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Start Over Graduate Program Computer Science and Engineering Committee Member Webb Colby Miller

1. ASSEMBLY ALGORITHMS FOR NEXT GENERATION SEQUENCE DATA

open_access
Open Access
Author:
Ratan, Aakrosh
Title:
ASSEMBLY ALGORITHMS FOR NEXT GENERATION SEQUENCE DATA
Graduate Program:
Computer Science and Engineering
Keywords:
next-generation sequencing
genome assembly
algorithms
File:
Download dissertation.pdf
Committee Members:
Webb Colby Miller, Dissertation Advisor/Co-Advisor
Webb Colby Miller, Committee Chair/Co-Chair
Piotr Berman, Committee Member
Stephan Schuster, Committee Member
Raj Acharya, Committee Member

2. Computational pipeline for the empirical detection of cleaved targets of small silencing RNAs using degradome sequencing data

open_access
Open Access
Author:
Addo-Quaye, Charles
Title:
Computational pipeline for the empirical detection of cleaved targets of small silencing RNAs using degradome sequencing data
Graduate Program:
Computer Science and Engineering
Keywords:
small RNAs microRNAs
File:
Download CAA154.pdf
Committee Members:
Webb Colby Miller, Dissertation Advisor/Co-Advisor
Webb Colby Miller, Committee Chair/Co-Chair
Michael Axtell, Committee Chair/Co-Chair
Ali Hurson, Committee Member
Raj Acharya, Committee Member
Padma Raghavan, Committee Member
John Edward Carlson, Committee Member

3. INFERENCE OF ORTHOLOGS, WHILE CONSIDERING GENE CONVERSION, TO EVALUATE WHOLE-GENOME MULTIPLE SEQUENCE ALIGNMENTS

open_access
Open Access
Author:
Hsu, Chih-Hao
Title:
INFERENCE OF ORTHOLOGS, WHILE CONSIDERING GENE CONVERSION, TO EVALUATE WHOLE-GENOME MULTIPLE SEQUENCE ALIGNMENTS
Graduate Program:
Computer Science and Engineering
Keywords:
Evolution
Gene conversion
Orthology
Multiple-Sequence Alignment
File:
Download Dissertation.pdf
Committee Members:
Webb Colby Miller, Dissertation Advisor/Co-Advisor
Webb Colby Miller, Committee Chair/Co-Chair
Raj Acharya, Committee Member
Wang Chien Lee, Committee Member
Ross Cameron Hardison, Committee Member

4. AUTOMATING ANALYSIS OF GENE CLUSTER EVOLUTION

open_access
Open Access
Author:
Song, Giltae
Title:
AUTOMATING ANALYSIS OF GENE CLUSTER EVOLUTION
Graduate Program:
Computer Science and Engineering
Keywords:
duplication
evolution
orthology
gene clusters
conversion
File:
Download giltae_song_dissertation.pdf
Committee Members:
Webb Colby Miller, Dissertation Advisor/Co-Advisor
Webb Colby Miller, Committee Chair/Co-Chair
Raj Acharya, Committee Member
Padma Raghavan, Committee Member
Ross Cameron Hardison, Committee Member
Yu Zhang, Committee Member

5. LEARNING SIGNALS IN GENOMIC SEQUENCE ALIGNMENTS FOR IDENTIFICATION OF FUNCTIONAL ELEMENTS

open_access
Open Access
Author:
Taylor, James
Title:
LEARNING SIGNALS IN GENOMIC SEQUENCE ALIGNMENTS FOR IDENTIFICATION OF FUNCTIONAL ELEMENTS
Graduate Program:
Computer Science and Engineering
Keywords:
functional element prediction
multiple sequence alignment
phylogeny
Markov Models
File:
Download James-Dissertation.pdf
Committee Members:
Webb Colby Miller, Committee Chair/Co-Chair
Francesca Chiaromonte, Committee Member
Ross Cameron Hardison, Committee Member
Hongyuan Zha, Committee Member
Piotr Berman, Committee Member

6. Algorithms for classification and prediction of protein structure and function

open_access
Open Access
Author:
JEONG, JIEUN
Title:
Algorithms for classification and prediction of protein structure and function
Graduate Program:
Computer Science and Engineering
Keywords:
protein structure
protein folds
hairpin loops
folding rules
approximation algorithms
gene regulatory network
File:
Download mythesis.pdf
Committee Members:
Piotr Berman, Committee Chair/Co-Chair
Arthur Mallay Lesk, Committee Member
Webb Colby Miller, Committee Member
Reka Z Albert, Committee Member

7. Information Fusion of Multiple Genomic Sensors for Clustering and Cis-Regulatory Element Identification

open_access
Open Access
Author:
Kasturi, Jyotsna
Title:
Information Fusion of Multiple Genomic Sensors for Clustering and Cis-Regulatory Element Identification
Graduate Program:
Computer Science and Engineering
Keywords:
Kullback-Leibler divergence
self-organizing map
multidimensional clustering
time-series
gene expression
motif finding
functional genomics
radial basis functions
information fusion
File:
Download JK_Thesis_05_2006.pdf
Committee Members:
Raj Acharya, Committee Chair/Co-Chair
Webb Colby Miller, Committee Member
Padma Raghavan, Committee Member
Ross Cameron Hardison, Committee Member
Francesca Chiaromonte, Committee Member

8. Reconstructing Contiguous Regions of an Ancestral Genome

open_access
Open Access
Author:
Ma, Jian
Title:
Reconstructing Contiguous Regions of an Ancestral Genome
Graduate Program:
Computer Science and Engineering
Keywords:
ancestral genome reconstruction
contiguous ancestral region
mammalian ancestor
genome rearrangement
File:
Download Jian_Ma_thesis.pdf
Committee Members:
Webb Colby Miller, Committee Chair/Co-Chair
Hongyuan Zha, Committee Member
Piotr Berman, Committee Member
Wojciech Makalowski, Committee Member
Ross Cameron Hardison, Committee Member

9. Algorithms for Aligning and Clustering Genomic Sequences that Contain Duplications

open_access
Open Access
Author:
Hou, Minmei
Title:
Algorithms for Aligning and Clustering Genomic Sequences that Contain Duplications
Graduate Program:
Computer Science and Engineering
Keywords:
algorithm
genomic sequence
duplication
alignment
homologous
orthologous
File:
Download MinmeiHou_Dissertation.pdf
Committee Members:
Webb Colby Miller, Committee Chair/Co-Chair
Piotr Berman, Committee Member
Hongyuan Zha, Committee Member
Ross Cameron Hardison, Committee Member