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147
Haplotyping as Perfect Phylogeny: Conceptual Framework and Efficient Solutions (Extended Abstract)
, 2002
"... The next highpriority phase of human genomics will involve the development of a full Haplotype Map of the human genome [12]. It will be used in largescale screens of populations to associate specific haplotypes with specific complex geneticinfluenced diseases. A prototype Haplotype Mapping strat ..."
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Cited by 109 (10 self)
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The next highpriority phase of human genomics will involve the development of a full Haplotype Map of the human genome [12]. It will be used in largescale screens of populations to associate specific haplotypes with specific complex geneticinfluenced diseases. A prototype Haplotype Mapping strategy is presently being finalized by an NIH workinggroup. The biological key to that strategy is the surprising fact that genomic DNA can be partitioned into long blocks where genetic recombination has been rare, leading to strikingly fewer distinct haplotypes in the population than previously expected [12, 6, 21, 7]. In this paper
Rigidity, Computation, and Randomization in Network Localization
 In Proceedings of IEEE INFOCOM ’04, Hong Kong
, 2004
"... In this paper we provide a theoretical foundation for the problem of network localization in which some nodes know their locations and other nodes determine their locations by measuring the distances to their neighbors. We construct grounded graphs to model network localization and apply graph rigid ..."
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Cited by 82 (14 self)
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In this paper we provide a theoretical foundation for the problem of network localization in which some nodes know their locations and other nodes determine their locations by measuring the distances to their neighbors. We construct grounded graphs to model network localization and apply graph rigidity theory to test the conditions for unique localizability and to construct uniquely localizable networks. We further study the computational complexity of network localization and investigate a subclass of grounded graphs where localization can be computed efficiently. We conclude with a discussion of localization in sensor networks where the sensors are placed randomly.
Upward Planarity Testing
 SIAM Journal on Computing
, 1995
"... Acyclic digraphs, such as the covering digraphs of ordered sets, are usually drawn upward, i.e., with the edges monotonically increasing in the vertical direction. A digraph is upward planar if it admits an upward planar drawing. In this survey paper, we overview the literature on the problem of upw ..."
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Cited by 81 (15 self)
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Acyclic digraphs, such as the covering digraphs of ordered sets, are usually drawn upward, i.e., with the edges monotonically increasing in the vertical direction. A digraph is upward planar if it admits an upward planar drawing. In this survey paper, we overview the literature on the problem of upward planarity testing. We present several characterizations of upward planarity and describe upward planarity testing algorithms for special classes of digraphs, such as embedded digraphs and singlesource digraphs. We also sketch the proof of NPcompleteness of upward planarity testing.
Drawing Planar Graphs Using the Canonical Ordering
 ALGORITHMICA
, 1996
"... We introduce a new method to optimize the required area, minimum angle and number of bends of planar drawings of graphs on a grid. The main tool is a new type of ordering on the vertices and faces of triconnected planar graphs. Using this method linear time and space algorithms can be designed for m ..."
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Cited by 65 (0 self)
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We introduce a new method to optimize the required area, minimum angle and number of bends of planar drawings of graphs on a grid. The main tool is a new type of ordering on the vertices and faces of triconnected planar graphs. Using this method linear time and space algorithms can be designed for many graph drawing problems.  Every triconnected planar graph G can be drawn convexly with straight lines on an (2n \Gamma 4) \Theta (n \Gamma 2) grid, where n is the number of vertices.  Every triconnected planar graph with maximum degree four can be drawn orthogonally on an n \Theta n grid with at most d 3n 2 e + 4, and if n ? 6 then every edge has at most two bends.  Every 3planar graph G can be drawn with at most b n 2 c + 1 bends on an b n 2 c \Theta b n 2 c grid.  Every triconnected planar graph G can be drawn planar on an (2n \Gamma 6) \Theta (3n \Gamma 9) grid with minimum angle larger than 2 d radians and at most 5n \Gamma 15 bends, with d the maximum d...
A Theory of Network Localization
, 2004
"... In this paper we provide a theoretical foundation for the problem of network localization in which some nodes know their locations and other nodes determine their locations by measuring the distances to their neighbors. We construct grounded graphs to model network localization and apply graph rigid ..."
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Cited by 62 (6 self)
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In this paper we provide a theoretical foundation for the problem of network localization in which some nodes know their locations and other nodes determine their locations by measuring the distances to their neighbors. We construct grounded graphs to model network localization and apply graph rigidity theory to test the conditions for unique localizability and to construct uniquely localizable networks. We further study the computational complexity of network localization and investigate a subclass of grounded graphs where localization can be computed efficiently. We conclude with a discussion of localization in sensor networks where the sensors are placed randomly.
The Molecule Problem Exploiting Structure In Global Optimization
 SIAM Journal on Optimization
, 1995
"... . The molecule problem is that of determining the relative locations of a set of objects in Euclidean space relying only upon a sparse set of pairwise distance measurements. This NPhard problem has applications in the determination of molecular conformation. The molecule problem can be naturally e ..."
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Cited by 60 (0 self)
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. The molecule problem is that of determining the relative locations of a set of objects in Euclidean space relying only upon a sparse set of pairwise distance measurements. This NPhard problem has applications in the determination of molecular conformation. The molecule problem can be naturally expressed as a continuous, global optimization problem, but it also has a rich combinatorial structure. This paper investigates how that structure can be exploited to simplify the optimization problem. In particular, we present a novel divideandconquer algorithm in which a large global optimization problem is replaced by a sequence of smaller ones. Since the cost of the optimization can grow exponentially with problem size, this approach holds the promise of a substantial improvement in performance. Our algorithmic development relies upon some recently published results in graph theory. We describe an implementation of this algorithm and report some results of its performance on a sample ...
Tree spanners
 SIAM J. Discrete Math
, 1995
"... A tree tspanner T of a graph G is a spanning tree in which the distance between every pair of vertices is at most t times their distance in G. This notion is motivated by applications in communication networks, distributed systems, and network design. This paper studies graph theoretic, algorithmic ..."
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Cited by 58 (1 self)
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A tree tspanner T of a graph G is a spanning tree in which the distance between every pair of vertices is at most t times their distance in G. This notion is motivated by applications in communication networks, distributed systems, and network design. This paper studies graph theoretic, algorithmic and complexity issues about tree spanners. It is shown that a tree 1spanner, if it exists, in a weighted graph with m edges and n vertices is a minimum spanning tree and can be found in O(m log β(m, n)) time, where β(m, n) = min{i  log (i) n ≤ m/n}. On the other hand, for any fixed t> 1, the problem of determining the existence of a tree tspanner in a weighted graph is proven to be NPcomplete. For unweighted graphs, it is shown that constructing a tree 2spanner takes linear time, whereas determining the existence of a tree tspanner is NPcomplete for any fixed t ≥ 4. A theorem which captures the structure of tree 2spanners is presented for unweighted graphs. For digraphs, an O((m+n)α(m, n)) algorithm is provided for
Permanents, Pfaffian Orientations, and Even Directed Circuits
, 1999
"... Given a 01 square matrix A, when can some of the 1’s be changed to −1’s in such a way that the permanent of A equals the determinant of the modified matrix? When does a real square matrix have the property that every real matrix with the same sign pattern (that is, the corresponding entries either ..."
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Cited by 57 (13 self)
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Given a 01 square matrix A, when can some of the 1’s be changed to −1’s in such a way that the permanent of A equals the determinant of the modified matrix? When does a real square matrix have the property that every real matrix with the same sign pattern (that is, the corresponding entries either have the same sign, or are both zero) is nonsingular? When is a hypergraph with n vertices and n hyperedges minimally nonbipartite? When does a bipartite graph have a “Pfaffian orientation”? Given a digraph, does it have no directed circuit of even length? Given a digraph, does it have a subdivision with no even directed circuit? It is known that all the above problems are equivalent. We prove a structural characterization of the feasible instances, which implies a polynomialtime algorithm to solve all of the above problems. The structural characterization says, roughly speaking, that a bipartite graph has a Pfaffian orientation if and only if it can be obtained by piecing together (in a specified way) planar bipartite graphs and one sporadic nonplanar bipartite graph.
A linear time algorithm for embedding graphs in an arbitrary surface
 SIAM J. Discrete Math
, 1999
"... Ljubljana, February 2, 2009A simpler linear time algorithm for embedding graphs into an arbitrary surface and the genus of graphs of bounded treewidth ..."
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Cited by 56 (10 self)
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Ljubljana, February 2, 2009A simpler linear time algorithm for embedding graphs into an arbitrary surface and the genus of graphs of bounded treewidth
A GraphConstructive Approach to Solving Systems of Geometric Constraints
 ACM TRANSACTIONS ON GRAPHICS
, 1997
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