Open Access. Powered by Scholars. Published by Universities.®
- Keyword
-
- Single nucleotide polymorphism (2)
- Algorithm (1)
- Alzheimer disease (1)
- Big data (1)
- Branch and bound (1)
-
- Branch and cut (1)
- Chitin (1)
- Clustering (1)
- Cognition (1)
- Combinatorial (1)
- Community detection (1)
- Cplex (1)
- Cut and solve (1)
- Cutting plane (1)
- Data mining (1)
- Distributed (1)
- Experimental evolution (1)
- Genome wide association study (1)
- Learning (1)
- Memory (1)
- Messenger RNA (1)
- Missing heritability (1)
- Mixed integer linear program (1)
- Mpi (1)
- Network clustering (1)
- Np hard (1)
- Optimization (1)
- Parallel (1)
- Polyadenation (1)
- Relaxation (1)
Articles 1 - 5 of 5
Full-Text Articles in Life Sciences
Polya Db3: A Database Cataloging Polyadenation Sites(Pas) Across Different Species And Their Conservation, Ram Mohan Nambiar
Polya Db3: A Database Cataloging Polyadenation Sites(Pas) Across Different Species And Their Conservation, Ram Mohan Nambiar
Theses
Polyadenation is an important process occurring in the messenger RNA that involves cleavage of 3 end nascent mRNAs and addition of poly(A) tails. For this thesis,I present PolyA DB3 ,a database cataloging cleavage and polyadenylation sites (PASs) in several genomes specifically for human,mouse,rat and chicken. This database is based on deep sequencing data. PASs are mapped by the 3’ region extraction and deep sequencing (3’READS) method, ensuring unequivocal PAS identification. Large volume of data based on diverse biological samples is used to increase PAS coverage and provide PAS usage information. Strand-specific RNA-seq data were used to extend annotated 3’ ends …
A Parallelized Implementation Of Cut-And-Solve And A Streamlined Mixed-Integer Linear Programming Model For Finding Genetic Patterns Optimally Associated With Complex Diseases, Michael Yip-Hin Chan
A Parallelized Implementation Of Cut-And-Solve And A Streamlined Mixed-Integer Linear Programming Model For Finding Genetic Patterns Optimally Associated With Complex Diseases, Michael Yip-Hin Chan
Theses
With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as late-onset Alzheimer’s disease (AD), but it has been a challenge to fully uncover the necessary information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases does not involve single markers working alone, but patterns of genetic markers interacting additively or epistatically. But as we move upwards beyond patterns of size two, it quickly becomes computationally infeasible to examine all combinations in the solution space. A common solution to solving …
Transcriptomics Of Learning, Pablo Iturralde
Transcriptomics Of Learning, Pablo Iturralde
Theses
Learning is a basic and important component of behavior yet we have very little empirical information about the interaction between mechanisms of learning and evolution. In our work, we are testing hypotheses about the neurogenetic mechanisms through which animal learning abilities evolve. We are able to test this directly by using experimentally evolved populations of flies, which differ in learning ability. These populations were previously evolved within the lab by creating worlds with different patterns of change following theoretically predicted effects on which enhanced learning will evolve. How has evolution acted to modulate genes and gene expression in the brain …
Hypoxic And Viral Contributions To The Etiopathogenesis Of Schizophrenia: A Whole Transcriptome Analysis, Kathryn A. Gorski
Hypoxic And Viral Contributions To The Etiopathogenesis Of Schizophrenia: A Whole Transcriptome Analysis, Kathryn A. Gorski
Theses
Schizophrenia is a mental illness with a complex and as of yet unclear etiology. It is highly heritable and has a strong polygenic character, however, studies examining the genetics of schizophrenia have not sufficiently explained all variability in its prevalence. Environmental causes are theorized to have a non trivial contribution to the pathoetiology of schizophrenia, including interactions with genetic components, but these mechanisms remain unclear. Analyzing schizophrenia dysfunction using transcriptomic approaches is a paradigm still in its infancy, and fewer studies still have examined non neurological contributions to schizophrenia pathology with next generation sequencing technologies. This pilot study uses several …
Efficient Reduced Bias Genetic Algorithm For Generic Community Detection Objectives, Aditya Karnam Gururaj Rao
Efficient Reduced Bias Genetic Algorithm For Generic Community Detection Objectives, Aditya Karnam Gururaj Rao
Theses
The problem of community structure identification has been an extensively investigated area for biology, physics, social sciences, and computer science in recent years for studying the properties of networks representing complex relationships. Most traditional methods, such as K-means and hierarchical clustering, are based on the assumption that communities have spherical configurations. Lately, Genetic Algorithms (GA) are being utilized for efficient community detection without imposing sphericity. GAs are machine learning methods which mimic natural selection and scale with the complexity of the network. However, traditional GA approaches employ a representation method that dramatically increases the solution space to be searched by …