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

  • 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

    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

    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

    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.


    OMSSA X!Tandem Mascot SEQUEST

    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

    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

    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.


    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
    • About PIR
    • PIR resources
    • UniProt resources
    • Search and retrieval
    • Analysis of retrieved results
    • Examples & tutorial