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1
November 2016
Discrete Applied Mathematics: Volume 213 Issue C, November 2016
Publisher: Elsevier Science Publishers B. V.
We study the classic Graph Motif problem. Given a graph G = ( V , E ) with a set of colors for each node, and a multiset M of colors, we seek a subtree T ź G , and a coloring assigning to each node in T a color ...
Keywords:
RGMRestricted GM, Guiding tree, GMGraph Motif, Graph motif, Parameterized algorithm, Representative family
2
March 2015
Journal of Discrete Algorithms: Volume 31 Issue C, March 2015
Publisher: Elsevier Science Publishers B. V.
We study the Partial Information Network Query (PINQ) problem, which generalizes two problems that often arise in bioinformatics: the Alignment Network Query (ANQ) problem and the TopologyFree Network Query (TFNQ) problem. In both ANQ and TFNQ we have a pattern P and a graph H, and we seek a subgraph ...
Keywords:
Partial information network query, Pattern matching, TopologyFree Network Query(TFNQ), Parameterized algorithm, Partial Information Network Query(PINQ), Topologyfree network query, Alignment Network Query(ANQ), Alignment network query
3
July 2014
Journal of Discrete Algorithms: Volume 27, July, 2014
Publisher: Elsevier Science Publishers B. V.
In this article we address two pattern matching problems which have important applications to bioinformatics. First we address the topologyfree network query problem: Given a set of labels L, a multiset P of labels from L, a graph H=(V"H,E"H) and a function Label"H:V"H>2^L, we need to find a subtree S ...
Keywords:
Alignment network query, Computational biology, Parameterized algorithm, Subgraph homeomorphism, Topologyfree network query
4
April 2012
ACM Transactions on Algorithms (TALG): Volume 8 Issue 2, April 2012
Publisher: ACM
Bibliometrics:
Citation Count: 0
Downloads (6 Weeks): 5, Downloads (12 Months): 37, Downloads (Overall): 346
Full text available:
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We introduce a generalization of interval graphs, which we call Dotted Interval Graphs (DIG). A dotted interval graph is an intersection graph of arithmetic progressions (dotted intervals). Coloring of dotted interval graphs naturally arises in the context of high throughput genotyping. We study the properties of dotted interval graphs, with ...
Keywords:
graph coloring, interval graph, intersection graph, circular arc graph, graph theory, Approximation algorithms
5
April 2010
RECOMB'10: Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
Publisher: SpringerVerlag
Metagenomic data enables the study of microbes and viruses through their DNA as retrieved directly from the environment in which they live Functional analysis of metagenomes explores the abundance of gene families, pathways, and systems, rather than their taxonomy Through such analysis researchers are able to identify those functional capabilities ...
Keywords:
Markov Chain Monte Carlo (MCMC), metagenomics, pathways, functional analysis
6
May 2009
RECOMB 2'09: Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
Publisher: SpringerVerlag
Metagenomicstudies consider the genetic makeup of microbial communities as a whole, rather than their individual member organisms. The functional and metabolic potential of microbial communities can be analyzed by comparing the relative abundance of gene families in their collective genomic sequences (metagenome) under different conditions. Such comparisons require accurate estimation ...
Keywords:
LanderWaterman, function comparison, functional analysis, metagenomics
7
October 2008
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB): Volume 5 Issue 4, October 2008
Publisher: IEEE Computer Society Press
Bibliometrics:
Citation Count: 9
Downloads (6 Weeks): 0, Downloads (12 Months): 3, Downloads (Overall): 260
Full text available:
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The optimal transformation of one tree into another by means of elementary edit operations is an important algorithmic problem that has several interesting applications to computational biology. Here we introduce a constrained form of this problem in which a partial mapping of a set of nodes (the "seeds") in one ...
Keywords:
Graph algorithms, Graph Theory, Discrete Mathematics, Mathematics of Computing, Trees, Biology and genetics, Life and Medical Sciences, Computer Applications
8
September 2008
Journal of Discrete Algorithms: Volume 6 Issue 3, September, 2008
Publisher: Elsevier Science Publishers B. V.
Given two undirected trees T and P, the Subtree Homeomorphism Problem is to find whether T has a subtree t that can be transformed into P by removing entire subtrees, as well as repeatedly removing a degree2 node and adding the edge joining its two neighbors. In this paper we ...
Keywords:
89.20.Ff, Approximate labelled matching, Tree similarity
9
August 2008
Journal of Computer and System Sciences: Volume 74 Issue 5, August, 2008
Publisher: Academic Press, Inc.
We study the problem of sorting binary sequences and permutations by lengthweighted reversals. We consider a wide class of cost functions, namely f(@?) [email protected]?^@a for all @a>=0, where @? is the length of the reversed subsequence. We present tight or nearly tight upper and lower bounds on the worstcase cost of ...
Keywords:
Dynamic programming, Modeling genome rearrangements, Potential functions, Sorting 0/1 sequences by reversals, Sorting by reversals
10
June 2008
Journal of Discrete Algorithms: Volume 6 Issue 2, June, 2008
Publisher: Elsevier Science Publishers B. V.
Consider a 01 matrix M(i,j) with columns C={c"1,c"2,...,c"m}, and rows R, orequivalentlya hypergraph M(R,C) having M as its adjacency matrix (where R are the vertices and C are the hyperedges). Denote r"i={c"jc" [email protected]?C and M(i,j)=1}. We consider the following two problems: (a) Is there a graph H, with vertex set C, ...
Keywords:
Hypergraph, Intersection representation of a matrix, Biological network clustering, Intersection graph, Unicycle graph
11
September 2007
WABI'07: Proceedings of the 7th international conference on Algorithms in Bioinformatics
Publisher: SpringerVerlag
The optimal transformation of one tree into another by means of elementary edit operations is an important algorithmic problem that has several interesting applications to computational biology. We introduce a constrained form of this problem in which a partial mapping of a set of nodes in one tree to a ...
12
August 2007
Bioinformatics: Volume 23 Issue 16, August 2007
Publisher: Oxford University Press
Motivation: Several recent studies attempted to establish measures for the similarity between genes that are based on the topological properties of metabolic networks. However, these approaches offer only a static description of the properties of interest and offer moderate (albeit significant) correlations with pertinent experimental data. Results: Using a constraintbased ...
13
September 2006
WABI'06: Proceedings of the 6th international conference on Algorithms in Bioinformatics
Publisher: SpringerVerlag
We present an effectively computable measure of functional gene similarity that is based on metabolic gene activity across a variety of growth media. We applied this measure to 750 genes comprising the metabolic network of the budding yeast. Comparing the in silico computed functional similarities to those obtained by using ...
14
August 2006
Journal of Combinatorial Theory Series A: Volume 113 Issue 6, August 2006
Publisher: Academic Press, Inc.
We investigate the number of different ways in which a rectangle containing a set of n noncorectilinear points can be partitioned into smaller rectangles by n (nonintersecting) segments, such that every point lies on a segment. We show that when the relative order of the points forms a separable permutation, ...
Keywords:
Guillotine partitions, Schröder numbers, separable permutations, Baxter permutations, rectangular partitions, rectangulations
15
July 2006
Discrete Applied Mathematics: Volume 154 Issue 12, 15 July 2006
Publisher: Elsevier Science Publishers B. V.
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 ...
Keywords:
separable permutations, Baxter permutations, slicing floorplans, mosaic floorplans
16
July 2006
CPM'06: Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
Publisher: SpringerVerlag
A new problem in phylogenetic inference is presented, based on recent biological findings indicating a strong association between reversals (aka inversions ) and repeats . These biological findings are formalized here in a new mathematical model, called repeatannotated phylogenetic trees (RAPT). We show that, under RAPT, the evolutionary process — ...
17
May 2006
Information Processing Letters: Volume 98 Issue 4, 31 May 2006
Publisher: Elsevier NorthHolland, Inc.
Guillotine partitions play an important role in many research areas and application domains, e.g., computational geometry, computer graphics, integrated circuit layout, and solid modeling, to mention just a few. In this paper we present an exact summation formula for the number of structurallydifferent guillotine partitions in d dimensions by n ...
Keywords:
binary space partitions, guillotine partitions, combinatorial problems
18
May 2006
Information Processing Letters: Volume 98 Issue 4, 31 May 2006
Publisher: Elsevier NorthHolland, Inc.
Guillotine partitions play an important role in many research areas and application domains, e.g., computational geometry, computer graphics, integrated circuit layout, and solid modeling, to mention just a few. In this paper we present an exact summation formula for the number of structurallydifferent guillotine partitions in d dimensions by n ...
Keywords:
Binary space partitions, Guillotine partitions, Combinatorial problems
19
September 2005
VLHCC '05: Proceedings of the 2005 IEEE Symposium on Visual Languages and HumanCentric Computing
Publisher: IEEE Computer Society
We present HyperFlow, a novel visual language for information analysis that combines features from visual dataflow and visual query languages into a unified framework. HyperFlow is designed to make it easier for users to retrieve, filter, and manipulate information, using databases alongside e.g. web services, in a transparent, intuitive, reproducible ...
20
August 2005
Proceedings of the 11th Annual International Conference on Computing and Combinatorics  Volume 3595
Publisher: SpringerVerlag New York, Inc.
We consider the number of different ways to divide a rectangle containing n noncorectilinear points into smaller rectangles by n nonintersecting axisparallel segments, such that every point is on a segment. Using a novel counting technique of Santos and Seidel[12], we show an upper bound of O20n/n4 on this number.

