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 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 | -- |
| 2010 Spring | Participant | Rotations or Research Group | Topic | References
NEED TO UPDATE ALL REFERENCES WITH CORRECT CITATIONS USING JACS FORMAT |
| 2010.01.27 | -- | GRD 500 | Introduction | No discussion. |
| 2010.02.03 | -- | GRD 500 | Scientific Misconduct | Discussion. |
| 2010.02.10 | -- | GRD 500 | Mentorship | Discussion. |
| 2010.02.17 | -- | GRD 500 | Authorship | Discussion. |
| 2010.02.24 | -- | GRD 500 | Plagiarism | Discussion. |
| 2010.03.03 | -- | GRD 500 | Managing Data | Discussion. |
| 2010.03.10 | -- | GRD 500 | Journalism | Discussion. |
| 2010.03.17 | -- | -- | -- | Research Rotation Presentations. |
| 2010.03.24 | Adler, Jeremy | Group | Topic | Citation. |
| 2010.03.31 | -- | -- | -- | Spring Break. |
| 2010.04.07 | Au, Loretta | Green | Neutral Networks | Bastolla, et al.; Connectivity of neutral networks, overdispersion and structural conservation in protein evolution. J Mol Evol 2003, 56, 243-254. |
| 2010.04.14 | Falk, Adam | Rizzo | Thermodynamic Integration | Steinbrecher, T., Mobley, D.L., Case, D.A.; Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations. J Chem Phys 2007, 127, 214108. |
| 2010.04.21 | Jiang, Lingling | Group | Topic | Citation. |
| 2010.04.28 | Vo, Emily | Rest | Binding Site Evolution | Lusk, R. W., Eisen, M. B.; Evolutionary Mirages: Selection on binding site composition creates the illusion of conserved grammars in drosophila enhancers. PLoS Genetics 2010, 6, (1), 1-8. |
| 2010.05.05 | Last, First | Group | Topic | Citation. |
