Analysis of nonsynonymous to synonymous nucleotide substitution rate ratios (Ka/Ks) indicates that positive selection may have been operating on this gene during the time of divergence of Bovinae and Antilopinae, starting from approximately 23 million years ago, a period that appears to account for most of the sequence difference between myostatin in this two groups.

Sites evolving under positive selection pressures were found both in the propeptide region and the C-terminal region of the gene.

3SAT in the hard region is a paradigmatic combinatorial optimization problem. I will present a study of a well-known heuristic search called walksat (Selman, Kautz & Cohen) that in fact has linear in N behaviour in median computation time up to M/N=4.14. (Numerical) concentration of the measure results will be presented in further support of this statement. These results on walksat are appearently new.

I will then further compare walksat to a somewhat complex algorithm called "survey propagation", which I will deduce as a variant of Belief Propagation in a fairly odd system of beliefs. The original derivation was framed in a 1-step replica symmetry breaking scenario in an equivalent diluted spin glass (Mezard, Parisi & Zecchina), and will not presented here. Survey propagation in polynomial in N in median computation time up to above 4.20,

This is joint work with Scott Kirkpatrick, to be presented at NIPS 2004.

Finally, a brief summary of the new network for all cancer researchers within KI , KICancer, will be presented.

Using a dataset with 327 families from SCOP 1.63 we compare the ability of two different methods to select an optimal conflict-free subset of equivalences. One is an implementation of Reinert et al.'s integer linear programming formulation (ILP) of the maximum weight trace problem (Reinert et al., 1997). This ILP formulation is a rigorous approach but its complexity is difficult to predict. The other method is T-Coffee (Notredame et al., 2000) which uses a heuristic enhancement of the equivalence weights which allow it to use the speed and simplicity of the progressive alignment approach while still incorporating information of all alignments in each step of building the MSTA. We find that although the ILP formulation consistently selects a more optimal set of conflict-free equivalences, the differences are small and the quality of the resulting MSTAs are essentially the same for both methods.

In a recently published study, we extended this revelation to show that reported SNPs in such domains were often not SNPs at all, but false interpretations of multi-site variability (MSV), reflecting the underlying copy-number differences. Most worryingly of all, MSVs masquerade as SNPs when genotyped with most common genotyping methods in use today. These issues must now be properly addressed in disease association studies and haplotype map construction, in order to avoid missing true signals or drawing invalid conclusions.

References:
Fredman, D. et al. Complex SNP-related sequence variation in segmental genome duplications. Nature Genetics (2004)
Iafrate, A.J. et al. Detection of large-scale variation in the human genome. Nature Genetics (2004).
Sebat, J. et al. Large-scale copy number polymorphism in the human genome. Science (2004)