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Start Over Committee Member Raj Acharya 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. 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

7. Uncovering hidden genomic features using computational approaches

open_access
Open Access
Author:
Chung, Wen-Yu
Title:
Uncovering hidden genomic features using computational approaches
Graduate Program:
Computer Science and Engineering
Keywords:
Computational Biology
Bioinformatics
Systems Biology
Molecular Evolution
File:
Download wychung-Dissertation.pdf
Committee Members:
Webb Colby Miller, Dissertation Advisor/Co-Advisor
Webb Colby Miller, Committee Chair/Co-Chair
Anton Nekrutenko, Committee Member
Raj Acharya, Committee Member
Padma Raghavan, Committee Member
Reka Z Albert, Committee Member

8. A Computational Framework For Inferring Structure, Function, and Evolution of Proteins

open_access
Open Access
Author:
Hong, Yoojin
Title:
A Computational Framework For Inferring Structure, Function, and Evolution of Proteins
Graduate Program:
Computer Science and Engineering
Keywords:
Proteins
Sequence Alignments
Twilight zone of Sequence Similarity
Position Specific Scoring Matrix
File:
Download 2010-PhD_dissertation_Yoojin_Hong.pdf
Committee Members:
Webb Colby Miller, Dissertation Advisor/Co-Advisor
Webb Colby Miller, Committee Chair/Co-Chair
Randen L Patterson, Committee Member
Padma Raghavan, Committee Member
Jayanth R Banavar, Committee Member
Damian B Van Rossum, Committee Member
Raj Acharya, Committee Member

9. Clustering Algorithms for Next-generation Sequencing Data from Heterogeneous Populations

open_access
Open Access
Author:
Prabhakara, Shruthi
Title:
Clustering Algorithms for Next-generation Sequencing Data from Heterogeneous Populations
Graduate Program:
Computer Science and Engineering
Keywords:
Clustering
Metagenomics
Mixture-modeling
Algorithms
File:
Download Shruthi_Prabhakara_Dissertation.pdf
Committee Members:
Raj Acharya, Dissertation Advisor/Co-Advisor
Webb Colby Miller, Committee Member
Mary Poss, Committee Member
Padma Raghavan, Committee Member