Spring 2008, CAP6938: Special Topics in Computational Genomics

Instructor: Shaojie Zhang

Lectures: Tu/Th 1:30-2:45pm ENGR 0383

Office hours: Shaojie Zhang, HEC 311, by appointment.

Background: The course should be self-contained. However, a concise introduction to Biology can be found at the Bioinformatics Algorithms web-site (chapter 3). Also, the text of Mol. Biol. of the Cell can be searched online.

There is no required text for the course. Current research papers (2003-2008) from "Nature", "Science", "PLOS Biology", "Genome Research", "Bioinformatics", and etc. are distributed along the course for different research topics. Optional Reference Books:

  • Richard C. Deonier, Simon Tavaré, and Michael S. Waterman Computational Genome Analysis: An Introduction
  • N.C, Jones and P.A. Pevzner. Introduction to Bioinformatics Algorithms.
  • Syllabus

    Proposals and Projects

    Assignments: Each student will be asked to write summaries for EACH paper, present TWO research papers in the class and accomplish ONE class project (or a research proposal)

    Grading: Summaries (30%), Paper presentations (30%), Final project (30%), Attendance (10%).

    Summaries Guide Line: Read the paper before lecture. Write a one-page summary of the paper that will be discussed on class. Make sure write down the biological problem and the computational problem hidden inside the paper. Send the summary by email to me before the lecture (12:00 pm sharp)

    Presentation Guide Line: Read paper first, meet with me 1-2 weeks before lecture to discuss the paper. Schedule a long meeting with me the day before lecture to discuss the slides. Slides due at noon (sharp) the lecture. Please make the appointments throught emails.

    Topics and Tentative Schedule:

    Date Topic Slides Papers Presenter
    L1: 01/08 Course Introduction PPT Shaojie Zhang
    L2: 01/10 1. Genome Rearrangement and Genome Evolution:
    1.1 Cancer Genomics
    PPT Reconstructing tumor genome architectures, Bioinformatics Shaojie Zhang
    L3: 01/15 1.2 Genome Rearrangment PPT Reconstructing contiguous regions of an ancestral genome, Genome Research Cunchong Zhong
    L4: 01/17 1.3 Genome Rearrangment Genome Rearrangements in Mammalian Evolution: Lessons From Human and Mouse Genomes, Genome Research Jonathan Cazalas
    L5 1.4 Whole Genome Duplication in Yeast Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae, Nature Shaojie Zhang
    L6 2. Repetitive DNA Detection and Classification and Segmental Duplication
    2.1 Repeat Identification
    De novo identification of repeat families in large genomes, Bioinformatics Chris Ellis
    L7 2.2 Segmental Duplication in Human Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution, Nature Genetics Joel Lehman
    L8 2.3 Gene Duplication in Fungi Natural history and evolutionary principles of gene duplication in fungi, Nature Ryan Lamers
    L9 2.4 Repeats and Phylogeny Orthologous repeats and mammalian phylogenetic inference , Genome Research Allyson Fenwick
    L10 3. Comparative Motif Finding and Gene Finding
    3.1 Human Motif Finding
    Systematic discovery of regulatory motifs in human promoters and 30 UTRs by comparison of several mammals , Nature Tisha Choudhury
    L11 3.2 Functional Elements in 12 Fly Genomes Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures , Nature Meenashi P. B.
    L12 3.3 Discovery of Regulatory Elements PPT Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting Genome Research
    L13 4. ncRNA Finding and ncRNA Regulation
    4.1 RNA Consensus Folding
    PPT Consensus Folding of Unaligned RNA Sequences Revisited, Journal of Computational Biology
    L14 4.2 RNA Homolog Search
    A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements, Bioinformatics
    L15 4.3 RNAz PPT 1. Fast and reliable prediction of noncoding RNAs , PNAS
    2. Genome-wide mapping of conserved RNA Secondary Structures Reveals Evidence for Thousands of functional Non-Coding RNAs in Human , Nature Biotechnology
    L16 4.4 New ncRNA Gene PPT An RNA gene expressed during cortical development evolved rapidly in humans, Nature
    L17 4.5 microRNA Target Recognition PPT The role of site accessibility in microRNA target recognition, Nature Genetics
    L18 4.6 microRNAs in Fly Genomes PPT Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes, Genome Research
    L19 4.7 microRNAs in Human Genome PPT Identification of hundreds of conserved and nonconsserved human microRNAs , Nature Genetics
    L20 5. Metagenomics: Global Ocean Sampling
    5.1 Introduction
    PPT 1. Metagenomics: A Call for Bringing a New Science into the Classroom (While It is Still New) , CBE Life Sciences Education
    2. Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes , Plos Biology
    3. Environmental Genome Shotgun Sequencing of the Sargasso Sea, Science
    4. The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific, Plos Biology
    L21 5.2 Protein Families Diversity PPT The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families, Plos Biology
    L22 5.3 Microbial Kinome Diversity PPT Structural and Functional Diversity of the Microbial Kinome, Plos Biology
    L23 6. Personal Genome sequencing PPT The Diploid Genome Sequence of an Individual Human, Plos Biology
    L24 7. Human Population Genetics
    7.1 SNPs in Human Populations
    PPT Whole-Genome Patterns of Common DNA Variation in Three Human Populations, Science
    L25 7.2 speciation of Humans and Chimps PPT Genetic evidence for complex speciation of humans and chimpanzees, Nature
    2. Genetic Structure of Human Populations, Science
    L27 7.4 Genomewide Admixture PPT A Genomewide Admixture Map for Latino Populations, American Journal of Human Genetics

    We are always looking for motivated students. If you are looking for research projects, please get in touch.