2009-2010 AMS-532 Fall-Spring

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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


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.
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


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.