The Experts below are selected from a list of 66294 Experts worldwide ranked by ideXlab platform
S Shiozawa - One of the best experts on this subject based on the ideXlab platform.
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Death receptor 3 (DR3) Gene Duplication in a chromosome region 1p36.3: Gene Duplication is more prevalent in rheumatoid arthritis
Genes & Immunity, 2004Co-Authors: K Osawa, N Takami, K Shiozawa, A Hashiramoto, S ShiozawaAbstract:The death receptor 3 ( DR3 ) Gene is a member of the apoptosis-inducing Fas Gene family. In the current study, fluorescence in situ hybridization (FISH) and Fiber-FISH revealed the existence of a second DR3 Gene ∼200 kb upstream of the original DR3 Gene. The existence of the duplicated DR3 Gene was confirmed by sequencing the corresponding human artificial chromosome clones as well as with quantitative PCR that measured the ratio of the DR3 Gene mutation (Rm), intrinsic to rheumatoid arthritis (RA) patients, by simultaneous amplification of the normal and mutated DR3 sequences. The DR3 Gene Duplication measured by FISH was found to be more frequent in patients with RA as compared to healthy individuals. We therefore surmise that the human DR3 Gene can be duplicated and that this Gene Duplication is more prevalent in patients with RA.
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Death receptor 3 (DR3) Gene Duplication in a chromosome region 1p36.3: Gene Duplication is more prevalent in rheumatoid arthritis.
Genes and immunity, 2004Co-Authors: K Osawa, N Takami, K Shiozawa, A Hashiramoto, S ShiozawaAbstract:The death receptor 3 (DR3) Gene is a member of the apoptosis-inducing Fas Gene family. In the current study, fluorescence in situ hybridization (FISH) and Fiber-FISH revealed the existence of a second DR3 Gene approximately 200 kb upstream of the original DR3 Gene. The existence of the duplicated DR3 Gene was confirmed by sequencing the corresponding human artificial chromosome clones as well as with quantitative PCR that measured the ratio of the DR3 Gene mutation (Rm), intrinsic to rheumatoid arthritis (RA) patients, by simultaneous amplification of the normal and mutated DR3 sequences. The DR3 Gene Duplication measured by FISH was found to be more frequent in patients with RA as compared to healthy individuals. We therefore surmise that the human DR3 Gene can be duplicated and that this Gene Duplication is more prevalent in patients with RA.
K Osawa - One of the best experts on this subject based on the ideXlab platform.
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Death receptor 3 (DR3) Gene Duplication in a chromosome region 1p36.3: Gene Duplication is more prevalent in rheumatoid arthritis
Genes & Immunity, 2004Co-Authors: K Osawa, N Takami, K Shiozawa, A Hashiramoto, S ShiozawaAbstract:The death receptor 3 ( DR3 ) Gene is a member of the apoptosis-inducing Fas Gene family. In the current study, fluorescence in situ hybridization (FISH) and Fiber-FISH revealed the existence of a second DR3 Gene ∼200 kb upstream of the original DR3 Gene. The existence of the duplicated DR3 Gene was confirmed by sequencing the corresponding human artificial chromosome clones as well as with quantitative PCR that measured the ratio of the DR3 Gene mutation (Rm), intrinsic to rheumatoid arthritis (RA) patients, by simultaneous amplification of the normal and mutated DR3 sequences. The DR3 Gene Duplication measured by FISH was found to be more frequent in patients with RA as compared to healthy individuals. We therefore surmise that the human DR3 Gene can be duplicated and that this Gene Duplication is more prevalent in patients with RA.
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Death receptor 3 (DR3) Gene Duplication in a chromosome region 1p36.3: Gene Duplication is more prevalent in rheumatoid arthritis.
Genes and immunity, 2004Co-Authors: K Osawa, N Takami, K Shiozawa, A Hashiramoto, S ShiozawaAbstract:The death receptor 3 (DR3) Gene is a member of the apoptosis-inducing Fas Gene family. In the current study, fluorescence in situ hybridization (FISH) and Fiber-FISH revealed the existence of a second DR3 Gene approximately 200 kb upstream of the original DR3 Gene. The existence of the duplicated DR3 Gene was confirmed by sequencing the corresponding human artificial chromosome clones as well as with quantitative PCR that measured the ratio of the DR3 Gene mutation (Rm), intrinsic to rheumatoid arthritis (RA) patients, by simultaneous amplification of the normal and mutated DR3 sequences. The DR3 Gene Duplication measured by FISH was found to be more frequent in patients with RA as compared to healthy individuals. We therefore surmise that the human DR3 Gene can be duplicated and that this Gene Duplication is more prevalent in patients with RA.
Oliver Eulenstein - One of the best experts on this subject based on the ideXlab platform.
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Mathematical properties of the Gene Duplication cost
Discrete Applied Mathematics, 2019Co-Authors: Paweł Górecki, Agnieszka Mykowiecka, Jarosław Paszek, Oliver EulensteinAbstract:Abstract The Gene Duplication problem seeks a species tree that reconciles given Gene trees with the minimum number of Gene Duplication events, called Gene Duplication cost. To better assess species trees inferred by the Gene Duplication problem we study diameters of the Gene Duplication cost, which describe elementary mathematical properties of this cost. The Gene Duplication cost is defined for a Gene tree, a species tree, and a leaf labeling function that maps the leaf-Genes of the Gene tree to the leaf-species. The diameters of this cost are its maximal values when one topology or both topologies of the trees involved are fixed under all possible leaf labelings and are fundamental in understanding how Gene trees and species trees relate. We describe the properties and formulas for these diameters for bijective and General leaf labelings, and present efficient algorithms to compute the diameters and their corresponding leaf labelings. Finally, we study these diameters under the unrooted reconciliation model in which Gene trees are unrooted. 1
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Consensus properties and their large-scale applications for the Gene Duplication problem.
Journal of bioinformatics and computational biology, 2016Co-Authors: Jucheol Moon, Harris T. Lin, Oliver EulensteinAbstract:Solving the Gene Duplication problem is a classical approach for species tree inference from Gene trees that are confounded by Gene Duplications. This problem takes a collection of Gene trees and seeks a species tree that implies the minimum number of Gene Duplications. Wilkinson et al. posed the conjecture that the Gene Duplication problem satisfies the desirable Pareto property for clusters. That is, for every instance of the problem, all clusters that are commonly present in the input Gene trees of this instance, called strict consensus, will also be found in every solution to this instance. We prove that this conjecture does not Generally hold. Despite this negative result we show that the Gene Duplication problem satisfies a weaker version of the Pareto property where the strict consensus is found in at least one solution (rather than all solutions). This weaker property contributes to our design of an efficient scalable algorithm for the Gene Duplication problem. We demonstrate the performance of our algorithm in analyzing large-scale empirical datasets. Finally, we utilize the algorithm to evaluate the accuracy of standard heuristics for the Gene Duplication problem using simulated datasets.
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An ILP solution for the Gene Duplication problem
BMC Bioinformatics, 2011Co-Authors: Wen-chieh Chang, Gordon J Burleigh, David Fernández-baca, Oliver EulensteinAbstract:Background The Gene Duplication (GD) problem seeks a species tree that implies the fewest Gene Duplication events across a given collection of Gene trees. Solving this problem makes it possible to use large Gene families with complex histories of Duplication and loss to infer phyloGenetic trees. However, the GD problem is NP-hard, and therefore, most analyses use heuristics that lack any performance guarantee.
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An ILP solution for the Gene Duplication problem.
BMC bioinformatics, 2011Co-Authors: Wen-chieh Chang, Gordon J Burleigh, David Fernández-baca, Oliver EulensteinAbstract:The Gene Duplication (GD) problem seeks a species tree that implies the fewest Gene Duplication events across a given collection of Gene trees. Solving this problem makes it possible to use large Gene families with complex histories of Duplication and loss to infer phyloGenetic trees. However, the GD problem is NP-hard, and therefore, most analyses use heuristics that lack any performance guarantee. We describe the first integer linear programming (ILP) formulation to solve instances of the Gene Duplication problem exactly. With simulations, we demonstrate that the ILP solution can solve problem instances with up to 14 taxa. Furthermore, we apply the new ILP solution to solve the Gene Duplication problem for the seed plant phylogeny using a 12-taxon, 6,084-Gene data set. The unique, optimal solution, which places Gnetales sister to the conifers, represents a new, large-scale genomic perspective on one of the most puzzling questions in plant systematics. Although the GD problem is NP-hard, our novel ILP solution for it can solve instances with data sets consisting of as many as 14 taxa and 1,000 Genes in a few hours. These are the largest instances that have been solved to optimally to date. Thus, this work can provide large-scale genomic perspectives on phyloGenetic questions that previously could only be addressed by heuristic estimates.
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An ILP solution for the Gene Duplication problem
BMC Bioinformatics, 2011Co-Authors: Wen-chieh Chang, Gordon J Burleigh, David Fernández-baca, Oliver EulensteinAbstract:Abstract Background The Gene Duplication (GD) problem seeks a species tree that implies the fewest Gene Duplication events across a given collection of Gene trees. Solving this problem makes it possible to use large Gene families with complex histories of Duplication and loss to infer phyloGenetic trees. However, the GD problem is NP-hard, and therefore, most analyses use heuristics that lack any performance guarantee. Results We describe the first integer linear programming (ILP) formulation to solve instances of the Gene Duplication problem exactly. With simulations, we demonstrate that the ILP solution can solve problem instances with up to 14 taxa. Furthermore, we apply the new ILP solution to solve the Gene Duplication problem for the seed plant phylogeny using a 12-taxon, 6, 084-Gene data set. The unique, optimal solution, which places Gnetales sister to the conifers, represents a new, large-scale genomic perspective on one of the most puzzling questions in plant systematics. Conclusions Although the GD problem is NP-hard, our novel ILP solution for it can solve instances with data sets consisting of as many as 14 taxa and 1, 000 Genes in a few hours. These are the largest instances that have been solved to optimally to date. Thus, this work can provide large-scale genomic perspectives on phyloGenetic questions that previously could only be addressed by heuristic estimates.
A Hashiramoto - One of the best experts on this subject based on the ideXlab platform.
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Death receptor 3 (DR3) Gene Duplication in a chromosome region 1p36.3: Gene Duplication is more prevalent in rheumatoid arthritis
Genes & Immunity, 2004Co-Authors: K Osawa, N Takami, K Shiozawa, A Hashiramoto, S ShiozawaAbstract:The death receptor 3 ( DR3 ) Gene is a member of the apoptosis-inducing Fas Gene family. In the current study, fluorescence in situ hybridization (FISH) and Fiber-FISH revealed the existence of a second DR3 Gene ∼200 kb upstream of the original DR3 Gene. The existence of the duplicated DR3 Gene was confirmed by sequencing the corresponding human artificial chromosome clones as well as with quantitative PCR that measured the ratio of the DR3 Gene mutation (Rm), intrinsic to rheumatoid arthritis (RA) patients, by simultaneous amplification of the normal and mutated DR3 sequences. The DR3 Gene Duplication measured by FISH was found to be more frequent in patients with RA as compared to healthy individuals. We therefore surmise that the human DR3 Gene can be duplicated and that this Gene Duplication is more prevalent in patients with RA.
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Death receptor 3 (DR3) Gene Duplication in a chromosome region 1p36.3: Gene Duplication is more prevalent in rheumatoid arthritis.
Genes and immunity, 2004Co-Authors: K Osawa, N Takami, K Shiozawa, A Hashiramoto, S ShiozawaAbstract:The death receptor 3 (DR3) Gene is a member of the apoptosis-inducing Fas Gene family. In the current study, fluorescence in situ hybridization (FISH) and Fiber-FISH revealed the existence of a second DR3 Gene approximately 200 kb upstream of the original DR3 Gene. The existence of the duplicated DR3 Gene was confirmed by sequencing the corresponding human artificial chromosome clones as well as with quantitative PCR that measured the ratio of the DR3 Gene mutation (Rm), intrinsic to rheumatoid arthritis (RA) patients, by simultaneous amplification of the normal and mutated DR3 sequences. The DR3 Gene Duplication measured by FISH was found to be more frequent in patients with RA as compared to healthy individuals. We therefore surmise that the human DR3 Gene can be duplicated and that this Gene Duplication is more prevalent in patients with RA.
K Shiozawa - One of the best experts on this subject based on the ideXlab platform.
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Death receptor 3 (DR3) Gene Duplication in a chromosome region 1p36.3: Gene Duplication is more prevalent in rheumatoid arthritis
Genes & Immunity, 2004Co-Authors: K Osawa, N Takami, K Shiozawa, A Hashiramoto, S ShiozawaAbstract:The death receptor 3 ( DR3 ) Gene is a member of the apoptosis-inducing Fas Gene family. In the current study, fluorescence in situ hybridization (FISH) and Fiber-FISH revealed the existence of a second DR3 Gene ∼200 kb upstream of the original DR3 Gene. The existence of the duplicated DR3 Gene was confirmed by sequencing the corresponding human artificial chromosome clones as well as with quantitative PCR that measured the ratio of the DR3 Gene mutation (Rm), intrinsic to rheumatoid arthritis (RA) patients, by simultaneous amplification of the normal and mutated DR3 sequences. The DR3 Gene Duplication measured by FISH was found to be more frequent in patients with RA as compared to healthy individuals. We therefore surmise that the human DR3 Gene can be duplicated and that this Gene Duplication is more prevalent in patients with RA.
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Death receptor 3 (DR3) Gene Duplication in a chromosome region 1p36.3: Gene Duplication is more prevalent in rheumatoid arthritis.
Genes and immunity, 2004Co-Authors: K Osawa, N Takami, K Shiozawa, A Hashiramoto, S ShiozawaAbstract:The death receptor 3 (DR3) Gene is a member of the apoptosis-inducing Fas Gene family. In the current study, fluorescence in situ hybridization (FISH) and Fiber-FISH revealed the existence of a second DR3 Gene approximately 200 kb upstream of the original DR3 Gene. The existence of the duplicated DR3 Gene was confirmed by sequencing the corresponding human artificial chromosome clones as well as with quantitative PCR that measured the ratio of the DR3 Gene mutation (Rm), intrinsic to rheumatoid arthritis (RA) patients, by simultaneous amplification of the normal and mutated DR3 sequences. The DR3 Gene Duplication measured by FISH was found to be more frequent in patients with RA as compared to healthy individuals. We therefore surmise that the human DR3 Gene can be duplicated and that this Gene Duplication is more prevalent in patients with RA.