2021-2022 AMS-532 Fall-Spring

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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)

2021 Fall Participant Rotations or Research Group Topic References


2021.08.26 Wed -- -- -- First year students will attend the AMS-539 ZOOM meeting
2021.09.02 Wed -- -- -- First year students will attend the AMS-539 ZOOM meeting
2021.09.09 Wed -- -- -- Faculty Research Presentations

Rizzo, Robert (11:45-12:05) Koo, Peter (12:10-12:40)

2021.09.16 Wed -- -- -- Organizational Meeting (First regular day of Journal Club).
2021.09.23 Wed Stepanenko, Darya -- -- Pabis et al; Influenza hemagglutinin drives viral entry via two sequential intramembrane mechanisms. PNAS 2020, 117, 7200-7207.
2021.09.30 Wed Samoilova, Khristina -- -- Babadi et al; Sparseness and Expansion in Sensory Representations. Neuron 2014, 83, 1-14.
2021.10.07 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.
2021.10.14 Wed Steier, Joshua -- -- Zhang et al; A Structured Table of Graphs with Symmetries and Other Special Propertiess. Symmetry 2020, 12, 2.
2021.10.21 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.
2021.10.28 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.
2021.11.04 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.
2021.11.11 Wed Stepanenko, Darya and Samoilova, Khristina -- -- Research Presentation
2021.11.18 Wed Steier, Joshua and Rajesh, Chandana -- -- Lab Rotation Presentations
2021.11.25 Wed -- -- -- THANKSGIVING BREAK
2021.12.02 Wed Chung, So Young and Hall, Carole and Foran, Chris -- -- Lab Rotation Presentations
2022 Spring Participant Rotations or Research Group Topic This semester (Spring 2022) students will take RCR training under AMS-500 and follow that schedule:


Required Syllabi Statements:

The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php

Student Accessibility Support Center Statement: If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.

Academic Integrity Statement: Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html

Critical Incident Management: Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of University Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Faculty in the HSC Schools and the School of Medicine are required to follow their school-specific procedures. Further information about most academic matters can be found in the Undergraduate Bulletin, the Undergraduate Class Schedule, and the Faculty-Employee Handbook.