Fast vicinity-upgrade algorithm for rectilinear steiner trees

Chua, Jacqueline Kia Kee; Lim, Yang Choon

doi:10.1049/el:19910710

Cited by 2 publications

(3 citation statements)

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“…The FTD seeds were mapped to the weighted interactome, and a FTD-related sub-network was constructed by adding new genes to connect FTD genes solving a Steiner tree problem [ 30 – 33 ], minimizing the sum of weights of every edge in the sub-graph. We applied a modified shortest path heuristic (SPH) distance algorithm, from Kou et al .…”

Section: Methodsmentioning

confidence: 99%

“…We applied a modified shortest path heuristic (SPH) distance algorithm, from Kou et al . solution [ 33 ], implemented in our subnet() R function. Our algorithm selected outgoing shortest paths combing the edge weights by Fisher’s method and testing the statistical significance (p < 0.05) with multiple comparison Bonferroni correction.…”

Section: Methodsmentioning

confidence: 99%

“…Genetic information encoded in the GWAS data was used to select seeds and weight the differential gene-gene co-variation, to reduce the network to its essential parts, removing non-informative noise and misleading nodes. To this end, we performed Steiner tree search [ 30 – 33 ], combined to Structural Equation Model (SEM) analysis [ 34 – 36 ]. Furthermore, we know that complex disorders tend to form specific sub-network structures, corresponding to groups of perturbed disease-associated genes [ 13 – 18 , 28 , 29 ].…”

Section: Introductionmentioning

confidence: 99%

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A novel network analysis approach reveals DNA damage, oxidative stress and calcium/cAMP homeostasis-associated biomarkers in frontotemporal dementia

et al. 2017

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Frontotemporal Dementia (FTD) is the form of neurodegenerative dementia with the highest prevalence after Alzheimer’s disease, equally distributed in men and women. It includes several variants, generally characterized by behavioural instability and language impairments. Although few mendelian genes (MAPT, GRN, and C9orf72) have been associated to the FTD phenotype, in most cases there is only evidence of multiple risk loci with relatively small effect size. To date, there are no comprehensive studies describing FTD at molecular level, highlighting possible genetic interactions and signalling pathways at the origin FTD-associated neurodegeneration. In this study, we designed a broad FTD genetic interaction map of the Italian population, through a novel network-based approach modelled on the concepts of disease-relevance and interaction perturbation, combining Steiner tree search and Structural Equation Model (SEM) analysis. Our results show a strong connection between Calcium/cAMP metabolism, oxidative stress-induced Serine/Threonine kinases activation, and postsynaptic membrane potentiation, suggesting a possible combination of neuronal damage and loss of neuroprotection, leading to cell death. In our model, Calcium/cAMP homeostasis and energetic metabolism impairments are primary causes of loss of neuroprotection and neural cell damage, respectively. Secondly, the altered postsynaptic membrane potentiation, due to the activation of stress-induced Serine/Threonine kinases, leads to neurodegeneration. Our study investigates the molecular underpinnings of these processes, evidencing key genes and gene interactions that may account for a significant fraction of unexplained FTD aetiology. We emphasized the key molecular actors in these processes, proposing them as novel FTD biomarkers that could be crucial for further epidemiological and molecular studies.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A novel network analysis approach reveals DNA damage, oxidative stress and calcium/cAMP homeostasis-associated biomarkers in frontotemporal dementia

et al. 2017

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A new generalized row-based global router

Swartz¹,

Sechen²

Proceedings of 1993 International Conference on Computer Aided Design (ICCAD)

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This paper presents a new generalized row-based global router suitable for standard cell, gate-array, and seaofgates integrated circuits. It is the jrst row-based global router to explicitly minimize chip area. This global router uses adaptive Steiner trees to minimize chip area. The results were vastly improved over typical minimum wire length Steiner trees. This global router automatically adapts to technologies. In addition, optimal feedthrough placement is accomplished using linear assignment. Throughout the algorithm, timing constraints are taken into account. Also, a unique vertical constraint cycle minimization step eases the task for LEA channel routers. Finally, it is shown that this global router outperformsother global routers for all of the MCNC benchmark circuits which were tested.

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Fast vicinity-upgrade algorithm for rectilinear steiner trees

Cited by 2 publications

References 0 publications

A novel network analysis approach reveals DNA damage, oxidative stress and calcium/cAMP homeostasis-associated biomarkers in frontotemporal dementia

A novel network analysis approach reveals DNA damage, oxidative stress and calcium/cAMP homeostasis-associated biomarkers in frontotemporal dementia

A new generalized row-based global router

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