By Joao Carlos Setubal, Sergio Verjovski-Almeida
This e-book constitutes the refereed court cases 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 offered including three invited papers have been conscientiously reviewed and chosen from fifty five submissions. The papers deal with a extensive diversity of present issues in computational biology and bioinformatics.
Read Online or Download Advances in Bioinformatics and Computational Biology: Brazilian Symposium on Bioinformatics, BSB 2005, Sao Leopoldo, Brazil, July 27-29, 2005, Proceedings PDF
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Additional resources for Advances in Bioinformatics and Computational Biology: Brazilian Symposium on Bioinformatics, BSB 2005, Sao Leopoldo, Brazil, July 27-29, 2005, Proceedings
Networks of reactions violating any of these laws are unphysical and cannot occur in nature. In this paper we describe a technique that perturbs an unfeasible network to produce a metabolic network that satisﬁes the two fundamental laws. This algorithm has been applied to study the metabolic pathways of E. coli. 1 Introduction With the availability of many completely sequenced genomes and much gene expression data the study of metabolic pathways  is entering a phase where constraint-based approaches will be useful in quantitative analysis .
N∗k , . . , 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 .
Type II pathways are those that have exchange ﬂuxes corresponding to metabolites like ATP, NADH, with the rest of the pathway being an internal cycle. These pathways represent futile cycles. Type III pathways have no exchange ﬂuxes, and these represent internal cycles corresponding to internal ﬂuxes. Type III loops in the ﬂux direction violate the second law of thermodynamics . For example, the pyruvate-kinase reaction ﬂux could be part of a type III loop. These loops are detected and removed by our algorithm.
Advances in Bioinformatics and Computational Biology: Brazilian Symposium on Bioinformatics, BSB 2005, Sao Leopoldo, Brazil, July 27-29, 2005, Proceedings by Joao Carlos Setubal, Sergio Verjovski-Almeida