2010-2011 AMS-532 Fall-Spring

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  • Posted on 09/01 by Trent:
  1. Each participant please update the Wiki as required
  • Posted on 09/10 by Lingling:
  1. Lab rotation is a very important part of this course. It is recommended (required for PhD track) that every new student in Computational Biology track to do three rotations in research groups of his/her special interests. Student must contacted four professors and get their permissions to do a rotation in their group. If you have any questions in regard to choosing a lab, please feel free to talk to professor Rizzo and his students (Trent Balius and Lingling Jiang). Rizzo lab is located in Room 3-129, Math Tower.
  • Posted on 09/15 by Lingling:
  1. Since some students find that the presentation is scheduled close to their AMS535 presentation, I modified the schedule so that people can prepare one at a time.
  • Posted on 11/17 by Lingling:
  1. I set up the rotation presentation schedule. Please prepare for a 15 minutes talk about your first rotation.
  2. We won't have journal club next Wednesday as it will follow a Friday schedule then.

Journal Club Participants, Topics, References, and Schedule

2010 Fall Participant Rotations or Research Group Topic References


2010.09.08 Adler, Jeremy -- Network identification Chu LH, Chen BS. Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targetsBMC Syst Biol. 2008 Jun 30;2:56.
2010.09.15 Vo, Emily -- GWAS Liu, J. Z.; et al., A versatile gene-based test for genome-wide association studies. Am. J. Hum. Genet. 2010, 87, 139-145.
2010.09.22 Jiang, Lingling -- HIV-gp41 Shi, W. X.; et al., Structural Characterization of HIV gp41 with the Membrane-proximal External Region. J. Bio. Che. 2010, 285, 24290-24298.
2010.09.29 Grinshpun, Boris Maslov Prokaryotic Metabolic Networks - Quadratic Scaling Maslov, S.; et al., Toolbox model of evolution of prokaryotic metabolic networks and their regulation. Proc. Natl. Acad. Sci. 2009, 106, 9743-9748.
2010.10.06 Liu, Jiangyang -- -- --
2010.10.13 Li, Miao Wei Zhu Normalization and DE Evaluation Bullard et al.: Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 2010 11:94.
2010.10.20 Yao, Yuan Wang Enzyme Conformation Wei Min; et al., Two-Dimensional Reaction Free Energy Surfaces of Catalytic Reaction: Effects of Protein Conformational Dynamics on Enzyme Catalysis. J. Phys. Chem. B 2008, 112, 454-466
2010.10.27 Gardin, Justin Michael -- -- --
2010.11.03 Chen, Jia Ruo -- -- --
2010.11.10 Cao, Yiwei Green Protein Design Shannon A. M.; et al., One- and two-body decomposable Poisson-Boltzmann methods for protein design calculations. Protein Sci. 2005, 14, 1293-1304.
2010.11.17 Balius, Trent Rizzo Drug design

Jorgensen W. L., Efficient Drug Lead Discovery and Optimization. Acc. Chem. Res. 2009, 42, (6), 724-733

2010.12.01 Grinshpun, B; Liu, J; Li, M -- rotation presentation --
2010.12.08 Gardin, J; Chen, J; Cao, Y; Yao, Y -- rotation presentation --
2010 Spring Participant Rotations or Research Group Topic References

Note: Readings and discussion questions in this section are taken from the Columbia University Responsible Conduct of Research website at http://ccnmtl.columbia.edu/projects/rcr

2010.01.27 Class discussion RCR / Ethics Introduction





Discussion: Why is the class important?

Discussion: How should we behave as scientists?

Discussion: How is science a social enterprise?

2010.02.03 Class discussion RCR / Ethics Scientific Misconduct


Readings (Introduction and Case Study #1 sections)

Discussion: How can the pressure to publish influence the conduct of research?

Discussion: Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?

Discussion: It seems clear that there is a problem with Samantha's data. What should Julio do now?

2010.02.10 Class discussion RCR / Ethics Mentorship Discussion.
2010.02.17 Class discussion RCR / Ethics Authorship Discussion.
2010.02.24 Class discussion RCR / Ethics Plagiarism Discussion.
2010.03.03 Class discussion RCR / Ethics Managing Data Discussion.
2010.03.10 Class discussion RCR / Ethics Journalism Discussion.
2010.03.24 Adler, Jeremy Group Topic Citation.
2010.03.31 -- -- -- Spring Break.