Advances in Bioinformatics and Computational Biology: by Joao Carlos Setubal, Sergio Verjovski-Almeida

By Joao Carlos Setubal, Sergio Verjovski-Almeida

This e-book constitutes the refereed complaints of the Brazilian Symposium on Bioinformatics, BSB 2005, held in Sao Leopoldo, Brazil in July 2005.

The 15 revised complete papers and 10 revised prolonged abstracts provided including three invited papers have been rigorously reviewed and chosen from fifty five submissions. The papers deal with a huge variety of present themes in computational biology and bioinformatics.

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Additional info for Advances in Bioinformatics and Computational Biology: Brazilian Symposium on Bioinformatics, BSB 2005, Sao Leopoldo, Brazil, July 27-29, 2005, Proceedings

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N∗i , . . , N∗nl ], where N∗k is the kth column vector of N . Also N∗k = [n1k , n2k , . . , nik , . . , nni k ]T , where nik is the (i, k) th entry of the matrix N . 4 No-Cycle Feasibility Constraint In this section we introduce a simple test to detect the presence of loops in a metabolic network that violate the second law of thermodynamics. To do so we take advantage of the directionality of the flow of fluxes in the cycle. The number of rows nl of the K matrix gives the number of loops or cycles in the network [11].

According to the second law, fluxes must flow from reactants of higher chemical potential to ones of lower chemical potential, since the entropy of the reaction is always non-decreasing [9]. The FBA analysis allows an infinite number of fluxes, many of these flux vectors violate the second law and hence are unfeasible. From a network topology point of view, the presence of cycles in the flux direction violates the law of production of entropy. Applying Kirchoff’s loop law, eliminates these entropy violating cycles.

2003 Oct 31;302(5646):842-6. 6. al, Identification of transcribed sequences in Arabidopsis thaliana by using highresolution genome tiling arrays, Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4453-8. Epub 2005 Mar 8. 7. al, A gene expression map for the euchromatic genome of Drosophila melanogaster, Science. 2004 Oct 22;306(5696):655-60. 8. al, Distribution of NF-kappaB-binding sites across human chromosome 22, Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12247-52. Epub 2003 Oct 3. 9. al, Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNA, Cell.

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