Contents
22.04.2009 Class Overview
- You can download lecture slides from here
29.04.2009 Linear Programming
- You can download lecture slides from here
- Recommended reading:
- E. Nabieva, K. Jim, A. Agarwal, B. Chazelle, and M. Singh, Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps, Bioinformatics, 21:i302-10, Suppl 1, 2005 (PubMed).
- V. Chandru and M.R. Rao, 175 Years of Linear Programming. Part 5: Max Flow = Min Cut, Reasonance 1999 (download from here)
- V. Vazirani, Introduction to LP-Duality, pp. 93-100, Approximation Algorithms, Springer 2001 (Amazon link or download from here).
- Linear Algebra pointers:
- A book by Gilbert Strang is recommended: Linear Algebra and Its Applications, Brooks Cole, 4th edition, 2005 (Amazon link).
- Video lectures of the MIT Linear Algebra course by Gilbert Strang can be accessed here.
06.05.2009 LP Rounding Algorithms
- You can download lecture slides from here
- Recommended reading:
- V. Vazirani, Multicut in General Graphs, pp. 167-174, Approximation Algorithms, Springer 2001 (Amazon link or download from here).
13.05.2009 LP Rounding Algorithms
- Recommended reading:
- same as the previous lecture
20.05.2009 Local Search Algorithm
- You can download Quiz 2 solutions here
- Recommended reading:
- B.W.Kernighan and S.Lin, An efficient heuristic procedure for partitioning graphs, Bell Report, 1970 (download from here).
27.05.2009 Linear Algebra in a Nutshell
- You can download Linear Algebra notes here
- Recommended reading:
- M. Jerrum, Two good counting algorithms, Counting, Sampling and Integrating: Algorithms and Complexity, book draft (download from here)
- G. Strang, The fundamental theorem of Linear Algebra,The American Mathematical Monthly 100:848-855, 1993 (download from here).
- Recommended links:
- Video lectures of the MIT Linear Algebra course by Gilbert Strang (access here).
- Video lecture by Martin Vingron from 2009 RECOMB Satellite on Bioinformatics Education, Sorting Gene Expression Matrices or, Linear Algebra Can Be Good for Something! (access here)
03.06.2009 Random Walks on Graphs
10.06.2009 Random Walks on Graphs
- You can download the slides from here
- You can download Random Walks notes from here
- Recommended reading:
- C. Chennubhotla and I. Bahar, Signal propagation in proteins and relation to equilibrium fluctuations, PLoS Computational Biology 3(9):e172, 2007 (PubMed link).
17.06.2009 Spectral Clustering
- You can download Quiz 4 solutions here
- Recommended reading:
- U. von Luxburg, A tutorial on Spectral Clustering, Statistics and Computing 17(4), 2007 (download from here).
24.06.2009 Global Network Alignment
- Recommended reading:
- R. Singh, J. Xu, and B. Berger Global alignment of multiple protein interaction networks with application to functional orthology detection, PNAS 105(35), 2008 (PubMed link).
- Recommended links:
- Video lecture by Martin Vingron from 2009 RECOMB Satellite on Bioinformatics Education, Sorting Gene Expression Matrices or, Linear Algebra Can Be Good for Something! (access here)
01.07.2009 Randomized Algorithms
08.07.2009 Randomized Algorithms
- Recommended reading:
- You can download scanned Stefan's notes from here
- N. Przulj, D.G.Corneil, and I.Jurisica, Modeling interactome: scale-free or geometric? Bioinformatics 20(18):3508-3515, 2004 (PubMed link)
- N. Alon et. al., Biomolecular network motif counting and discovery by color coding., Bioinformatics 24(13):i241-249, 2008 (PubMed link).
- N. Alon, R. Yuster, and U. Zwick Color-Coding, Journal of the ACM 42(4):844-856 (download from here).
- Recommended links:
- Video lecture by Natasa Przulj from 2009 RECOMB Satellite on Bioinformatics Education, From Network Topology to Biological Function and Disease. (access here)
An excellent introduction into the biological application of the algorithm that Stefan will describe during the next two lectures.