Analysis of Biological Networks, Spring 2011


Instructor: Roded Sharan
Time: Tuesday 13-16

Syllabus and Handouts

The syllabus for the course is here

A recommended book on biological networks is: "Biological networks" by Kepes. A recommended book on introduction to biology is 'Molecular Biology of the Cell' by Alberts et al.

Scribe instructions can be found here

Following is a tentative outline of the course, which will be updated according to what is actually studied in class:




Lecture scribes

Read more

(refs. are below)


22 Feb

Introduction to cell biology and networks

Molecular biology of the cell, Alberts et al.


1 Mar

Network measures and random network models

Network motif papers


8 Mar

Protein-protein interaction networks : data processing & functional annotation

PPI preprocessing papers; Functional annotation papers


15 Mar

Integer Linear Programming


22 Mar

(Shiur Halshlama on 26.4)

Network querying

Shlomi'06; Dost'07; Bruckner'09


29 Mar

Global network alignment

Bandyopadhyay'05; Yosef'08; Singh '08


5 Apr

Network modules

Alon'95; Scott'05


12 Apr

Local network alignment

Kelley'03; Sharan'05a; Sharan'05b; Koyuturk'05


3 May

Networks in disease

Liu '07; Kutalik '08; Goh '07;  Yilderim '07


17 May

Networks in drug development


24 May

Network integration

Zhang'05; Tan'07; Gunsalus'05; Yeang'04; Luscombe'04


31 May

Functional subnetwork inference


Reviews/tutorials on Biological Networks

1.      N. Pruzlj et al. Graph theory analysis of protein-protein interactions. In "Knowledge discovery in proteomics", edited by Igor Jurisica and Dennis Wigle, CRC Press, 2005.

2.      A.-L. Barabsi and Z.N. Oltvai. Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5:101-113, 2004.

3.      M.E.J. Newman. The structure and function of complex networks. SIAM Reviews 45:167-256, 2003.

4.      R. Albert and A.-L. Barabasi. Statistical mechanics of complex networks. Rev. Modern Phys. 74:47-97, 2002.

Network motifs

1.      S. Shen-Orr et al. Network motifs in the transcriptional regulation of E. Coli. Nat. Genet. 31:64-8, 2002.

2.      R. Milo et al. Network motifs: simple building blocks of complex networks. Science 298:824-7, 2002. (see also comment by Y. Artzy-Randrup et al.)

3.      R. Milo et al. Superfamilies of evolved and designed networks. Science 303:1538-42, 2003.

4.      S. Itzkovitz et al. Subgraphs in random networks. Phys. Rev. E 68:026127, 2003.

5.      N. Kashtan et al. Efficient sampling algorithms for estimating subgraph concentrations and detecting network motifs. Bioinformatics 20:1746-58, 2004.

6.      S. Wuchty et al. Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat. Genet. 35:176-9, 2003.

7.      G.C. Conant and A. Wagner. Convergent evolution of gene circuits. Nat. Genet. 34:264-6, 2003.

PPI Preprocessing

1.      C. von Mering et al. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417: 399-403, 2002.

2.      G.D. Bader & C.W.V. Hogue. Analyzing protein-protein interaction data obtained from different sources. Nature Biotech. 20:991-7, 2002.

3.      C.M. Deane et al. PPIs: Two methods for assessment of the reliability of high throughput observations. Molecular and Cellular Proteomics 1:349-56, 2002.

4.      L.R. Matthews et al. Identification of potential interaction networks using sequence-based searches for conserved PPIs or "Interologs". Genome Res. 11:2120-6, 2001.

5.      A. Grigoriev. On the number of PPIs in the yeast proteome. NAR 31:4157-61, 2003.

6.      D.S. Goldberg & F.P. Roth. Assessing experimentally derived interactions in a small world. PNAS 100:4372-6, 2003.

7.      M. Deng et al. Assessment of the reliability of PPIs and protein function prediction. PSB 140-51, 2003.

8.      J.S. Bader et al. Gaining confidence in high-throughput PPI networks. Nature Biotech. 22:78-85, 2004.

9.      S. Suthram et al. Comparison of PPI confidence schemes. Proc. First Annual RECOMB Systems Biology Workshop, 2005.

Functional Annotation

1.      B. Schwikowski et al. A network of PPIs in yeast. Nature Biotech. 18:1257-61, 2000.

2.      H. Hishigaki et al. Assessment of prediction accuracy of protein function from PPI data. Yeast 18:523-31, 2001.

3.      A. Vazquez et al. Global protein function prediction from PPI networks. Nature Biotech. 21:697-700, 2003.

4.      M. Deng et al. Prediction of protein function using PPI data. JCB 10:947-60, 2003.

5.      M. Deng et al. PPI Preprocessing papers, article 7.

6.      S. Letovsky and S. Kasif. Predicting protein function from PPI data: a probabilistic approach. Bioinformatics 19(Suppl. 1):197-204, 2003.

7.      U. Karaoz et al. Whole genome annotation by using evidence integration in functional linkage networks. PNAS 101:2888-93, 2004.

8.      E. Nabieva et al. Whole proteome prediction of protein function via graph theoretic analysis of interaction maps. Bioinformatics 21(Suppl. 1):302-10, 2005.

9.      A. Tanay et al. Clustering and Biclustering papers, article 5.