Difference between revisions of "2009-2010 AMS-532 Fall-Spring"

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| 2009.00.00 || Jackson, Michael || Jones || Example Citation || Altman, M. D.; et al., HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants.'' J Am Chem Soc'' '''2008''', ''130, (19)'', 6099-113.
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| 2009.09.09 || Adler, Jeremy || Entcheva|| modeling of neural behavior||Global Structure, Robustness, and Modulation of Neuronal Models. J Neurosci. 2001 Jul 15;21(14):5229-38..
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| 2009.09.09 || Adler, Jeremy || Group|| Topic|| Citation.
 
 
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| 2009.09.23 || Au, Loretta || Green|| Protein Design|| Taylor, M. S.; et al., Mutations affecting the oligomerization interface of G-protein-coupled receptors revealed by a novel de novo protein design framework. ''Biophys J'' '''2008''', ''94, (7)'', 2470-2481.  
 
| 2009.09.23 || Au, Loretta || Green|| Protein Design|| Taylor, M. S.; et al., Mutations affecting the oligomerization interface of G-protein-coupled receptors revealed by a novel de novo protein design framework. ''Biophys J'' '''2008''', ''94, (7)'', 2470-2481.  
 
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| 2009.00.00 || Brody, Dustin || Green || Gene Regulatory Networks || Pomerance, A., et al; The effect of network topology on the stability of discrete state models of genetic control. ''PNAS'' '''2009''', 8209-8214.
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| 2009.09.30 || Brody, Dustin || Green || Gene Regulatory Networks || Pomerance, A., et al; The effect of network topology on the stability of discrete state models of genetic control. ''PNAS'' '''2009''', 8209-8214.
 
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| 2009.00.00 || Chen, Yong || Group|| Topic|| Citation.
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| 2009.10.07 || Chen, Yong || Ahn|| Biostatistic|| A multiple testing procedure to associate gene expression levels with survival. ''Statist.Med.'' '''2005''',3077-3088.
 
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| 2009.00.00 || Falk, Adam || Group|| Topic|| Citation.
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| 2009.10.14 || Falk, Adam || Green|| Protein Design|| Havranek, J.J.; Baker, D., Motif-directed flexible backbone design of functional interactions. ''Protein Science'' '''2009''', ''18'', 1293-1305.  
 
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| 2009.00.00 || Guan, Xinyu || Group|| Topic|| Defining network topologies that can achieve biochemical adaptation.
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| 2009.10.21 || Guan, Xinyu || Group|| Topic|| Tsai, TY., et al; Robust, tunable biological oscillations from interlinked positive and negative feedback loops. ''Science.'' '''2008''',321(5885):126-9.
 
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| 2009.00.00 || Jiang, Lingling || Group|| Topic|| Citation.
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| 2009.10.28 || Jiang, Lingling || Group|| Pharmacophore modelling|| Gerhard Wolver, Thierry Langer; LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters. ''J.chem. Inf. Model.'' '''2005''', ''45'', 160-169.
 
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| 2009.00.00 || Hu, Yijing || Group|| Topic|| Citation.
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| 2009.11.04 || Hu, Yijing || Group|| Cell Migration|| Thomas P. Kole, Yiider Tseng, et al; Intracellular Mechanics of Migrating Fibroblasts. ''Molecular Biology of the Cell'' '''2005''', ''16'', 328-338.
 
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| 2009.00.00 || Kim, Seunglee || Group|| Topic|| Citation.
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| 2009.11.11 || Balius, Trent || Rizzo Group || Clustering MD simulations || Shao, J., et al.; Clustering molecular dynamics trajectories: 1. Characterizing the Performance of Different Clustering Algorithms. ''J. Chem. Theory Comput.'' '''2007''', ''3'', 2312-2334.
 
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| 2009.00.00 || Song, Bowen || Group|| Topic|| Citation.
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| 2009.11.18 || Song, Bowen || Zhu || Biostatistics || Joshi, T.; et al., Cellular function prediction and biological pathway discovery in Arabidopsis thaliana using microarray data. ''Int. J. Bioin. Res. and App.'' '''2006''', ''1'', 335-350.
 
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| 2009.00.00 || Vo, Emily || Group|| Topic|| Citation.
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| 2009.12.02 || Wong, Chia || Group|| Survival Analysis|| Akritas, M. G.; Nonparametric Survival Analysis. ''Stat. Sci.'' '''2004''', ''19'', 615-623.
 
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| 2009.00.00 || Wong, Chia || Group|| Topic|| Citation.
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| 2009.12.09 || Vo, Emily || Green || Sugar Conformation || Auzanneau, F-I.; et al., Stochastic conformational search on the Lewis X (Le<sup>x</sup>) trisaccharide and three Le<sup>x</sup> analogues. ''Can. J. Chem.'' '''2002''', ''80'', 1088-1095.
 
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| 2009.00.00 || Zhou, Ji || Group|| Topic|| Citation.
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|2009.00.00 || Zhou, Ji || -- || -- || --
 
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| 2010.00.00 || Last, First|| Group|| Topic|| Citation.
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| 2010.01.27 || -- || GRD 500 || Introduction || No discussion.
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| 2010.02.03 || -- || GRD 500 || Scientific Misconduct|| Discussion.
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| 2010.02.10 || -- || GRD 500 || Mentorship || Discussion.
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| 2010.02.17 || -- || GRD 500 || Authorship || Discussion.
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| 2010.02.24 || -- || GRD 500 || Plagiarism || Discussion.
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| 2010.03.03 || -- || GRD 500 || Managing Data || Discussion.
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| 2010.03.10 || -- || GRD 500 || Journalism || Discussion.
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| 2010.03.17 || -- || -- || -- || Research Rotation Presentations.
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| 2010.03.24 || Adler, Jeremy|| Group|| Topic|| Citation.
 
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| 2010.00.00 || Last, First|| Group|| Topic|| Citation.
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| 2010.03.31 || -- || -- || -- || Spring Break.
 
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| 2010.00.00 || Last, First|| Group|| Topic|| Citation.
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| 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.
 
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| 2010.00.00 || Last, First|| Group|| Topic|| Citation.
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| 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.
 
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| 2010.00.00 || Last, First|| Group|| Topic|| Citation.
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| 2010.04.21 || Jiang, Lingling|| Group||Topic ||Citation.  
 
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| 2010.00.00 || Last, First|| Group|| Topic|| Citation.
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| 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.
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| 2010.05.05 || Last, First|| Group|| Topic|| Citation.
 
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Latest revision as of 11:32, 12 August 2010

Journal Club Participants, Topics, References, and Schedule

Note: Each participant please update the Wiki as required


2009 Fall Participant Rotations or Research Group Topic References

NEED TO UPDATE ALL REFERENCES WITH CORRECT CITATIONS USING JACS FORMAT

2009.09.09 Adler, Jeremy Entcheva modeling of neural behavior Global Structure, Robustness, and Modulation of Neuronal Models. J Neurosci. 2001 Jul 15;21(14):5229-38..
2009.09.23 Au, Loretta Green Protein Design Taylor, M. S.; et al., Mutations affecting the oligomerization interface of G-protein-coupled receptors revealed by a novel de novo protein design framework. Biophys J 2008, 94, (7), 2470-2481.
2009.09.30 Brody, Dustin Green Gene Regulatory Networks Pomerance, A., et al; The effect of network topology on the stability of discrete state models of genetic control. PNAS 2009, 8209-8214.
2009.10.07 Chen, Yong Ahn Biostatistic A multiple testing procedure to associate gene expression levels with survival. Statist.Med. 2005,3077-3088.
2009.10.14 Falk, Adam Green Protein Design Havranek, J.J.; Baker, D., Motif-directed flexible backbone design of functional interactions. Protein Science 2009, 18, 1293-1305.
2009.10.21 Guan, Xinyu Group Topic Tsai, TY., et al; Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science. 2008,321(5885):126-9.
2009.10.28 Jiang, Lingling Group Pharmacophore modelling Gerhard Wolver, Thierry Langer; LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters. J.chem. Inf. Model. 2005, 45, 160-169.
2009.11.04 Hu, Yijing Group Cell Migration Thomas P. Kole, Yiider Tseng, et al; Intracellular Mechanics of Migrating Fibroblasts. Molecular Biology of the Cell 2005, 16, 328-338.
2009.11.11 Balius, Trent Rizzo Group Clustering MD simulations Shao, J., et al.; Clustering molecular dynamics trajectories: 1. Characterizing the Performance of Different Clustering Algorithms. J. Chem. Theory Comput. 2007, 3, 2312-2334.
2009.11.18 Song, Bowen Zhu Biostatistics Joshi, T.; et al., Cellular function prediction and biological pathway discovery in Arabidopsis thaliana using microarray data. Int. J. Bioin. Res. and App. 2006, 1, 335-350.
2009.12.02 Wong, Chia Group Survival Analysis Akritas, M. G.; Nonparametric Survival Analysis. Stat. Sci. 2004, 19, 615-623.
2009.12.09 Vo, Emily Green Sugar Conformation Auzanneau, F-I.; et al., Stochastic conformational search on the Lewis X (Lex) trisaccharide and three Lex analogues. Can. J. Chem. 2002, 80, 1088-1095.
2009.00.00 Zhou, Ji -- -- --
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.
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