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Title: Atom distance and interaction between DNA and acetylated histone tails.
Creator: Goordeen, Victoria, Snyder, Patricia Ann
Date Issued: 2013-04-05
PURL: http://purl.flvc.org/fcla/dt/3361087
Subject Headings: Transcription, Genetic, Histones, DNA
Format: Document (PDF)

Title: Characterization of normal mitochondrial inheritance in C. elegans and a reverse genetic approach to identify possible genes involved.
Creator: Wilson, Amber Diane, Florida Atlantic University, LaMunyon, Craig W.
Abstract/Description: Mitochondria are inherited uniparentally in almost all eukaryotic models studied to date. The fathers mitochondria are eliminated and there have been several hypothesis as to how this occurs. One hypothesis is that the sperm mitochondria are actively targeted and destroyed. Ubiquitin has been proposed a possible candidate involved in this process. My research investigated the normal mitochondrial inheritance pattern in C. elegans. I also examined the possible role of the C34F11.1 gene in...
Show moreMitochondria are inherited uniparentally in almost all eukaryotic models studied to date. The fathers mitochondria are eliminated and there have been several hypothesis as to how this occurs. One hypothesis is that the sperm mitochondria are actively targeted and destroyed. Ubiquitin has been proposed a possible candidate involved in this process. My research investigated the normal mitochondrial inheritance pattern in C. elegans. I also examined the possible role of the C34F11.1 gene in mitochondrial inheritance. This gene is sperm-specific and has ubiquitin-ligase properties. It was determined that the normal mitochondrial inheritance pattern in C. elegans is maternal and that the sperm mitochondria are eliminated. It was also concluded that the C34F11.1 gene does not have a role in normal mitochondrial inheritance.
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Date Issued: 2003
PURL: http://purl.flvc.org/fcla/dt/13049
Subject Headings: Caenorhabditis elegans, Mitochondrial DNA
Format: Document (PDF)

Title: A review of the stability of feature selection techniques for bioinformatics data.
Creator: Awada, Wael, Khoshgoftaar, Taghi M., Dittman, David, Wald, Randall, Napolitano, Amri E., Graduate College
Date Issued: 2013-04-12
PURL: http://purl.flvc.org/fcla/dt/3361293
Subject Headings: Bioinformatics, DNA microarrays, Data mining
Format: Document (PDF)

Title: Is there an error correcting code in the base sequence in DNA?.
Creator: Liebovitch, Larry S., Levine, Leo, Tao, Yi, Todorov, Angelo T.
Date Issued: 1996-09
PURL: http://purl.flvc.org/fau/165441
Subject Headings: Biophysics--Research, DNA, Genetics, DNA Repair--genetics, DNA--Analysis--Mathematical models, Genetic code
Format: Document (PDF)

Title: Analysis of Tardigrade Damage Suppressor Protein (Dsup) Expressed in Tobacco.
Creator: Kirke, Justin, Zhang, Xing-Hai, Florida Atlantic University, Department of Biological Sciences, Charles E. Schmidt College of Science
Abstract/Description: DNA damage is one of the most harmful stress inducers in living organisms. Studies have shown that exposure to high doses of various types of radiation cause DNA sequence changes (mutation) and disturb protein synthesis, hormone balance, leaf gas exchange and enzyme activity. Recent discovery of a protein called Damage Suppressor Protein (Dsup), found in the tardigrade species Ramazzotius varieornatus, has shown to reduce the effects of radiation damage in human cell lines. We have generated...
Show moreDNA damage is one of the most harmful stress inducers in living organisms. Studies have shown that exposure to high doses of various types of radiation cause DNA sequence changes (mutation) and disturb protein synthesis, hormone balance, leaf gas exchange and enzyme activity. Recent discovery of a protein called Damage Suppressor Protein (Dsup), found in the tardigrade species Ramazzotius varieornatus, has shown to reduce the effects of radiation damage in human cell lines. We have generated multiple lines of tobacco plants expressing the Dsup gene and preformed numerous tests to show viability and response of these transgenic plants when exposed to mutagenic chemicals, UV radiation and ionizing radiation. We have also investigated Dsup function in association to DNA damage and repair in plants by analyzing the expression of related genes using RT-qPCR. We have also analyzed DNA damage from X-ray and UV treatments using an Alkaline Comet Assay. This project has the potential to help generate plants that are tolerant to more extreme stress environments, particularly DNA damage and mutation, unshielded by our atmosphere. The possibility of growing plants accompanying human space travel and extraterrestrial colonization inspires our imagination. Extremotolerant tardigrade genes such as Dsup may be a valuable avenue in helping to cultivate crops in these future endeavors.
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Date Issued: 2019
PURL: http://purl.flvc.org/fau/fd/FA00013384
Subject Headings: DNA damage, DNA Damage--radiation effects, Tardigrada, DNA Repair, Transgenic plants
Format: Document (PDF)

Title: Relationships between the global structure of genetic networks and mRNA levels measured by cDNA microarrays.
Creator: Liebovitch, Larry S., Shehadeh, Lina A., Jirsa, Viktor K.
Date Issued: 2006-05-16
PURL: http://purl.flvc.org/fau/165446
Subject Headings: DNA microarrays, DNA--genetics, Gene Expression Regulation, DNA- protein interactions, Genetic regulation, Messenger RNA--Analysis
Format: Document (PDF)

Title: DNA fingerprinting of human oral microbiome: a first step towards development of early diagnosis of oral diseases.
Creator: Chakraborty, Shreyasee, Graduate College
Date Issued: 2013-04-12
PURL: http://purl.flvc.org/fcla/dt/3361916
Subject Headings: DNA fingerprinting, Mouth--Diseases, Metagenomics
Format: Document (PDF)

Title: Devising a novel protocol to study 5-hydroxymethylcytosine's role in the consolidation of a methamphatamine [sic] associated contextual memory.
Creator: Odom, John David., Harriet L. Wilkes Honors College
Abstract/Description: DNA methylation, the addition of a methyl group to the 5' position of DNA cytosines (5mC), is generally associated with transcriptional repression during early embryo formation ; however, in the adult brain, it is dynamically regulated and plays an important role in the formation and maintenance of memory. Very recently, it has been hypothesized that DNA hydroxymethylation, the addition of a hydroxyl group to methylated cytosines (5mC), serves as an intermediate in the DNA demethylation...
Show moreDNA methylation, the addition of a methyl group to the 5' position of DNA cytosines (5mC), is generally associated with transcriptional repression during early embryo formation ; however, in the adult brain, it is dynamically regulated and plays an important role in the formation and maintenance of memory. Very recently, it has been hypothesized that DNA hydroxymethylation, the addition of a hydroxyl group to methylated cytosines (5mC), serves as an intermediate in the DNA demethylation pathway. GIven its recent discovery, the role of DNA hydroxymethylation in memory has not yet been explored. In this study, we developed an immunofluorescent triple labeling protocol in order to begin examining the involvement of 5mC and 5hmC in neurons activated by consolidation of a contextual memory associated with methamphetamine in the brain's reward center, the nucleus accumbens.
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Date Issued: 2012
PURL: http://purl.flvc.org/FAU/3359318
Subject Headings: Memory, Physiological aspects, Cognitive neuroscience, DNA, Methylation
Format: Document (PDF)

Title: Bioinformatic analysis of viral genomic sequences and concepts of genome-specific national vaccine design.
Creator: Chatterjee, Sharmistha P., College of Engineering and Computer Science, Department of Computer and Electrical Engineering and Computer Science
Abstract/Description: This research is concerned with analyzing a set of viral genomes to elucidate the underlying characteristics and determine the information-theoretic aspects of the genomic signatures. The goal of this study thereof, is tailored to address the following: (i) Reviewing various methods available to deduce the features and characteristics of genomic sequences of organisms in general, and particularly focusing on the genomes pertinent to viruses; (ii) applying the concepts of information...
Show moreThis research is concerned with analyzing a set of viral genomes to elucidate the underlying characteristics and determine the information-theoretic aspects of the genomic signatures. The goal of this study thereof, is tailored to address the following: (i) Reviewing various methods available to deduce the features and characteristics of genomic sequences of organisms in general, and particularly focusing on the genomes pertinent to viruses; (ii) applying the concepts of information-theoretics (entropy principles) to analyze genomic sequences; (iii) envisaging various aspects of biothermodynamic energetics so as to determine the framework and architecture that decide the stability and patterns of the subsequences in a genome; (iv) evaluating the genomic details using spectral-domain techniques; (v) studying fuzzy considerations to ascertain the overlapping details in genomic sequences; (vi) determining the common subsequences among various strains of a virus by logistically regressing the data obtained via entropic, energetics and spectral-domain exercises; (vii) differentiating informational profiles of coding and non-coding regions in a DNA sequence to locate aberrant (cryptic) attributes evolved as a result of mutational changes and (viii) finding the signatures of CDS of genomes of viral strains toward rationally conceiving plausible designs of vaccines. Commensurate with the topics indicated above, necessary simulations are proposed and computational exercises are performed (with MatLabTM R2009b and other software as needed). Extensive data gathered from open-literature are used thereof and, simulation results are verified. Lastly, results are discussed, inferences are made and open-questions are identified for future research.
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Date Issued: 2013
PURL: http://purl.flvc.org/FAU/3360772
Subject Headings: Genetic engineering, Bioinformatics, Genomics, DNA microarrays, Proteomics
Format: Document (PDF)

Title: Detection and purification of lupus B cells.
Creator: Saccocio, Seth., Florida Atlantic University, Hartmann, James X.
Abstract/Description: This study developed a method for positive selection of anti-single stranded (ss)DNA B cells from peripheral blood mononuclear cells (PBMCs) using a twenty nucleotide oligomer of deoxythymidine (oligo(dT) 20mer), coupled to microscopie magnetic beads. Oligo(dT) 20mer specificity for plasma anti-ssDNA antibody (Ab) was established through indirect enzyme linked immunosorbent assay (ELISA) and flow cytometry. A novel method for semi-quantitative detection of ssDNA specific, B cells from PBMC...
Show moreThis study developed a method for positive selection of anti-single stranded (ss)DNA B cells from peripheral blood mononuclear cells (PBMCs) using a twenty nucleotide oligomer of deoxythymidine (oligo(dT) 20mer), coupled to microscopie magnetic beads. Oligo(dT) 20mer specificity for plasma anti-ssDNA antibody (Ab) was established through indirect enzyme linked immunosorbent assay (ELISA) and flow cytometry. A novel method for semi-quantitative detection of ssDNA specific, B cells from PBMC purified peripheral blood that utilized flow cytometric analysis of oligo(dT) 20mer Texas Red labeled cells was developed. Qualitative purification of ssDNA specific, B cells using oligo(dT) coupled magnetic beads was determined through light microscopy and flow cytometric analysis of positive sclected cell populations. Cross-reaetivity of oligo(dT) 20mer with receptors distinct from membrane Ab, resulted in the use of oligo(dC) 20mer as a useful blocking agent. Results show anti-ssDNA Ab titer does not correlate with numbers of peripheral blood ssDNA specific, B cells.
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Date Issued: 2003
PURL: http://purl.flvc.org/fcla/dt/13086
Subject Headings: Systemic lupus erythematosus, B cells, DNA antibodies
Format: Document (PDF)

Title: EFFECT OF N-METHYL-N'-NITRO-N-NITROSOGUANIDINE (MNNG) ON DNA OF CULTURED RAT HEPATOMA CELLS.
Creator: JHABVALA, PERSEUS, Florida Atlantic University, Stein, Abraham, Charles E. Schmidt College of Science, Department of Biological Sciences
Abstract/Description: The objective of this study was to elucidate the interaction of the carcinogen MNNG with nuclear DNA of Rat Hepatoma cells. The effect of a range of MNNG concentrations on RH cell DNA was studied by an analysis of the DNA fragments obtained in linear alkaline sucrose gradients. A macromolecular analysis of the sedimentation profile for 0.06 mM MNNG (Experiment I), and 0.1 mM MNNG (Experiment III), suggested that the system was paucidisperse and contained at least three components. The major...
Show moreThe objective of this study was to elucidate the interaction of the carcinogen MNNG with nuclear DNA of Rat Hepatoma cells. The effect of a range of MNNG concentrations on RH cell DNA was studied by an analysis of the DNA fragments obtained in linear alkaline sucrose gradients. A macromolecular analysis of the sedimentation profile for 0.06 mM MNNG (Experiment I), and 0.1 mM MNNG (Experiment III), suggested that the system was paucidisperse and contained at least three components. The major component Max 1 has a molecular weight comparable to that known for the mammalian replicon. Max 2 has a molecular weight twice that of Max 1 and Max 3 has a molecular weight half that of Max 1. The size of the replicon is comparable to that obtained by others. Inferences were drawn regarding the structure of chromatin and the role of the distribution of sites hypersensitive to methylation with respect to the oncogenes.
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Date Issued: 1985
PURL: http://purl.flvc.org/fcla/dt/14260
Subject Headings: Carcinogenicity testing, Cancer--Genetic aspects, DNA
Format: Document (PDF)

Title: MITOCHONDRIAL GENETIC DIVERSITY OF THE RED-TAILED MONKEY, CERCOPITHECUS ASCANIUS, IN AFRICAN RAINFORESTS.
Creator: Dutra, Vitor Daniel, Detwiler, Kate M., Florida Atlantic University, Department of Biological Sciences, Charles E. Schmidt College of Science
Abstract/Description: Cercopithecus ascanius is an African primate species encompassing five geographic types with unresolved taxonomy. Recent publications have analyzed C. ascanius genetic diversity and taxonomy; however, few publications have addressed the genetic diversity and phylogenetic relationships of C. ascanius from wild populations. My objectives for this thesis were to determine mtDNA diversity within the C. Ascanius species and investigate C. ascanius genetic structure. Results from this thesis...
Show moreCercopithecus ascanius is an African primate species encompassing five geographic types with unresolved taxonomy. Recent publications have analyzed C. ascanius genetic diversity and taxonomy; however, few publications have addressed the genetic diversity and phylogenetic relationships of C. ascanius from wild populations. My objectives for this thesis were to determine mtDNA diversity within the C. Ascanius species and investigate C. ascanius genetic structure. Results from this thesis support findings from previous studies wherein C. ascanius depicted high mitochondrial diversity and all C. ascanius subspecies form a monophyletic clade within the Cercopithecus genus. Analyzing additional samples of C. ascanius monkeys will strengthen molecular diversity estimation and clarify genetic structure within the C. ascanius lineage.
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Date Issued: 2023
PURL: http://purl.flvc.org/fau/fd/FA00014325
Subject Headings: Mitochondrial DNA, Cercopithecus ascanius, Genetics, Phylogeny
Format: Document (PDF)

Title: A molecular systematic survey of sponge derived microbes.
Creator: Sandell, K., Peterson, C. L., Harmody, Dedra K., McCarthy, Peter J., Pomponi, Shirley A., Lopez, Jose V.
Date Issued: 2004
PURL: http://purl.flvc.org/fau/fd/FA00007425
Subject Headings: Sponges, Marine microbiology, Symbiosis, Polymorphism, Restriction Fragment Length, DNA Fingerprinting
Format: Document (PDF)

Title: Construction of mitochondrion-targeted telomerase for analysis in Saccharomyces cerevisiae.
Creator: Martin, Ricardo., Harriet L. Wilkes Honors College
Abstract/Description: Telomerase is associated with telomere production and nDNA protection. However, studies by Santos et al. have demonstrated that human telomerase has a mitochondrial entry sequence and in the presence of hydrogen peroxide it has been found inside the mitochondrion and may cause mitochondrial DNA mutations. Saccharomyces cerevisiae contains telomerase, but it does not have the mitochondrial entry sequence. To determine if the presence of telomerase in the mitochondria can induce mutations an...
Show moreTelomerase is associated with telomere production and nDNA protection. However, studies by Santos et al. have demonstrated that human telomerase has a mitochondrial entry sequence and in the presence of hydrogen peroxide it has been found inside the mitochondrion and may cause mitochondrial DNA mutations. Saccharomyces cerevisiae contains telomerase, but it does not have the mitochondrial entry sequence. To determine if the presence of telomerase in the mitochondria can induce mutations an experiment was developed in which a mitochondrion entry sequence would be fused to the S. cerevisiae telomerase enzyme. This fusion could then be screened in S. cerevisiae with an ade2 mutation for a simple color assay of mitochondrial activity. To date, no successful transformant has been identified. The frequency of incorrect ligations has been recognized and may indicate that the desired fusion is lethal to E. coli cells.
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Date Issued: 2009
PURL: http://purl.flvc.org/FAU/209994
Subject Headings: Cell membranes, Formation, Mitochondrial DNA, Mutation (Biology), Cell metabolism
Format: Document (PDF)

Title: The Role of Exoribonucleases and MutT Pyrophosphohydrolase in the Surveillance of Oxidatively-damaged RNA.
Creator: Zhang, Jianan, Li, Zhongwei, Florida Atlantic University
Abstract/Description: Three important exoribonucleases degrading RNAs in sequence-independent manner, RNase II, RNase Rand polynucleotide phosphorylase (PNPase), were shown to protect cells against oxidative stress. This is presumably due to the function of the exoribonucleases in the removal of oxidized RNA in cells. MutT pyrophosphohydrolase .was previously reported to scavenge oxidized nucleotides 8-oxoGTP and 8-oxoGDP, prevent their incorporation into RNA. Deficiency of MutT may lead to an increase in the...
Show moreThree important exoribonucleases degrading RNAs in sequence-independent manner, RNase II, RNase Rand polynucleotide phosphorylase (PNPase), were shown to protect cells against oxidative stress. This is presumably due to the function of the exoribonucleases in the removal of oxidized RNA in cells. MutT pyrophosphohydrolase .was previously reported to scavenge oxidized nucleotides 8-oxoGTP and 8-oxoGDP, prevent their incorporation into RNA. Deficiency of MutT may lead to an increase in the level of 8-oxoG in RNA, which may enhance the requirement of the RNA surveillance function of the exoribonucleases. This study focuses on the roles of the RNA-degradation exoribonucleases in the removal of oxidatively-damaged RNA in the mutT background. This work shows that mutT mutation enhances the sensitivity of the RNase mutants to hydrogen peroxide. Growth defect of the pnp mutT mutant was detected even under normal aeration, but was rescued to the level of pnp mutant under anaerobic conditions. The pnp mutT mutant shows high mutator activity observed from LacZ reporter system and high level of 8-oxoG in RNA, strongly suggest that PNPase is responsible for removing 8-oxoG containing RNAs elevated in mutT background. Additionally, genetic instability observed from the mutant lacking RNase II and MutT supports the idea that RNase II may adopt a distinct pathway to reduce deleterious effect from oxidation challenge.
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Date Issued: 2007
PURL: http://purl.flvc.org/fau/fd/FA00000856
Subject Headings: Nucleic acids--Oxidation, DNA repair, Chemical mutagenesis
Format: Document (PDF)

Title: ANTI-DNA ANTIBODIES IN SYSTEMIC LUPUS.
Creator: Cavallo, Michelle Fay, Hartmann, James X., Florida Atlantic University, Department of Biological Sciences, Charles E. Schmidt College of Science
Abstract/Description: Two novel methodologies were developed for purification and functional (DNA hydrolytic) assessment of anti-DNA antibodies of IgG isotype from patients with Systemic Lupus Erythematosus (SLE). Earlier protocols for purification and analysis of antibody hydrolytic abilities were lengthy, laborious, and potentially disruptive to antibody function. Purification protocols failed to capture all four IgG subclasses and produced multiple bands outside the range of IgG on electrophoretic separation....
Show moreTwo novel methodologies were developed for purification and functional (DNA hydrolytic) assessment of anti-DNA antibodies of IgG isotype from patients with Systemic Lupus Erythematosus (SLE). Earlier protocols for purification and analysis of antibody hydrolytic abilities were lengthy, laborious, and potentially disruptive to antibody function. Purification protocols failed to capture all four IgG subclasses and produced multiple bands outside the range of IgG on electrophoretic separation. Hydrolysis assays were discontinuous increasing the likelihood of introducing error and making them better suited to analysis of endpoint kinetics rather than reaction kinetics. A two-step, affinity-based purification protocol was developed which utilized magnetic Dynabeads to capture serum components with binding affinity for a thymine 20mer followed by capture of the antibody components of this initial anti-T 20mer serum fraction using Protein G. A fluorescence-based method for real-time, continuous analysis of anti-DNA antibody hydrolytic activity utilizing hydrolysis probes was developed and used to characterize abzyme reaction kinetic parameters. Anti-DNA antibodies demonstrated significantly different Vmax and Km values in the hydrolysis assay (p <0.001) when compared with a DNAse I control.
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Date Issued: 2019
PURL: http://purl.flvc.org/fau/fd/FA00013363
Subject Headings: Systemic lupus erythematosus, Anti-DNA antibodies, DNA antibodies, Antibodies, Catalytic, Autoantibodies--Analysis, Antibodies--isolation & purification
Format: Document (PDF)

Title: Iron and mitochondrial aging.
Creator: Paez, Rafael., Harriet L. Wilkes Honors College
Abstract/Description: Aging is a process characterized by accumulated oxidative damage to DNA, proteins, and lipids,which leads to the gradual degeneration of cellular activity. Mitochondria play a central role in aging because they produce both cellular energy and oxidative stress. As resultof accumulated oxidative damage, mitochondria function decays, which leads to a cellular energy deficit and compromises cellular function. Iron is an essential nutrient reequired by mitodhondria to function optimally. It has...
Show moreAging is a process characterized by accumulated oxidative damage to DNA, proteins, and lipids,which leads to the gradual degeneration of cellular activity. Mitochondria play a central role in aging because they produce both cellular energy and oxidative stress. As resultof accumulated oxidative damage, mitochondria function decays, which leads to a cellular energy deficit and compromises cellular function. Iron is an essential nutrient reequired by mitodhondria to function optimally. It has been proved that iron supplementation increases the lifespan of several yeast strains, including superoxide dismutase mutants. We are interested in finding where the iron is going and what it might be doing that is beneficial to the cell. We have used Saccharomyces cerevisiae as our molecular model of aging. Our results indicate that the extra iron is being transported into the mitochoindria.
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Date Issued: 2012
PURL: http://purl.flvc.org/FAU/3359313
Subject Headings: Oxidation, Physiological, Aging, Molecular aspects, Mitochondrial DNA, Yeast fungi, Research, Methodology, Free radicals (Chemistry), Pathophysiology
Format: Document (PDF)

Title: Cytogenic bioinformatics of chromosomal aberrations and genetic disorders: data-mining of relevant biostatistical features.
Creator: Karri, Jagadeshwari., College of Engineering and Computer Science, Department of Computer and Electrical Engineering and Computer Science
Abstract/Description: Cytogenetics is a study on the genetic considerations associated with structural and functional aspects of the cells with reference to chromosomal inclusions. Chromosomes are structures within the cells containing body's information in the form of strings of DNA. When atypical version or structural abnormality in one or more chromosomes prevails, it is defined as chromosomal aberrations (CA) depicting certain genetic pathogeny (known as genetic disorders). The present study assumes the...
Show moreCytogenetics is a study on the genetic considerations associated with structural and functional aspects of the cells with reference to chromosomal inclusions. Chromosomes are structures within the cells containing body's information in the form of strings of DNA. When atypical version or structural abnormality in one or more chromosomes prevails, it is defined as chromosomal aberrations (CA) depicting certain genetic pathogeny (known as genetic disorders). The present study assumes the presence of normal and abnormal chromosomal sets in varying proportions in the cytogenetic complex ; and, stochastical mixture theory is invoked to ascertain the information redundancy as a function of fractional abnormal chromosome population. This bioinformatic measure of redundancy is indicated as a track-parameter towards the progression of genetic disorder, for example, the growth of cancer. Lastly, using the results obtained, conclusions are enumerated, inferences are outlined and directions for future studies are considered.
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Date Issued: 2012
PURL: http://purl.flvc.org/FAU/3358597
Subject Headings: Medical genetics, Chromosome abnormalities, Cancer, Genetic aspects, Mutation (Biology), DNA damage
Format: Document (PDF)

Title: Effects of gene selection and data sampling on prediction of breast cancer treatments.
Creator: Heredia, Brian, Khoshgoftaar, Taghi M., Florida Atlantic University, College of Engineering and Computer Science, Department of Computer and Electrical Engineering and Computer Science
Abstract/Description: In recent years more and more researchers have begun to use data mining and machine learning tools to analyze gene microarray data. In this thesis we have collected a selection of datasets revolving around prediction of patient response in the specific area of breast cancer treatment. The datasets collected in this paper are all obtained from gene chips, which have become the industry standard in measurement of gene expression. In this thesis we will discuss the methods and procedures used in...
Show moreIn recent years more and more researchers have begun to use data mining and machine learning tools to analyze gene microarray data. In this thesis we have collected a selection of datasets revolving around prediction of patient response in the specific area of breast cancer treatment. The datasets collected in this paper are all obtained from gene chips, which have become the industry standard in measurement of gene expression. In this thesis we will discuss the methods and procedures used in the studies to analyze the datasets and their effects on treatment prediction with a particular interest in the selection of genes for predicting patient response. We will also analyze the datasets on our own in a uniform manner to determine the validity of these datasets in terms of learning potential and provide strategies for future work which explore how to best identify gene signatures.
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Date Issued: 2014
PURL: http://purl.flvc.org/fau/fd/FA00004292, http://purl.flvc.org/fau/fd/FA00004292
Subject Headings: Antineoplastic agents -- Development, Breast -- Cancer -- Treatment, Cancer -- Genetic aspects, DNA mircroarrays, Estimation theory, Gene expression
Format: Document (PDF)

Title: Gene selection for sample sets with biased distribution.
Creator: Kamal, Abu Hena Mustafa., College of Engineering and Computer Science, Department of Computer and Electrical Engineering and Computer Science
Abstract/Description: Microarray expression data which contains the expression levels of a large number of simultaneously observed genes have been used in many scientific research and clinical studies. Due to its high dimensionalities, selecting a small number of genes has shown to be beneficial for many tasks such as building prediction models from the microarray expression data or gene regulatory network discovery. Traditional gene selection methods, however, fail to take the class distribution into the...
Show moreMicroarray expression data which contains the expression levels of a large number of simultaneously observed genes have been used in many scientific research and clinical studies. Due to its high dimensionalities, selecting a small number of genes has shown to be beneficial for many tasks such as building prediction models from the microarray expression data or gene regulatory network discovery. Traditional gene selection methods, however, fail to take the class distribution into the selection process. In biomedical science, it is very common to have microarray expression data which is severely biased with one class of examples (e.g., diseased samples) significantly less than other classes (e.g., normal samples). These sample sets with biased distributions require special attention from researchers for identification of genes responsible for a particular disease. In this thesis, we propose three filtering techniques, Higher Weight ReliefF, ReliefF with Differential Minority Repeat and ReliefF with Balanced Minority Repeat to identify genes responsible for fatal diseases from biased microarray expression data. Our solutions are evaluated on five well-known microarray datasets, Colon, Central Nervous System, DLBCL Tumor, Lymphoma and ECML Pancreas. Experimental comparisons with the traditional ReliefF filtering method demonstrate the effectiveness of the proposed methods in selecting informative genes from microarray expression data with biased sample distributions.
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Date Issued: 2009
PURL: http://purl.flvc.org/FAU/186330
Subject Headings: Gene expression, Research, Methodology, Medical informatics, Apoptosis, Molecular aspects, DNA microarrays, Research
Format: Document (PDF)

FAU Theses and Dissertations (21)	+ -
Honors Student Theses (4)	+ -
FAU College Collections (3)	+ -
FAU Graduate Student Research (2)	+ -
HBOI Faculty Contributions (1)	+ -

DNA microarrays (6)	+ -
Mitochondrial DNA (6)	+ -
Bioinformatics (4)	+ -
DNA (4)	+ -
Mutation (Biology) (4)	+ -

Cancer--Genetic aspects (3)	+ -
Cell metabolism (3)	+ -
DNA antibodies (3)	+ -
Medical informatics (3)	+ -
Molecular aspects (3)	+ -
Systemic lupus erythematosus (3)	+ -
Aging (2)	+ -
Apoptosis--Molecular aspects (2)	+ -
Cellular signal transduction (2)	+ -
DNA damage (2)	+ -
DNA fingerprinting (2)	+ -
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Gene expression (2)	+ -
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Research (2)	+ -
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Electronic Thesis or Dissertation (21)	+ -
thesis (4)	+ -
article (3)	+ -
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poster (1)	+ -

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Charles E. Schmidt College of Science (10)	+ -
Department of Biological Sciences (10)	+ -
College of Engineering and Computer Science (5)	+ -
Department of Computer and Electrical Engineering and Computer Science (5)	+ -

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