Difference between revisions of "2010-2011 AMS-532 Fall-Spring"
From Rizzo_Lab
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| − | *From Case Study 1: A reporter from a major newspaper is scheduled to do a story on | + | *From Case Study 1: A reporter from a major newspaper is scheduled to do a story on a drug which you think might be causing premature death among second generation mice. Do you call the reporter and disclose your concerns? Why? |
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*From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why? | *From Case Study 2: Your adviser says that any disclosure of her secrete research o Anthrax would be illegal? What do you do? Why? | ||
| − | *From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly | + | *From Case Study 3: What do you do when you find out that there might be an undercover reporter working secretly to uncover the truth in an apparently poorly hospital which might violate patients privacy? |
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Revision as of 18:46, 3 January 2011
Announcement
- Posted on 09/01 by Trent:
- Each participant please update the Wiki as required
- Posted on 09/10 by Lingling:
- 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:
- 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:
- I set up the rotation presentation schedule. Please prepare for a 15 minutes talk about your first rotation.
- 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
NEED TO UPDATE ALL REFERENCES WITH CORRECT CITATIONS USING JACS FORMAT |
| 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 | -- |
| 2011 Spring | Participant | Rotations or Research Group | Topic | References
NEED TO UPDATE ALL REFERENCES WITH CORRECT CITATIONS USING JACS FORMAT |
| 2010.01.27 | Outside of class | Scientific Integrity Course | (0) Additional requirements to fulfill RCR training |
Requirements
|
| 2010.01.27 | Class discussion | Scientific Integrity Course | (1) Introduction to the Course & to Ethics and Science |
Stony Brook Lecture
|
| 2010.02.03 | Class discussion | Scientific Integrity Course | (2) Scientific Misconduct |
Stony Brook Lecture
|
| 2010.02.10 | Class discussion | Scientific Integrity Course | (3) Mentorship |
Stony Brook Lecture
|
| 2010.02.17 | Class discussion | Scientific Integrity Course | (4) Authorship |
Stony Brook Lecture
|
| 2010.02.24 | Class discussion | Scientific Integrity Course | (5) Plagiarism |
Stony Brook Lecture
|
| 2010.03.03 | Class discussion | Scientific Integrity Course | (6) Managing Data |
Stony Brook Lecture
|
| 2010.03.10 | Class discussion | Scientific Integrity Course | (7) Journalism |
Stony Brok Lecture Readings (3 Case Studies)
|
| 2010.03.31 | -- | -- | -- | Spring Break. |
