Bioinformatics 2014
Instructor: Cheol-Koo Lee, Ph.D.
Discussion assistants: Seung-Soo Kim, Young-Yon Kwon, Seok-Jin Hong
9.2(Tue): Class introduction and schedule
9.4(Thu): Chapter 1
Homework: read P1 & P2
9.11(Thu): P1 discussion
9.16(Tue): P1 student presentation
9.18(Thu): P2 discussion
9.23(Tue): P2 student presentation
9.25(Thu): Chapter 2-1
9.30(Tue): Chapter 2-2
Homework: read P3
10.2(Thu): P3 discussion
10.7(Tue): P3 student presentation
10.14(Tue): Chapter 3-1
10.16(Thu): Chapter 3-2
10.21 or 10.23: Mid-term exam
10.28(Tue): Chapter 3-3
Homework: read P4
10.30(Thu): P4 discussion
11.4(Tue): P4 student presentation
11.6(Thu): Chapter 3-4
11.11(Tue): Chapter 4
Homework: read P5
11.13(Thu): P5 discussion
11.18(Tue): P5 student presentation

11.20(Thu): Chapter 5
11.25(Tue): Chapter 6-1
Homework: read P6 & P7
11.27(Thu): P6 discussion
12.2(Tue): P6 student presentation
12.4(Thu): P7 discussion
12.9(Tue): P7 student presentation
12.11(Thu): Chapter 6-2
12.16 or 12.18: Final exam
Reading homework for discussion and student presentation:
P1: Guri Giaever and Corey Nislow (2014). The Yeast Deletion Collection: A Decade of Functional
Genomics. Genetics, Vol. 197, 451–465.
P2: Caitlin F. Connelly, Jon Wakefield, Joshua M. Akey (2014). Evolution and Genetic Architecture of
Chromatin Accessibility and Function in Yeast. PLoS Genet 10(7): e1004427.
P3: Hannah Carter, Matan Hofree and Trey Ideker (2013). Genotype to phenotype via network analysis.
Current Opinion in Genetics & Development, 23:611–621.
P4: Janusz Dutkowski, Michael Kramer, Michal A Surma, Rama Balakrishnan, J Michael Cherry, Nevan J
Krogan & Trey Ideker (2013). A gene ontology inferred from molecular networks. Nat Biotechnol.
31(1):38-45.
P5: Dutkowski J, Ono K, Kramer M, Yu M, Pratt D, Demchak B, Ideker T (2014). NeXO Web: the NeXO ontology database and visualization platform. Nucleic Acids Res. 42(Database issue):D1269-74.
P6: Tanya Barrett1, Stephen E. Wilhite, Pierre Ledoux, Carlos Evangelista, Irene F. Kim, Maxim
Tomashevsky, Kimberly A. Marshall, Katherine H. Phillippy, Patti M. Sherman, Michelle Holko, Andrey
Yefanov, Hyeseung Lee, Naigong Zhang, Cynthia L. Robertson, Nadezhda Serova, Sean Davis and
Alexandra Soboleva (2013). NCBI GEO: archive for functional genomics data sets—update. Nucleic Acids
Research, Vol. 41, Database issue D991–D995.
P7: Gentleman et al. (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biology 2004, 5:R80.
Student presentation: Presentation by students on some specific topics in the reading materials.

Lecture
Chapter 1. Introduction: Bioinformatics
Chapter 2. Access to sequence data and literature information
Chapter 3. Pairwise sequence alignment
Chapter 4. Basic local alignment search tool (BLAST)
Chapter 5. Bioinformatics approaches to ribonucleic acid (RNA)
Chapter 6. Gene expression: microarray data analysis