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Bioinformatics @ CSSE

In: SOBS Research Linkage Seminars, South 1, Clayton, Monash University, 3pm Friday 7th September 2001

alphabetic order :Bioinformatics
track record interest useful technology, e.g.

Lloyd Allison

IPL.V23 1986... * MML, algorithms, data mining

Trevor Dix

* algorithms, parallel sys', data mining

David Dowe

HICSS-26 1993... * MML, Stats

Maria Garcia de la Banda

  * constraints, optimization

Emeritus Professor C. S. Wallace

J.Theor.Biol.V23 1969... * MML, inductive inference, clustering
This document can be found at  www.csse.monash.edu.au/~lloyd/Seminars/2001-VBC01/index.shtml   and contains hyper-links to other resources - © L. Allison, 7 September 2001.
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>>programme>>   
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In: SOBS Research Linkage Seminars, Friday September 7th 2001

3.00 - 3.10
Dr. Brian Cooke and A/Prof. John Davies. Dept. Microbiology, Monash University. SOBS Research Linkage Seminars - introduction and overview.
Session 1 Genomes (Chair: A/Prof. John Davies)
3.10 - 3.25 Prof. Ross Coppel. Dept. Microbiology, Monash University. Genomes. Why are they important?
3.25 - 3.40
Dr. Sue Forrest. Australian Genome Research Facility. Facilitating Genome Research - inside the AGRF.
3.40 - 3.55
Prof. Ross Coppel. Dept. Microbiology, Monash University. The Victorian Bioinformatics Consortium (VBC).
3.55 - 4.10
Dr. Lloyd Allison. School of Computer Science and Software Engineering, Monash University. Bioinformatics @ CSSE     (left).
Break
Session 2 Immediate post-genome (Chair: Dr. Brian Cooke)
4.30 - 4.45
A/Prof. John Davies. Dept. Microbiology, Monash University. A DNA core facility. Oligos, sequencing and robotics.
4.45 - 5.00
Dr. John Boyce. Dept. Microbiology, Monash University. Real-time PCR; accurate quantitation at the speed of light.
5.00 - 5.15
A/Prof. John Davies. Dept. Microbiology, Monash University. Microarrays.
5.15 - 5.30
Dr. James Whisstock. Dept. Biochemistry and Molecular Biology, Monash University. Utilising genomic data.
5.30 - 5.35
Prof. Warwick Anderson. Dept. Physiology, Monash University. Genomes and beyond.
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Some past work in CS / CSSE

L. Allison & T.I. Dix. A Bit-String Longest-Common-Subsequence Algorithm, Inf. Proc. Lett., V23, Dec' 1986, p305-310

fast, bit, longest common subsequence algorithm LCS LCSS related to Dynamic Programming Algorithm DPA for sequence analysis homology HMM PHMM

LCS ~ edit distance,  bit-operation algorithm,  about |word|× faster,  e.g. 32×.

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. . . some past work, e.g. . . .

Clustering:
C. S. Wallace & D. M. Boulton. An Information Measure for Classification. Computer J. 11(2) pp.185-194, August 1968

Estimation, complexity & entropy
D. M. Boulton & C. S. Wallace. The Information Content of a Multistate Distribution. J. Theor. Biol. 23 pp.269-278, 1969

Restriction site mapping:
T. I. Dix & D. H. Kieronska. Tree Pruning in Restriction Site Mapping, Aus. Comp. Sci. Comm. 9(1), 1987

Multiple alignment & evolutionary trees:
L. Allison, C. S. Wallace & C. N. Yee, Minimum Message Length Encoding, Evolutionary Trees and Multiple-Alignment. 25th Hawaii Int. Conf. Sys. Sci., 1 pp.663-674, Jan. 1992

Protein secondary structure
D. L. Dowe, J. Oliver, T. I. Dix, L. Allison, C. S. Wallace, A Decision Graph Explanation of Protein Secondary Structure Prediction. 26th Hawaii Int. Conf. Sys. Sci., 1, pp.669-678, Jan. 1993 [graph]

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Some current work in CSSE

Compression for pattern discovery and for alignment of non-random seq's
Plasmodium falciparum (malaria)
highly repetitive DNA chr10 Plasmodium falciparum PF by approximate repeats model 2D pattern discovery plot, nb not by DOTTER
with Linda Stern (CS, Melbourne), Ross Coppel (Microb', Monash), & Trevor Dix (CSSE, Monash),

Highly compressible DNA (<0.61 bits/base)

Left: NOT a dot-plot. By [approx repeats model], no manual adjustment of parameters needed, significant repeat obvious.

v. DOTTER [click], "snow" from many common short repeats, best tweaking of parameters but significant repeat still well hidden with DOTTER.

More: [1] [2]

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"Sequence data was obtained through early release from The Institute for Genomic Research at www.tigr.org"

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Some possible future applications of . . .

. . . to . . .


© L. Allison, School of Computer Science and Software Engineering, Monash University, Australia 3168.
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