CBCB Seminar Series
Fall 2004
12:30 p.m. Tuesday September 14, 2004
Title: organizational meeting
Speaker: Stephen M. Mount, Ph.D.
Venue: Biomolecular Science
Building Room 3118
Abstract: To discuss the schedule
in Fall 2004.
12:30 p.m. Tuesday September 21, 2004
Title: Future of bioinformtics
workflows
Speaker: Michael Cummings, Ph.D.
Venue: Biomolecular Science
Building Room 3118
Reference:
Abstracting
Workflows: Unifying Bioinformatics Task Conceptualization and
Specification Through Semantic Web Services
12:30 p.m. Tuesday September 28, 2004
Title: Molecular evolution for the
computer scientist
Speaker: Charles Delwiche,
Ph.D.
Venue: Biomolecular Science
Building Room 3118
2 p.m. Tuesday October 5, 2004
Title: Computational Analysis of
Genes and Genomes
Speaker: Steven L.
Salzberg, Ph.D. (The Institute for Genomic Research)
Venue: A.V. Williams Room 2460
Abstract:
In this talk, I will review the work of my group on several different
research areas in bioinformatics. First, I will discuss our research on
genome assembly, a computationally challenging problem that continues to
evolve as new sequencing technology appears. Second, I will describe our
most recent developments in gene finding, particularly our Pair hidden
Markov model (PHMM) for finding genes simultaneously in two organisms.
Third, I will discuss our biodefense-oriented work on Bacillus anthracis,
the causative agent of anthrax, including a brief review of our forensic
work and recent developments on a new high-density gene chip for
single-nucleotide polymorphism (SNP) discovery.
Background References:
- Comparative genome sequencing for discovery of novel polymorphisms in
Bacillus anthracis. T.D. Read, S.L. Salzberg, M. Pop, M. Shumway, L.
Umayam, L. Jiang, E. Holtzapple, J. Busch, K.L. Smith, J.M. Schupp, D.
Solomon, P. Keim, and C.M. Fraser. Science 296 (2002),
2028-2033.
- Comparative genome assembly. M. Pop, A. Phillippy, A.L. Delcher, S.L.
Salzberg, Briefings in Bioinformatics 5:3 (2004), 237-248.
- Versatile and open software for comparing large genomes. S. Kurtz, A.
Phillippy, A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu, and S.L.
Salzberg. Genome Biology 5:R12 (2004).
- TigrScan and GlimmerHMM: two open-source ab initio eukaryotic gene
finders. W.H. Majoros, M. Pertea, and S.L. Salzberg. Bioinformatics
(2004).
12:30 p.m. Tuesday October 12, 2004
Title: Random pieces of random
models (computer science for the biologist)
Speaker: Dianne O'Leary, Ph.D.
Venue: Biomolecular Science
Building Room 3118
12:30 p.m. October 19, 2004
Title: Hierarchical clustering
explorer
Speaker: Ben Shneiderman, Ph.D. and Jinwook Seo
Venue: Biomolecular Science
Building Room 3118
Reference:
Hierarchical Clustering Explorer
for Interactive Exploration of Multidimensional Data
12:30 p.m. Tuesday October 26, 2004
Title: Identifying Proteins Using
Mass Spectrometry
Speaker: Chau-Wen Tseng, Ph.D., Woei-Jyh (Adam) Lee and Xue Wu
Venue: Biomolecular Science
Building Room 3118
Abstract:
Large numbers of MS/MS peptide spectra generated in proteomics experiments
require efficient, sensitive and specific algorithms for peptide
identification. In the Open Mass Spectrometry Search Algorithm (OMSSA),
specificity is calculated by a classic probability score using an explicit
model for matching experimental spectra to sequences. At default
thresholds, OMSSA matches more spectra from a standard protein cocktail
than a comparable algorithm. OMSSA is designed to be faster than published
algorithms in searching large MS/MS datasets.
References:
OMSSA
- Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, Yang X,
Shi W, Bryant SH, "Open
Mass Spectrometry Search Algorithm", J Proteome Res. 2004 Oct
11;3(5):958-964
X!Tandem
Mascot
SEQUEST
- Link AJ, Eng J, Schieltz DM, Carmack E, Mize GJ, Morris DR, Garvik BM,
Yates JR 3rd, "Direct
analysis of protein complexes using mass spectrometry", Nat
Biotechnol. 1999 Jul;17(7):676-82
- Dongre AR, Eng JK, Yates JR 3rd, "Emerging
tandem-mass-spectrometry techniques for the rapid identification of
proteins", Trends Biotechnol. 1997 Oct;15(10):418-25
- Yates JR 3rd, Eng JK, Clauser KR, Burlingame AL, "Search
of Sequence Databases with Uninterpreted High-Energy Collision-Induced
Dissociation Spectra of Peptides", J Am Soc Mass Spectom. 1996
Nov;7(11):1089-98
12:30 p.m. Tuesday November 2, 2004
Title: Protein Identification
Using Tandem Mass Spectrometry
Speaker: Nathan Edwards, Ph.D.
Venue: Biomolecular Science
Building Room 3118
11 a.m. Tuesday November 9, 2004
Title: Improving Genome Assembly
(doctoral defense)
Speaker: Cevat Ustun
Venue: Energy Research Facility
Building #223 Room 1207
Abstract:
12:30 p.m. Tuesday November 16, 2004
Title: Primate hormonal evolution
Speaker: Lisa Pfiefer
Venue: Biomolecular Science
Building Room 3118
12:30 p.m. Tuesday November 30, 2004
Title: Protein structure
Speaker: Elena Zotenko
Venue: Biomolecular Science
Building Room 3118
Abstract:
Given a query protein the ability to identify all structurally similar
proteins is of primary importance in the study of protein evolution and
function. As the number of protein structures grows there is a need to
develop screening methods that will perform quick yet accurate filtering
of the database before a more computationally expensive protein structure
comparison method is applied.
Our long term goal is to develop such screening method for VAST (Vector
Alignment Search Tool), a protein structure comparison method used at
NCBI. Average crossing number, a geometric invariant based on the writhing
number of a knot, was used by several researchers to provide a global
descriptor of protein shape. We suggest a screening method that uses
average crossing number to detect locally similar substructures. Local
similarities are then efficiently combined to detect similar protein
structures.
In this talk I am going to give an overview of protein structure and
protein structure comparison methods. Then I will describe our screening
method and the preliminary results that we are getting.
References:
- L.Holm, C.Sander, "3-D
lookup: fast protein structure database searches at 90% reliability",
Proc Int Conf Intell Syst Mol Biol, 1995,3:179-87
- P.Rogen, B.Fain, "Automatic
classification of protein structure by using Gauss integrals",
PNAS, 2003, 100:119-124
- P.Rogen, B.Henrik, "A
new family of global protein shape descriptors", Mathematical
Biosciences, 2003, 182:167-181
12:30 p.m. Tuesday November 7, 2004
Title: PIR and UniProt Resources
Speaker: Raja Mazumder,
Ph.D. (Georgetown University)
Venue: Plant Science Building Room
1129
Outline:
- About PIR
- PIR resources
- UniProt resources
- Search and retrieval
- Analysis of retrieved results
- Examples & tutorial
References:
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