During my Ph.D. and Master's work at UNL, I have done many presentations over different areas
of my work and interests. Here is a list of the presentations that I have given (Chronological
order, most recent first):
Randomized Online
Algorithms: This is the presentation that I gave
over a two-week span for the Randomized Algorithms seminar.
Simulating Families of ``Twilight Zone''
proteins: Protein identification using only sequence
information is a difficult task, and for any method that attempts to perform it, there must be
a method that can validate the results. This is mostly done through the use of simulated
sequences, so that the evolution of the protein sequences is known. However, before my method,
there has been no simulation package that could create realistic twilight-zone proteins. This
presentation is a discussion of the method I used to create such a package.
Moriyama Lab 3: Gaps in
alignments are often treated as missing information. However, gaps in alignments represent
substantial evolutionary events, such as insertion or deletion events. This type of
information should be usable to infer evolutionary history among sets of proteins. In this
presentation, I present many methods of using these events in phylogenetic construction, using
these papers [4,5,6,7,8].
Bioinformatic Seminar (um... OLD) Presentation over
indel-PSeq-Gen: indel-PSeq-Gen is a sequence
generator that uses PSeq-Gen [1] to simulate amino acid substitutions, while
indel-PSeq-Gen simulates insertion and deletion events (indels) based on empirical evidence
given in Chang and Benner [3] and Benner et al. [2].
Moriyama Lab 2: A paper
presentation. The paper discussed the selective advantage for survival of a Horizontal Gene
Transfer based on the codon usage index of the gene versus the organism receiving the gene.
Moriyama Lab 1: This is a
basic presentation over simulation study, beginning with PSeq-Gen (a protein sequence
generator), discussing the algorithm behind converting protein scoring matrices into
transition matrices, then moving on to three types of phylogenetic tree reconstruction:
Neighbor-Joining, Maximum Parsimony, and Maximum Likelihood.
Grassly,N., Adachi,J., Rambaut,A. (1997) PSeq-Gen: an application for the
monte carlo simulation of protein sequence evolution along phylogenetic trees, Bioinformatics, 13, 559-560.
Benner,S., Cohen,M., Gonnett,G. (1993) Empirical and structural models for
insertions and deletions in the divergent evolution of proteins, J. Mol. Biol., 229, 1065-1082.
Chang,M.S.S., Benner,S.A. (2004) Empirical analysis of protein insertions
and deletions determining parameters for the correct placement of gaps in protein sequence
alignments, J. Mol. Biol., 341, 617-631.
