Algorithms for Computational Biology: First International - download pdf or read online

By Adrian-Horia Dediu, Carlos Martín-Vide, Bianca Truthe (eds.)

ISBN-10: 3319079522

ISBN-13: 9783319079523

ISBN-10: 3319079530

ISBN-13: 9783319079530

This publication constitutes the refereed complaints of the 1st foreign convention, AlCoB 2014, held in July 2014 in Tarragona, Spain.

The 20 revised complete papers have been conscientiously reviewed and chosen from 39 submissions. The scope of AlCoB contains themes of both theoretical or utilized curiosity, specifically: particular series research, approximate series research, pairwise series alignment, a number of series alignment, series meeting, genome rearrangement, regulatory motif discovering, phylogeny reconstruction, phylogeny comparability, constitution prediction, proteomics: molecular pathways, interplay networks, transcriptomics: splicing versions, isoform inference and quantification, differential research, next-generation sequencing: inhabitants genomics, metagenomics, metatranscriptomics, microbiome research, platforms biology.

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Additional info for Algorithms for Computational Biology: First International Conference, AlCoB 2014, Tarragona, Spain, July 1-3, 2014, Proceedigns

Example text

Vester’s Impact Matrix has only positive entries and therefore we work with the absolute value of the estimated matrix A, without affecting the forthcoming analysis, given that the Impact Matrix has information only about the magnitude of the interactions, and not about their sign. We then calculate the indicators AS, PS and the Indices of Influence Q, P. Afterwards, we identify the most active, reactive, critical and buffering genes in the network, and thus determine their Systemic Role. Finally, the corresponding interpretation of their role is briefly discussed.

Furthermore, we observed that the number of distance computations is slightly larger for the benchmarks from the application. 32 E. Althaus, A. K. Hildebrandt Table 1. seconds) and the number of distance evaluations (in billion) together with the respective standard deviation for different sizes of the priority queue, either having constant size queues or having size growing linearly with the number of points in the cluster. Furthermore, we show the space requirement (in megabyte) of our algorithm.

In our method, we compute the matrix A by means of linear programming. We minimize the L1 -norm of the matrix A, in order to get the simplest matrix that can explain the system’s dynamical behavior (cf. Occam’s razor). Our core question is, is there more information that can be retrieved from analyzing the matrix A? We try to gain insights into the behavior of the individual genes and their role in the system as a total. In the economical literature, we found a method called Sensitivity Model (or Paper Computer ), proposed by Vester and von Hesler in 1980 [9] (usually referred to as Vester’s model).

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Algorithms for Computational Biology: First International Conference, AlCoB 2014, Tarragona, Spain, July 1-3, 2014, Proceedigns by Adrian-Horia Dediu, Carlos Martín-Vide, Bianca Truthe (eds.)

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