Results 1  10
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88
Four Strikes against Physical Mapping of DNA
 JOURNAL OF COMPUTATIONAL BIOLOGY
, 1993
"... Physical Mapping is a central problem in molecular biology ... and the human genome project. The problem is to reconstruct the relative position of fragments of DNA along the genome from information on their pairwise overlaps. We show that four simplified models of the problem lead to NPcomplete ..."
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Cited by 55 (8 self)
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Physical Mapping is a central problem in molecular biology ... and the human genome project. The problem is to reconstruct the relative position of fragments of DNA along the genome from information on their pairwise overlaps. We show that four simplified models of the problem lead to NPcomplete decision problems: Colored unit interval graph completion, the maximum interval (or unit interval) subgraph, the pathwidth of a bipartite graph, and the kconsecutive ones problem for k >= 2. These models have been chosen to reflect various features typical in biological data, including false negative and positive errors, small width of the map and chimericism.
Lethal oxidative damage and mutagenesis are generated by iron in fur mutants of Escherichia coli: protective role of superoxide dismutase
 J Bacteriol
, 1995
"... Lethal oxidative damage and mutagenesis are generated by iron in delta fur mutants of Escherichia coli: protective role of superoxide dismutase. ..."
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Cited by 48 (1 self)
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Lethal oxidative damage and mutagenesis are generated by iron in delta fur mutants of Escherichia coli: protective role of superoxide dismutase.
On the Complexity of DNA Physical Mapping
, 1994
"... The Physical Mapping Problem is to reconstruct the relative position of fragments (clones) of DNA along the genome from information on their pairwise overlaps. We show that two simplified versions of the problem belong to the class of NPcomplete problems, which are conjectured to be computationa ..."
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Cited by 41 (7 self)
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The Physical Mapping Problem is to reconstruct the relative position of fragments (clones) of DNA along the genome from information on their pairwise overlaps. We show that two simplified versions of the problem belong to the class of NPcomplete problems, which are conjectured to be computationally intractable. In one version all clones have equal length, and in another, clone lengths may be arbitrary. The proof uses tools from graph theory and complexity.
Tractability of Parameterized Completion Problems on Chordal, Strongly Chordal and Proper Interval Graphs
, 1994
"... We study the parameterized complexity of three NPhard graph completion problems. The MINIMUM FILLIN problem is to decide if a graph can be triangulated by adding at most k edges. We develop O(c m) and O(k mn + f(k)) algorithms for this problem on a graph with n vertices and m edges. Here f(k ..."
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Cited by 40 (5 self)
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We study the parameterized complexity of three NPhard graph completion problems. The MINIMUM FILLIN problem is to decide if a graph can be triangulated by adding at most k edges. We develop O(c m) and O(k mn + f(k)) algorithms for this problem on a graph with n vertices and m edges. Here f(k) is exponential in k and the constants hidden by the bigO notation are small and do not depend on k. In particular, this implies that the problem is fixedparameter tractable (FPT). The PROPER
Genetic and functional analysis of the multiple antibiotic resistance (mar) locus in Escherichia coli
 J
, 1993
"... Genetic and functional analysis of the multiple antibiotic resistance (mar) locus in Escherichia coli. ..."
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Cited by 38 (10 self)
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Genetic and functional analysis of the multiple antibiotic resistance (mar) locus in Escherichia coli.
Pathwidth, Bandwidth and Completion Problems to Proper Interval Graphs with Small Cliques
 SIAM Journal on Computing
, 1996
"... We study two related problems motivated by molecular biology: ffl Given a graph G and a constant k, does there exist a supergraph G of G which is a unit interval graph and has clique size at most k? ffl Given a graph G and a proper kcoloring c of G, does there exist a supergraph We show th ..."
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Cited by 29 (6 self)
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We study two related problems motivated by molecular biology: ffl Given a graph G and a constant k, does there exist a supergraph G of G which is a unit interval graph and has clique size at most k? ffl Given a graph G and a proper kcoloring c of G, does there exist a supergraph We show that those problems are polynomial for fixed k. On the other hand we prove that the first problem is equivalent to deciding if the bandwidth of G is at most k \Gamma 1. Hence, it is NPhard, and W [t]hard for all t. We also show that the second problem is W [1]hard. This implies that for fixed k, both of the problems are unlikely to have an O(n ) algorithm, where ff is a constant independent of k.
Organization of the Escherichia coli K12 gene cluster responsible for production of the extracellular polysaccharide colanic acid
 J. Bacteriol. 178:4885
, 1996
"... Organization of the Escherichia coli K12 gene cluster responsible for production of the extracellular polysaccharide colanic acid. ..."
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Cited by 24 (1 self)
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Organization of the Escherichia coli K12 gene cluster responsible for production of the extracellular polysaccharide colanic acid.
Identification and molecular characterization of csrA, a pleiotropic gene from Escherichia coli that affects glycogen biosynthesis, gluconeogenesis, cell size, and surface properties
 J Bacteriol
, 1993
"... Identification and molecular characterization of csrA, a pleiotropic gene from Escherichia coli that affects glycogen biosynthesis, gluconeogenesis, cell size, and surface properties. ..."
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Cited by 19 (10 self)
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Identification and molecular characterization of csrA, a pleiotropic gene from Escherichia coli that affects glycogen biosynthesis, gluconeogenesis, cell size, and surface properties.
Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K12 ORF archive): unique resources for biological research. DNA Res
 Sir Paul Nurse, Cancer Research UK Your
, 2005
"... Based on the genomic sequence data of Escherichia coli K12 strain, we have constructed a complete set of cloned individual genes encoding Histidinetagged proteins with or without GFP fused for functional genomic analysis. Each clone encodes a protein of predicted ORF attached by Histidines and sev ..."
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Cited by 18 (1 self)
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Based on the genomic sequence data of Escherichia coli K12 strain, we have constructed a complete set of cloned individual genes encoding Histidinetagged proteins with or without GFP fused for functional genomic analysis. Each clone encodes a protein of predicted ORF attached by Histidines and seven spacer amino acids at the Nterminal end, and five spacer amino acids and GFP at the Cterminal end. SfiI restriction sites are generated at both the N and Cterminal boundaries of ORF upon cloning, which enables easy transfer of ORF to other vector systems by cutting with SfiI. Expression of cloned ORF is under the control of an IPTGinducible promoter, which is strictly repressed by lacI q repressor gene product. The set of cloned ORFs described here should provide unique resources for systematic functional genomic approaches including (i) construction of DNA microarray, (ii) production and purification of proteins, (iii) analysis of protein localization by monitoring GFP fluorescence and (iv) analysis of protein–protein interaction. Key words: Escherichia coli; bacterial functional genomics; ORF clone; resource 1.
Organic solvent tolerance and antibiotic resistance increased by overexpression of marA in Escherichia coli
 Appl. Environ
, 1997
"... of ..."