2015-2016 AMS-532 Fall-Spring
From Rizzo_Lab
Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage
Instructor | Dr. Robert C. Rizzo [631-632-9340, rizzorc@gmail.com] |
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Course No. | AMS-532 |
Location/Time | Physics P127 Wed 12:00PM - 12:53PM |
Office Hours | Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics |
Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring)
2015 Fall | Participant | Rotations or Research Group | Topic | References
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT |
2015.08.26 Wed | Last name, First name | -- | -- | Organizational Meeting |
2015.09.02 Wed | Belfon, Kellon | Dr. Simmerling's Group | Protein Dynamics | Hornak, V. et al. HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. PNAS. 2006 January. 103(4). 915-920. [1] |
2015.09.09 Wed | Tian, Chuan | Dr. Simmerling's Group | Force Field Development | Hornak, V. et al. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins: Structure, Function, and Bioinformatics. 2006 June. 65(3). 712-725. [2] |
2015.09.16 Wed | -- | -- | -- | AMS Grad Student BBQ |
2015.09.23 Wed | Cortes, Michael | Dr. Balazsi's Group | Gene regulation | Weitz, J. S. et al. Collective decision making in bacterial viruses. Biophys J. 2008 September. 95(6). 2673-2680. [3] |
2015.09.30 Wed | Singleton, Courtney | Dr. Rizzo's Group | Genetic Algorithms for De Novo Design | Kawai, K. et al. De Novo Design of Drug-Like Molecules by a Fragment-Based Molecular Evolutionary Approach. J. Chem. Inf. Model. 2014. 54(1). 49-56. |
2015.10.07 Wed | Jones, Peter | -- | Gene Circuit's | Nevozha, D. et al. Mapping the Environmental Fitness Landscape of a Synthetic Gene Circuit. PLOS Comp Bio. 2012. 8, e1002480 |
2015.10.14 Wed | Awwa, Monaf | -- | Modelling ECGC in Cancer Implicated Proteins | Van Aller, Glenn S., et al. "Epigallocatechin gallate (EGCG), a major component of green tea, is a dual phosphoinositide-3-kinase/mTOR inhibitor." Biochemical and biophysical research communications 406.2 (2011): 194-199. |
2015.10.21 Wed | Xue, Jing | -- | PIPER:An FFT-Based Protein Docking Program with Pairwise Potentials | Kozakov, D., Brenke, R., Comeau, S. R. and Vajda, S. (2006), PIPER: An FFT-based protein docking program with pairwise potentials. Proteins, 65: 392–406. doi: 10.1002/prot.21117 |
2015.10.28 Wed | Shapiro, Maxwell | Dr. Rest Lab | Gene Expression, Fitness Functions | Rest JS, Morales CM, Waldron JB, et al. Nonlinear Fitness Consequences of Variation in Expression Level of a Eukaryotic Gene. Molecular Biology and Evolution. 2013;30(2):448-456. doi:10.1093/molbev/mss248. [4] |
2015.11.04 Wed | Banisafar, Sahar | -- | Image Processing | ANGENENT, S. et al. MATHEMATICAL METHODS IN MEDICAL IMAGE PROCESSING. BULLETIN (New Series) OF THE AMERICAN MATHEMATICAL SOCIETY. 2006. 43. 365. |
2015.11.11 Wed | Guo, Haoyue | -- | Gene Expression Noise | Charlebois, D. A. et al. Gene Expression Noise Facilitates Adaptation and Drug Resistance Independently of Mutation. PHYSICAL REVIEW LETTERS. 2011. 107. 218101. |
2015.11.18 Wed | Jiang, Beilei | -- | Structure-based Design | Lai, C-T. et al. Rational Modulation of the Induced-Fit Conformational Change for Slow-Onset Inhibition in Mycobacterium tuberculosis InhA. Biochemistry, 2015, 54, 4683−4691 |
2015.11.25 Wed | - | -- | -- | THANKSGIVING BREAK |
2015.12.02 Wed | Tuznik, Stanley | -- | Cancer Networks | Sandhu, R. et al. Graph curvature for differentiating cancer networks. Sci Rep. 2014 July. 5:12323. |
2016 Spring | Participant | Rotations or Research Group | Topic | References
SEMESTER STARTS WITH RESPONSIBLE CONDUCT OF RESEARCH |
2016.01.27 Wed | Class discussion | Responsible Conduct of Research (RCR) | (1) Course Overview: Fulfilling Responsible Conduct in Research Training |
Discussion of Overall Course Requirements which include:
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2016.02.03 Wed | Class discussion | Responsible Conduct of Research (RCR) | (2) Integrity in Scholarship (Introduction to Ethics and Science) |
Stony Brook Lecture
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2016.02.10 Wed | Class discussion | Responsible Conduct of Research (RCR) | (3) Scientific Misconduct |
Stony Brook Lecture
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2016.02.17 Wed | Class discussion | Responsible Conduct of Research (RCR) | (4) Mentoring |
Stony Brook Lecture
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2016.02.24 Wed | Class discussion | Responsible Conduct of Research (RCR) | (5) Ownership and Authorship |
Stony Brook Lecture
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2016.03.02 Wed | Class discussion | Responsible Conduct of Research (RCR) | (6) Plagiarism |
Stony Brook Lecture
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2016.03.09 Wed | Class discussion | Responsible Conduct of Research (RCR) | (7) Data Management |
Stony Brook Lecture
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2016.03.16 Wed | -- | -- | -- | SPRING BREAK |
2016.03.23 Wed | Class discussion | Responsible Conduct of Research (RCR) | (8) Journalism and Science |
Stony Brook Lecture
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2016.03.30 Wed | Class discussion | Responsible Conduct of Research (RCR) | (9) Responsible Conduct of Research Involving Human Subjects |
Stony Brook Lecture
Discussion
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2016.04.13 Wed | Class discussion | Responsible Conduct of Research (RCR) | (10) Responsible Conduct of Research Involving Laboratory Animals |
Stony Brook Lecture
Discussion
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2016.04.20 Wed | Last name, First name | -- | -- | ROTATION/RESEARCH PRESENTATIONS |
2016.04.27 Wed | Last name, First name | -- | -- | ROTATION/RESEARCH PRESENTATIONS |
2016.05.04 Wed | Last name, First name | -- | -- | ROTATION/RESEARCH PRESENTATIONS |