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:
| 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 |
PPT | 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 |
| L26 | 7.3 Sub-structures of Human Population | PPT | 1. GENEALOGICAL TREES,COALESCENT
THEORY AND THE ANALYSIS OF
GENETIC POLYMORPHISMS, Nature Reviews
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 |