- 6 Feb 2012 (M): course overview, genome rearrangements and sorting by reversals
**Reading:**

Brian Hayes. Sorting Out the Genome, American Scientist, 95(5):386-391, 2007.

Sections 5.1 and 5.2 of*Introduction to Bioinformatics Algorithms*

(optional background) Chapter 3 of*Introduction to Bioinformatics Algorithms*

- 8 Feb 2012 (W): genome rearrangements - sorting by reversals (a 4-approximation)
**Reading:**

Sections 5.3 and 5.4 of*Introduction to Bioinformatics Algorithms*

(optional) Alberto Caprara. Sorting by Reversals is Difficult. In*Proceedings of the First Annual International Conference on Computational Molecular Biology*, 1997.

(optional) P. Berman, S. Hannenhalli, and M. Karpinski. 1.375-Approximation Algorithm for Sorting by Reversals. In*Proceedings of the European Symposium on Algorithms (ESA)*, 2002. - 10 Feb 2012 (F): genome rearrangements - sorting by reversals (a 2-approximation) and pancake sorting intro
**Reading:**

Sections 1 and 2 of John Kececioglu and David Sankoff. Exact and approximation algorithms for sorting by reversals, with application to genome rearrangment.*Algorithmica*, 13(1):180-210, 1995.

- 13 Feb 2012 (M): pancake sorting
**Reading:**

Sections 1 and 2 of William Gates and Christos Papadimitriou. Bounds for Sorting by Prefix Reversals.*Discrete Mathematics*, 27:47-57, 1979.

(optional) L. Bulteau, G. Fertin, and I. Rusu. Pancake Flipping is Hard. CoRR abs/1111.0434: 2011.

(optional) J. Fischer and S.W. Ginzinger. A 2-Approximation Algorithm for Sorting by Prefix Reversals. In*Proceedings of the European Symposium on Algorithms (ESA)*, 2005.

(optional) B. Chitturi, W. Fahle, Z. Meng, L. Morales, C.O. Shields, I.H. Sudborough, and W. Voit. An (18/11)n upper bound for sorting by prefix reversals.*Journal of Theoretical Computer Science*, 410:3372-3390, 2009.

- 15 Feb 2012 (W): local & global sequence alignment
**Reading:**

Sections 6.1, 6.4, and 6.6 of*Introduction to Bioinformatics Algorithms*or Section 6.6 of*Algorithm Design*for Needleman-Wunsch algorithm

Sections 6.8 of*Introduction to Bioinformatics Algorithms*for Smith-Waterman algorithm

(optional) Section 6.7 of*Algorithm Design*or Section 7.2 of*Introduction to Bioinformatics Algorithms*for space-efficient version of Needleman-Wunsch - 17 Feb 2012 (F): multiple sequence alignment
**Reading:**

Section 6.10 of*Introduction to Bioinformatics Algorithms*

Sections 14.5 and 14.6.2 of Gusfield's*Algorithms on Strings, Trees, and Sequences*

(optional) Lusheng Wang and Tao Jiang. On the Complexity of Multiple Sequence Alignment, Journal of Computational Biology, 1(4):337-348, 1994.

- Group Homework #1 is due on Wednesday

- 20 Feb 2012 (M): phylogenetic alignment
**Reading:**

Section 14.8 of Gusfield's*Algorithms on Strings, Trees, and Sequences*

(optional) David Sankoff. The early introduction of dynamic programming into computational biology, Bioinformatics, 16(1):41-47, 2000. - 22 Feb 2012 (W): linear programming intro and application to vertex cover
**Reading:**

Section 11.6 of*Algorithm Design*

(optional) The wikipedia entry on linear programming

- 24 Feb 2012 (F): LP-based 2-approximation for load balancing
**Reading:**

Section 11.7 of*Algorithm Design*

- Solo Homework #1 is due on Friday

- 27 Feb 2012 (M): LP duality theory
**Reading:**

Section 12.1 of Vazirani's*Approximation Algorithms*

- 29 Feb 2012 (W): LP duality applied to max-flow and min-cut
**Reading:**

Section 12.2 of*Approximation Algorithms*

(optional) Section 12.3 of*Approximation Algorithms*

- 2 Mar 2012 (F): multicut and integer multicommodity flow in trees
**Reading:**

Sections 18.1, 18.2 of*Approximation Algorithms*

- 5 Mar 2012 (M): probability review via MAX 3-SAT
**Reading:**

Sections 13.12 and 13.3 of*Algorithm Design*

(review from cs280) Sections 13.2 and 13.4 of*Algorithm Design*

- 7 Mar 2012 (W): randomized rounding of the set cover LP
**Reading:**

Chapter 14 of*Approximation Algorithms* - 9 Mar 2012 (F): 2-approximation for Steiner Tree

- Group Homework #2 is due on Wednesday

- 12 Mar 2012 (M): randomized algorithm for the connected facility location problem
**Reading:**

Section 12.2 of Williamson and Shmoys'*The Design of Approximation Algorithms*

- 14 Mar 2012 (W): the offline and online caching problem
**Reading:**

Section 4.3 of*Algorithm Design*for the offline version - 16 Mar 2012 (F): randomized marking algorithm for paging
**Reading:**

Section 13.8 of*Algorithm Design*

- Solo Homework #2 is due on Friday

- 19 Mar 2012 (M): introduction to the multicast game
**Reading:**

start of Section 12.7 of*Algorithm Design* - 21 Mar 2012 (W): multicast game
**Reading:**

rest of Section 12.7 of*Algorithm Design* - 23 Mar 2012 (F): Braess' paradox and routing games

- 2 Apr 2012 (M): the facility location game and its price of stability
**Reading:**

Sections 19.4.1 and 19.4.2 of*Algorithmic Game Theory* - 4 Apr 2012 (W): utility games and their price of anarchy
**Reading:**

Sections 19.4.3-19.4.5 of*Algorithmic Game Theory* - 6 Apr 2012 (F): cascading behavior in networks
**Reading:**

Sections 19.1-19.5 of Easley and Kleinberg's*Networks, Crowds, and Markets*

- Group Homework #3 is due on Wednesday

- 9 Apr 2012 (M): more on the cascade model, including the cascade capacity
**Reading:**

Sections 19.5-19.7B of Easley and Kleinberg's*Networks, Crowds, and Markets* - 11 Apr 2012 (W): compatibility and its role in cascades
**Reading:**

Section 19.7C of Easley and Kleinberg's*Networks, Crowds, and Markets* - 13 Apr 2012 (F): bargaining and power in networks
**Reading:**

Sections 12.1-12.6 of Easley and Kleinberg's*Networks, Crowds, and Markets*

- Solo Homework #3 is due on Friday

- 16 Apr 2012 (M): balanced outcomes in social exchange networks
**Reading:**

Jon Kleinberg and Eva Tardos. Balanced Outcomes in Social Exchange Networks. In*Proceedings of the Symposium on Theory of Computing (STOC)*, 2008. - 18 Apr 2012 (W): balanced outcomes in social exchange networks, continued
- 20 Apr 2012 (F): strong and weak ties
**Reading:**

Sections 3.1-3.3.4 of Easley and Kleinberg's*Networks, Crowds, and Markets*

- An outline of your paper is due on Wednesday, via email.

- 23 Apr 2012 (M): structural holes
**Reading:**

Section 3.5 of Easley and Kleinberg's*Networks, Crowds, and Markets*

Sections 1 and 2 of J. Kleinberg, S. Suri, E. Tardos, T. Wexler. Strategic Network Formation with Structural Holes. Conference on Electronic Commerce (EC), 2008. - 25 Apr 2012 (W): structural holes, continued
**Reading:**

Section 3 of J. Kleinberg, S. Suri, E. Tardos, T. Wexler. Strategic Network Formation with Structural Holes. Conference on Electronic Commerce (EC), 2008. - 27 Apr 2012 (F): pageRank
**Reading:**

Sections 14.1-14.3 of Easley and Kleinberg's*Networks, Crowds, and Martkets*

- Group Homework #4 is due on Wednesday

- 30 Apr 2012 (M):
- 2 May 2012 (W): final presentations (Veronica, TBA)
- 4 May 2012 (F): final presentations (Andre, Margaret?)

- Solo Homework #4 is due on Friday
- A pdf draft of your paper is due on Sunday, 13 May, via email.

- 7 May 2012 (M): final presentations
- 9 May 2012 (W): final presentations
- 11 May 2012 (F): final presentations

- Final Projects are due on Thursday, May 17 by 9pm.