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Isaac Newton Institute for Mathematical Sciences

Neural Networks and Machine Learning

July - December 1997

Organisers: C M Bishop (Aston), D Haussler (UCSC), G E Hinton (Toronto), M Niranjan (Cambridge), L G Valiant (Harvard)

Statistical Analysis of DNA and Protein Sequences

20 - 24 October 1997

(Updated 14/10/97)

Organisers: D Haussler (UCSC), R Durbin (Sanger) and C M Bishop (Aston)

Monday 20 October

15.00 - 16.30 Registration

16.30 - 17.00 Tea

17.00 - 18.00 David Haussler (UCSC) Statistical genome analysis: hidden Markov methods

18.00 - 19.00 Wine Reception

Tuesday 21 October

08.30 - 09.20 Registration

09.20 - 10.20 Richard Durbin (Sanger) Pairwise sequence alignment

10.20 - 11.00 Chip Lawrence (Albany, NY) A fully Bayesian approach to biopolymer sequence analysis: sequence alignment illustration

11.00 - 11.30 Coffee

11.30 - 12.10 Steven Altschul (NCBI) Empirical statistics for the local alignment of simple sequences with position-specific score matrices

12.10 - 12.50 Alan Lapedes (Santa Fe Inst) Correlated mutations in protein sequences: Phylogenetic and structural effects

12.50-15.30 Lunch

15.30 - 16.00 Tea

16.00 - 16.40 Bill Bruno (Los Alamos) Weighted neighbor joining: A fast approximation to ML phylogeny reconstruction

16.40 - 17.20 Graeme Mitchison (Cambridge) Using hidden Markov models for phylogeny

17.20 - 18.00 Nick Goldman (Cambridge) A hidden Markov model for sequence evolution

18.00 - 19.00 Wine Reception

Wednesday 22 October

09.20 - 10.20 Cyrus Chothia (Cambridge) Protein structures, assessing sequence comparisons and genome sequences

10.20 - 11.00 Liisa Holm (EBI) Mapping the protein universe

11.00 - 11.30 Coffee

11.30 - 12.10 Philipp Bucher (Lausanne) Paradoxes of sequence profiles and hidden Markov models

12.10 - 12.50 Chris Sander (EBI) TBA

12.50-15.30 Lunch

15.30 - 16.00 Tea

16.00 - 16.40 Jun Liu (Stanford) Decoupling the hidden Markov model: strategies for increasing sensitivities

16.40 - 17.20 Pierre Baldi (Caltech) Hidden Markov models in computational molecular biology: from protein families to DNA bending

17.20 - 18.00 Stephen Muggleton (York) Protein binding site analysis using inductive logic programming

18.00 - 19.00 Wine Reception

Thursday 23 October

09.20 - 10.20 Anders Krogh (Denmark) Computational methods for finding genes in human DNA

10.20 - 11.00 Mark Borodovsky (Atlanta) Evolution of GeneMark

11.00 - 11.30 Coffee

11.30 - 12.10 Victor Solovyev (Sanger) Using statistical characteristics of functional gene regions for gene structure prediction

12.10 - 12.50 Chris Burge (Stanford) TBA

12.50-15.30 Lunch

15.30 - 16.00 Tea

16.00 - 16.40 David Kulp (USCS) & Martin Reese (Berkeley) Integration of neural networks for gene features into a hidden Markov model based genefinder

16.40 - 17.20 Kiyoshi Asai (Tokyo) Toward more flexible use of hidden Markov models in computational biology

17.20 - 18.00 Sean Eddy (St Louis) A computational genetic screen for small nucleolar RNA genes in yeast, using probabilistic models

19.30 - 22.00 Conference Dinner at the University Arms Hotel

Friday 24 October

09.00 - 09.40 Phil Green (Seattle) Heterogeneity of genomic sequence composition

09.40 - 10.20 Mikhail Gelfand (Moscow) Avoidance of palindromes in bacterial genomes: how is it connected with restriction-modification systems

10.20 - 11.00 Gary Stormo (Colorado) Uncovering the regulatory networks in whole genomes

11.00 - 11.30 Coffee

11.30 - 12.10 N A Kolchanov (Novosibirsk) Computer technology for prediction of functional site activities based on their nucleotide sequences

12.10 - 12.50 Soren Brunak (Denmark) DNA replication and genome organization

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