http://www.teses.usp.br Últimas 10 publicaciones de la Biblioteca Digital de Tesis y Disertaciones de la Universidad de São Paulo Bioinformatics es Wed, 02 Jan 2013 00:00:00 -0300 http://www.teses.usp.br/teses/disponiveis/95/95131/tde-29112012-144348/?&lang=es http://www.teses.usp.br/teses/disponiveis/95/95131/tde-29112012-144348/?&lang=es Ethanol production improvements give rise to the breeding of yeast strains, that became the investigation focus in several research centers. Recently, a wild strain used in Brazilian sugarcane industry was sequenced, the PE-2 strain of Saccharomyces cerevisiae, and this event brought an interest in studying the dynamics of the fermentation of this strain in order to understand which aspects this strain become more adapted to the fermentation conditions, maintaining a high capacity to produce bioethanol.... tde@sc.usp.br (Noronha, Melline Fontes) Disertación de Máster Wed, 02 Jan 2013 00:00:00 -0300 http://www.teses.usp.br/teses/disponiveis/95/95131/tde-27112012-185423/?&lang=es http://www.teses.usp.br/teses/disponiveis/95/95131/tde-27112012-185423/?&lang=es The protein structure prediction can be seen as an optimization problem where given an amino acid sequence, the tertiary protein structure must be found amongst many possible by obtaining energy functions minima. Many researchers have been proposing Evolutionary Computation strategies to find tridimensional structures of proteins; however results are not always satisfactory since among other factors, there are always a great number of local optima in the search space. Usually, the fitness functions... tde@sc.usp.br (Ishivatari, Luís Henrique Uchida) Disertación de Máster Tue, 25 Sep 2012 00:00:00 -0300 http://www.teses.usp.br/teses/disponiveis/95/95131/tde-04092012-134137/?&lang=es http://www.teses.usp.br/teses/disponiveis/95/95131/tde-04092012-134137/?&lang=es The São Paulo Blood Center is responsible to maintain a database with information on each donation. However, this database does not have the quality required by techniques of analysis. For this reason, it is difficult to use it directly to establish systematic relationships between the variables. The main contribution of this paper is a provenance description of attributes selected using classification criteria defined by specialists. We show that it is possible to make detailed investigations using... tde@sc.usp.br (Almeida, Fernanda Nascimento) Tesis Doctoral Mon, 10 Sep 2012 00:00:00 -0300 http://www.teses.usp.br/teses/disponiveis/95/95131/tde-30082012-161501/?&lang=es http://www.teses.usp.br/teses/disponiveis/95/95131/tde-30082012-161501/?&lang=es Many real world problems can be described as optimization problems. In bioinformatics in special, there is multiple sequence alignment, filogeny and RNA and Protein structure prediction, among others. Population based metaheuristics are techniques based in the interaction of a set of candidate solutions as elements of a population. Its use is specially interesting in optimization problems where there is little or no knowledge of the search space. The objective of this work is to study the use of... tde@sc.usp.br (Shimo, Helder Ken) Disertación de Máster Wed, 11 Jul 2012 00:00:00 -0300 http://www.teses.usp.br/teses/disponiveis/95/95131/tde-03072012-172159/?&lang=es http://www.teses.usp.br/teses/disponiveis/95/95131/tde-03072012-172159/?&lang=es This dissertation develops and applies methods to characterize brain regions during resting state. Graphs are used to represent functional MRI connectivity from different brain regions. Vertices represent brain regions and edges represent connectivity. To overcome the visualization and interpretation problems of this form of representation, we developed quantitative methods to characterize its patterns. Methods: For each subject: 1) The reduction of spatial dimensionality of functional magnetic... tde@sc.usp.br (Vieira, Gilson) Disertación de Máster Thu, 28 Jun 2012 00:00:00 -0300 http://www.teses.usp.br/teses/disponiveis/95/95131/tde-22062012-150304/?&lang=es http://www.teses.usp.br/teses/disponiveis/95/95131/tde-22062012-150304/?&lang=es Molecular biology researches are increasingly producing large amounts of data regarding underlying biological phenomena. Bioinformatics is a multidisciplinary research field whose main objective is the development of theories and information systems to help the process of knowledge discovery from biological data. Functional genomics is a field of study bioinformatics concerned with the study of gene function through parallel and large scale expression measurements of a genome. A variety of software... tde@sc.usp.br (Miyazaki, Flavia Akemi) Disertación de Máster Fri, 15 Jun 2012 00:00:00 -0300 http://www.teses.usp.br/teses/disponiveis/95/95131/tde-24042012-223141/?&lang=es http://www.teses.usp.br/teses/disponiveis/95/95131/tde-24042012-223141/?&lang=es Genomic medicine has suggested that the exposure to risk factors since conception may influence gene expression and consequently induce the development of chronic diseases in adulthood. Scientific papers bringing up these discoveries indicate that epigenetics must be exploited to prevent diseases of high prevalence, such as cardiovascular diseases, diabetes and obesity. A large amount of scientific information burdens health care professionals interested in being updated, once searches for accurate... tde@sc.usp.br (Pollettini, Juliana Tarossi) Disertación de Máster Fri, 15 Jun 2012 00:00:00 -0300 http://www.teses.usp.br/teses/disponiveis/95/95131/tde-27052012-225515/?&lang=es http://www.teses.usp.br/teses/disponiveis/95/95131/tde-27052012-225515/?&lang=es Gene expression studies have been of great importance, allowing the development of new therapies, diagnostic exams, drugs and the understanding of a variety of biological processes. Nevertheless, those studies involve some obstacles: a huge number of genes, while only a very few of them are really relevant to the problem at hand; data with the presence of noise; among others. This research project consists of: the study of decision tree induction algorithms; the definition of a methodology capable... tde@sc.usp.br (Perez, Pedro Santoro) Disertación de Máster Tue, 13 Mar 2012 00:00:00 -0300 http://www.teses.usp.br/teses/disponiveis/95/95131/tde-24012012-154506/?&lang=es http://www.teses.usp.br/teses/disponiveis/95/95131/tde-24012012-154506/?&lang=es Histopathology is considered one of the most important diagnostic tools in medical routine and is characterized by the study of structural and morphological changes of the cells in biological tissues caused by diseases. Currently, the visual assessment of the pathologist is the main method used in the histopathological diagnosis of microscopic images obtained from biopsy samples. This diagnosis is usually based on the experience of the pathologist. The use of computational techniques in the processing... tde@sc.usp.br (Miranda, Gisele Helena Barboni) Disertación de Máster Tue, 14 Feb 2012 00:00:00 -0300 http://www.teses.usp.br/teses/disponiveis/95/95131/tde-26012012-161321/?&lang=es http://www.teses.usp.br/teses/disponiveis/95/95131/tde-26012012-161321/?&lang=es Proteins exhibit an enormous variety of biology functions. The knowledge of tertiary structures can help the understanding of the proteins function. According to Anfisen, the native tertiary structure of a protein can be determined by its primary structure information, what could allow that computational methods could be used to predict the tertiary structure when the primary structure is available. However, there is still not a computational tool to solve the structure prediction problem for a large... tde@sc.usp.br (Oliveira, Lariza Laura de) Disertación de Máster Tue, 09 Aug 2011 00:00:00 -0300 http://www.teses.usp.br/teses/disponiveis/95/95131/tde-14072011-052430/?&lang=es http://www.teses.usp.br/teses/disponiveis/95/95131/tde-14072011-052430/?&lang=es The identification and characterization of geometrical and physical-chemical properties in protein vacant spaces aggregates important information for steering rational drug designing and functional characterization of binding and catalytic sites. Therefore, several softwares have been develop during the past two decades in order to perform such characterization. Nevertheless, the existing tools still present a series of limitations such as lack of precision, lack of integrability in large scale protocols,... tde@sc.usp.br (Oliveira, Saulo Henrique Pires de) Disertación de Máster Tue, 09 Aug 2011 00:00:00 -0300 http://www.teses.usp.br/teses/disponiveis/95/95131/tde-27072011-105810/?&lang=es http://www.teses.usp.br/teses/disponiveis/95/95131/tde-27072011-105810/?&lang=es Thanks to recent advances in molecular biology and biochemistry, allied to an ever increasing amount of experimental data, the functional state of thousands of genes can now be extracted simultaneously by using methods such as DNA microarrays, SAGE, and more recently RNA-Seq, generating a massive volume of biological data. The mapping of gene transcription levels at large scale is motivated by the proposition that information of the functional state of an organism is broadly determined by its gene... tde@sc.usp.br (Lopes, Fabricio Martins) Tesis Doctoral Tue, 07 Jun 2011 00:00:00 -0300 http://www.teses.usp.br/teses/disponiveis/95/95131/tde-07062011-115256/?&lang=es http://www.teses.usp.br/teses/disponiveis/95/95131/tde-07062011-115256/?&lang=es We study the relationship between different measures of causality or information flow. We show that the concept of partial measures of dependence are related to the definition of inverse random variables. tde@sc.usp.br (Takahashi, Daniel Yasumasa) Tesis Doctoral Tue, 07 Jun 2011 00:00:00 -0300 http://www.teses.usp.br/teses/disponiveis/95/95131/tde-30052011-223151/?&lang=es http://www.teses.usp.br/teses/disponiveis/95/95131/tde-30052011-223151/?&lang=es In biological systems, the study of gene regulatory networks stability is seen as an important contribution that Mathematics can make to cancer research and that of other genetic diseases. In this work, we consider the concept of ``canalization'' as a consequence of stability in gene regulatory networks. The characteristics of canalized regulatory networks are superficially understood. Hence, we study the canalization concept under a computational framework: a simplified model is proposed to describe... tde@sc.usp.br (Patricio, Vitor Hugo Louzada) Disertación de Máster Thu, 12 May 2011 00:00:00 -0300 http://www.teses.usp.br/teses/disponiveis/95/95131/tde-13022009-150320/?&lang=es http://www.teses.usp.br/teses/disponiveis/95/95131/tde-13022009-150320/?&lang=es Structural Bioinformatics of Proteins modified by Alternative Splicing tde@sc.usp.br (Durham, Elza Helena Andrade Barbosa) Tesis Doctoral Thu, 12 May 2011 00:00:00 -0300 http://www.teses.usp.br/teses/disponiveis/95/95131/tde-02122010-212001/?&lang=es http://www.teses.usp.br/teses/disponiveis/95/95131/tde-02122010-212001/?&lang=es The reason for low rates of sustained viral response (SVR) in HCV patients remains unknown. Several studies suggest that viral load is closely associated to viral and host factors, such age, sex, body weight, transaminase levels and HCV genotype. Moreover, an strong CD8+ T-cell immunity in acute resolving hepatitis C is matched by strong and sustained CD4+ T-cell proliferation to multiple recombinant structural and non-structural viral proteins is responsible for the control of viraemia in HCV infection.... tde@sc.usp.br (Queiróz, Artur Trancoso Lopo de) Tesis Doctoral Thu, 12 May 2011 00:00:00 -0300 http://www.teses.usp.br/teses/disponiveis/95/95131/tde-14122010-095648/?&lang=es http://www.teses.usp.br/teses/disponiveis/95/95131/tde-14122010-095648/?&lang=es Bioinformatics tools are becoming the choice for aiding scientists for gene annotation and for studying gene in physiological conditions of interest. Among those efforts, phylogenetics clustering algorithms and tools for predicting short DNA patterns, such as binding sites for transcription factor, are outlined as essential. To develop a mixture procedure merging this two distant fields of bioinformatics research is a challenge hard to overcome. In the present study, we present our results of trying... tde@sc.usp.br (Almeida, Marcio Augusto Afonso de) Tesis Doctoral Wed, 05 Jan 2011 00:00:00 -0300 http://www.teses.usp.br/teses/disponiveis/95/95131/tde-17092010-123112/?&lang=es http://www.teses.usp.br/teses/disponiveis/95/95131/tde-17092010-123112/?&lang=es Due to the wide diversity of unknown organisms in the environment, 99% of them cannot be grown in traditional culture medium in laboratories. Therefore, metagenomics projects are proposed to study microbial communities present in the environment, from molecular techniques, especially the sequencing. Thereby, for the coming years it is expected an accumulation of sequences produced by these projects. Thus, the sequences produced by genomics and metagenomics projects present several challenges for... tde@sc.usp.br (Cantão, Mauricio Egidio) Tesis Doctoral Tue, 21 Sep 2010 00:00:00 -0300 http://www.teses.usp.br/teses/disponiveis/95/95131/tde-18122008-133618/?&lang=es http://www.teses.usp.br/teses/disponiveis/95/95131/tde-18122008-133618/?&lang=es Recent studies have shown that variation of allelic-specific gene expression is more common than previously thought, reaching up to 50% of human genes. To identify genes displaying differential expression among alleles it is important for the understanding of several diseases, including the cancer. Identification of genes submitted to allelic-specific differential expression is hard, mostly due to the difficulty in evaluating the expression levels of each allele independently. In this work, we developed... tde@sc.usp.br (Souza, Jorge Estefano Santana de) Tesis Doctoral Tue, 21 Sep 2010 00:00:00 -0300 http://www.teses.usp.br/teses/disponiveis/95/95131/tde-31102009-194730/?&lang=es http://www.teses.usp.br/teses/disponiveis/95/95131/tde-31102009-194730/?&lang=es Cellular signaling paths through molecules are one of the main processes of functional control of an organism. The comprehension of signaling molecules functions enables one to understand the metabolic pathways of an organism, along with related biological events and several diseases. The signaling through retinoic acid (RA) and its secondary products is responsible for controlling several functions, such as cellular growth and differentiation, retinas formation and cardio development, and is also... tde@sc.usp.br (Sobreira, Tiago José Paschoal) Tesis Doctoral