell, 1993
Gutell, R. R. (1993).
Collection of small subunit (16S and 16S-like) ribosomal RNA structures.
NAR, 21, 3051-3054.

Guthrie & Abelson, 1982
Guthrie, C. & Abelson, J. (1982).
Organization and expression of tRNA genes in Saccharomyces cerevisiae.
In J. Strathern, E. Jones, & J. Broach (Eds.), The Molecular Biology of the Yeast Saccharomyces: Metabolism and Gene Expression. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory.

Guthrie & Patterson, 1988
Guthrie, C. & Patterson, B. (1988).
Spliceosomal snRNAs.
Ann. Rev. Genet., 22, 387-419.

Hadjiolov, 1985
Hadjiolov, A. (1985).
The Nucleolus and Ribosome Biogenesis.
New York: Springer-Verlag.

Hani & Feldmann, 1998
Hani, J. & Feldmann, H. (1998).
tRNA genes and retroelements in the yeast genome.
Nucleic Acids Res, 26, 689-96.

Hatlen & Attardi, 1971
Hatlen, L. & Attardi, G. (1971).
Proportion of HeLa cell genome complementary to transfer RNA and 5S RNA.
J Mol Biol, 56, 535-53.

Hayes & Borodovsky, 1998
Hayes, W. & Borodovsky, M. (1998).
How to interpret an anonymous bacterial genome: machine learning approach to gene identification.
Genome Res, 8, 1154-71.

Henras et al., 1998
Henras, A., Henry, Y., Bousquet-Antonelli, C., Noaillac-Depeyre, J., Gelugne, J., & Caizergues-Ferrer, M. (1998).
Nhp2p and Nop10p are essential for the function of H/ACA snoRNPs.
EMBO J, 17, 7078-90.

Higgins et al., 1992
Higgins, D., Bleasby, A., & Fuchs, R. (1992).
ClustalV: Improved software for multiple sequence alignment.
Comput. Applic. Biosci., 8, 189-191.

Ikemura, 1982
Ikemura, T. (1982).
Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs.
J Mol Biol, 158, 573-97.

Jarmolowski et al., 1990
Jarmolowski, A., Zagorski, J., Li, H., & Fournier, M. (1990).
Identification of essential elements in U14 RNA of Saccharomyces cerevisiae.
EMBO J, 9, 4503-9.

Johnson & Abelson, 1983
Johnson, P. & Abelson, J. (1983).
The yeast tRNA-Tyr gene intron is essential for correct modification of its tRNA product.
Nature, 302, 681-7.

Kano et al., 1993
Kano, A., Ohama, T., Abe, R., & Osawa, S. (1993).
Unassigned or nonsense codons in Micrococcus luteus.
J Mol Biol, 230, 51-6.

Keeney et al., 1995
Keeney, J. B., Chapman, K. B., Lauermann, V., Voytas, D. F., Astrom, S. U., von Pawel-Rammingen, U., Bystrom, A., & Boeke, J. D. (1995).
Multiple molecular determinants for retrotransposition in a primer tRNA.
Mol. Cell. Biol., 15, 217-226.

Kiss-Laszlo et al., 1996
Kiss-Laszlo, Z., Henry, Y., Bachellerie, J., Caizergues-Ferrer, M., & Kiss, T. (1996).
Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs.
Cell, 85, 1077-88.

Kiss-Laszlo et al., 1998
Kiss-Laszlo, Z., Henry, Y., & Kiss, T. (1998).
Sequence and structural elements of methylation guide snoRNAs essential for site-specific ribose methylation of pre-rRNA.
EMBO J, 17, 797-807.

Klootwijk & Planta, 1973
Klootwijk, J. & Planta, R. J. (1973).
Analysis of the methylation sites in yeast ribosomal RNA.
Eur. J. Biochem., 39, 325-333.

Krogh et al., 1994
Krogh, A., Brown, M., Mian, I. S., Sjolander, K., & Haussler, D. (1994).
Hidden Markov models in computational biology: Applications to protein modeling.
J. Mol. Biol., 235, 1501-1531.

Krzyzosiak et al., 1987
Krzyzosiak, W., Denman, R., Nurse, K., Hellmann, W., Boublik, M., Gehrke, C., Agris, P., & Ofengand, J. (1987).
In vitro synthesis of 16S ribosomal RNA containing single base changes and assembly into a functional 30S ribosome.
Biochemistry, 26, 2353-64.

Laferriere et al., 1994
Laferriere, A., Gautheret, D., & Cedergren, R. (1994).
An RNA pattern matching program with enhanced performance and portability.
Comput Appl Biosci, 10, 211-2.

Lafontaine & Tollervey, 1998
Lafontaine, D. & Tollervey, D. (1998).
Birth of the snoRNPs: the evolution of the modification-guide snoRNAs.
Trends Biochem Sci, 23, 383-8.

Leader et al., 1997
Leader, D., Clark, G., Watters, J., Beven, A., Shaw, P., & Brown, J. (1997).
Clusters of multiple different small nucleolar RNA genes in plants are expressed as and processed from polycistronic pre-snoRNAs.
EMBO J, 16, 5742-51.

Levitan et al., 1998
Levitan, A., Xu, Y., Ben-Dov, C., Ben-Shlomo, H., Zhang, Y., & Michaeli, S. (1998).
Characterization of a novel trypanosomatid small nucleolar RNA.
Nucleic Acids Res, 26, 1775-83.

Liang & Fournier, 1995
Liang, W. & Fournier, M. (1995).
U14 base-pairs with 18S rRNA: a novel snoRNA interaction required for rRNA processing.
Genes Dev, 9, 2433-43.

Lisacek et al., 1994
Lisacek, F., Diaz, Y., & Michel, F. (1994).
Automatic identification of group I intron cores in genomic DNA sequences.
J. Mol. Biol., 235, 1206-1217.

Lowe & Eddy, 1999
Lowe, T. & Eddy, S. (1999).
A computational screen for methylation guide snoRNAs in yeast.
Science, 283, 1168-71.

Lowe & Eddy, 1997
Lowe, T. M. & Eddy, S. R. (1997).
tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence.
Nucl. Acids Res., 25, 955-964.

Lowe & Eddy, 1998
Lowe, T. M. & Eddy, S. R. (1998).
The Eddy Lab snoRNA Database.
Available at http://rna.wustl.edu/snoRNAdb/.

Maden & Hughes, 1997
Maden, B. & Hughes, J. (1997).
Eukaryotic ribosomal RNA: the recent excitement in the nucleotide modification problem.
Chromosoma, 105, 391-400.

Maden, 1990
Maden, B. E. H. (1990).
The numerous modified nucleotides in eukaryotic ribosomal RNA.
Prog. Nucl. Acids Res. Mol. Biol., 39, 241-303.

Maden et al., 1995
Maden, B. E. H., Corbett, M. E., Heeney, P. A., Pugh, K., & Ajuh, P. M. (1995).
Classical and novel approaches to the detection and localization of the numerous modified nucleotides in eukaryotic ribosomal RNA.
Biochimie, 77, 22-29.

Marvel, 1986
Marvel, C. C. (1986).
A program for the identification of tRNA-like structures in DNA sequence data.
Nucl. Acids Res., 14, 431-435.

Mattaj et al., 1993
Mattaj, I., Tollervey, D., & Seraphin, B. (1993).
Small nuclear RNAs in messenger RNA and ribosomal RNA processing.
FASEB J, 7, 47-53.

Mattaj, 1993
Mattaj, I. W. (1993).
RNA recognition: A family matter?
Cell, 73, 837-840.

Maxwell & Fournier, 1995
Maxwell, E. & Fournier, M. (1995).
The small nucleolar RNAs.
Annu Rev Biochem, 6, 897-934.

Mizuta et al., 1995
Mizuta, K., Hashimoto, T., & Otaka, E. (1995).
The evolutionary relationships between homologs of ribosomal YL8 protein and YL8-like proteins.
Curr Genet, 28, 19-25.

Ni, 1998
Ni, J. (1998).
The Major Function of Eukaryotic Small Nucleolar RNAs is Nucleotide Modification in Ribosomal RNA.
PhD thesis, University of Massachusetts, Amherst.

Ni et al., 1997
Ni, J., Tien, A., & Fournier, M. (1997).
Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA.
Cell, 89, 565-73.

Nicoloso et al., 1994
Nicoloso, M., Caizergues-Ferrer, M., Michot, B., Azum, M., & Bachellerie, J. (1994).
U20, a novel small nucleolar RNA, is encoded in an intron of the nucleolin gene in mammals.
Mol Cell Biol, 14, 5766-76.

Nicoloso et al., 1996
Nicoloso, M., Qu, L., Michot, B., & Bachellerie, J. (1996).
Intron-encoded, antisense small nucleolar RNAs: the characterization of nine novel species points to their direct role as guides for the 2'-O-ribose methylation of rRNAs.
J Mol Biol, 260, 178-95.

Noon et al., 1998
Noon, K. R., Bruenger, E., & McCloskey, J. A. (1998).
Posttranscriptional modifications in 16S and 23S rRNAs of the Archaeal hyperthermophile Sulfolobus solfataricus.
J. Bacteriol., 180, 2883-2888.

Oba et al., 1991
Oba, T., Andachi, Y., Muto, A., & Osawa, S. (1991).
CGG: an unassigned or nonsense codon in Mycoplasma capricolum.
Proc Natl Acad Sci U S A, 88, 921-5.

Ofengand & Fournier, 1998
Ofengand, J. & Fournier, M. (1998).
The pseudouridine residues of rRNA: Number, location, biosynthesis, and function.
In H. Grosjean & R. Benne (Eds.), Modification and Editing of RNA (pp. 229-254). ASM Press.

Paolella & Russo, 1985
Paolella, G. & Russo, T. (1985).
A microcomputer program for the identification of tRNA genes.
Comput Appl Biosci, 1, 149-51.

Parker et al., 1988
Parker, R., Simmons, T., Shuster, E., Siliciano, P., & Guthrie, C. (1988).
Genetic analysis of small nuclear RNAs in Saccharomyces cerevisiae: viable sextuple mutant.
Mol Cell Biol, 8, 3150-9.

Pavesi et al., 1994
Pavesi, A., Conterlo, F., Bolchi, A., Dieci, G., & Ottonello, S. (1994).
Identification of new eukaryotic tRNA genes in genomic DNA databases by a multistep weight matrix analysis of transcriptional control regions.
Nucl. Acids Res., 22, 1247-1256.

Pearson & Lipman, 1988
Pearson, W. & Lipman, D. (1988).
Improved tools for biological sequence comparison.
Proc Natl Acad Sci U S A, 85, 2444-8.

Percudani et al., 1997
Percudani, R., Pavesi, A., & Ottonello, S. (1997).
Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae.
J Mol Biol, 268, 322-30.

Petfalski et al., 1998
Petfalski, E., Dandekar, T., Henry, Y., & Tollervey, D. (1998).
Processing of the precursors to small nucleolar RNAs and rRNAs requires common components.
Mol Cell Biol, 18, 1181-9.

Planta & Mager, 1998
Planta, R. & Mager, W. (1998).
The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae.
Yeast, 14, 471-7.

Qu et al., 1999
Qu, L., Henras, A., Lu, Y., Zhou, H., Zhou, W., Zhu, Y., Zhao, J., Henry, Y., Caizergues-Ferrer, M., & Bachellerie, J. (1999).
Seven novel methylation guide small nucleolar RNAs are processed from a common polycistronic transcript by Rat1p and RNase III in yeast.
Mol Cell Biol, 19, 1144-58.

Raue et al., 1988
Raue, H., Klootwijk, J., & Musters, W. (1988).
Evolutionary conservation of structure and function of high molecular weight ribosomal RNA.
Prog Biophys Mol Biol, 51, 77-129.

Reynolds, 1995
Reynolds, W. (1995).
Developmental stage-specific regulation of Xenopus tRNA genes by an upstream promoter element.
J Biol Chem, 270, 10703-10.

Rice et al., 1993
Rice, C. M., Fuchs, R., Higgins, D. G., Stoehr, P. J., & Cameron, G. N. (1993).
The EMBL data library.
Nucl. Acids Res., 21, 2967-2971.

Riedel et al., 1986
Riedel, N., Wise, J., Swerdlow, H., Mak, A., & Guthrie, C. (1986).
Small nuclear RNAs from Saccharomyces cerevisiae: unexpected diversity in abundance, size, and molecular complexity.
Proc Natl Acad Sci U S A, 83, 8097-101.

Roberts et al., 1998
Roberts, T., Sturm, N., Yee, B., Yu, M., Hartshorne, T., Agabian, N., & Campbell, D. (1998).
Three small nucleolar RNAs identified from the spliced leader-associated RNA locus in kinetoplastid protozoans.
Mol Cell Biol, 18, 4409-17.

Sakakibara et al., 1994a
Sakakibara, Y., Brown, M., Hughey, R., Mian, I. S., Sjolander, K., Underwood, R. C., & Haussler, D. (1994a).
Stochastic context-free grammars for tRNA modeling.
Nucl. Acids Res., 22, 5112-5120.

Sakakibara et al., 1994b
Sakakibara, Y., Brown, M., Underwood, R. C., Mian, I. S., & Haussler, D. (1994b).
Stochastic context-free grammars for modeling RNA.
In L. Hunter (Ed.), Proceedings of the Twenty-Seventh Annual Hawaii International Conference on System Sciences: Biotechnology Computing, volume V (pp. 284-293). Los Alamitos, CA: IEEE Computer Society Press.

Salzberg et al., 1998
Salzberg, S., Delcher, A., Kasif, S., & White, O. (1998).
Microbial gene identification using interpolated markov models.
Nucleic Acids Res, 26, 544-8.

Samarsky & Fournier, 1999
Samarsky, D. & Fournier, M. (1999).
A comprehensive database for the small nucleolar RNAs from Saccharomyces cerevisiae.
Nucleic Acids Res, 27, 161-164.
Available from
http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA _DataBase.html.

Saurin & Marliere, 1987
Saurin, W. & Marliere, P. (1987).
Matching relational patterns in nucleic acid sequences.
Comput. Applic. Biosci., 3, 115-120.

Schiestl et al., 1993
Schiestl, R., Manivasakam, P., Woods, R., & Gietz, R. (1993).
Introducing DNA into yeast by transformation.
Methods, 4, 79-85.

Sharp et al., 1993
Sharp, P., Stenico, M., Peden, J., & Lloyd, A. (1993).
Codon usage: mutational bias, translational selection, or both?
Biochem Soc Trans, 21, 835-41.

Shaw et al., 1998
Shaw, P., Beven, A., Leader, D., & Brown, J. (1998).
Localization and processing from a polycistronic precursor of novel snoRNAs in maize.
J Cell Sci, 111, 2121-8.

Shortridge et al., 1986
Shortridge, R., Pirtle, I., & Pirtle, R. (1986).
IBM microcomputer programs that analyze DNA sequences for tRNA genes.
Comput Appl Biosci, 2, 13-7.

Sibbald et al., 1992
Sibbald, P., Sommerfeldt, H., & Argos, P. (1992).
Overseer: a nucleotide sequence searching tool.
Comput Appl Biosci, 8, 45-8.

Smith & Steitz, 1997
Smith, C. M. & Steitz, J. A. (1997).
Sno storm in the nucleolus: New roles for myriad small RNPs.
Cell, 89, 669-672.

Smith et al., 1997
Smith, D. R., Doucette-Stamm, L. A., Deloughery, C., Lee, H., Dubois, J., Aldredge, T., Bashirzadeh, R., Blakely, D., Cook, R., Gilbert, K., Harrison, D., Hoang, L., Keagle, P., Lumm, W., Pothier, B., Qiu, D., Spadafora, R., Vicaire, R., Wang, Y., Wierzbowski, J., Gibson, R., Jiwani, N., Caruso, A., Bush, D., Safer, H., Patwell, D., Prabhakar, S., McDougall, S., Shimer, G., Goyal, A., Pietrokovski, S., Church, G. M., Daniels, C. J., Mao, J., Rice, P., Nolling, J., & Reeve, J. N. (1997).
Complete genome sequence of Methanobacterium thermoautotrophicum $\Delta$H: Functional analysis and comparative genomics.
J Bacteriol., 179, 7135-7155.

Staden, 1980
Staden, R. (1980).
A computer program to search for tRNA genes.
Nucl. Acids Res., 8, 817-825.

Staden, 1988
Staden, R. (1988).
Methods to define and locate patterns of motifs in sequences.
Comput. Applic. Biosci., 4(1), 53-60.

Steinberg et al., 1993
Steinberg, S., Misch, A., & Sprinzl, M. (1993).
Compilation of tRNA sequences and sequences of tRNA genes.
Nucl. Acids Res., 21, 3011-3015.
Database available at http://www.uni-bayreuth.de/departments/biochemie/trna/.

Stenico et al., 1994
Stenico, M., Lloyd, A., & Sharp, P. (1994).
Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases.
Nucleic Acids Res, 22, 2437-46.

Strobel & Abelson, 1986
Strobel, M. & Abelson, J. (1986).
Effect of intron mutations on processing and function of Saccharomyces cerevisiae SUP53 tRNA in vitro and in vivo.
Mol Cell Biol, 6, 2663-73.

Tateno & Gojobori, 1997
Tateno, Y. & Gojobori, T. (1997).
DNA Data Bank of Japan in the age of information biology.
Nucleic Acids Res, 25, 14-7.

Tollervey & Kiss, 1997
Tollervey, D. & Kiss, T. (1997).
Function and synthesis of small nucleolar RNAs.
Curr Opin Cell Biol, 9, 337-42.

Tollervey et al., 1991
Tollervey, D., Lehtonen, H., Carmo-Fonseca, M., & Hurt, E. (1991).
The small nucleolar RNP protein NOP1 (fibrillarin) is required for pre-rRNA processing in yeast.
EMBO J, 10, 573-83.

Tollervey et al., 1993
Tollervey, D., Lehtonen, H., Jansen, R., Kern, H., & Hurt, E. C. (1993).
Temperature-sensitive mutations demonstrate roles for yeast fibrillarin in pre-rRNA processing, pre-rRNA methylation, and ribosome assembly.
Cell, 72, 443-457.

Tranquilla et al., 1982
Tranquilla, T., Cortese, R., Melton, D., & Smith, J. (1982).
Sequences of four tRNA genes from Caenorhabditis elegans and the expression of C. elegans tRNALeu (anticodon IAG) in Xenopus oocytes.
Nucleic Acids Res, 10, 7919-34.

Tycowski et al., 1996
Tycowski, K., Smith, C., Shu, M., & Steitz, J. (1996).
A small nucleolar RNA requirement for site-specific ribose methylation of rRNA in Xenopus.
Proc Natl Acad Sci U S A, 93, 14480-5.

Tycowski et al., 1998
Tycowski, K., You, Z., Graham, P., & Steitz, J. (1998).
Modification of U6 spliceosomal RNA is guided by other small RNAs.
Mol Cell, 2, 629-38.

Veldman et al., 1981
Veldman, G., Klootwijk, J., de Regt, V., Planta, R., Branlant, C., Krol, A., & Ebel, J. (1981).
The primary and secondary structure of yeast 26S rRNA.
Nucleic Acids Res, 9, 6935-52.

Watkins et al., 1998a
Watkins, N., Gottschalk, A., Neubauer, G., Kastner, B., Fabrizio, P., Mann, M., & Luhrmann, R. (1998a).
Cbf5p, a potential pseudouridine synthase, and Nhp2p, a putative RNA-binding protein, are present together with Gar1p in all H box/ACA-motif snoRNPs and constitute a common bipartite structure.
RNA, 4, 1549-68.

Watkins et al., 1998b
Watkins, N., Newman, D., Kuhn, J., & Maxwell, E. (1998b).
In vitro assembly of the mouse U14 snoRNP core complex and identification of a 65-kDa box C/D-binding protein.
RNA, 4, 582-93.

Weinstein & Steitz, 1999
Weinstein, L. & Steitz, J. (1999).
Guided tours: from precursor snoRNA to functional snoRNP.
Curr Opin Cell Biol, 11, 378-84.

Westaway & Abelson, 1995
Westaway, S. & Abelson, J. (1995).
Splicing of tRNA precursors.
In D. Soll & U. L. RajBhandary (Eds.), tRNA: Structure, Biosynthesis, and Function (pp. 79-92). ASM Press.

Wheelan & Boguski, 1998
Wheelan, S. J. & Boguski, M. S. (1998).
Late-night thoughts on the sequence annotation problem.
Genome Res., 8, 168-169.

Wilson et al., 1985
Wilson, E., Larson, D., Young, L., & Sprague, K. (1985).
A large region controls tRNA gene transcription.
J Mol Biol, 183, 153-63.

Woese et al., 1990
Woese, C., Kandler, O., & Wheelis, M. (1990).
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
Proc Natl Acad Sci U S A, 87, 4576-9.

Woolford, 1991
Woolford, J. (1991).
The structure and biogenesis of yeast ribosomes.
Adv Genet, 2, 63-118.

Wozniak & Makalowski, 1990
Wozniak, P. & Makalowski, W. (1990).
Searching for tRNA genes in DNA sequences-an IBM microcomputer program.
Comput Appl Biosci, 6, 49-50.

Wu et al., 1998
Wu, P., Brockenbrough, J., Metcalfe, A., Chen, S., & Aris, J. (1998).
Nop5p is a small nucleolar ribonucleoprotein component required for pre-18 S rRNA processing in yeast.
J Biol Chem, 273, 16453-63.

Young et al., 1986
Young, L., Takahashi, N., & Sprague, K. (1986).
Upstream sequences confer distinctive transcriptional properties on genes encoding silkgland-specific tRNA-Ala.
Proc Natl Acad Sci U S A, 83, 374-8.

Yu et al., 1997
Yu, Y., Shu, M., & Steitz, J. (1997).
A new method for detecting sites of 2'-O-methylation in RNA molecules.
RNA, 3, 324-31.

Zagorski et al., 1988
Zagorski, J., Tollervey, D., & Fournier, M. (1988).
Characterization of an SNR gene locus in Saccharomyces cerevisiae that specifies both dispensible and essential small nuclear RNAs.
Mol Cell Biol, 8, 3282-90.


Todd M. Lowe
2000-03-31