AMS-531 Laboratory Rotations in Computational Biology

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Instructor Dr. Robert C. Rizzo [631-632-9340, rizzorc -at-]
Course No. AMS-531
Location/Time Individual
Office Hours Anytime or by appointment, Room 1-111, Dept. of Applied Math & Statistics

GENERAL INFORMATION: This is two semester course in which first year PhD students spend at least 8 weeks in each of three different laboratories actively participating in the research of participating Computational Biology faculty. At the end of each rotation, students give a presentation of their lab activities and accomplishments. The primary goal of rotations is to help students choose a research advisor and to help faculty members choose students. Students register for AMS 531 in both the Fall and Spring semesters of the first year. Fall and Spring, 0 - 3 credits, S/U grading. Crosslisted with PHY 584.

Learning Objectives:

  • (1) Learn how research is conducted at a "very high research" University.
  • (2) Actively participate in research of three Computational Biology faculty.
  • (3) Gain experience working as a part of a team.
  • (4) Learn to use cutting edge research tools in Computational Biology.
  • (5) Explore research projects that could lead to dissertation work.
  • (6) Gain experience giving group-meeting presentations on lab activities and accomplishments.

The goal of "Lab Rotations" 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. Note that Lab Rotations are required of all PhD students. For Masters students, Lab Rotations are optional and may be pursued with interested faculty on a case-by-case basis. At the end of each rotation, students give a brief synopsis (~15 minutes) of their lab activities and accomplishments. 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-531 instructor, three rotations are then scheduled for the following dates:

  • Rotation 1: ~ Sep 29 – Nov 28 (Fall)
  • Rotation 2: ~ Dec 01 – Feb 27 (Fall-Spring)
  • Rotation 3: ~ Mar 02 – May 01 (Spring)

Lab Rotation Guidelines: The goal of lab rotations is to help students choose a research advisor and to help faculty members choose students. In particular, faculty members use rotations as a way to help gauge how a student will work in a laboratory setting and if they would be a productive team member of the lab. With this objective in mind it is important to consider the following points when doing each rotation.

  • Become fully engaged in the lab during your rotation. Make arrangements with the group leader to have a desk or other place at which you can work and be sure to go to the lab everyday. If you need to work on class assignments do your homework in the lab. Students that rarely show up leave a less than favorable impression.
  • Show interest in the lab's research. Ask questions.
  • Read key papers from the lab. Become well-acquainted with tools being used in the group.
  • Be proactive in communicating with others in the lab. Ask for help and guidance to get started.
  • Attend lab meetings. Ask questions.
  • Be proactive in asking your rotation advisor to discuss with you research projects which could be pursued should you join the group permanently.
  • Keep in mind that faculty members must devote considerable time, effort, as well as provide financial assistance when they commit to becoming an advisor to a student. Thus, faculty members want to be sure that before they make such a commitment a student has good work habits, can communicate, is easy to work with, is interested in the lab's research, and wants to succeed in graduate school. Lab rotations can be used to show to potential advisors you have such qualities.

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.

Required Syllabi Statements: The University Senate has authorized that the following required statements appear in all teaching syllabi on the Stony Brook Campus. This information is also located on the Provost’s website:

Americans with Disabilities Act: If you have a physical, psychological, medical or learning disability that may impact your course work, please contact Disability Support Services, ECC(Educational Communications Center) Building, Room 128, (631)632-6748. They will determine with you what accommodations, if any, are necessary and appropriate. All information and documentation is confidential.

Academic Integrity: 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

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.

Rotation Schedules[edit]

Academic Year Participant Track Rotation 1 (~ Sep 29 to Nov 28) Rotation 2 (~ Dec 01 to Feb 27) Rotation 3 (~ Mar 02 to May 01)
2018-2017 last, first PhD - DEPT lab1 lab2 lab3
2018-2017 last, first PhD - DEPT lab1 lab2 lab3
2018-2017 last, first PhD - DEPT lab1 lab2 lab3
2018-2017 last, first PhD - DEPT lab1 lab2 lab3
2018-2017 last, first PhD - DEPT lab1 lab2 lab3
2017-2016 Cao, Xin PhD - AMS Coutsias Tannenbaum Balazi
2017-2016 Fallon, Zachary PhD - CHE Rizzo Simmerling Kosakov
2017-2016 Nassar, Roy PhD - CHE Dill Rizzo Simmerling
2017-2016 O'Connell, Daniel PhD - AMS Dill Rizzo Futcher
2017-2016 Telehany, Stephen PhD - CHE Simmerling Raleigh Rizzo
2016-2015 Awwa, Monaf PhD - CHE Rizzo Simmerling Kosakov
2016-2015 Banisafar, Sahar PhD - AMS Tannenbaum Kosakov Coutsias
2016-2015 Guo, Haoyue PhD - CHE Balazi MacCarthy Simmerling
2016-2015 Jiang, Beilei PhD - CHE Simmerling Rizzo Kosakov
2016-2015 Tuznik, Stanley PhD - AMS Tannenbaum Kosakov Rizzo
2016-2015 Hu, Yu MS - AMS TBD TBD Balazi
2016-2015 Shapiro, Maxwell MS - AMS Rest MacCarthy Patro
2016-2015 Xue, Jing MS - AMS Kosakov TBD TBD
2015-2014 Belfon, Kellon PhD CHE Simmerling Rizzo Raleigh
2015-2014 Cortes, Michael PhD AMS Rizzo Balazsi Green
2015-2014 Elkin, Rena PhD AMS MacCarthy Tannenbaum Balazsi
2015-2014 Lee, Stella PhD AMS Levy MacCarthy Dill
2015-2014 Sam-Ang, Panu PhD AMS Balazsi Green Reuter
2015-2014 Santos, Ruda PhD BSB Green Li Rizzo
2015-2014 Hassan, Mosavverul MS AMS Seeliger Coutsias Simmerling
2015-2014 Yin, Xingyu PhD BSB Glyn Rizzo Garcia-Diaz
2014-2013 Kennedy, Chelsea PhD AMS Zhu Rizzo Green
2014-2013 Li, Fangfei PhD AMS Rizzo Green Coutsias
2014-2013 Yu, Bihua PhD AMS Green Coutsias Zhu
2014-2013 Zhou, Junjie PhD CHE Rizzo Raleigh Simmerling
2013-2012 Krantsevich, Artyom PhD AMS MacCarthy Schatz Green
2013-2012 Krantsevich, Nick PhD AMS Rizzo MacCarthy Schatz
2013-2012 Li, Xindy PhD AMS Rizzo Green MacCarthy
2013-2012 Yuan, Chaohui PhD AMS MacCarthy Rizzo Green
2013-2012 Guo, Jiaye PhD BSB Boon Rizzo -
2013-2012 Shan, Emma MS AMS - MacCarthy -
2013-2012 Chen, Ye MS AMS - - MacCarthy
2013-2012 Amgalan, Anar PhD PHY Dill Rizzo Maslov
2012-2011 Jeewon, Sin PhD AMS Rizzo Green MacCarthy
2012-2011 Chen, Jeff PhD AMS Schatz Maslov MacCarthy
2012-2011 Sinayev, Roman AMS MS Green Rizzo Simmerling
2012-2011 Xia, Yunting AMS MS Rizzo MacCarthy Green
2012-2011 Zhou, Yuchen AMS MS Green Rizzo MacCarthy