COS 598F, Spring 2008: Home Page

Princeton University
Computer Science Department

Computer Science 598F
AdTop CS: Biological Networks: Analysis and Prediction

Mona Singh

Spring 2008

Course Summary

In this seminar course, we will discuss recent research on computational analysis of biological networks. Potential topics to be discussed include: network dynamics, predicting protein-protein and protein-DNA interactions; comparing, partitioning and interrogating interaction networks; network-based protein function prediction, and uncovering network organizational principles.

Most of the class will consist of student presentations of recent papers. Typically, in each class, we will cover and critically discuss 2-3 papers. In addition to presenting papers a couple of times during the term, students are required to attend all classes and participate in discussions.

Administrative Information

Lectures: F 1330-1620, Room: CS 401

Professor: Mona Singh - 420 CS Building - 258-2087 mona@cs.princeton.edu

Graduate Coordinator: Melissa Lawson - 310 CS Building - 258-5387 mml@cs.princeton.edu

Schedule / Syllabus

Date	Papers	Presenter
2/8	Introduction Hartfield, Hopfield, Liebler, Murray. From molecular to modular cell biology. Nature (1999) 402: C47. Zhu, Gerstein, Snyder. Getting Connected: Analysis and principles of biological networks. Genes and Development (2007) 21: 1010 Aittokallio, Schwikowski. Graph-based methods for analysing networks in cell biology. Briefs in Bioinformatics (2006) 7: 243 Nabieva, Singh. Protein function prediction via analysis of interactomes. (Preprint) In: Prediction of protein structures, functions and interactions (Ed. J. Bujnicki)	Mona Singh
2/15	Luscombe, Babu, Yu, Snyder, Teichmann, Gerstein (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431:308-312. de Lichtenberg U, Jensen LJ, Brunak S, Bork P (2005) Dynamic complex formation during the yeast cell cycle. Science 307: 724–727.	Alex Ochoa Tony Capra
2/22	1. Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, et al. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature. 2004;430:88–93. 2. Batada, ,Reguly, Breitkreutz, Boucher, Breitkreutz, Hurst,Tyers. Stratus not altocumulus: A new view of the yeast protein interaction network. (2006) PLoS Biol. 4:e317. 3. Batada,Reguly, Breitkreutz, Boucher, Breitkreutz, Hurst,Tyers. Still Stratus Not Altocumulus: Further Evidence against the Date/Party Hub Distinction (2007) PLoS Biol. 5:e154.	Tao Yue*
2/29	1. Beyer, Bandyopadhyay, Ideker. (2007) Integrating physical and genetic maps: from genomes to interaction networks. Nature Reviews Genetics 8: 699-710. 2. Kelley, Ideker (2005) Systematic interpretation of genetic interactions using protein networks. Nature Biotechnol. 23: 561.	Chris Park*
3/7	Gunsalus, Ge, Schetter et al. (2005) Predictive models of molecular machines involved in C. elegans early embryogenesis. Nature 436: 861. 2. Komurov, White (2007) Revealing static and dynamic modular architecture of the eukaryotic protein interaction network Molecular Systems Biology 3:110	Lindsay Gorman Jimin Song
3/14	Gandhi, Zhong, Mathivanan et al. Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat. Genet. 38:285-293, 2006. Goh, Cusick, Valle, Childs, Vidal, Barabási. The human disease network (2007) PNAS 104(21): 8685-8690.	Yuhui Luo*
3/21	NO CLASS - SPRING BREAK
3/28	1. Ptacek, Devgan, Michaud, Zhu et al. Global analysis of protein phosphorylation in yeast. (2005) Nature 438: 679. 2. Olsen, Blagoev, Gnad, Macek, Kumar, Mortensen, Mann. Global, In vivo, and site-specific phosphorylation dynamics in signaling networks. (2006) Cell 3(3): 635. 3. Linding, Jensen, Ostheimer et al. Systematic discovery of in vivo phosphorylation networks. (2007) Cell 129: 1415.	Tiago Guerra*
4/4	1. Campillos, von Mering, Jensen, Bork. Identification and analysis of of evolutionary cohesive functional modules in protein networks.(2006) Genome Res. 16: 37. 2. Tan, Shlomi, Feizi, Ideker, Sharan (2007) Transcriptional regulation of protein complexes within and across species PNAS 104: 1283.	Lindsay Gorman Jimin Song
4/11	1. Xia, Xue, Dong, Zhu, Wang et al. (2006) Identification of the Proliferation/Differentiation Switch in the Cellular Network of Multicellular Organisms PLoS Comput Biol 2(11): e145 2. Ulitsky, Shamir. Identification of functional modules using network topology and high-throughput data. (2008) BMC Systems Biology 1:8.	Adam Sanders
4/18	1. Hu, Killion, Iyer. Genetic reconstruction of a functional transcriptional regulatory network. (2007) Nature Genetics 39: 683. 2. Ernst, Vainas, Harbison, Simon and Bar-Joseph. Reconstructing dynamic regulatory maps. (2007) Molecular Systems Biology 3:74.	Dario Amodei*
4/25	1. Farkas, Jeong, Vicsek, Barabasi and Oltvai. The topology of the transcription regulatory network in the yeast S. cerevisiae. (2002) Physica A 318: 601. 2. Ohn, Kim and Kim. Genomic characterization of perturbation sensitivity. (2007) Bioinformatics 23(13): i354.	Peng Jiang*

Princeton University
Computer Science Department

Computer Science 598F
AdTop CS: Biological Networks: Analysis and Prediction

Mona Singh

Spring 2008

Course Summary

Administrative Information

Lectures: F 1330-1620, Room: CS 401

Schedule / Syllabus

2. Komurov, White (2007) Revealing static and dynamic modular architecture of the eukaryotic protein interaction network Molecular Systems Biology 3:110

1. Campillos, von Mering, Jensen, Bork. Identification and analysis of of evolutionary cohesive functional modules in protein networks.(2006) Genome Res. 16: 37.

2. Tan, Shlomi, Feizi, Ideker, Sharan (2007) Transcriptional regulation of protein complexes within and across species PNAS 104: 1283.

1. Xia, Xue, Dong, Zhu, Wang et al. (2006) Identification of the Proliferation/Differentiation Switch in the Cellular Network of Multicellular Organisms PLoS Comput Biol 2(11): e145

2. Ulitsky, Shamir. Identification of functional modules using network topology and high-throughput data. (2008) BMC Systems Biology 1:8.

Princeton University Computer Science Department

Computer Science 598F AdTop CS: Biological Networks: Analysis and Prediction Mona Singh

Spring 2008

Course Summary

Administrative Information

Lectures: F 1330-1620, Room: CS 401

Schedule / Syllabus

2. Komurov, White (2007) Revealing static and dynamic modular architecture of the eukaryotic protein interaction network Molecular Systems Biology 3:110

1. Campillos, von Mering, Jensen, Bork. Identification and analysis of of evolutionary cohesive functional modules in protein networks.(2006) Genome Res. 16: 37.

2. Tan, Shlomi, Feizi, Ideker, Sharan (2007) Transcriptional regulation of protein complexes within and across species PNAS 104: 1283.

1. Xia, Xue, Dong, Zhu, Wang et al. (2006) Identification of the Proliferation/Differentiation Switch in the Cellular Network of Multicellular Organisms PLoS Comput Biol 2(11): e145

2. Ulitsky, Shamir. Identification of functional modules using network topology and high-throughput data. (2008) BMC Systems Biology 1:8.

Princeton University
Computer Science Department

Computer Science 598F
AdTop CS: Biological Networks: Analysis and Prediction

Mona Singh