F. Abe,17 H. Akimoto,39 A. Akopian,31 M. G. Albrow,7 A. Amadon,5 S. R. Amendolia,27 D. Amidei,20 J. Antos,33 S. Aota,37 G. Apollinari,31 T. Arisawa,39 T. Asakawa,37 W. Ashmanskas,18 M. Atac,7 P. Azzi-Bacchetta,25 N. Bacchetta,25 S. Bagdasarov,31 M. W. Bailey,22 P. de Barbaro,30 A. Barbaro-Galtieri,18 V. E. Barnes,29 B. A. Barnett,15 M. Barone,9 G. Bauer,19 T. Baumann,11 F. Bedeschi,27 S. Behren...

Time-series data from multicomponent systems capture the dynamics of the ongoing processes and reflect the interactions between the components. The progression of processes in such systems usually involves check-points and events at which the relationships between the components are altered in response to stimuli. Detecting these events together with the implicated components can help understan...

mRNA decapping is a common step shared between two important mRNA decay pathways in yeast, Saccharomyces cerevisiae. To investigate how mRNAs are decapped, we have developed an assay that can be easily used to measure the decapping activity. This assay has been used to isolate yeast strains with altered decapping activities. The results demonstrated that decreased decapping activity in vitro co...

We propose a general method to predict functions of vertices where (i) the wiring of the network is somehow related to the vertex functionality and (ii) a fraction of the vertices are functionally classified. The method is influenced by role-similarity measures of social network analysis. The two versions of our prediction scheme are tested on model networks where the functions of the vertices ...

Here it is demonstrated that the yeast Saccharomyces cerevisiae can take up and assemble at least 38 overlapping single-stranded oligonucleotides and a linear double-stranded vector in one transformation event. These oligonucleotides can overlap by as few as 20 bp, and can be as long as 200 nucleotides in length. This straightforward scheme for assembling chemically-synthesized oligonucleotides...

Predicting the biological function of all the genes of an organism is one of the fundamental goals of computational system biology. In the last decade, high-throughput experimental methods for studying the functional interactions between gene products (GPs) have been combined with computational approaches based on Bayesian networks for data integration. The result of these computational approac...

Yeast species such as Saccharomyces cerevisiae have been exploited by humans for millennia and so it is therefore unsurprising that they are attractive cells to re-engineer for industrial use. Despite many beneficial traits yeast has for synthetic biology, it currently lags behind Escherichia coli in the number of synthetic networks that have been described. While the eukaryotic nature of yeast...

Palindromic sequences in single-stranded DNA and RNA have the potential for intrastrand base pairing, resulting in formation of "hairpin" structures. We previously reported a genetic method for detecting such structures in vivo in the yeast Saccharomyces cerevisiae. Below, we describe evidence indicating that a 14-base-pair palindrome (7 bp per inverted repeat) is sufficient for formation of a ...