Genomes

Prerequisites:

Biology 100 or Biochemistry 100A and Biology 105

Course description:

Advanced elective for biology majors, examining biology on the genome scale. Topics include sequencing techniques, genome assembly, analysis of gene expression data, and comparative and evolutionary analysis of genomes. Although much of the course material is from the Genomes 3 text, students will also read primary literature and review articles.

 

Course goals:

  1. Learn the fundamental techniques involved in sequencing, assembling, and annotating genomes.

  2. Learn the rationale behind functional characterization of genome information including expression profiling and proteomics.

  3. Learn the principles of genome architectures across the domains of life.

  4. Learn basic comparative genomics principles including phylogenetic reconstruction and population genetics with special focus on human genetics.

  5. Increase proficiency in reading and evaluating primary literature and review articles.

  6. Through student-led literature discussions, increase proficiency in scientific communication.

 

Text: Genomes 3 by T.A. Brown and assigned review articles

Time: 10:00-11:45 am Tu/Th; PSB 140

Instructor: Ed Green (PSB 312; ed@soe.ucsc.edu)

 

Office hours: Wednesdays 4:00-5:00 pm

 

Academic integrity:

All the information you can handle can be found on the UCSC site for Academic Integrity. For this class, you are encouraged to discuss your assignments with your classmates and anyone else. However, the written work that you submit for a grade shall be written by you and you alone. If you think it might be a violation of academic integrity, it probably is. Ask me, before you submit your work, if you ever need clarification.

 

Syllabus:

 

Number

Date

Topic

Reading

1 (Th)

22 Sept

Overview / history of genomics

 

2 (Tu)

27 Sept

Mapping genomes

Ch. 1, 2, and 3

3 (Th)

29 Sept

Sequencing technology and assembly 1 (the bad old days); HW1 assigned

Ch. 4; papers

4 (Tu)

4 Oct

Sequencing technology and assembly 2 (Next generation sequencing)

Review articles

6 (Th)

6 Oct

Next-gen genome assembly; Midterm review

Review articles

7 (Tu)

11 Oct

Midterm 1

 

8 (Th)

13 Oct

Genome anatomies (euk., prok., viral) I

Ch. 7, 8, 9

9 (Tu)

18 Oct

Genome anatomies II

Ch. 7, 8, 9

10 (Th)

20 Oct

Genes finding, function and transcriptional profiling (RNAseq and sequencing-based methods); HW2 assigned

Ch. 5, 6 and RNAseq review article

11 (Tu)

25 Oct

Student-led paper presentations

Transposon-mediated rewiring of gene regulatory networks & pregnancy in mammals

Sea Anemone Genome

12 (Th)

27 Oct

Gene expression and RNA-seq; HW2 due

Ch. 5, 6, and RNAseq review article

14 (Tu)

1 Nov

Chromatin, gene expression, and splicing;

 Ch. 10, 12;

Tilgner et al., Mikkelsen et al.,and Kelly et al.

15 (Th)

3 Nov

Midterm 2

 

16 (Tu)

8 Nov

Genome Evolution I - mutations, repair, and recombination

Ch. 16, 17

17 (Th)

10 Nov

Student-led paper presentations

Alu elements and hominid phylogenetics

Genome-wide SNP and haplotype analysis reveal a rich history underlying dog domestication

18 (Tu)

15 Nov

Recombination, origin of life, and gene evolution

Ch. 17 & 18

19 (Th)

17 Nov

Molecular phylogenies and pop-gen I; HW3 assigned

Ch. 19

20 (Tu)

22 Nov

Population genomics I;

Jakobsson et al., Novembre and Ramachandran

21 (Tu)

29 Nov

Population genomics II; HW3 returned

 articles

22 (Th)

1 Dec

Final review

 articles

 

 

 


 

Grading:

 

There will be 2 midterms, a final, 3 homeworks, and 1 student-led paper discussion.

 

The final grade will be calculated as follows:

 

Midterms: 15% each

 

Final: 35%

 

Homeworks: highest two will be 10% each

 

Student-led paper discussion: 10%
In-class group assignments: 5%

 

 

 

 

Instructors and Assistants