2020-2021 AMS-532 Fall-Spring
Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage
| Instructor | Dr. Robert C. Rizzo [631-632-9340, rizzorc -at- gmail (dot) com] |
|---|---|
| Course No. | AMS-532 |
| Location/Time | online, Wed 11:45PM - 12:40PM |
| Office Hours | Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics |
GENERAL INFORMATION: GENERAL INFORMATION: AMS-532 is a two semester course in which students attend and actively participate in research discussions at weekly Journal Club meetings on topics from the current literature using the skills and knowledge acquired during laboratory rotations (AMS-531), or, if they have already joined a research lab, on topics relevant to their own research projects. In the Spring, a new component is added which is devoted to Responsible Conduct of Research (RCR) training as mandated by the University and Federal funding agencies (e.g. NIH, NSF, DOE, DOD). Note that Journal Club and Responsible Conduct of Research are required of all PhD and Masters students.
Learning Objectives:
- (1) Actively participate in Journal Club discussions on Computationally Biology literature.
- (2) Hone critical reading skills and lead discussions on literature related to Laboratory Rotations (AMS-531).
- (3) Give oral presentations on specific rotation projects performed during Laboratory Rotations (AMS-531).
- (4) Gain training in responsible conduct of research (RCR), as mandated by the university and federal funding agencies (e.g. NIH, NSF, DOE, DOD), arranged in the following sections:
- (i) Course Overview: Fulfilling Responsible Conduct in Research Training
- (ii) Integrity in Scholarship
- (iii) Scientific Misconduct
- (iv) Mentoring
- (v) Ownership and Authorship
- (vi) Plagiarism
- (vii) Data Management
- (viii) Journalism and Science
- (ix) Responsible Conduct of Research Involving Human Subjects
- (x) Responsible Conduct of Research Involving Laboratory Animals
(1) Journal Club: The goal of the "Journal Club" portion of AMS-532 is for students to hone critical reading and analytic skills through group discussion of literature related to lab rotation research programs. Participants take turn being "discussion leader" who informally guides the group through a manuscript for which all Journal Club members will have read in advance of the meeting. Normally, research papers are suggested by the PI of the laboratory hosting the student. An interactive WIKI page is maintained at http://ringo.ams.sunysb.edu/index.php which list papers covered to date in Journal Club along with a Course Schedule listing each week's discussion leader.
(2) Responsible Conduct of Research (RCR): The first ten Journal Club meetings in the Spring are devoted to training in "Responsible Conduct of Research" arranged in the following sections: (1) Course Overview: Fulfilling Responsible Conduct in Research Training, (2) Integrity in Scholarship, (3) Scientific Misconduct, (4) Mentoring, (5) Ownership and Authorship, (6) Plagiarism, (7) Data Management, (8) Journalism and Science, (9) Responsible Conduct of Research Involving Human Subjects, and (10) Responsible Conduct of Research Involving Laboratory Animals. Prior to each meeting, students will view online lectures by Stony Brook faculty and read additional relevant materials, which often include case studies. The RCR meetings will be run as small group breakout sessions followed by group discussion. To fully fulfill RCR training, students must also complete a relevant RCR module, and achieve a passing grade of at least 80% on subsequent quizzes, within the web-based Collaborative Institutional Training Initiative (CITI) located at www.citiprogram.org. See Course Schedule at the bottom of the WIKI page ( http://ringo.ams.sunysb.edu/index.php ) for more information including relevant links, topics, and dates for RCR meetings.
LITERATURE DISCLAIMER: Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.
PRESENTATION DISCLAIMER: Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.
Journal Club Schedule (Fall & Spring) and Responsible Conduct of Research Schedule (Spring)
| 2020 Fall | Participant | Rotations or Research Group | Topic | References
REFERENCES SHOULD USE J. AM. CHEM. SOC. FORMAT |
| 2020.08.26 Wed | -- | -- | -- | First year students will attend the AMS-539 ZOOM meeting |
| 2020.09.02 Wed | -- | -- | -- | First year students will attend the AMS-539 ZOOM meeting |
| 2020.09.09 Wed | -- | -- | -- | Faculty Research Presentations
Rizzo, Robert (11:45-12:05) Koo, Peter (12:10-12:40) |
| 2020.09.16 Wed | -- | -- | -- | Organizational Meeting (First regular day of Journal Club). |
| 2020.09.23 Wed | Stepanenko, Darya | -- | -- | Pabis et al; Influenza hemagglutinin drives viral entry via two sequential intramembrane mechanisms. PNAS 2020, 117, 7200-7207. |
| 2020.09.30 Wed | Samoilova, Khristina | -- | -- | Babadi et al; Sparseness and Expansion in Sensory Representations. Neuron 2014, 83, 1-14. |
| 2020.10.07 Wed | Foran, Chris | -- | -- | Cloutier et al; Machine Learning Models of Antibody−Excipient Preferential Interactions for Use in Computational Formulation Design. Mol. Pharmaceutics 2020, 17, 3589-3599. |
| 2020.10.14 Wed | Steier, Joshua | -- | -- | Zhang et al; A Structured Table of Graphs with Symmetries and Other Special Propertiess. Symmetry 2020, 12, 2. |
| 2020.10.21 Wed | Hall, Carole | -- | -- | Ferreira et al; Structural Rearrangements Maintain the Glycan Shield of an HIV-1 Envelope Trimer After the Loss of a Glycan. Scientific Reports 2018, 8, 05031. |
| 2020.10.28 Wed | Chung, So Young | -- | -- | Kursa et al; Quantifying the antiviral effect of APOBEC3 on HIV-1 infection in humanized mouse model. J Theoretical Biology 2020, 498, 110295. |
| 2020.11.04 Wed | Rajesh, Chandana | -- | -- | Shaytan et al; Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomic Insights into Nucleosome Functions. J Mol Biol 2016, '428, 221-237. |
| 2020.11.11 Wed | Stepanenko, Darya and Samoilova, Khristina | -- | -- | Research Presentation |
| 2020.11.18 Wed | Steier, Joshua and Rajesh, Chandana | -- | -- | Lab Rotation Presentations |
| 2020.11.25 Wed | -- | -- | -- | THANKSGIVING BREAK |
| 2020.12.02 Wed | Chung, So Young and Hall, Carole and Foran, Chris | -- | -- | Lab Rotation Presentations |
| 2021 Spring | Participant | Rotations or Research Group | Topic | This semester (Spring 2021) students will take RCR training under AMS-500 and follow that schedule:
https://www.stonybrook.edu/commcms/ams/graduate/_courses/ams500 |
Required Syllabi Statements:
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