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1.
Efficient construction of accurate multiple alignments and large-scale phylogenies
by Wheeler, Travis John, Ph.D.  The University of Arizona. 2009: 185 pages; 3369689.
2.
Improving Multiple Sequence Alignments by Revising Sequence Families with Alignment Scoring Approaches
by Levchuk, Aleksandr Olegovich, M.S.  University of California, Riverside. 2011: 72 pages; 1505602.
4.
Algorithms for biological network alignment
by Flannick, Jason, Ph.D.  Stanford University. 2009: 152 pages; 3343954.
5.
Clustering, searching and evaluating biological sequence data
by Ghodsi, Mohammadreza, Ph.D.  University of Maryland, College Park. 2012: 104 pages; 3543455.
6.
Structural RNA homology search and alignment using covariance models
by Nawrocki, Eric Paul, Ph.D.  Washington University in St. Louis. 2009: 281 pages; 3372748.
7.
Novel algorithms for structural alignment of non-coding RNAs
by Kolbe, Diana Lynn, Ph.D.  Washington University in St. Louis. 2010: 175 pages; 3408095.
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A flexible comparative genomics framework for integrating heterogeneous sequence data
by Regier, Allison Ann Penner, Ph.D.  University of Notre Dame. 2011: 102 pages; 3496613.
10.
Structure-Preserving Rearrangements: Algorithms for Structural Comparison and Protein Analysis
by Bliven, Spencer Edward, Ph.D.  University of California, San Diego. 2015: 159 pages; 3716489.
11.
Statistical phylogenetic methods with applications to virus evolution
by Westesson, Oscar, Ph.D.  University of California, Berkeley. 2012: 258 pages; 3555992.
12.
The structural and functional landscape of protein superfamilies: From the thioredoxin fold to parasite peptidases
by Atkinson, Holly J., Ph.D.  University of California, San Francisco. 2009: 159 pages; 3359576.
13.
Ambiguous fragment assignment for high-throughput sequencing experiments
by Roberts, Adam, Ph.D.  University of California, Berkeley. 2013: 93 pages; 3616509.
15.
The human gut microbiota: New analyses and methods on the continuum between disease and health
by Hartman, Amber Laura, Ph.D.  The Johns Hopkins University. 2009: 216 pages; 3399101.
16.
Analyzing comparative sequence data to understand genome function and evolution
by Prasad, Arjun B., Ph.D.  The George Washington University. 2010: 223 pages; 3389713.
17.
Remote Homology Detection in Proteins Using Graphical Models
by Daniels, Noah Manus, Ph.D.  Tufts University. 2013: 122 pages; 3563611.
18.
Intron position in RNA polymerase genes and their relationship to eukaryotic phylogenies
by Robinson, Matthew C., M.S.  East Carolina University. 2010: 90 pages; 1484138.
20.
Efficiency of pair-wise and multiple alignment algorithms in computational biology
by Vu, Man H., M.S.  California State University, Long Beach. 2010: 67 pages; 1486717.
21.
Evolution and Function of Compositional Patterns in Mammalian Genomes
by Prakash, Ashwin, Ph.D.  The University of Toledo. 2011: 185 pages; 3490731.
22.
Computational Pan-Genomics: Algorithms and Applications
by Cleary, Alan Michael, Ph.D.  Montana State University. 2018: 133 pages; 10792396.
23.
Characterization of protein residue surface accessibility using sequence homology
by Mishra, Radhika Pallavi, M.S.  San Jose State University. 2010: 155 pages; 1477358.
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Genome Assembly: Novel Applications by Harnessing Emerging Sequencing Technologies and Graph Algorithms
by Koren, Sergey, Ph.D.  University of Maryland, College Park. 2012: 238 pages; 3517547.
26.
Inferring dinoflagellate genome structure, function, and evolution from short-read high-throughput RNA-Seq
by Gibbons, Theodore Robert, Ph.D.  University of Maryland, College Park. 2015: 132 pages; 10011582.
27.
Identification of microRNA targets
by Krek, Azra, Ph.D.  New York University. 2009: 92 pages; 3365704.
28.
Improving gene annotation and understanding of mammalian evolution by identifying retrocopies of mRNA transcripts
by Baertsch, Robert D., Ph.D.  University of California, Santa Cruz. 2010: 92 pages; 3421298.
29.
The Paladin Suite: Multifaceted Characterization of Whole Metagenome Shotgun Sequences
by Westbrook, Anthony, M.S.  University of New Hampshire. 2017: 101 pages; 10685940.
30.
Platyrrhine phylogenetics with a focus on callitrichine life history adaptations
by Jameson, Natalie Mae, Ph.D.  Wayne State University. 2013: 199 pages; 3601745.
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