2010-2011 AMS-532 Fall-Spring
From Rizzo_Lab
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 Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring)
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 | -- | First rotation presentations | -- |
2010.12.08 | Gardin, J; Chen, J; Cao, Y; Yao, Y | -- | First rotation presentations | -- |
2011 Spring | Participant | Rotations or Research Group | Topic | References
NEED TO UPDATE ALL REFERENCES WITH CORRECT CITATIONS USING JACS FORMAT |
-- | Work to be Done Outside of class | Responsible Conduct of Research (RCR) | (0) Additional requirements to fulfill RCR training |
Requirements
|
2011.02.02 (first class) | Class Cancelled due to Ice Storm | -- | -- | -- |
2011.02.09 | Class discussion | Responsible Conduct of Research (RCR) | (1) Introduction to Ethics and Science |
Stony Brook Lecture
|
2011.02.16 | Class discussion | Responsible Conduct of Research (RCR) | (2) Scientific Misconduct |
Stony Brook Lecture
|
2011.02.23 | Class discussion | Responsible Conduct of Research (RCR) | (3) Mentorship |
Stony Brook Lecture
|
2011.03.02 | Class discussion | Responsible Conduct of Research (RCR) | (4) Authorship |
Stony Brook Lecture
|
2010.03.09 | Class discussion | Responsible Conduct of Research (RCR) | (5) Plagiarism |
Stony Brook Lecture
|
2011.03.16 | Class discussion | Responsible Conduct of Research (RCR) | (6) Managing Data |
Stony Brook Lecture
|
2010.03.23 | Class discussion | Responsible Conduct of Research (RCR) | (7) Journalism |
Stony Brok Lecture
|
2011.03.30 | Grinshpun, B; Gardin, J | -- | Second rotation presentations | -- |
2011.04.06 | Yao, Y; Cao, Y | -- | Second rotation presentations | -- |
2011.04.13 | Chen, J; | -- | Second rotation presentations | -- |
2011.04.20 | Spring Break | Spring Break | Spring Break | Spring Break |
2011.04.27 | URECA Celebration | URECA Celebration | SAC Ballrooms A&B | 10am-4 pm ALL DAY |
2011.05.04 | Cao, Y | -- | Second & Third rotation presentations | -- |
2011.05.11 (last class) | Yao, Y; Chen, J; Gardin, J; Grinshpun, B | -- | Third rotation presentations | -- |