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1,282
On the complexity of computing minimum energy consumption broadcast subgraphs
 in Symposium on Theoretical Aspects of Computer Science
, 2001
"... Abstract. We consider the problem of computing an optimal range assignment in a wireless network which allows a specified source station to perform a broadcast operation. In particular, we consider this problem as a special case of the following more general combinatorial optimization problem, calle ..."
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Cited by 115 (13 self)
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Abstract. We consider the problem of computing an optimal range assignment in a wireless network which allows a specified source station to perform a broadcast operation. In particular, we consider this problem as a special case of the following more general combinatorial optimization problem, called Minimum Energy Consumption Broadcast Subgraph (in short, MECBS): Given a weighted directed graph and a specified source node, find a minimum cost range assignment to the nodes, whose corresponding transmission graph contains a spanning tree rooted at the source node. We first prove that MECBS is not approximable within a constant factor (unless P=NP). We then consider the restriction of MECBS to wireless networks and we prove several positive and negative results, depending on the geometric space dimension and on the distancepower gradient. The main result is a polynomialtime approximation algorithm for the NPhard case in which both the dimension and the gradient are equal to 2: This algorithm can be generalized to the case in which the gradient is greater than or equal to the dimension. 1
Monetary policy rules in the open economy: effects on welfare and business cycles
 Journal of Monetary Economics
, 2002
"... This paper computes welfare maximizing Taylorstyle interest rate rules, in a business cycle model of a small open economy. The model assumes staggered price setting and shocks to domestic productivity, to the world interest rate, to world inflation, and to the uncovered interest rate parity conditi ..."
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Cited by 85 (5 self)
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This paper computes welfare maximizing Taylorstyle interest rate rules, in a business cycle model of a small open economy. The model assumes staggered price setting and shocks to domestic productivity, to the world interest rate, to world inflation, and to the uncovered interest rate parity condition. Optimized policy rules have a pronounced antiinflation stance and entail significant nominal and real exchange rate volatility. The country responds to an increase in external volatility by holding more foreign assets. The policy rule affects the variance and the mean of consumption. The effect on the mean matters significantly for welfare. JEL classification: E4; F3; F4
Approximating Minimum Quartet Inconsistency (Abstract)
, 2002
"... A fundamental problem in computational biology which has been widely studied in the last decades is the reconstruction of evolutionary trees from biological data. Unfortunately, almost all its known formulations are NPhard. The compelling need for having efficient computational tools to solve this ..."
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Cited by 5 (0 self)
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A fundamental problem in computational biology which has been widely studied in the last decades is the reconstruction of evolutionary trees from biological data. Unfortunately, almost all its known formulations are NPhard. The compelling need for having efficient computational tools to solve this biologcal problem has brought a lot of attention to the analysis of the quartet paradigm for inferring evolutionary trees [1, 2, 8]. Given a quartet of taxa {a, b, c, d}, there are 3 possible degree3 trees connecting the taxa as terminals. Each such tree is called a quartet topology. The quartet methods proceed by first estimating the topology of each quartet of taxa and then recombining the inferred quartet topologies into an evolutionary tree. A major difficulty in this approach derives from the fact that quartet topology inference methods often make mistakes, and thus may result in a set Q of quartet topologies that is inconsistent with any evolutionary tree. Therefore, the problem of recombining the quartet topologies of Q to form an estimate of the correct evolutionary tree is naturally formulated as an optimization problem that looks for a tree T maximizing the number of consistent quartets (i.e.
Analysis of bacterial community composition by oligonucleotide fingerprinting of rRNA genes
 Applied and Environmental Microbiology
, 2002
"... One of the first steps in characterizing an ecosystem is to describe the organisms inhabiting it. For microbial studies, experimental limitations have hindered the ability to depict diverse communities. Here we describe oligonucleotide fingerprinting of rRNA genes (OFRG), a method that permits ident ..."
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Cited by 18 (9 self)
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One of the first steps in characterizing an ecosystem is to describe the organisms inhabiting it. For microbial studies, experimental limitations have hindered the ability to depict diverse communities. Here we describe oligonucleotide fingerprinting of rRNA genes (OFRG), a method that permits identification of arrayed rRNA genes (rDNA) through a series of hybridization experiments using small DNA probes. To demonstrate this strategy, we examined the bacteria inhabiting two different soils. Analysis of 1,536 rDNA clones revealed 766 clusters grouped into five major taxa: Bacillus, Actinobacteria, Proteobacteria, and two undefined assemblages. Soilspecific taxa were identified and then independently confirmed through clusterspecific PCR of the original soil DNA. Nearspecieslevel resolution was obtained by this analysis as clones with average sequence identities of 97 % were grouped in the same cluster. A comparison of these OFRG results with the results obtained in a denaturing gradient gel electrophoresis analysis of the same two soils demonstrated the significance of this methodological advance. OFRG provides a costeffective means to extensively analyze microbial communities and should have applications in medicine, biotechnology, and ecosystem studies. How diverse are microbial communities? Does microbial diversity lead to ecosystem stability? What are the relationships between microbial community composition and ecosystem
Computational Complexity Of Multiple Sequence Alignment With SpScore
 Journal of Computational Biology
, 1999
"... . It is shown that the multiple alignment problem with SPscore is NPhard for each scoring matrix in a broad class M that includes most scoring matrices actually used in biological applications. The problem remains NP hard even if sequences can only be shifted relative to each other and no inte ..."
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Cited by 37 (1 self)
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. It is shown that the multiple alignment problem with SPscore is NPhard for each scoring matrix in a broad class M that includes most scoring matrices actually used in biological applications. The problem remains NP hard even if sequences can only be shifted relative to each other and no internal gaps are allowed. It is also shown that there is a scoring matrix M 0 such that the multiple alignment problem for M 0 is MAXSNPhard, regardless of whether or not internal gaps are allowed. Key words and phrases. sequence alignment, scoring matrix, NPhardness, MAXSNP  hardness, polynomial time approximation scheme. email: just@math.ohiou.edu phone: (740)5931260 fax: (740)5939805. 1 2 WINFRIED JUST 1. Introduction The importance of good multiple sequence alignment algorithms is evidenced by the large number of programs that have been developed for this task (Fasman and Salzberg 1998). Finding an optimal alignment of k sequences appears to quickly become computationall...
Approximating Minimum Quartet Inconsistency (Abstract)
"... A fundamental problem in computational biology which has been widely studied in the last decades is the reconstruction of evolutionary trees from biological data. Unfortunately, almost all its known formulations are NPhard. The compelling need for having efficient computational tools to solve this b ..."
Abstract
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A fundamental problem in computational biology which has been widely studied in the last decades is the reconstruction of evolutionary trees from biological data. Unfortunately, almost all its known formulations are NPhard. The compelling need for having efficient computational tools to solve this biological problem has brought a lot of attention to the analysis of the quartet paradigm for inferring evolutionary trees [1, 2, 8]. Given a quartet of taxa {a, b, c, d}, there are 3 possible degree3 trees connecting the taxa as terminals. Each such tree is called a quartet topology. The quartet methods proceed by first estimating the topology of each quartet of taxa and then recombining the inferred quartet topologies into an evolutionary tree. A major difficulty in this approach derives from the fact that quartet topology
Approximating Minimum Quartet Inconsistency (Abstract)
, 2002
"... A fundamental problem in computational biology which has been widely studied in the last decades is the reconstruction of evolutionary trees from biological data. Unfortunately, almost all its known formulations are NPhard. The compelling need for having efficient computational tools to solve this ..."
Abstract
 Add to MetaCart
A fundamental problem in computational biology which has been widely studied in the last decades is the reconstruction of evolutionary trees from biological data. Unfortunately, almost all its known formulations are NPhard. The compelling need for having efficient computational tools to solve this biological problem has brought a lot of attention to the analysis of the quartet paradigm for inferring evolutionary trees [1, 2, 8]. Given a quartet of taxa {a, b, c, d}, there are 3 possible degree3 trees connecting the taxa as terminals. Each such tree is called a quartet topology. The quartet methods proceed by first estimating the topology of each quartet of taxa and then recombining the inferred quartet topologies into an evolutionary tree. A major difficulty in this approach derives from the fact that quartet topology
The complexity of multiple sequence alignment with SPscore that is a metric
 TCS
, 2001
"... This paper analyzes the computational complexity of computing the optimal alignment of a set of sequences under the SP (sum of all pairs) score scheme. We solve an open question by showing that the problem is NP complete in the very restricted case in which the sequences are over a binary alphabet ..."
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Cited by 34 (0 self)
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This paper analyzes the computational complexity of computing the optimal alignment of a set of sequences under the SP (sum of all pairs) score scheme. We solve an open question by showing that the problem is NP complete in the very restricted case in which the sequences are over a binary alphabet and the score is a metric. This result establishes the intractability of multiple sequence alignment under a score function of mathematical interest, which has indeed received much attention in biological sequence comparison.
Probe Selection Algorithms with Applications in the Analysis of Microbial Communities (Extended Abstract)
, 2001
"... We propose two efficient heuristics for minimizing the number of oligonucleotide probes needed for analyzing populations of ribosomal RNA gene (rDNA) clones by hybridization experiments on DNA microarrays. Such analyses have applications in the study of microbial communities. Unlike in the classical ..."
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Cited by 27 (9 self)
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We propose two efficient heuristics for minimizing the number of oligonucleotide probes needed for analyzing populations of ribosomal RNA gene (rDNA) clones by hybridization experiments on DNA microarrays. Such analyses have applications in the study of microbial communities. Unlike in the classical SBH (sequencing by hybridization) procedure, where multiple probes are on a DNA chip, in our applications we perform a series of experiments, each one consisting of applying a single probe to a DNA microarray containing a large sample of rDNA sequences from the studied population. The overall cost of the analysis is thus roughly proportional to the number of experiments, underscoring the need for minimizing the number of probes. Our algorithms are based on two wellknown optimization techniques, i.e. simulated annealing and Lagrangian relaxation, and our preliminary tests demonstrate that both algorithms are able to find satisfactory probe sets for real rDNA data.
Results 1  10
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1,282