2010-2011 AMS-532 Fall-Spring

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  • Posted on 09/01 by Trent:
  1. Each participant please update the Wiki as required
  • Posted on 09/10 by Lingling:
  1. 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:
  1. 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:
  1. I set up the rotation presentation schedule. Please prepare for a 15 minutes talk about your first rotation.
  2. 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


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


2010.01.27 Class discussion Scientific Integrity Course Introduction to the Course & to Ethics and Science

Stony Brook Lecture

Readings (Nature articles)


  • Why is the class important?
  • How should we behave as scientists?
  • How is science a social enterprise?
2010.02.03 Class discussion Scientific Integrity Course Scientific Misconduct

Stony Brook Lecture

Readings (Taken from Columbia University http://ccnmtl.columbia.edu/projects/rcr)

Discussion (Taken from Columbia University http://ccnmtl.columbia.edu/projects/rcr)

  • How can the pressure to publish influence the conduct of research?
  • Was it appropriate for Dr. Chan to promise Samantha second authorship based on performing some assays?
  • It seems clear that there is a problem with Samantha's data. What should Julio do now?
2010.02.10 Class discussion Scientific Integrity Course Mentorship

Rubin Lecture

2010.02.17 Class discussion Scientific Integrity Course Authorship

Gergen Lecture

2010.02.24 Class discussion Scientific Integrity Course Plagiarism

[https://meeting.sinc.stonybrook.edu/p41971516 Clark Lecture

2010.03.03 Class discussion Scientific Integrity Course Managing Data

[https://meeting.sinc.stonybrook.edu/p68134598 Huddy Lecture

2010.03.10 Class discussion Scientific Integrity Course Journalism

[https://meeting.sinc.stonybrook.edu/p99353453 Schneider Lecture

2010.03.31 -- -- -- Spring Break.