Biostatistics Commons^™

An Application In Bioinformatics : A Comparison Of Affymetrix And Compugen Human Genome Microarrays, Milind Misra

Theses

The human genome microarrays from Compugen® and Affymetrix® were compared in the context of the emerging field of computational biology. The two premier database servers for genomic sequence data, the National Center for Biotechnology Information and the European Bioinformatics Institute, were described in detail. The various databases and data mining tools available through these data servers were also discussed. Microarrays were examined from a historical perspective and their main current applications-expression analysis, mutation analysis, and comparative genomic hybridization-were discussed. The two main types of microarrays, cDNA spotted microarrays and high-density spotted microarrays were analyzed by exploring the human genome microarray …

A Method For Developing In-Silico Protein Homologs, Susan Mcclatchy

Theses

Computational methods for identifying and screening the most promising drug receptor candidates in the human genome are of great interest to drug discovery researchers. Successful methods will accurately identify and narrow the field of potential drug receptor candidates. This study details one such method.

The method described here begins with the assumption that novel drug receptors have high sequence similarity to established drug receptors. The similarity search program FASTA3 aligns translated sequences of the human genome to known drug receptor sequences and ranks these alignments by measuring their statistical significance. Query results returned by FASTA3 are assembled into "in-silico proteins" …

Analysis Of Gene Expression Data Using Expressionist 3.1 And Genespring 4.2, Indu Shrivastava

Theses

The purpose of this study was to determine the differences in the gene expression analysis methods of two data mining tools, Expressionistic^TM 3.1 and GeneSpring^TM 4.2 with focus on basic statistical analysis and clustering algorithms. The data for this analysis was derived from the hybridization of Rattus norvegicus RNA to the Affymetrix RG34A GeneChip. This analysis was derived from experiments designed to identify changes in gene expression patterns that were induced in vivo by an experimental treatment.

The tools were found to be comparable with respect to the list of statistically significant genes that were up-regulated by more …

Statistical Image Analysis Of Spotted Arrays, Filippo Posta

Theses

There is a lot of systematic and specific variability in microarray experiments, this variability affects measured gene expression levels, leading to unreliable gene profiling or an heavy load of extra experiment to statistically confirm the data observed in one experiment.

The aim of this work is to systematically analyze, using statistics, the image derived from a cDNA microarray experiment to have a better understanding of this variability and thus a better confidence over the data obtained from an experiment.

Using technologies available at the Center for Applied Genomics, Newark, New Jersey. Selected images derived from different type of microarray experiments …

An Algorithm For Estimating The Quality Of Microarrays, Ajeet S. Sodhi

Theses

Microarray technology is currently one of the most valuable gene expression tools in molecular biology allowing the experimenter to simultaneously quantify the expression of thousands of genes. It is also one of the most difficult tools to use accurately as each microarray produces a large amount of information that needs to be inspected and normalized before analysis. As the size of a microarray or number of replicates increase, the use of manual inspection becomes impractical. The aim of this thesis is to introduce an algorithm that evaluates each feature of a microarray from the scanned data file. A quality score …

Comparative Molecular Field Analysis (Comfa) Of Protonated Methylphenidate Phenyl-Substituted Analogs, Kathleen Mary Gilbert

Theses

Protonated methylphenidate (pMP) and several phenyl-substituted pMP analogs were analyzed using Comparative Molecular Field Analysis (CoMFA) to develop a pharmacophore for dopamine transporter (DAT) binding. This research is a part of an interdisciplinary study on using methylphenidate (MP) analogs to block the binding of cocaine to the DAT as a treatment for addiction.

A random search conformational analysis using key pMP torsional angles was performed to create conformer families representing possible bioactive conformations. The lowest energy pMP conformer of each family was used as a template to create phenyl-substituted pMP analogs.

Partial least squares analysis was used to determine the …

Bottom-Up Design Of Artificial Neural Network For Single-Lead Electrocardiogram Beat And Rhythm Classification, Srikanth Thiagarajan

Doctoral Dissertations

Performance improvement in computerized Electrocardiogram (ECG) classification is vital to improve reliability in this life-saving technology. The non-linearly overlapping nature of the ECG classification task prevents the statistical and the syntactic procedures from reaching the maximum performance. A new approach, a neural network-based classification scheme, has been implemented in clinical ECG problems with much success. The focus, however, has been on narrow clinical problem domains and the implementations lacked engineering precision. An optimal utilization of frequency information was missing. This dissertation attempts to improve the accuracy of neural network-based single-lead (lead-II) ECG beat and rhythm classification. A bottom-up approach defined …