DNA sequence alignment and single-nucleotide polymorphism (SNP) detection are two important tasks in genomics research. A common genome resequencing analysis workflow is to first perform sequence alignment and then detect SNPs among the aligned sequences. In practice, the performance bottleneck in this workflow is usually the intermediate result I/O due to the separation of the two components, ...

The ability to make sense of the massive amounts high-dimensional data generated from molecular dynamics (MD) simulations is heavily dependent on knowledge a low dimensional manifold (parameterized by reaction coordinate or RC) that typically distinguishes between relevant metastable states and which captures slow interest. Methods based machine learning artificial intelligence have been propos...

Central issues concerning protein structure prediction have been highlighted by the recently published summary of the fourth community-wide protein structure prediction experiment (CASP4). Although sequence/structure alignment remains the bottleneck in comparative modeling, there has been substantial progress in fully automated remote homolog detection and in de novo structure prediction. Signi...

Abstract This paper introduces a bottleneck game with finite sets of commuters and departing time slots as an extension congestion games Konishi et al. (J Econ Theory 72:225–237, 1997a). After characterizing Nash equilibrium the game, we provide sufficient conditions for which equivalence between strong equilibria holds. Somewhat surprisingly, unlike in games, pure strategies may often fail to ...