The Bioinformatics and Computational Biology graduate program emphasizes interdisciplinary training in nine related areas of focus: Bioinformatics, Computational Molecular Biology, Structural and Functional Genomics, Macromolecular Structure and Function, Metabolic and Developmental Networks, Integrative Systems Biology, Information Integration and Data Mining, Biological Statistics, and Mathematical Biology.

Participating Departments

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Theses/Dissertations from 2007

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Assembly and analysis of complex plant genomes, Scott Joseph Emrich

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Bioinformatics in maize genome research, Ling Guo

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Analysis of protein-RNA and protein-peptide interactions in Equine Infectious Anemia Virus (EIAV) infection, Jae-Hyung Lee

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Studies of protein designability using reduced models, Myron Peto

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Computational annotation of eukaryotic gene structures: algorithms development and software systems, Michael Edward Sparks

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Boundary value approaches to molecular dynamics simulation, Peter Thomas Vedell

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Genesis of gene structures and computational analysis of U12-type introns, Matthew Devin Wilkerson

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The design and analysis of microarray experiments using pooled samples for the study of quantitative traits, Wuyan Zhang

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Functional divergence after gene duplication and sequence-structure relationship: a case-study of G-protein alpha subunits, Ying Zheng

Theses/Dissertations from 2006

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Improving text clustering for functional analysis of genes, Jing Ding

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Algorithms and procedures to analyze physiological signals in psychophysiological research, Joset Amy Etzel

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Bayesian recombination detection modeling and application, Fang Fang

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CAVEMol: an immersive 3D molecule viewer, Darrin W. Lemmer

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From pathway to regulon in Arabidopsis, Wiesława Izabela Mentzen

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New methods for designing and analyzing microarray experiments for the detection of differential expression, Justin C. Recknor

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Plant genome informatics: evaluation and analysis of genomic DNA features involved in the transcriptional processing of protein coding genes , Shannon Dwayne Schlueter

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A modular data analysis pipeline for the discovery of novel RNA motifs , Justin Schonfeld

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Computational studies with ESTs: assembly, SNP detection, and applications in alternative splicing , Jianmin Wang

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Distance-based protein structure modeling , Di Wu

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Use of linkage disequilibrium for quantitative trait loci mapping in livestock , Honghua Zhao

Theses/Dissertations from 2005

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Distance-based NMR structure determination and refinement, Feng Cui

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Multi-scale genetic network inference based on time series gene expression profiles, Pan Du

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Identification of interface residues involved in protein-protein and protein-DNA interactions from sequence using machine learning approaches , Changhui Yan

Theses/Dissertations from 2004

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Genomic differences between humans and primates, Tyra Ellen Dunn-Thomas

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EIAV DB: a comprehensive equine infectious anemia (EIAV) virus database, LaRon Maurice Hughes

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Investigation of soybean sudden death syndrome caused by Fusarium solani f. sp. glycines cell-free-culture-filtrates, Junli Ji

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An agent-based computational model of the evolution of reproductive isolation in populations of digital plants , Nicole Patricia Leahy

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BACAP: an assembly program for hierarchical shotgun sequencing, Haining Lin

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The effect of tags on non-local adaptation, Bradley James Powers

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Comparative genomics: multiple genome rearrangement and efficient algorithm development , Shiquan Wu

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Statistical analysis of gene expression profiles, Zhongqi Zhang

Theses/Dissertations from 2003

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Genome wide recognition of tumor necrosis factor (TNF) like ligands in human and Arabidopsis genomes: a structural genomics approach, Zhong Gao

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Functional divergence and genome evolution of vertebrate protein kinases (kinome), Jianying Gu

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Protein-carbohydrate and protein-protein interactions: using models to better understand and predict specific molecular recognition, Alain Teboho Laederach

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Identification of regional motifs in the 5'UTR and their implication in translational control mechanisms, Sachet Ashok Shukla

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Identification and functional analysis of thylakoid membrane proteome , Yingchun Wang

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The mechanism of integration preference to heterochromatin of yeast retrotransposon Ty5 , Weiwu Xie

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DNA sequence-specific recognition by transcriptional factors, Wu Xu

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Branching process models for HIV-1 drug resistant mutants, Hua Zhou

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Statistical analysis of functional divergence in gene families, Huaijun Zhou

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Spliced alignment and its application in Arabidopsis thaliana , Wei Zhu

Theses/Dissertations from 2002

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Consensus properties of supertree construction methods, Lixia Diao

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Spatial clustering of differences in measured homoplasy with respect to protein structure, Kent Allan Vander Velden

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Data-driven discovery of rules for protein function classification based on sequence motifs, Xiangyun Wang

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MetNet DB: a comprehensive metabolic and regulatory network database, Hailong Zhang

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Gene expression pattern analysis, Xiaosi Zhang

Theses/Dissertations from 2001

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Studying the replication mechanism of the yeast retrotransposon Ty5 by molecular and computational approaches, Xiang Gao

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The relationship of sequence similarity and expression pattern similarity between yeast genes within gene families, Yuan Lin

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Functional divergence and age distribution of vertebrate gene families , Yufeng Wang

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Functional analysis of photosystem I complex by site-directed mutagenesis , Wu Xu