This dissertation presents applications of machine learning and statistical approaches to infer protein-DNA bindings in the presence of epigenetic modifications. Epigenetic modifications are alterations to the DNA resulting in gene expression regulation where the structure of the DNA remains unaltered. It is a heritable and reversible modification and often involves addition or deletion of certain chemical compounds to the DNA. Histone modification is an epigenetic change that involves alteration of the histone proteins – thus changing the chromatin (DNA wound around histone proteins) structure – or addition of methyl-groups to the Cytosine base adjacent to a Guanine base. Epigenetic factors often interfere in gene expression regulation by promoting or inhibiting protein-DNA bindings. Such proteins are known as transcription factors. Transcription is the first step of gene expression where a particular segment of DNA is copied into the messenger-RNA (mRNA). Transcription factors orchestrate gene activity and are crucial for normal cell function in any organism. For example, deletion/mutation of certain transcription factors such as MEF2 have been associated with neurological disorders such as autism and schizophrenia. In this dissertation, different computational pipelines are described that use mathematical models to explain how the protein-DNA bindings are mediated by histone modifications and DNA-methylation affecting different regions of the brain at different stages of development. Multi-layer Markov models, Inhomogeneous Poisson analyses are used on data from brain to show the impact of epigenetic factors on protein-DNA bindings. Such data driven approaches reinforce the importance of epigenetic factors in governing brain cell differentiation into different neuron types, regulation of memory and promotion of normal brain development at the early stages of life. / Doctor of Philosophy / A cell is the basic unit of any living organism. Cells contain nucleus that contains DNA, self replicating material often called the blueprint of life. For sustenance of life, cells must respond to changes in our environment. Gene expression regulation, a process where specific regions of the DNA (genes) are copied into messenger RNA (mRNA) molecules and then translated into proteins, determines the fate of a cell. It is known that various environmental (such as diet, stress, social interaction) and biological factors often indirectly affect gene expression regulation. In this dissertation, we use machine learning approaches to predict how certain biological factors interfere indirectly with gene expression by changing specific properties of DNA. We expect our findings will help in understanding the interplay of these factors on gene expression.

Pesquisas recentes em medicina genômica sugerem que fatores de risco que incidem desde a concepção de uma criança até o final de sua adolescência podem influenciar no desenvolvimento de doenças crônicas da idade adulta. Artigos científicos com descobertas e estudos inovadores sobre o tema indicam que a epigenética deve ser explorada para prevenir doenças de alta prevalência como doenças cardiovasculares, diabetes e obesidade. A grande quantidade de artigos disponibilizados diariamente dificulta a atualização de profissionais, uma vez que buscas por informação exata se tornam complexas e dispendiosas em relação ao tempo gasto na procura e análise dos resultados. Algumas tecnologias e técnicas computacionais podem apoiar a manipulação dos grandes repositórios de informações biomédicas, assim como a geração de conhecimento. O presente trabalho pesquisa a descoberta automática de artigos científicos que relacionem doenças crônicas e fatores de risco para as mesmas em registros clínicos de pacientes. Este trabalho também apresenta o desenvolvimento de um arcabouço de software para sistemas de vigilância que alertem profissionais de saúde sobre problemas no desenvolvimento humano. A efetiva transformação dos resultados de pesquisas biomédicas em conhecimento possível de ser utilizado para beneficiar a saúde pública tem sido considerada um domínio importante da informática. Este domínio é denominado Bioinformática Translacional (BUTTE,2008). Considerando-se que doenças crônicas são, mundialmente, um problema sério de saúde e lideram as causas de mortalidade com 60% de todas as mortes, o presente trabalho poderá possibilitar o uso direto dos resultados dessas pesquisas na saúde pública e pode ser considerado um trabalho de Bioinformática Translacional. / 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 information become complex and expensive. Some computational techniques might support management of large biomedical information repositories and discovery of knowledge. This study presents a framework to support surveillance systems to alert health professionals about human development problems, retrieving scientific papers that relate chronic diseases to risk factors detected on a patient\'s clinical record. As a contribution, healthcare professionals will be able to create a routine with the family, setting up the best growing conditions. According to Butte, the effective transformation of results from biomedical research into knowledge that actually improves public health has been considered an important domain of informatics and has been called Translational Bioinformatics. Since chronic diseases are a serious health problem worldwide and leads the causes of mortality with 60% of all deaths, this scientific investigation will probably enable results from bioinformatics researches to directly benefit public health.

Pesquisas recentes em medicina genômica sugerem que fatores de risco que incidem desde a concepção de uma criança até o final de sua adolescência podem influenciar no desenvolvimento de doenças crônicas da idade adulta. Artigos científicos com descobertas e estudos inovadores sobre o tema indicam que a epigenética deve ser explorada para prevenir doenças de alta prevalência como doenças cardiovasculares, diabetes e obesidade. A grande quantidade de artigos disponibilizados diariamente dificulta a atualização de profissionais, uma vez que buscas por informação exata se tornam complexas e dispendiosas em relação ao tempo gasto na procura e análise dos resultados. Algumas tecnologias e técnicas computacionais podem apoiar a manipulação dos grandes repositórios de informações biomédicas, assim como a geração de conhecimento. O presente trabalho pesquisa a descoberta automática de artigos científicos que relacionem doenças crônicas e fatores de risco para as mesmas em registros clínicos de pacientes. Este trabalho também apresenta o desenvolvimento de um arcabouço de software para sistemas de vigilância que alertem profissionais de saúde sobre problemas no desenvolvimento humano. A efetiva transformação dos resultados de pesquisas biomédicas em conhecimento possível de ser utilizado para beneficiar a saúde pública tem sido considerada um domínio importante da informática. Este domínio é denominado Bioinformática Translacional (BUTTE,2008). Considerando-se que doenças crônicas são, mundialmente, um problema sério de saúde e lideram as causas de mortalidade com 60% de todas as mortes, o presente trabalho poderá possibilitar o uso direto dos resultados dessas pesquisas na saúde pública e pode ser considerado um trabalho de Bioinformática Translacional. / 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 information become complex and expensive. Some computational techniques might support management of large biomedical information repositories and discovery of knowledge. This study presents a framework to support surveillance systems to alert health professionals about human development problems, retrieving scientific papers that relate chronic diseases to risk factors detected on a patient\'s clinical record. As a contribution, healthcare professionals will be able to create a routine with the family, setting up the best growing conditions. According to Butte, the effective transformation of results from biomedical research into knowledge that actually improves public health has been considered an important domain of informatics and has been called Translational Bioinformatics. Since chronic diseases are a serious health problem worldwide and leads the causes of mortality with 60% of all deaths, this scientific investigation will probably enable results from bioinformatics researches to directly benefit public health.