Ron Y. Pinter

Photosystem I gene cassettes are present in marine virus genomes.

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 evidence for the presence of photosystem I (PSI) genes in the genomes of viruses that infect these marine cyanobacteria, using pre-existing metagenomic data from the global ocean sampling expedition as well as from viral biomes. The seven cyanobacterial core PSI genes identified in this study, psaA, B, C, D, E, K and a unique J and F fusion, form a cluster in cyanophage genomes, suggestive of selection for a distinct function in the virus life cycle. The existence of this PSI cluster was confirmed with overlapping and long polymerase chain reaction on environmental DNA from the Northern Line Islands. Potentially, the seven proteins encoded by the viral genes are sufficient to form an intact monomeric PSI complex. Projection of viral predicted peptides on the cyanobacterial PSI crystal structure suggested that the viral–PSI components might provide a unique way of funnelling reducing power from respiratory and other electron transfer chains to the PSI.

Optimal Chaining of CMOS Transistors in a Functional Cell

We describe an algorithm that maps a CMOS circuit diagram into an area-efficient, high-performance layout in the style of a transistor chain. It is superior to other published algorithms of this kind in terms of the class of input circuits it accepts, its efficiency, and the quality of the results it produces. This algorithm is intended for the automatic generation of basic cells in a custom or semicustom design environment, thereby removing the burden of arduous mask definition from the designer. We show how our method was used to compose cells in a row into a functional slice (e.g. an adder) that can be used in, say, a data path.

Trapezoid graphs and their coloring

Abstract We define trapezoid graphs, an extension of both interval and permutation graphs. We show that this new class properly contains the union of the two former classes, and that trapezoid graphs are equivalent to the incomparability graphs of partially ordered sets having interval order dimension at most two. We provide an optimal coloring algorithm for trapezoid graphs that runs in time O(nk), where n is the number of nodes and k is the chromatic number of the graph. Our coloring algorithm has direct applications to channel routing on integrated circuits.

Spill code minimization techniques for optimizing compliers

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 algorithms, universally outperforming them. In our approach, we extend the capability of the existing algorithms in several ways. First, we use multiple heuristic functions to increase the likelihood that less spill code will be inserted. We have found three complementary heuristic functions which together appear to span a large proportion of good spill decisions. Second, we use a specially tuned greedy heuristic for determining the order of deleting (and hence coloring) the unconstrained vertices. Third, we have developed a “cleaning” technique which avoids some of the insertion of spill code in non-busy regions.

Comparative metagenomics of microbial traits within oceanic viral communities

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 datasets, we characterize previously undetected microbial metabolic capabilities concealed within the genomes of uncultured marine viral communities. A total of 34 microbial gene families were detected on 452 viral GOS scaffolds. The majority of auxiliary metabolic genes found on these scaffolds have never been reported in phages. Host genes detected in viruses were mainly divided between genes encoding for different energy metabolism pathways, such as electron transport and newly identified photosystem genes, or translation and post-translation mechanism related. Our findings suggest previously undetected ways, in which marine phages adapt to their hosts and improve their fitness, including translation and post-translation level control over the host rather than the already known transcription level control.

Optimal Placement for River Routing

River routing is the problem of connecting a set of terminals a 1,…,a n on a line to another set b 1,…,b n in order across a rectangular channel. When the terminals are located on modules, the modules must be placed relative to one another before routing. This placement problem arises frequently in design systems like bristle-blocks where stretch lines through a module can effectively break it into several chunks, each of which must be placed separately. This paper gives concise necessary and sufficient conditions for wirability which are applied to reduce the optimal placement problem to the graph-theoretic single-source-longest-paths problem. By exploiting the special structure of graphs that arise from the placement problem for rectilinear wiring, an optimal solution may be determined in linear time.

River Routing: Methodology and Analysis

The problem of river routing across a channel is only a special case of more general routing configurations. Both its methodological and combinatorial characteristics can be extended in useful ways which will be explored in this paper. The two characteristics that we generalize here are planarity and grouping. Planarity means that the connections are realizable in one layer; ie the interconnection pattern of the nets is planar. Grouping means that the connections are made in order, that is to say that the routing of net i+l is adjacent, conceptually and preferably physically, to the routing of net I.

On Routing Two-Point Nets Across a Channel

Many problems that arise in general channel routing manifest themselves in simpler situations. We consider connecting a set of n terminals on a line to another set on a parallel line across a rectangular channel. We show that in any solution to the problem that (almost) minimizes the width of the channel (i.e. the distance between the lines the terminals reside on) a net may require as many as ?(?n) horizontal jogs no net routed from top to bottom need ever turn upward in the middle We also present an efficient algorithm to obtain minimal jogging in river routing, and provide necessary and sufficient conditions for conflict cycle resolution. These and other results are presented in the context of a general survey on routing from a combinatorial complexity point of view.

Efficient String Matching with Don’t-Care Patterns

The occurrences of a constant pattern in a given text string can be found in linear time using the famous algorithm of Knuth, Morris, and Pratt [KMP]. Aho and Corasick [AC] independently solved the problem for patterns consisting of a set of strings, where the occurrence of one member is considered a match. Both algorithms preprocess the pattern so that the text can be searched efficiently. This paper considers the extension of their methods to, deal with patterns involving more expressive descriptions, such as don’t-care (wild-card) symbols, complements, etc. Such extensions are useful in the context of clever text-editors and the analysis of chemical compounds.

A computational approach for genome-wide mapping of splicing factor binding sites

Alternative splicing is regulated by splicing factors that serve as positive or negative effectors, interacting with regulatory elements along exons and introns. Here we present a novel computational method for genome-wide mapping of splicing factor binding sites that considers both the genomic environment and the evolutionary conservation of the regulatory elements. The method was applied to study the regulation of different alternative splicing events, uncovering an interesting network of interactions among splicing factors.