H. C. (Paul) LEE  

Preprints/Archives
Selected papers
Articles in Chinese
All publications
- Books

Course material for the SyBBi Paper Reading Class


Powerpoint Introduction by HCL (PDF)
Fall 2006 - Student Groups and paper assignment    Schedule
Spring 2007 - Student Groups and paper assignment    Schedule
Fall 2007 - Student Groups and paper assignment    Schedule
Spring 2008 - Student Groups and paper assignment    Schedule
Fall 2008 - Student Groups and paper assignment    Schedule
Fall 2009 - Suggest Reading List (PDF) Suggest Reading List (htm)
Fall 2009 - Some Powerpoint Files (htm)
Spring 2010 - Suggest Reading List (htm)

References

Systems Biology General

- Looking beyond the details: a rise in system-oriented approaches ... Hiroaki Kitano. Curr Genet 2002, 41:1-10 (PDF)
- The Meaning of Systems Biology. MW Kirchner. Cell 2005, 121:503-504 (PDF)
- The evolution of molecularbiology into systems biology. Westerhoff et al. Nature Biotech. 2004, 22:1249-1252. (PDF)
- Systems Biology: A Brief Overview. Hiroaki Kitano Science 2002, 295:1662-1664. (PDF)
- Overview of biological networks. Harvard_MIT Ph.D. Program in Bioinformatics and Integrative Genomics (http://insilico.mit.edu/2002/) 2002/09/12 Lecture 1
- Structure of biological networks: curcuits, modules and motifs. Harvard_MIT Ph.D. Program ... 2002/09/16 Lecture 2

Database & software

- Kyoto encyclopedia of genes and genomes (KEGG). Kanehisa & Goto, Nucl. Acids Res. (2000) 28:27-30. (PDF)
- Systems biology mark-up language (SBML). Hucka et al. Bioinformatics 2003, 4:524-531 (PDF)

Measurement and instrument

- Exploring the new world of the genome with DNA microarrays. Brown & Botstein, Nat. Gen. Supplement. 1999, 21:33-37. (PDF)
- Fabrication of microfluidic systems in poly(dimethylsiloxane). JC McDonald et al. Electrophoresis 2000, 21, 27-40. (PDF)
- Mass Spectometry. R Aebersold & M Mann. Nature 2003, 422:199-207. (PDF)

Systems Biology experiment and theory

- A genomic code for nucleosome positioning. Eran Segal1 et al. Nature online 16 June 2006. (PDF)
- A Protein Interaction Map of Drosophila melanogaster. Giot et al. Sienceexpress 6 November 2003 pp1-19 (PDF)
- A first-draft human protein-interaction map. Lehner & Fraser. Gen Biology 5:R93 pp1-9 (PDF)
- A Panoramic View of Yeast Noncoding RNA Processing. WT Peng et al. Cell 2003, 113:919-933. (PDF)
- Robustness of Cellular Functions. J. Sterlling et al. Cell 2004, 118:675-685. (PDF)

Modeling and simulation

- Stochastic Kinetic Analysis of Developmental Pathway Bifurcation in Phage-Infected Escherichia coli Cells. A Arkin et al. Genetics 1998, 149:1633-1648. (PDF)
- Limit Cycle Models for Circadian Rhythms Based on Transcriptional Regulation in Drosophila and Neurospora. Leloup and Goldbeter. J Bio. Rhythms 1999, 14:433-448. (PDF)
- Dynamics of the p53-Mdm2 feedback loop in individual cells. Lahav et al. Nat Gen 2004, 36:147-150. (PDF)
- (Bacterial chemotaxis) Robustness in simple biochemical networks. Barkai & Leibler. Nature 1997, 387:913-917. (PDF)
- Yeast cycle. Chen et al. Mol. Biology of the Cell 2000, 11:369-391. (PDF)
- Network biology. Barabasi & Oltvai. Nature Rev. 2004, 5:101-114. (PDF)
- Sniffers, buzzers, toggles and blinkers: dynamics of ... pathways ... Tyson et al. Curr. Op. Cell Bio. 2003, 15:221-231 (PDF)
- Advances in flux balance analysis. Kauffman et al. Curr. Op. Biotech. 2003, 14:491-496. (PDF)
- The yeast cell-cycle network is robustly designed. Fangting Li, et al. PNAS April 6, 2004 vol. 101 no.14, 4781-4786.

Further reading

Nature Review. Systems biology: a user's guide (2006)

The Human Genome

- The Sequence of the Human Genome. J. Craig Venter et al. Science 2001, 291:1304-1351 (16 February 2001)  Online
- Initial sequencing and analysis of the human genome. ES Lander et al. Nature 2001, 409:860-921 (15 February 2001)  Online

Protein Networks and Maps
- A Genomic Regulatory Network for Development. Eric H. Davidson Science 2002, 295:1669 (2002)
- Gene_Regulatory_Networks and the Evolution of Animal Body Plans. EH Davidson and DH Erwin. Science 311:796-800 (2006) Supporting Online Material
- Network Motifs: Simple Building Blocks of Complex Networks. R. Milo et al. Science. 2002 Oct 25;298(5594):763-4.
- Automated modelling of signal transduction networks. Martin Steffen et al. BMC Bioinformatics. 2002 Nov 1;3(1):34.]
- Hierarchical Organization of Modularity in Metabolic Networks. E. Ravasz et al. Science. 2002 Aug 30;297(5586):1551-5.
- Inferring domain-domain interactions from protein-protein interactions. Deng M, Mehta S, Sun F, Chen T. Genome Res. 2002 Oct;12(10):1540-8.
- Transcriptional Regulatory Networks in Saccharomyces cerevisiae. Tong Ihn Lee et al. Science. 2002 Oct 25;298(5594):799-804.
- Evolution of transcription factors and the gene regulatory network in Escherichia coli. M. Madan Babu and Sarah A. Teichmann Nucleic Acids Research, 2003, 31:1234-1244.
- Topological structure analysis of the protein-protein interaction network in budding yeast Dongbo Bu et al. Runsheng Chen. Nucleic Acids Research, 2003, 31:2443-2450. (PDF)
- Molecular network modeling and data analysis. R. Somogyi, et al. Harvard_MIT Prog. Bioinformatics \& Integrative Genomics (PDF)
- Protein-Protein Interaction. Rain et al. Nature 2001, 409: (PDF)
- Regulatory Network for Development. Davidson et al. Science 2002 (PDF)
- Protein-Protein Interaction. von Mering et al. Nature 2002, 417: (PDF)

Miscellaneous

- A Mathematical Theory of Communication. C.E. Shannon The Bell System Technical Journal 1948, 27:379-423; 623-656 (PDF)
- Self-Organized Criticality: An Explanation of $1/f$ Noise. Per Bak, Chao Tang, Kurt Wiesenfeld Phys. Rev. Lett. 59 (1987) 831-834 (PDF)

Links

Computational and systems biology at MIT
Department of Systems Biology, Harvard Medical School
Systems Biology at Pacific Northwest National Laboratory
Ottawa Institute of Systems Biology
Institute for Systems Biology
Institute of Molecular Systems Biology (IMSB)
A portal site for systems biology


H. C. (Paul) Lee