References

• Bonfield, James K. and Staden, Rodger. ZTR: a new format for DNA sequence trace data. Bioinformatics 18, 3-10, (2002).

• Bonfield, James, K., Beal, Kathryn F., Betts, Matthew J. and Staden, Rodger. Trev: a DNA trace editor and viewer. Bioinformatics 18, 194-195, (2002)

• Rodger Staden, David P. Judge and James K. Bonfield SEQUENCE ASSEMBLY AND FINISHING METHODS Bioinformatics. A Practical Guide to the Analysis of Genes and Proteins. Second Edition Eds. Andreas D. Baxevanis and B. F. Francis Ouellette. John Wiley & Sons, New York, NY, USA.

• The C. elegans Sequencing Consortium. Genome Sequence of the Nematode C. elegans: A Platform for Investigating Biology. Science 282, 2012-2018 (1998)

• Rodger Staden, Kathryn F. Beal and James K. Bonfield The Staden Package, 1998. Computer Methods in Molecular Biology, pages 115-130, vol. 132: Bioinformatics Methods and Protocols Eds Stephen Misener and Steve A. Krawetz. The Humana Press Inc., Totowa, NJ 07512

• Bonfield, J.K., Rada, C. and Staden, R. Automated detection of point mutations using flourescent sequence trace subtraction. Nucleic Acids Res. 26, 3404-3409 (1998)

• Cesar Milstein, Michael S. Neuberger and Rodger Staden. Both DNA strands of antibody genes are hypermutation targets. Proc. Natl. Acad. Sci. USA, 95, 8791-8794 (1998)

• Flint, J., Sims, M., Clark, K., Staden, R. and Thomas, K. An Oligo-Screening Strategy to Fill Gaps Found During Shotgun Sequencing Projects. DNA Sequence 8, 241-245 (1998)

• Staden, R. The Staden Sequence Analysis Package. Molecular Biotechnology 5, 233-241 (1996)

• Bonfield, J.K. and Staden, R. Experiment files and their application during large-scale sequencing projects. DNA Sequence 6, 109-117 (1996)

• Staden, R. Indexing and using sequence databases. Methods in Enzymology 266, 105-114 (1996)

• Bonfield, J.K., Smith, K.F. and Staden, R. A new DNA sequence assembly program. Nucleic Acids Res. 23, 4992-4999 (1995)

• Bonfield, J.K. and Staden, R. The application of numerical estimates of base calling accuracy to DNA sequencing projects. Nucleic Acids Res. 23, 1406-1410 (1995)

• Dear, S. and Staden, R. A standard file format for data from DNA sequencing instruments. DNA Sequence 3, 107-110 (1992)

• Staden, R. and Dear, S. Indexing the sequence libraries: Software providing a common indexing system for all the standard sequence libraries. DNA Sequence 3, 99-105 (1992).

• Dear, S. and Staden, R. A sequence assembly and editing program for efficient management of large projects. Nucleic Acid Res. 19, 3907-3911 (1991).

• Staden, R. Screening protein and nucleic acid sequences against libraries of patterns. DNA Sequence 1, 369-374 (1991).

• Staden, R. Searching for patterns in protein and nucleic acid sequences. Methods in Enzymology 183, 193-211. (1990).

• Staden, R. Finding protein coding regions in genomic sequences. Methods in Enzymology 183, 163-180. (1990).

  Not so recent publications from the group include:

• Staden, R. Methods for discovering novel motifs in nucleic acid sequences. CABIOS 5, 293-298 (1989)

• Staden R, Methods for calculating the probabilities of finding patterns in sequences. CABIOS 5 89-96 (1989)

• Staden R, Methods to define and locate patterns of motifs in sequences. CABIOS 4, 53-60 (1988)

• Staden, R. Graphic methods to determine the function of nucleic acid sequences. Nucleic Acid Res. 12, 521-538 (1984)

• Staden, R. Computer methods to locate signals in nucleic acid sequences. Nucleic Acid Res. 12, 505-519 (1984)

• Staden, R. A computer program to enter DNA gel reading data into a computer. Nucleic Acid Res. 12, 499-503 (1984)

• Staden, R. Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes. Nucleic Acid Res. 12, 551-567 (1984)

• Staden, R. and McLachlan, A.D. Codon preference and its use in identifying protein coding regions in long DNA sequences. Nucleic Acid Res. 10 141-156 (1982)

• Staden, R. Automation of the computer handling of gel reading data produced by the shotgun method of DNA sequencing. Nucleic Acid Res. 10, 4731-4751 (1982)

• Staden, R. An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences. Nucleic Acid Res. 10, 2951-2961 (1982)

• Staden, R. A new computer method for the storage and manipulation of DNA gel reading data. Nucleic Acid Res. 8, 3673-3694 (1980)

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