Thesis Archive
The UC San Diego Libraries provide access to official copies of all UC San Diego dissertations. Use Roger (in the UC San Diego Libraries Catalog) to search for UC San Diego Bioinformatics dissertations (and a 2nd search since they're not consistently classified).
| Thesis | Links | |
|---|---|---|
| 2009 | ||
| Nitin Gupta, Ph.D., Bioinformatics and Systems Biology (2009) Computational and Comparative Proteogenomics: Annotating Genomes and Proteomes using Tandem Mass Spectrometry Advisors: Pavel Pevzner, Steven Briggs | Library | |
| Suchit Jhunjhunwala, Ph.D., Biology with a specialization in Bioinformatics (2009) The 3-D Structure of the Immunoglobulin Heavy Chain Locus: Implications for Long-Range Genomic Interactions Advisors: Cornelis Murre, Maho Niwa | Library | Abstract |
| Noah Aaron Zaitlen, Ph.D., Bioinformatics and Systems Biology (2009) Methods for the Analysis of Human Genetic Variation in the Search for the Genetic Basis of Human Disease Advisors: Vineet Bafna, Eleazar Eskin | Library | Abstract |
| Juan Lorenzo Rodriguez Flores, Ph.D., Bioinformatics and Systems Biology (2009) In Silico, In Vitro, In Vivo and In Populo: Regulatory Genetics of Single Nucleotide Polymorphisms in the Phenylethanolamine N-Methyltransferase Promoter Advisors: Daniel T. O'Connor, Shankar Subramaniam | Library | Abstract |
| Gary Chung Hon, Ph.D., Bioinformatics and Systems Biology (2009) Understanding the Global Architecture of Gene Regulation in Human Cells through Analysis of Chromatin Signatures Advisors: Bing Ren, Wei Wang | Library | Abstract |
| Ines Thiele, Ph.D., Bioinformatics (2009) A Stoichiometric Model of E. Coli's Macromolecular Synthesis Machinery and its Integration with Metabolism Advisors: Bernhard Palsson, Steven Briggs | Library | Abstract |
| Ali Bashir, Ph.D., Bioinformatics (2009) Computational Methods for Analyzing and Detecting Genomic Structural Variation: Applications to Cancer Advisors: Vineet Bafna, Nicholas Schork | Library | Abstract |
| Ryan Kelley, Ph.D., Bioinformatics (2009) The Analysis and Integration of High-Throughput Biological Data for Pathway Discovery Advisors: Trey Ideker, Vineet Bafna | Library | Abstract |
| 2008 | ||
| Kasey Robert Hutt, Ph.D., Bioinformatics (2008) High-throughput genomic assays: Applications and analysis of DSL technology and next-generation sequencing Advisors: Michael Rosenfeld, Terry Gaasterland | Library | Abstract |
| Christopher Benner, Ph.D., Bioinformatics (2008) Identification of a Conserved Periodic Promoter Structure in Metazoans Advisors: Christopher Glass, Shankar Subramaniam | Library | Abstract |
| Mark Chaisson, Ph.D., Bioinformatics (2008) Combinatorial Methods for Computational Genomics: Mammalian Phylogenetics Using Micro Inversions and Fragment Assembly with Short Reads Advisors: Pavel Pevzner, Vineet Bafna | Library | Abstract |
| Michele Elizabeth Day, Ph.D., Bioinformatics (2008) Insights into the functionality and targeting of PKA regulatory subunit RIα Advisors: Susan Taylor, Lynn Ten Eyck | Library | Abstract |
| Elaine Ellen Thompson, Ph.D., Bioinformatics (2008) Characterizing Protein Structures by Surface Mapping Advisors: Lynn Ten Eyck, Vineet Bafna | Library | Abstract |
| Samuel Harris Payne, Ph.D., Bioinformatics (2008) Advances in Computational Mass Spectrometry Phosphoprotoemics and Proteogenomics Advisors: Vineet Bafna, William Loomis | Library | Abstract |
| Max W. Chang, Ph.D., Bioinformatics (2008) Computational Structure-Based Methods to Anticipate HIV Drug Resistance Evolution and Accelerate Inhibitor Discovery Advisor: Richard Belew | Abstract | |
| Kristine Mary Briedis, Ph.D., Bioinformatics (2008) The distribution and evolution of protein kinase and phosphatase families in the three superkingdoms of life Advisor: Philip Bourne | Library | Abstract |
| Silpa Suthram, Ph.D., Bioinformatics (2008) Understanding cellular function through the analysis of protein interaction networks Advisor: Trey Ideker | Abstract | |
| 2007 | ||
| Leah Ortiz-Luis Barrera, Ph.D., Bioinformatics (2007) Genome-Wide Mapping And Analysis Of Mammalian Promoters Advisors: Bing Ren, Philip Bourne | Library | Abstract |
| Andrew Robert Joyce, Ph.D., Bioinformatics (2007) Modeling and analysis of the E. coli transcriptional regulatory network: an assessment of its properties, plasticity and role in adaptive evolution Advisors: Bernhard Palsson, Bing Ren | Library | Abstract |
| Stephen Will Tanner, Ph.D., Bioinformatics (2007) Efficient and accurate bioinformatics algorithms for peptide mass spectrometry Advisors: Vineet Bafna, Julian Schroeder | Library | Abstract |
| Derren Barken, Ph.D., Bioinformatics (2007) Temporal encoding and homeostatic control in the IKK-IκB-NF-κB signaling system Advisors: Alexander Hoffmann, Shankar Subramaniam | Abstract | |
| 2006 | ||
| Thuy D. Vo, Ph.D., Bioinformatics (2006) Systems analysis of energy metabolism elucidates the roles of mitochondria in human health and disease Advisors: Bernhard Palsson, Andrew McCulloch | Library | Abstract |
| Coleman A. Mosley, Ph.D., Bioinformatics (2006) Global views of human genetic variation: Single Nucleotide Polymorphisms' (SNPs) effects and their random nature Advisors: Nicholas Schork, Daniel O'Connor | Library | Abstract |
| John Mongan, Ph.D., Bioinformatics (2006) Implicit Solvent Method Development and Application: Fast Molecular Surfaces, Constant PH and Accelerated Dynamics, and Rational Drug Design Advisors: J. Andrew McCammon, Gary Huber | Library | Abstract |
| Degui Zhi, Ph.D., Bioinformatics (2006) Discovery and analysis of mosaic arrangements in biological sequences and structures Advisors: Pavel Pevzner, William Loomis | Library | Abstract |
| 2005 | ||
| Nathan Daniel Price, Ph.D., Bioengineering with a Specialization in Bioinformatics (2005) Unbiased Assessment of Genome-Scale Metabolic Network States Advisors: Bernhard Palsson, Shankar Subramaniam | Library | Abstract |
| Albert Hsiao, Ph.D., Bioengineering with a Specialization in Bioinformatics (2005) Comparative functional genomics of energy metabolism and insulin resistance in mammalian systems Advisors: Shankar Subramaniam, Jerrold Olefsky | Library | Abstract |
| Jason Aaron Papin, Ph.D., Bioengineering with a Specialization in Bioinformatics (2005) Systems Analysis of Cellular Signaling Networks Advisor: Bernhard Palsson | Library | |
| 2004 | ||
| Markus Juhana Herrgard, Ph.D., Bioengineering with a Specialization in Bioinformatics (2004) Reconstruction and systems analysis of genome-scale metabolic and regulatory networks in Saccharomyces cerevisiae Advisor: Bernhard Palsson | Library | Abstract |
| Iman Famili, Ph.D., Bioengineering with a Specialization in Bioinformatics (2004) Systemic analysis of the stoichiometric matrix and kinetic characterization of metabolic networks Advisor: Bernhard Palsson | Library | Abstract |
| 2003 | ||
| Markus Willard Covert, Ph.D., Bioengineering with a Specialization in Bioinformatics (2003) Transcriptional Regulation In Escherichia coli: A Systems Biology Approach Advisor: Bernhard Palsson | Library | Abstract |
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