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 2016

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Dynamic self-assembling DNA nanosystems: design and engineering, Divita Mathur

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Scalable and reproducible genome analysis in the age of next-generation genome sequencing, Daniel Scott Standage

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Computational methods for integrated analysis of omics and pathway data, Jesse R. Walsh

Theses/Dissertations from 2015

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Sociogenomics of social organization: mechanistic and evolutionary underpinnings of caste development and facial recognition in paper wasps, Ali Berens

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Computational prediction, experiment design and statistical validations of non-coding regulatory RNA, Hyejin Cho

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Use of NGS for discovery of viruses in the soybean aphid, Ying Feng

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Studies on the causes and consequences of sex determination in turtles, Srihari Radhakrishnan

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Representing protein native states using weighted conformation ensembles, Vijay Vammi

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Mechanisms and impact of alternative transposition-induced segmental duplications, Tao Zuo

Theses/Dissertations from 2014

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Cytonuclear and small RNA evolution in diploid and polyploid plant species, Lei Gong

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Understanding conformational transitions in RAS proteins using all-atom and coarse-grained molecular dynamics, Abhijeet Kapoor

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A next generation of studies: Heterosis and inbreeding depression, Shreyartha Mukherjee

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The mitochondrial ratchet: Examples from non-bilaterian animals, Walker Pett

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Topics in cancer genomics, Sachet Ashok Shukla

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Coarsegrained modeling and electrostatics of phospholipid monolayers, Sweta Vangaveti

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Sequence-based prediction of RNA-protein interactions, Rasna Rani Walia

Theses/Dissertations from 2013

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Molecular regulation of IL-2 inducible T-cell kinase (Itk) and the Tec kinases: A combined experimental and computational study, with emphasis on the N-terminal Pleckstrin Homology domain, Scott Edward Boyken

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Computational and experimental analysis of TAL effector-DNA binding, Erin Lynn Doyle

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Understand biological regulatory systems using computational models: Reconstruction, Analysis and Integration, Yao Fu

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Statistical summary of protein structures, Yuanyuan Huang

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Building and simulating protein machines, Ataur Rahim Katebi

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Computational prediction of RNA-protein interaction partners and interfaces, Usha Muppirala

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On inferring and interpreting genetic population structure - applications to conservation, and the estimation of pairwise genetic relatedness, Arun Sethuraman

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Integration of large datasets for plant model organisms, Yves Sucaet

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Workflow tools for biological applications, Marie C. Vendettuoli

Theses/Dissertations from 2012

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Immunoglobulin motions and antigen binding effects examined by elastic network models, Debkanta Chakraborty

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Local assembly and pre-mRNA splicing analyses by high-throughput sequencing data, Hsien-chao Chou

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Borrowing information across genes and experiments for improved error variance estimation in microarray data analysis and statistical inferences for gene expression heterosis, Tieming Ji

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Parallel Algorithms for Bayesian Networks Structure Learning with Applications in Systems Biology, Olga Nikolova

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Sequence homology based protein-protein interacting residue predictions and the applications in ranking docked conformations, Li Xue

Theses/Dissertations from 2011

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Bioinformatics methods for metabolomics based biomarker detection in functional genomics studies, Preeti Bais

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Computational prediction of Ds transposon insertion sites in plants using DNA structural features, Xianyan Kuang

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Investigation and development of statistical method for gene expression data analysis, Nicholas Bradley Larson

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Application of comparative genomics for detection of genomic features and transcriptional regulatory elements, Hong Lu

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Extraction of an Effective Pairwise Potential for Amino Acids, Jie Luo

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Genome engineering using DNA-binding proteins: zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), Deepak Reyon

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Fast learning optimized prediction methodology for protein secondary structure prediction, relative solvent accessibility prediction and phosphorylation prediction, Saraswathi Sundararajan

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Modular Algorithms for Biomolecular Network Alignment, Fadi George Towfic

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Error correction and clustering algorithms for next generation sequencing, Xiao Yang

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Machine learning methods for omics data integration, Wengang Zhou

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Mechanistic insights on important biomolecules derived using simple dynamics models from extending the reach of elastic network modeling, Michael Thomas Zimmermann

Theses/Dissertations from 2010

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Characterization of the signal sequence binding domain of Ffh by genetics and comparative analysis, Stacy Stamey Duncan

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Computational approaches to understand interactions between zinc finger proteins and DNA, Fengli Fu

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An evolutionary study of human microRNAs, Yong Huang

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Deciphering the transcriptional regulation and response of barley to obligate fungal biotroph invasion, Matthew James Moscou

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Improving statistical inference for gene expression profiling data by borrowing information, Long Qu

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Detecting recombination and its mechanistic association with genomic features via statistical models, Misha Rajaram

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Transcriptional defense response of the soybean plant, Glycine max, in reaction to infestation by the soybean aphid, Aphis glycines, Matthew Edward Studham

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Diagnostics for nonlinear models with application to population pharmacokinetic modeling, Xiaoyong Sun

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Methods for integrated biochemical pathway analysis, John Louis Van Hemert

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The evolution of mitochondrial genome and proteome in animals, Xiujuan Wang

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Network modeling in systems biology, Tian Xia

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A macroscopic study of the Swedish human population, Chaoliang Zhang

Theses/Dissertations from 2009

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Using a seed-network to query multiple large-scale gene expression datasets from the developing retina in order to identify and prioritize experimental targets, Timothy Alcon

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Protein structure prediction and conformational transitions, Haitao Cheng

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Insights into the rice and Arabidopsis genomes: intron fates, paralogs, and lineage-specific genes, Haining Lin

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Modeling, simulation, synthesis, and optimization of biochemical networks, Kent Allan Vander Velden

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Protein-protein interface: database, analysis and prediction, Feihong Wu

Theses/Dissertations from 2008

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Exploring host-pathogen relationships through computer simulations of intracellular infection, Garrett Marc Dancik

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Hypothesis building using the Animal Trait Ontology, LaRon Maurice Hughes

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Assembly and annotation tools for analysis of large contiguous regions of the maize genome, Brent Anson Kronmiller

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Interactive graphics, graphical user interfaces and software interfaces for the analysis of biological experimental data and networks, Michael Lawrence

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Data integration for biological network databases: MetNetDB labeled graph model and graph matching algorithm, Jie Li

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Evolutionary variance of gene network model via simulated annealing, Kyoungmin Roh

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Characterization and design of C2H2 zinc finger proteins as custom DNA binding domains, Jeffry D. Sander

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Computational analysis and prediction of protein-RNA interactions, Michael Terribilini

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Analysis on protein structures using statistical and bioinformatical methods, Aimin Yan

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Understanding protein motions by computational modeling and statistical approaches, Lei Yang

Theses/Dissertations from 2007

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Characterizing and influencing differentiation of Retinal Progenitor Cells, Tyra Ellen Dunn-Thomas

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

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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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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 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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Spliced alignment and its application in Arabidopsis thaliana , Wei Zhu

Theses/Dissertations from 2001

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