Ron Y. Pinter

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Genes and proteins generate molecular circuitry that enables the cell to process information and respond to stimuli. A major challenge is to identify characteristic patterns in this network of interactions that may shed light on basic cellular mechanisms. Previous studies have analyzed aspects of this network, concentrating on either(More)
MOTIVATION Several genome-scale efforts are underway to reconstruct metabolic networks for a variety of organisms. As the resulting data accumulates, the need for analysis tools increases. A notable requirement is a pathway alignment finder that enables both the detection of conserved metabolic pathways among different species as well as divergent metabolic(More)
Global register allocation and spilling is commonly performed by solving a graph coloring problem. In this paper we present a new coherent set of heuristic methods for reducing the amount of spill code generated. This results in more efficient (and shorter) compiled code. Our approach has been compared to both standard and priority-based coloring(More)
Cyanobacteria of the Synechococcus and Prochlorococcus genera are important contributors to photosynthetic productivity in the open oceans. Recently, core photosystem II (PSII) genes were identified in cyanophages and proposed to function in photosynthesis and in increasing viral fitness by supplementing the host production of these proteins. Here we show(More)
Current algorithmic studies of genome rearrangement ignore the length of reversals (or inversions); rather, they only count their number. We introduce a new cost model in which the lengths of the reversed sequences play a role, allowing more flexibility in accounting for mutation phenomena. Our focus is on sorting unsigned (unoriented) permutations by(More)
A floorplan represents the relative relations between modules on an integrated circuit. Floorplans are commonly classified as slicing, mosaic, or general. Separable and Baxter permutations are classes of permutations that can be defined in terms of forbidden subsequences. It is known that the number of slicing floorplans equals the number of separable(More)
Viral genomes often contain genes recently acquired from microbes. In some cases (for example, psbA) the proteins encoded by these genes have been shown to be important for viral replication. In this study, using a unique search strategy on the Global Ocean Survey (GOS) metagenomes in combination with marine virome and microbiome pyrosequencing-based(More)
Programs in languages such as Fortran, Pascal, and C were designed and written for a sequential machine model. During the last decade, several methods to vectorize such programs and recover other forms of parallelism that apply to more advanced machine architectures have been developed (particularly for Fortran, due to its pointer-free semantics). We(More)
We study the problem of sorting integer sequences and permutations by length-weighted reversals. We consider a wide class of cost functions, namely <i>f(l)</i> = <i>l</i><sup>&alpha;</sup> for all &alpha; &#8805; 0, where <i>l</i> is the length of the reversed subsequence. We present tight or nearly tight upper and lower bounds on the worst-case cost of(More)