AMS-532 Laboratory Rotations and Journal Club in Computational Biology

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Instructor Dr. Robert C. Rizzo [631-632-9340,]
Course No. AMS-532
Location/Time Math Tower, Room 1-122, Wednesday 11:45-12:40 pm
Office Hours Anytime or by appointment, Room 1-101, Dept. of Applied Math & Statistics

GENERAL INFORMATION: AMS-532 is a two semester course in which PhD students in the AMS Computational Biology Track spend at least 8 weeks in each of three different laboratories actively participating in the research of participating Computational Biology faculty. In addition, students will 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 the rotations. Students register for AMS-532 each semester. All students (in other tracks, graduate programs, or already in a research group) are fully welcome to participate in the Journal Club component.

Note that Lab Rotations and Journal Club are required of PhD students. Masters students who register for AMS-532 participate only in Journal Club. However, outside of AMS-532, interested Masters students may pursue arrangements to engage in research with interested faculty on a case-by-case basis.

Each semester AMS-532 has two components for which guidlines are posted at AMS-532: Lab Rotations/Journal Club Guidelines.

(1) Lab Rotations: The goal of the "Lab Rotations" portion of AMS-532 is for PhD students in the AMS Computational Biology Track to learn in detail what and how research is conducted in at least three groups over the Fall and Spring semesters of the first year. The goal of the rotations is to help students choose a research advisor and to help faculty members choose students. Students should consult the AMS compbio track webpage at, talk with senior Stony Brook students, and contact potential PI's in an effort to narrow down a list to 3-4 potential laboratories. Depending on availability, and in conjunction with the AMS-532 instructor, three rotations are then scheduled for the following dates:

  • Rotation 1: Sep 20th – Nov 15th (Fall)
  • Rotation 2: Nov 15th – Feb 14th (Fall-Spring)
  • Rotation 3: Feb 14th – April 18th (Spring)

At the end of each of the three rotations students will give a brief synopsis (~15 minutes in ppt format) of their lab activities and accomplishments. Presentations will be given at the Journal Club.

(2) 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 which list papers covered to date in Journal Club along with the discussion leader schedule.

DISABILITY SUPPORT SERVICES (DSS) STATEMENT: If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact Disability Support Services (631) 632-6748 or 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 Disability Support Services. For procedures and information go to the following website:

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 are required to report any suspected instance of academic dishonesty to the Academic Judiciary. For more comprehensive information on academic integrity, including categories of academic dishonesty, please refer to the academic judiciary website at

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 Judicial Affairs any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, and/or inhibits students' ability to learn.

LITERATURE: Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.

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.

Course Schedules