CS273

Spring 2006/2007 Schedule
This was the schedule for the Spring 2006/2007 offering of CS273a.

 DateTitleHW
Related Material
14/3/07Introduction; UCSC Genome Browser & Table Browser 
  1. http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml
  2. BLAT - The BLAST-like alignment tool
  3. The UCSC Genome Browser Database: update 2006
  4. The UCSC Genome Browser Database: update 2007
  5. The UCSC Known Genes
  6. Exploring relationships and mining data with the UCSC Gene Sorter
  7. Piloting the Zebrafish Genome Browser
  8. The UCSC Table Browser data retrieval tool
  9. Computational screening of conserved genomic DNA in search of functional noncoding elements
24/5UCSC Code Tree; Genome Variation & Assemblies; Repeats 
  1. Genome assembly comparison identifies structural variants in the human genome
  2. Structural Variation in the Human Genome
  3. Copy-number variations add a new layer of complexity in the human genome
  4. Global variation in copy number in the human genome
  5. Finishing the euchromatic sequence of the human genome
  6. An assessment of the sequence gaps: unfinished business in a finished human genome
  7. Quality assessment of the human genome sequence
  8. Mobile Elements: Drivers of Genome Evolution
  9. Junk DNA as an evolutionary force
  10. The Shocking Details of Genome.ucsc.edu
  11. Sequencing the Human Genome - NOVA interviews
34/10DNA Sequencing 
 
44/12DNA Sequencing (cont.)HW 1 out
 
54/17Genome Assemblies 
  1. The illumina genotyping technology
  2. Reconstruction of synteny and orthology
  3. Dog genome assembly
  4. Historic paper (1997) in favor of human whole genome shotgun sequencing
  5. Historic paper (1997) against human whole genome shotgun sequencing
64/19UCSC Known Genes (by Jim Kent) 
  1. http://en.wikipedia.org/wiki/Jim_Kent
74/24Vertebrate Comparative Genomics 
  1. Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay
  2. Ultraconserved elements in the human genome
  3. Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements
  4. Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants
  5. In vivo enhancer analysis of human conserved non-coding sequences
  6. Autism and ultraconserved non-coding sequence on chromosome 7q
  7. The share of human genomic DNA under selection estimated from human-mouse genomic alignments
  8. Distribution and intensity of constraint in mammalian genomic sequence
  9. Genome-wide identification of human functional DNA using a neutral indel model
  10. Initial sequencing and comparative analysis of the mouse genome
  11. Ultraconserved regions in multiple sclerosis
  12. Sequence variation in ultraconserved and highly conserved elements does not cause X-linked mental retardation
84/26Genome EvolutionHW 1 due

HW 2 out

  1. Mammalian ancestral genome reconstruction
  2. Gene inparalogs and outparalogs
  3. The threaded blockset multiple aligner
  4. Multiple whole genome alignment--a review
  5. The LAGAN multiple aligner
95/1Genes and Gene Regulation 
  1. The Sequence of the Human Genome
  2. Initial sequencing and analysis of the human genome
  3. Horizontal gene transfer: A critical view
  4. Transcriptional Regulatory Elements in the Human Genome
105/3Transcription Regulation in Vertebrates 
  1. Epigenetics: A Landscape Takes Shape
  2. Long-Range Control of Gene Expression: Emerging Mechanisms and Disruption in Disease
115/8Whole Genome Motif Discovery 
  1. Whole-genome comparative motif discovery in yeast
  2. Whole-genome comparative motif discovery in human promoters and 3' UTRs
  3. A non-parametric TF binding site motif model
125/10Gene Finding and Cis Regulatory ElementsHW 2 due
  1. Twinscan: gene prediction guided by a pairwise alignment
  2. NSCAN: gene prediction guided by a multiple alignment
  3. Assessment of gene prediction accuracy on 1% of the human genome
  4. Genome-wide prediction of conserved Cis Regulatory Modules
135/15Insulators in the Human Genome  
  1. CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease
  2. A distal enhancer and an ultraconserved exon are derived from a novel retroposon
  3. Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome
  4. Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites
  5. Supplementary Figure 5
  6. Supplementary Figure 8
145/17Co-option in the human genomeProject out
  1. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes
155/22Human population genetics 
  1. Analysis of the Phase I Hapmap Project data
  2. Conserved Noncoding Sequences are still negatively selected in humans
  3. Tests for positive selection
  4. The EHH test for positive selection
  5. A genome-wide scan for recent positive selection in humans
  6. Human brain size may be still evolving
165/24Vertebrate Comparative Genomics (by Ivan Ovcharenko) 
  1. http://www.dcode.org/
  2. http://ivan.dcode.org/
175/29Ancestral Reconstruction (by Jian Ma) 
  1. http://www.soe.ucsc.edu/~jianma/
185/31Chains & Nets; Non-coding transcripts 
  1. Genome-wide transcription and the implications for genomic organization
  2. Identification and Classification of Conserved RNA Secondary Structures in the Human Genome
  3. An RNA gene expressed during cortical development evolved rapidly in humans
  4. Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome
196/5Metagenomics 
 
206/12Final Project Presentations (3:30pm, S361)