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WELCOME!
It is our great pleasure to welcome you to Stony Brook University and the PhD Program in Microbiology
& Immunology! We are looking forward to getting to know each of you and as you embark on your
graduate studies. We hope you will soon feel comfortable in your new surroundings and that you won’t
hesitate to come to us with questions or concerns.
This handbook contains a great deal of useful information regarding the curriculum, registering for
courses, health insurance, etc. as well as program policies and forms you will need throughout your
graduate studies. We encourage you to maintain a copy of this handbook for future reference.
Graduate Program Director
Nick Carpino, Ph.D.
Associate Professor
Department of Microbiology and Immunology
Life Sciences 160
Mailing address:
Department of Microbiology and Immunology
Life Sciences Building, Room 130
Stony Brook, NY 11794-5222
Telephone: 631-632-4610
Fax: 631-632-9797
Email: [email protected]
Graduate Program Coordinator
Jennifer Jokinen
Department of Microbiology and Immunology
Life Sciences Building, Room 130
Stony Brook, NY 11794-5222
Telephone: 631-632-8812
Fax: 631-632-9797
Email: Jennifer.Jokinen@stonybrook.edu
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Table of Contents
Page
Welcome & Contact Information
2
Organizational Overview
4
Getting Started
4
Identification Cards
4
Facilities Access
4
Parking and Permits
5
Transportation
5
Vehicle Registration
5
E-Mail Account
5
Campus Mail
6
Student Mailboxes
6
Photocopies
6
Research Compliance
6
Appointments
7
Payroll Designations: TAs, GAs, RAs and Fellows
7
Pay Days and Direct Deposit
8
Time Reporting
9
Social Security Cards (International students)
9
Federal and State Income Tax Information
9
FAFSA and Financial Aid
9
Graduate Student Health Insurance and Benefits
9
Vacations
10
Childbirth Accommodation Program
11
Leave of Absence
11
Establishing New York State Residency
11
Graduate Student Organization (GSO)
12
Academics and Registration
13
Graduate Bulletin
13
Academic Classification
13
Registration and Deadlines
13
Registration Blocks
14
Laboratory Rotations
14
Rotations at Cold Spring Harbor Laboratory
14
Grades and GPAs
15
Teaching Practicum
15
Attendance at Scientific Conferences
15
Conferences at Cold Spring Harbor Laboratory
15
MI Annual Retreat
16
SBU Symposia and Colloquia
16
The Fishbowl
16
MI Program Policies
17
Dissertation Proposal Defense
17
Monitoring Student Progress
17
Graduate Student Seminar
17
Publication Policy
18
Dissertation Proposal and Dissertation Examining Committee
18
Dissertation Defense Policy
18
Individual Development Plan Program
18
Forms
19
Rotation Evaluation Form
19-20
CSHL Rotating Grad Student Form
21
CSHL Rotating Grad Student Checklist
22
MI Dissertation Proposal Summary Report
23
MI Dissertation Research Progress Report
24
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ORGANIZATIONAL OVERVIEW
Stony Brook University (SBU) is a flagship institution of the State University of New York (SUNY)
system and one of the top research institutions in the nation. Admission to the Graduate Program in
Microbiology & Immunology (HBM) is highly competitive and you have been invited to join us because
of your unique qualifications and accomplishments. We are confident in your ability to excel in your
studies and future career and have high expectations for each and every one of you!
Students in the Microbiology & Immunology Program are part of the School of Medicine while students
in the Genetics (BGE) Program and the Molecular and Cell Biology (MCB) Program, for example, are
part of the College of Arts and Sciences. Although the MI and BGE Programs belong to different
administrative units, they have a special relationship. The same Graduate Program Coordinator serves
students in both programs, and new students in MI and BGE share office space during the first year (the
Fishbowl; more about this later). The Graduate Program in Microbiology & Immunology is “owned and
operated” by the Department Microbiology and Immunology(MI). Key personnel in MI are shown below.
Name
Role in MI
Dr. David Thanassi
Chair
Julianna Pryor
Department Administrator
Ms. Christina Babzien
Senior Administrative Assistant
Dr. Srinivas Sistla
Director of Laboratories
As your studies progress and you choose a mentor for your graduate research, you may become affiliated
with another academic department at SBU or at Cold Spring Harbor Laboratory. However, you will still
be members of the HBM Program and the academic policies and procedures that govern your studies will
continue to fall under the jurisdiction HBM and the SBU Graduate School. The Graduate School web site
contains a great deal of useful information including upcoming deadlines, links to the Graduate Bulletin,
policies that apply to all PhD students, and various forms.
GETTING STARTED
IDENTIFICATION CARDS
Your Stony Brook ID card and SOLAR number are critical forms of campus identification. Please obtain
your photo ID as soon as possible. Take your SOLAR ID number, as well as another form of government-
issued photo ID (driver’s license, passport) to one of the Campus Card Offices located in the
Administration Building or the Health Sciences Center (HSC Level 3). Your Stony Brook photo ID may
be scanned to record your attendance at the mandatory Graduate Student Orientation sessions, so
obtaining this card should be one of your first priorities.
Pease take steps to safeguard your ID card, as you will be charged a fee for a replacement. Further, your
ID card will be programmed to grant you access to various buildings or facilities (next).
FACILITIES ACCESS
Your photo ID card, once programmed, provides your access to the Life Sciences/Centers for Molecular
Medicine complex at night, on weekends and on holidays. The building manager, Lou Capuano (Life
Sciences room 051) will encrypt your “prox card” and issue keys to provide the access you need. Some
laboratories have specific access restrictions. If you rotate in, or join, one of those labs, please email
the building manager (Louis.Capuano@stonybrook.edu) and cc your mentor. Include your ID number, as
well as the number printed ON THE BACK of your card. Note that keys must be returned when you leave
the institution or graduate.
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PARKING AND PERMITS
Please take some time to review the Transportation and Parking Services website. As a Graduate Student
RA, GA, TA or Fellow, you are entitled to a Faculty/Staff parking permit, provided your car is registered
in your name. To obtain a permit you need to take your vehicle registration and Stony Brook photo ID
to the Bursar’s office in the Administration building. Note that you will be eligible for a Staff permit only
after you have completed payroll paperwork, because your employee designation must be activated in the
SOLAR system. It usually takes at least a week after submission of your paperwork to the Payroll
department for this to be accomplished.
There is no charge for a Faculty/Staff or Resident parking permit, though you may choose to sign up to
park in one of the paid lots, such as the Administration or HSC garages, or a Life Sciences “premium” lot.
Students living in on-campus housing may obtain a resident student-parking permit.
Please note that campus parking regulations strictly enforced. Never park in a handicap spot, and be
careful to park in designated areas. Also note that you should not park in residential lots, unless you are,
in fact, a campus resident and have the proper permit. Parking tickets can add up quite quickly, and
unpaid parking tickets will prevent you from registering and can delay your graduation or the issuance of
your diploma. Refer to the latest map, which can be found on the “Where to Park” link on the
Transportation and Parking website.
TRANSPORTATION
Stony Brook University Transportation Services provides a wide variety of transportation options. It
operates a bus service all year long, to make it easier to get from one side of campus to another, as well as
to off campus destinations. On weekdays the buses run from roughly 5:30am until 11:30pm. On
weekends, additional “Shopping” service is provided. The SBU Transit Tracking System provides real-
time locations of all the campus buses.
Biking on campus is encouraged. The Stony Brook train station (on the Port Jefferson Station Long Island
Railroad line) is located adjacent to campus. For faster train service to/from New York City, many
students use the Ronkonkoma line. The Ronkonkoma station is about a 15-minute drive from campus.
VEHICLE REGISTRATION
To register a car in NY you need the original title, your social security card and other forms of
identification. If your car is financed, you may have to write to your bank to obtain the title. We suggest
you start this process as soon as possible, as it can take several weeks. There is a Department of Motor
Vehicles office at 3 Roads Plaza, Port Jefferson Station, NY.
E-MAIL ACCOUNT
Please establish a Stony Brook e-mail account as soon as possible upon arriving at SBU. You may set up
your email account from your SOLAR home page (see the section: Security and Personal Data). The
Program and the University will use your “@stonybrook.edu” email address for all official
communications, so it is essential to use this account (or forward emails from this account to your
preferred email address).
CAMPUS MAIL
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Mail within the University is distributed through the campus mail system. To send campus mail, address
it with the individual’s name, department, and the 4-digit campus zip code. You can find this information
in the on-line Campus Directory. The MI campus zip code is 5222.
Convenient branches of the US Post Office are located at:
129 Main St, Stony Brook, NY (631) 246-9239
325 Lake Ave, St James, NY (631) 584-4138
450 Route 25A, East Setauket, NY (631) 941-4005
STUDENT MAILBOXES
You will each have a mailbox in the room next to the copy room on the 2
nd
floor of the Life Sciences
Building. Please check your mailbox frequently as important notices (particularly mailings from the
Graduate School or other campus departments) are not always sent by email.
RESEARCH COMPLIANCE AND SAFETY
You are responsible for your own safety, and for learning which training is required for your specific
research. Environmental Health and Safety offers numerous live training sessions throughout the year as
well as online training for many courses. You are also required to attend the Research Compliance
Workshop held during Orientation. The MI Laboratory Director, Srinivas Sistla, can also refer you to the
appropriate sources for training you may need. Cold Spring Harbor Laboratory has its own safety training
requirements and it is your responsibility to obtain the required training if you rotate in, or join, a CSHL
lab.
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APPOINTMENTS
Appointment paperwork is time-critical to ensure your first paycheck is issued on time. In order to
appoint you to the payroll system, you must provide your local address plus the following forms of
identification:
US students: Valid passport OR valid driver’s license plus Social Security card
Permanent Residents: Proof of permanent residency plus Social Security card
International students: Valid passport, Visa (I-94), SEVIS I-20.
Address changes: It is important to notify the Graduate Program Coordinator, as well as update your
SOLAR account immediately. This is essential since payroll, Visa and Immigration Services, and all
academic records are tied to your SOLAR account.
PAYROLL DESIGNATIONS: ARE YOU A TA, GA, RA OR FELLOW?
As a graduate student in the MI Program, you will be appointed to the payroll as a Teaching Assistant,
Graduate Assistant, Research Assistant or Fellow. These distinctions are important primarily because of
the impact they have on your pay periods and health insurance enrollment. The reason for the difference
between these classifications is the source of funding for your support.
Teaching Assistants (TAs) and Graduate Assistants (GAs) are paid from funds provided by the State
of New York. Most first-year students are supported, at least in part, by State funds. As a GA or TA, you
are a member of a collective bargaining unit (GSEU union) that has negotiated certain benefits for its
members. You should attend the insurance orientation session for TAs and GAs to enroll in the SUNY
Student Employee Health Plan (NYSHIP) and learn about the benefits.
After your first year it is quite likely you will be re-appointed as a Research Assistant (RA) and it is
likely this will be your payroll designation throughout your graduate studies at Stony Brook unless you
receive a fellowship appointment. RAs are paid from research funds managed by The Research
Foundation of the State University of New York and are represented by the RA union. When you make
the change to Research payroll, you should attend the insurance orientation session for RAs to enroll in
the RA insurance program, and learn more about your coverage.
Important note:
When changing payroll status from State Funds to Research or Fellowship funds, or vice versa, it is
necessary to complete new tax withholding forms, as well as new Health Insurance enrollment and Direct
Deposit forms. The Graduate Program Coordinator can assist you.
Some of you may have, or will receive, a fellowship to support your graduate studies. There are several
different types of fellowships available to Stony Brook University students in our program:
Training Grant Fellowships: A number of Stony Brook University faculty members have obtained
highly competitive federally funded training grants (NIH T32 grants). MI graduate students
conducting research in the laboratories of participating faculty may be eligible for appointment to the
Molecular and Cell Biology of Infectious Diseases (Principal Investigator Dr. James Konopka) or
Chemical Biology (Principal Investigators Dr. Nicole Sampson and Dr. Peter Tonge) training grants.
Research mentors nominate their students for appointment to these training grants.
Appointment to one of the NIH training grants is competitive and only domestic (US citizen or
Permanent Resident) students are eligible. Criteria for appointment vary, but students appointed to
these grants excel both academically and in research. For payroll and taxation purposes, training grant
fellows are not classified as “employees” of the University. Rather, the stipend is considered an
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academic award. Fellows should consult the Internal Revenue Service website (and/or a tax
professional) for information regarding taxation of fellowship stipends.
Graduate Council Fellowships: GCFs are awarded by Stony Brook University during the
admissions process. Each GCF Fellow is nominated by the graduate program seeking to recruit the
student.
NSF and NIH Fellowships: Domestic students are also encouraged to apply for their own individual
predoctoral National Science Foundation (NSF) or National Institutes of Health (NIH) fellowships. In
addition to being a prestigious addition to your Curriculum Vitae, recipients of individual fellowships
typically receive a bonus, above and beyond the standard program stipend and may provide additional
funds to cover fees, travel to scientific meetings, etc. Individual fellowships are also academic
awards, as opposed to salaries. Recipients of these fellowships should consult the IRS website (and/or
a tax professional) for information on taxation of fellowship stipends.
W. Burghardt Turner Fellowships: Domestic students who are from groups underrepresented in the
STEM disciplines may be nominated for a Turner Fellowship, funded by New York State. These are
competitive fellowships, and most are awarded during the admissions process. Additional Turner
Fellowships are awarded to more senior graduate students as they near completion of their
dissertation research. Unlike federally funded training grant Fellowships, stipends from Turner
Fellowships are taxable.
Scholars in Biomedical Sciences: The Scholars in Biomedical Sciences Program, nicknamed the
“Med-into-Grad” program, enables biomedical PhD students to receive additional training in
translational medicine. This opportunity is available to both international and domestic students.
Students in years two or three of graduate school may apply for this competitive fellowship. The track
aims to give graduate students an understanding of the presentation, progression and treatment of
diseases related to their area of research. Scholars in Biomedical Sciences Fellows work with a
clinician and complete additional coursework during the fellowship year.
Additional Fellowships: The Graduate School provides information, resources and assistance
regarding external funding opportunities. The Center for Inclusive Education also offers assistance
and funding opportunities for graduate students and postdoctoral fellows.
PAY DAYS and DIRECT DEPOSIT
Throughout your studies your stipend may be derived from a fellowship, State teaching assistantship, a
research assistantship – or a combination of these various sources of funding. It is likely that you will be
paid as a research assistant on your mentor’s research grant after your first year, unless you join a
laboratory at Cold Spring Harbor. Students conducting research at CSHL become CSHL graduate student
employees and participate in a different benefit program.
Research Foundation employees (Research Assistants and most Fellows) will receive their paychecks on
Fridays, every two weeks. State employees (Teaching Assistants, Turner or SUNY Fellows) will receive
their checks on Wednesdays, every two weeks. Please consult with the Graduate Program Coordinator if
you have any questions regarding your pay or deductions.
All graduate students and University employees are asked to set up direct deposit of payroll checks. This
is especially helpful for those of you conducting rotations at off-campus (or cross-campus) locations. It
often takes two pay periods (or more) for the direct deposit to become active, and you must re-enroll in
the Direct Deposit program if you change status (from RA to Fellow or vice versa). Also note that any
changes to your Direct Deposit instructions must be filed with Human Resources, Administration
Building Room 390. Information for setting up Direct Deposit of your paycheck may be found here.
Research Assistants enroll in Direct Deposit using the RF Self Service website. You must provide your
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account number and bank electronic routing number, both of which are printed on your checks. Please
provide a voided check or a direct-deposit letter from your bank in order to ensure these numbers are
recorded properly. Remember to check your pay stub regularly, especially if you have Direct Deposit.
Errors can occur, so the sooner you notice a discrepancy, the sooner we can resolve any issues or errors.
Deductions (especially for insurance) can sometimes be confusing – so please ask if there are any
concerns.
TIME REPORTING
It is your responsibility to report your attendance every month (protocol varies according to appointment
type). Failure to report your attendance may result in a delayed paycheck.
SOCIAL SECURITY CARDS (International Students)
The purpose of a Social Security Number (SSN) is to help the government keep track of an individual's
earnings in the US for tax purposes. International students must apply for a Social Security number as
quickly as possible after completing registration, as this number is required for both payroll and insurance
enrollment purposes, and must be in our files no later than October 30
th
. Detailed instructions, a link to
the application form and a list of required documents are included on the Visa and Immigration Services’
web site.
Please bring your social security card to the GPC office as soon as you receive it so photocopies may be
made for your permanent record and for the Payroll and Insurance offices.
FEDERAL AND STATE INCOME TAXES
When completing your original appointment paperwork, you will complete both State and Federal tax
withholding forms. You may make changes to your withholding instructions at any time, by visiting
Human Resources, Administration Building Room 390. Most students will be entitled to a tax refund each
year, so it is important to file State and Federal tax returns on a timely basis (April 15 deadline each year).
Domestic students must file tax returns prior to filing the FAFSA application. Refer to the Human
Resources Tax Forms and Information page for forms, tax changes for the current year as well as
information specifically for International Students. All students filing taxes for the first time are strongly
encouraged to attend the Tax Workshops sponsored by the Graduate Student Organization (“GSO”) each
year.
Some international students qualify for special tax treatment. Please refer to Non-Resident Alien
Frequently Asked Tax Questions for more information. Depending upon your personal circumstance, you
may wish to visit the Human Resources Office for clarification.
FAFSA AND FINANCIAL AID
All domestic students are encouraged (but not required) to complete the “FAFSA” (Free Application for
Federal Student Aid) each year to ensure eligibility for any student loans that may be needed. The Office
of Student Financial Aid and Scholarship Services can assist, and has numerous on line resources to help
with the process. Remember you will need your tax return information to complete the FAFSA.
GRADUATE STUDENT HEALTH INSURANCE AND BENEFITS
“Required” Student Health Insurance and Health Insurance Waiver: Stony Brook now requires every
student to have basic health insurance and automatically enrolls all students in the Student Health
Insurance Plan (SHIP) or International Student Health Insurance Plan (ISHIP) to ensure no one is
overlooked. These plans are intended primarily for undergraduate students and provide limited coverage.
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The MI Graduate Program provides you with employee health insurance as a benefit, so it is important to
waive the mandatory health insurance on SOLAR every semester. If you decide to remain on a family
health insurance policy, you may do so, and will still qualify for a waiver of the insurance premium
provided you complete the waiver request on SOLAR. If you discover an insurance charge is still on your
SOLAR account in late September, please let the GPC know. No waivers will be granted after October 1.
As a Graduate Student Research Assistant (RA), Teaching Assistant (TA), Graduate Assistant (GA) or
Research Fellow, you are provided with graduate student health insurance benefits. There are some
differences in the plans for State GAs/TAs versus the plan for research assistants and fellows. There will
be several orientation sessions – please plan to attend to learn more about the insurance plan, as well as
how to enroll your spouse, dependents and/or Domestic Partner. Graduate student insurance includes
dental and vision coverage, in addition to medical benefits. For specific information, forms, premium
rates and other useful links, refer to the appropriate website indicated below.
STATE Graduate Students:
Graduate student TAs and GAs (paid with State funds) can find detailed information on their benefits on
the Human Resource Services “State Graduate Student” benefits website. To view your Benefits
Handbook, log on as a “graduate student” at NYSHIP online.
RESEARCH Graduate Students:
Graduate students paid solely with Research funds (RAs and some Fellows) can find detailed information
on their benefits on the Human Resource Services “RF Graduate Student” benefits website.
INTERNATIONAL Graduate Students:
The University provides certain services specifically for International Students. For example, you are
covered by (mandatory) Emergency Medical Evacuation coverage. This enables you to return home if
you become seriously ill, and you will see this charge on your SOLAR account each fall and spring
semester. It is especially important for you to enroll in your Graduate Student Employee health insurance
within 30 days of your appointment date. Once you enroll and payroll deductions begin, the mandatory
ISHIP health insurance fee will be removed from your student bill, usually in October. You must present
your Social Security card to complete your enrollment in the RA or TA health insurance plan, so, again, it
is critical to apply for the Social Security card as soon as possible.
VACATIONS
First-year laboratory rotations run from the end of August into early May, so students are expected to be
working during this time. We understand that many of you will have holiday plans and/or family
obligations on certain holidays. Since you also have laboratory obligations, absences from rotations
during your first year require pre-approval of your rotation advisor. A brief trip home during the holidays
or a planned absence for religious observation does not require approval but you should let your rotation
advisor know that you will be absent. If there should be an emergency that requires you to leave the
University unexpectedly, be sure to contact the Program Director as soon as possible.
Once you join a research group, your mentor will be responsible for approving your vacation leave. In
order to remain in good standing, discuss vacation plans with your advisor well in advance. It is suggested
that graduate students take no more than 2-3 weeks off each year. Students needing more time (such as
international students returning home for a month) should discuss these plans with the advisor. It is also
customary to take less time off the following year.
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CHILDBIRTH ACCOMMODATION PROGRAM
The Graduate School has established a special program for students who bear children during the course
of their PhD studies. This program enables pregnant and childbearing graduate students to maintain full-
time, registered student status and facilitate their return to full participation in class work, research,
teaching and clinical training.
The Childbirth Accommodation Program, SB-CAP, includes provisions for academic extensions, relief
from regular teaching, research, or training duties and short-term financial support for students normally
paid as Teaching Assistants, Grad Assistants or Research Assistants. Under this program, the Graduate
School pays the student’s stipend, so that the mentor’s financial resources are not strained during the
period the student is not in the lab. Leave is granted for a period of 12 weeks. More information,
including the application for Leave may be found at the Childbirth Accommodation page.
Please note that pregnant graduate students must inform their Program Directors and Research Mentors
that they wish to take leave by the 24th week of pregnancy. Students must have the knowledge and
consent of their advisor, program directors, professors and a doctor's note to be eligible for SB-
CAP. International students must also consult with Visa and Immigration Services.
LEAVE OF ABSENCE
A student may need to take a leave of absence from graduate studies under some circumstances. A leave
of absence may be taken for a single semester or for as long as one year. Your Graduate Program Director
and the Dean of the Graduate School must approve a request for a leave of absence. The Request for
Leave of Absence form may be found on the Graduate School website.
NEW YORK STATE RESIDENCY (US Citizens or Permanent Residents only)
All graduate students who are US citizens or permanent residents must establish New York State
Residency before the start of the fall semester following your first year and should begin this
process upon arrival at SBU. If you are not a New York State resident, but are eligible to establish
residency, and have not completed this process by then, you will be charged for the difference between
in-state tuition and the out of state rate – $2,000 or more, per semester. This will be your responsibility,
since, beginning in year two, your tuition scholarship is calculated at the in-state tuition rate.
Detailed information on how to apply for residency, along with the Residency Application Form.\, are
posted on the Bursar’s website. To establish residency, you should register to vote (at a local post office),
and obtain a New York State driver’s license. If you own a car that is registered in your name, and you
wish to use free Faculty/Staff parking, you will need to change to New York State registration and
register your automobile in NY State. Other documents that can be used to support your application for
residency are a local bank account (with statements mailed to your local address), or a utility bill in your
name, showing a local address. Students who wish to remain on their parents’ health insurance policy
may still establish residency, providing all other documents have a valid NY address.
Please note that if you have a vehicle on campus registered to your parents who reside out-of-state, you
cannot be considered independent and therefore will be charged the out-of-state tuition rate. As a result,
the vehicle must be leased or registered in your name.
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GRADUATE STUDENT ORGANIZATION
The Graduate Student Organization (GSO) is the graduate student governing body at the Stony Brook
University. It is incorporated in the State of New York as a nonprofit organization and is legally, and
structurally, independent of the University. The GSO purpose aims to protect the rights of graduate
students, advance their interests, provide a forum for public debate, and promote graduate student
participation in University affairs. GSO sponsors numerous activities, provides various services (tax and
legal clinics, emergency loans and more) and promotes interaction between graduate students from
various disciplines. Check out the links on their webpage, including the latest “Survival Guide.”
The GSO also assists graduate students with the costs of travel related to your research. Reimbursement
of up to $350 is available through the Resource Access Project (RAP) program. The competitive
Distinguished Travel Award will provide up to $1,500 for attendance at prestigious conferences or
symposia. Note that there are two nomination cycles per year for the Distinguished Travel Award and
each Graduate Program may only nominate two students per nomination cycle. The MI Program selects
students for nominations on a first-come first-serve basis. Learn more about these funding opportunities
by exploring the Forms page on the GSO website.
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ACADEMICS AND REGISTRATION
GRADUATE BULLETIN
The Graduate Bulletin is updated every semester, and includes important information on academic
policies and degree requirements. Each graduate program has its own section of the Bulletin and you may
find the Bulletin to be a useful source of information for finding electives.
ACADEMIC CLASSIFICATON
The number of credits for which you should register is determined by your academic classification. Each
entering MI graduate student is classified as either a “G3” or a “G4”:
G3 First-year graduate student who has completed less than 24 graduate-level
credit hours by the start of the semester and is enrolling in a doctoral
degree program. G3 students register for 9 credits during the fall
and spring semesters in year one.
G4 Advanced graduate student who has completed 18 or more SUNY
credits or has a master’s degree. G4 students register for a total of 9 credits
each fall and spring semester.
G3 students will become a G4 student in the fall semester of the second year and all students will become
a G5 student after presenting a successful dissertation proposal and “Advancing to Candidacy”. Both G4
and G5 students register for a total of 9 credits each fall and spring semester – no more, no less.
REGISTRATION AND DEADLINES
After your individual advisory session with your Program Director, please register as soon as possible.
Date specific calendars and deadlines are posted on the Registrar’s Academic Calendar web page. To
avoid late registration charges, you must always be registered for at least one credit before the first
day of classes in the fall and spring semesters.
! The last day to drop a class, without incurring tuition liability, is the end of the first week of
classes.
! The last day to “swap” classes (exchange one course for another, equal number of credits) is the
last day of the second week of classes. After this deadline you must petition the Graduate School
to make any changes to your registration.
! The deadline to complete any registration changes is the end of the third week of classes. If you
are not registered as a full-time student by the end of late registration, you will lose your tuition
scholarship, as well as jeopardize your full-time student (and F-1 visa) status.
! As a general rule, it is always easier to ADD, rather than drop, classes, so long as you do so
before the end of Late Registration.
Late registration and tuition liability fees are your responsibility, so please make it a point to register early
each year. Contact your Program Director (and/or Administrator) if you do not know which courses to
take or encounter registration difficulties.
You must be registered as a full time student throughout your graduate studies, in order to receive
tuition scholarships and/or maintain F-1 visa status. You must also register for 0 (zero) credits of
HBM 800 Summer Research EVERY YEAR to continue your full-time student status. Please be very
careful to register for the appropriate number of credits, as significant tuition liabilities will be incurred if
you are under or over the proper load and/or miss the critical deadlines. Consult your Program Director to
obtain permission to register for any additional or alternate courses. International students who are required to
take ESL classes may register for more than 12 credits without additional tuition charges.
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REGISTRATION BLOCKS
If you are “blocked” from registration, first check your SOLAR messages and account balance. In most
cases you are prevented from registering if you owe any fees (parking tickets, e.g.), or have not responded
to a SOLAR message or need to submit documents to the Graduate School. The Graduate Program
Coordinator can help you sort out any problems but don’t wait until the registration deadline to seek help.
LABORATORY ROTATIONS
Laboratory rotations are a critical part of your first year of graduate studies and you are required to
complete at least three rotations. Your rotation experiences will help you to find the appropriate lab for
the duration of your graduate studies. Once you join a lab, your mentor will be responsible for paying
your stipend. You are expected to find a permanent laboratory no later than the end of your first year of
study. You should make every effort to participate fully in laboratory activities during your rotations and
demonstrate your interest and ability to contribute to the group’s research. The rotation period is very
much a courtship (you are looking for a laboratory in which to conduct your dissertation research and the
faculty are looking to recruit the best student to their group), as well as an opportunity to learn new
techniques and build collaborations. Each rotation must be pre-approved by the Program Director. You
will receive a rotation evaluation at the end of each rotation that will become part of your permanent
academic record (a blank copy of the rotation evaluation form is included in this handbook). Many PIs
will ask their rotation students to present his/her rotation project at a group meeting toward the end of the
rotation as one way to assess the student’s understanding of the project and his/her ability to present and
interpret data.
Not all biomedical graduate programs follow the same rotation schedule, so it is important to inform your
rotation mentor of the dates. With the approval of your Program Director and the laboratory PI, the
rotation period may be adjusted if needed. A summer rotation is scheduled for students who have not
been successful in finding a laboratory during the academic year. Since classes are not in session during
the summer and students may work full-time in a summer rotation, the length of a summer rotation is
determined by the PI and Graduate Program Director. For 2019-20 the rotation dates are:
Fall: August 22 through November 18, 2022
Winter: November 28 through February 10, 2023
Spring: February 13 through May 5, 2023
Students must wait until the end of the spring rotation period, May 1, 2023, before asking to join a lab.
ROTATIONS AT COLD SPRING HARBOR LABORATORY
Students who wish to rotate at CSHL usually find that the winter rotation gives them the necessary time
in the laboratory as classes are not in session from mid-December to approximately the third week of
January. CSHL requires that you complete a Rotation Checklist and turn in a Rotation Requisition before
you may begin a rotation there. This procedure ensures that CSHL is aware of your presence in one of
their labs and that you can be informed of important regulations, procedures and safety information. The
checklist and Rotation Requisition are included at the end of this handbook. If you use public
transportation for the commute to Cold Spring Harbor, be sure to check out the partial reimbursement
available from the Graduate Student Organization.
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GRADES AND GPAs
The Graduate School requires all Stony Brook graduate students to maintain a Grade Point Average
(GPA) of 3.0 (B) or higher. The Graduate School’s policy specifies “If a student’s cumulative GPA falls
below 3.0, he/she will be placed on academic probation for one semester. If the overall graduate average
has been raised to B by the end of the semester following notice of probation, the student will
automatically return to regular status. A student on academic probation who fails to achieve a 3.0
cumulative GPA by the end of the second semester of probation will usually not be permitted to re-
enroll.”
Students receiving a grade lower than B in a required course should consult the Graduate Program
Director, as it is likely the course must be repeated. A higher grade for a repeated course will replace the
original grade.
TEACHING PRACTICUM
SUNY requires all Ph.D. students to gain teaching experience consisting of a minimum of one semester
of supervised teaching. MI graduate students currently fulfill the teaching practicum requirement by
serving as a TA in the medical microbiology course taught to first-year medical and dental students.
ATTENDANCE AT SCIENTIFIC CONFERENCES
Students are encouraged to attend scientific conferences and present their research findings as part of their
training. The costs associated with attending a conference are paid by the student’s mentor’s research
grants and may be supplemented with funds from a number of sources:
! Students appointed to a training grant may receive funding to attend scientific conferences
! Sigma Xi (call for applications usually issued in March)
! Graduate Student Organization travel award; note that the Program may only nominate two
students per funding cycle and these nominations are made on a first-come first-served basis
! Professional Development Award from the Graduate Student Employees Union (members only)
! Organizations sponsoring conferences often provide travel awards (e.g., American Society for
Microbiology student travel awards)
ATTENDING CONFERENCES AT COLD SPRING HARBOR LABORATORY
As a Stony Brook graduate student, you are welcome to attend conferences and symposia held at CSHL
without charge as long as you are not presenting a poster or platform talk at the meeting. However, you
do need to register online and select “check to follow,” so that there will be a nametag waiting for you.
The nametag will grant you free admission to the meeting, wine and cheese reception (if any), etc., but no
meals will be provided. Abstract books for CSHL meetings are delivered to MI several days before the
start of the meeting and copies may be found next to the student mailboxes on the second floor of the Life
Sciences Building as well as in the MI main office (Life Sciences Building, room 130).
Before you register online please contact Val Pakaluk in the meetings department and provide the
following information:
• Your Name
• Your SBU Graduate Program
• The meeting you plan to attend
Send this information to: Val Pakaluk, Meetings Administrator [email protected] 516-367-6895
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MI ANNUAL RETREAT
The Department of Microbiology and Immunology holds a retreat every year, usually in late September or
early October, to help new students become familiar with research opportunities in the Department and
become better acquainted with the faculty, other graduate students, postdoctoral fellows and staff
members. All MI graduate students are expected to attend the retreat every year. Students who have
joined a research group are expected to present a poster every year at the retreat. The retreat also provides
a forum for presentation of graduate student awards.
SBU SYMPOSIA AND COLLOQUIA
The Department of Microbiology and Immunology periodically sponsors a colloquium on human
diseases. Other departments and institutes at SBU also sponsor annual symposia (e.g., the annual Institute
for Chemical Biology and Drug Discovery Symposium, Cancer Center Symposia). Attendance at these
intramural scientific meetings is without cost to SBU graduate students but may require preregistration
online. Students are encouraged to take advantage of these excellent scientific meetings.
THE FISHBOWL
The first-year MI and BGE student office will be your special refuge and study area throughout the first
year. We encourage you to make good use of it for study sessions, as well as for good times together. You
will need to work together to keep the space reasonably clean and comfortable. The cleaning staff will
empty the trashcans but other cleaning is up to you.
We have provided a computer and printer, as well as other useful items. The previous denizens have left
you sample exam questions, as well as carryout menus and other odds and ends. If there are any technical
issues with the computer, or other items needing attention, please let the Graduate Program Coordinator
know. Access to nearby electrical outlets is limited at some of the office carrels. If you prefer to use one
of these carrels, please use a power strip to connect to the closest electrical outlet (additional power strips
may be obtained from Srinivas Sistla). The use of extension cords in conjunction with power strips
creates the risk of fire and is prohibited by the SBU Fire Marshal.
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MI PROGRAM POLICIES
GRADUATE STUDENT SEMINAR
Graduate students in the MI Program will register for HBM 696 Professional Development in
Microbiology and Immunology every fall and spring semester, and present their research in an annual
seminar as part of this course. Graduate students whose advisory committees have given them written
permission to write and defend their dissertations in the upcoming fall or spring semester in a given
academic year will not be required to give a seminar as part of HBM 696 that academic year. The
student’s dissertation seminar will fulfill the requirement for an annual seminar under these
circumstances.
DISSERTATION COMMITTEE
MI graduate students form an advisory committee for the dissertation proposal defense with the advice of
the advisor and approval of the Graduate Program. This committee is composed of a minimum of two
members of the training faculty (“inside members”), one of whom who serves as chair of the advisory
committee, and a minimum of one faculty member who is not a member of the MI training faculty
(“outside member”). The outside member may be from another department at SBU or another university.
The chair of the committee is responsible for submitting the Dissertation Proposal Defense Report and the
annual Dissertation Research Progress Report. Upon successful defense of the dissertation proposal, the
student’s advisor joins the above faculty members to form the Dissertation Committee. The Dissertation
Committee contributes to the development of the dissertation project, monitors the student’s progress,
reads the student’s dissertation, attends the dissertation seminar, and questions the student after the public
dissertation seminar. The Committee may request changes to the dissertation before signing the signature
page and recommending acceptance of the dissertation. A request for appointment of the Dissertation
Examining Committee must be submitted to the Graduate School at least four weeks before the
dissertation defense. The Graduate Program Director will submit this request will be submitted to the
Graduate School on behalf of the student. Note that a current CV must be provided for an outside
committee member who is not a member of a SBU graduate program.
DISSERTATION PROPOSAL DEFENSE
After completing all required courses and passing the qualifying exam, students in the MI Program must
write and orally defend a dissertation proposal in order to advance to candidacy. Students must submit the
written proposal to their committee and defend the proposal within 10 months of the qualifying exam.
The student’s committee will decide if the student has passed the proposal defense and make
recommendations to the Program’s Executive Committee with regards to corrective actions and timelines
in instances where the student does not pass the proposal defense. Under exceptional circumstances, a
student may petition the Executive Committee for an extension to this 10-month rule.
MONITORING STUDENT PROGRESS
All students who have successfully defended their dissertation proposal are required to meet with their
advisory committee once a year (annual report) and submit a written report six months after every
meeting (6-month report).
Annual Report:
1. Students will provide a written summary of the dissertation research and distribute the summary
to each member of the advisory committee at least five working days prior to the annual meeting.
2. The advisor will provide a brief statement that summarizes his/her perspective on the student’s
progress and the direction of the project to each member of the advisory committee in advance of
08/01/22
18
the annual meeting.
3. The chair of the advisory committee will complete the Dissertation Research Progress Report that
indicates whether the progress made by the student and his/her effort on the project since the
previous meeting exceeds expectations, meets expectations, or falls short of expectation. If the
student’s progress and/or effort have fallen short of expectations, the report will also specify steps
to be taken by the student in order to meet expectations within six months.
Six-Month Report:
1. Students shall submit a written report six months after every annual meeting to all members of
their advisory committee and the Graduate Program Director.
2. The six-month report should be a concise summary of the dissertation research organized by
specific aims.
3. If the student’s progress fell short of the committee’s expectations at the previous meeting, the
report should also summarize the steps taken by the student to address their concerns.
PUBLICATION POLICY
All MI students must be the first-author of at least one publication of original research to graduate. This
policy was reviewed and endorsed by the Program’s Executive Committee on March 30, 2007. The
Committee further decided that a student who has submitted a first-author paper for publication, but has
not yet received a decision from the journal, might request permission to schedule the dissertation defense
provided the student’s advisor and dissertation committee supports this request.
DISSERTATION DEFENSE POLICY
In order to ensure that adequate time will be available to make all requested changes to the dissertation,
students must schedule their dissertation seminars and defense a minimum of 14 days before the Graduate
School’s deadline for submission of dissertations.
INDIVIDUAL DEVELOPMENT PLAN PROGRAM
All first- and second-year MI graduate students and graduate students appointed to the Molecular and Cell
Biology of Infectious Diseases training grant are expected to participate in the MI Individual
Development Plan (IDP) Program. The IDP Program provides a mechanism for setting short- and long-
term professional goals and for the periodic review and refinement of these goals. The IDP Program is
presented in conjunction with career development activities to assist students in their professional growth.! !
08/01/22
19
!
GRADUATE!STUDENT!LABORATORY!ROTATION!EVALUATION!
!
The$purpose$of$this$evaluation$is$to$provide$constructive$feedback$to$the$rotation$student.$$A$copy$is$also$
needed$to$document$the$student’s$pro gres s$an d$be $plac ed$in$the$stu den t’s$aca de m ic$file.$$All$evaluatio ns$
will$be$shared$with$the$student,$as$well$as$his/her$Graduate$Program$Director.$
$
Please$describe$the$student’s$laboratory$performance,$indicating$both$his/her$strengths$as$well$as$areas$
in$which $th e $st u d en t$c a n $improve.$$P le a se $a d d re ss $a ny $d e la ys $o r$d iffic u ltie s$th e $s tu d en t $m a y $be$
experiencing.$$$
If$you$ha v e$c o n ce rn s $o r$co mmen t s$y o u $pr e fer $n o t$to $s h a re $w it h$t h e$s tu d e n t,$p lea s e $co n ta c t$th e $Gradu a te$
Program$Director$directly.$$Contact$information$is$on$page$2.$
!
Student!Name:!!! !
!
Rotation!Period!! FALL! WINTER! !! SPRING!!!
!
Rotation!Mentor:! !
! ! ! ! ! ! ! ! !
After!reviewing!the!descriptions!below,!please!rate!this!student’s!performance!by!checking!the!appropriate!rating:!!
! !
OUTSTANDING! EXCELLENT!!!!!! VERY!GOOD!!!!!! PASSING!!!!!! UNSATISFACTORY!
!
Outstanding>!
Performance!is!well!beyond!that!expected!of!a!firstByear!student,!at!the!level!of!an!advanced!graduate!
student.!The!student!works!independ ently!and!has!devoted !substantial!time!and!though t!to!project!
goals!and!independent!background!readings.!He/she!demonstrates!an!ability!to!improve!experimental!
design.!The!student’s!technical!skills!are!very!good!and!he/she!is!able!to!master!new!techniques!quickly.!
This!grade!should!be!reserved!for!exceptional!firstByear!graduate!students.!
!
Excellent>!
Work!is!at!a!level!above!that!of!an!average!firstByear!student.!The!student!shows!strong!motivation,!
works!diligently!on!the!project,!and!thinks!about!the!basic!scientific!issues!the!experiments!are!meant!
to!address.!This!grade!should!indicate!that!you!are!confident!of!the!student’s!potential!as!a!researcher!
and!are!very!satisfied!with!the!student’s!performance!in!the!laboratory.!
!
Very!Good>!
Work!is!as!expected!for!a !ty p ica l!firs tBye ar!graduate!student.!The!student!shows !clear!potential!for!
productive!graduate!level!research,!but!may!need!to!work!on!technical!skills,!intellectual!independence,!
effort!in!laboratory,!etc.!This!grade!should!be!given!for!an!average!rotation!performance,!to!a!graduate!
student!showing!reasonable!skill!levels!and!interest.!This!grade!may!also!be!appropriate!for!an!excellent!
student!who!has!entered!the!program!without!extensive!laboratory!experience,!especially!during!first!
rotations.!
!
Passing>!
The!student!shows !potential!but!will!need!significant!improvement!technically!and/or!intellectually!in!
order!to!successfully!complete!a!Ph.D.!This!grade!indicates!that!you!have!some!concerns!about!the!
student’s!ability!to!succeed!in!the!program.!
08/01/22
20
!
Unsatisfactory>!
Performance!was!below!that!expected!for!a!firstByear!graduate!student.!The!student!shows!
inadequate!motivation,!effort!and/or!ability!in!the!laboratory.!!
!
Overall!impression!of!the!student:!!!
!
!
!
What!are!the!student’s!strengths?!!
!
!
!
How!can!the!student!improve!his/her!performance?!
!
!
If!fundin g!is !a va ila b le ,!w o u ld !y o u !co n s id er !ta k in g!t h is!s tu d e n t!in to !y o u r!la b !fo r !h is/ h e r!d is se r ta tio n !r es e a rc h ?!
!
!
!
Evaluation!completed!by:!!!
!
!
!(Name !/!Da te)!
!
Please!return!a!copy!of!the!completed!evaluation!to!the!student,!with !a !copy!to!the!Gradu ate !Pro gr am !
Coordinator!and!Graduate!Program!Director.!!Additional!or!confidential!comments!may!be!sent!to!the!Graduate!
Program!Director.!
!
Graduate!Program!Coordinator!
Jennifer!Jokinen !(Je nn ifer.Jo kine n@stonyb roo k.e du )! (631)!632B8812!
!
Graduate!Program!Director,!!Microbiology!&!Immunology!
Nick!Carpino!([email protected])! (631)!632B4610!
! !
08/01/22
21
!
COLD SPRING HARBOR LABORATORY
Graduate Student Rotation Requisition Form
Student Personal Information
Name: _____________________________________
Local Address: Home Telephone:
Lab Telephone:
E-mail address: Cell#:
Emergency contact (name and telephone number):
Home Institution Information
School (e.g., SUNY Stony Brook):
Program/Department:
Matriculation Date:
Program Coordinator:
Name Signature Date
CSHL Information (to be completed by CSHL Faculty Advisor)
CSHL Rotation Start Date: End Date:
CSHL Rotation Faculty Advisor:
Name Signature Date
I understand that acceptance as a Rotating Graduate Student is not a guarantee of placement for future full-time
research in a CSHL laboratory. I have discussed the availability of future funding with my faculty advisor prior to
being accepted as a rotating student. I understand that ALL full-time student placements are subject to written
_____________________________________ ____________________________
Student’s Signature Date
_____________________________________ ____________________________
HR Signature Date
cc: Kimberly Geer, Watson School
Carol DuPree, Office of Sponsored Programs
SBU Program Coordinator
!
!
!
8/16/2022
COLD SPRING HARBOR LABORATORY
ROTATION STUDENT’S CHECKLIST
We are pleased that you have decided to do a graduate school laboratory rotation here at Cold
Spring Harbor Laboratory and welcome you to our campus. The following are the required steps
which must be completed prior to the start of your rotation. If at any point during this process you
have questions, please contact Michele Borriello at 516-367-6984, or mborriel@cshl.edu.
Complete Graduate Student Rotation Requisition Form (Mandatory)
This form is available from your Stony Brook program coordinator. Obtain all required signatures,
including your SBU program coordinator and the CSHL faculty advisor who accepted you for a
rotation. Note: A new form is required for every new rotation. If a new form is not submitted, your
building and computer access will cease on the end date of your
original rotation.
Submit Graduate Student Requisition Form (Mandatory)
Your completed requisition form must be returned to Michele Borriello in the CSHL Human
Resources Department, Luke Building (Tel. 516-367-6984) prior to the start of your rotation. An
information packet will be provided.
Schedule Safety Orientation (Mandatory)
Before any work in the Lab may begin, you must attend a mandatory Laboratory safety
orientation given by the CSHL Department of Environmental Health and Safety. Please contact
Graham Wildt at wildt@cshl.edu, or at
516-367-8336, to be included in the next scheduled
training session.
Obtain CSHL Security Identification Card (Mandatory)
Complete the Security Information Sheet and 1) present it to Michelle Borriello in the Human
Resources Department who will authorize your status and assign an employee number and 2) bring it
to the CSHL Security Department in
the Richards
Building where a picture ID card will be issued for
you. A security ID card is required to gain access to campus buildings, obtain a computer account or
purchase discounted meal cards. Give all completed forms to the HRIS
Assistant for data entry.
Purchase Meal Ticket (Optional)
Discounted meal tickets for use in the Blackford Dining Hall may be purchased from the cash-
register attendant in the dining hall. In order to qualify for the discount, show your CSHL security
identification card. (A $20 meal card is available to graduate students for $16.)
Shuttle Transportation Service (Optional)
The Lab provides a shuttle van service to and from the main campus, the Woodbury campus and the
Syosset train station. The schedule for our van service may be found on the Cold Spring Harbor
Laboratory intranet site under General Information (
http://meetings.cshl.edu/shuttle.pdf
)
On-campus Housing (Optional)
Occasionally, you may find the need to spend the night on campus. We do have limited on site rooms
available to graduate students on a first-come, first-serve basis. Please contact Andrea Newell in our
Meetings Office at 367-6847, or newell@cshl.edu, if you need a room for the night. We cannot
guarantee that rooms will be available. Therefore, it is important for you to contact the Meetings
Office, identifying yourself as a Rotating Graduate Student, as soon as know you may need a room.
There is a $51.00 per night charge for staying in our on-campus rooms. (Note: Rooms are generally
not available from Wednesday-Sunday when meetings are in session.)
Watson School of Biological Sciences
You are invited to visit the Watson School of Biological Sciences, located in Urey Cottage, whose
staff will be happy to assist you with any questions you may have as a rotating graduate student.
08/01/22
23
MICROBIOLOGY AND IMMUNOLOGY GRADUATE PROGRAM
DISSERTATION PROPOSAL SUMMARY REPORT
Student: ___________________________________________
Title of Proposal:
________________________________________________________________________
Advisor: _____________________________
Defense Date: _____________________________
Attach a summary of the proposal defense, including recommendations of the committee, to this signed
form (pass/conditional pass/fail).
Dissertation Proposal Committee
Chair of the Committee
Second Inside Member
Third Inside Member (optional)
Outside Member
Second Outside Member (optional)
Together with the advisor, this committee becomes the Dissertation Research Committee. This
committee must meet at least once per year to monitor the progress of the dissertation research and
review six-month reports submitted by the student between annual meetings. The chairperson is
responsible for submitting a summary of the proceedings of the annual meetings to the Program Office.
cc: Dissertation Advisor
Graduate Program Director
08/01/22
24
GRADUATE PROGRAM IN MICROBIOLOGY AND IMMUNOLOGY
DISSERTATION RESEARCH PROGRESS REPORT
This form certifies that the dissertation research committee for ___________________________
(Student’s name)
met on __________________ to review his/her progress.
(Date)
The progress made by the student and his/her effort on the research since the previous meeting:
___ Exceeds expectations
___ Meets expectations
___ Falls short of expectations
Please attach a report that summarizes the progress of the research and suggestions made at the
meeting.
The summary should also describe the reasons the student’s progress and/or effort has fallen short
of expectations, if applicable, and steps to be taken by the student to meet the committee’s
expectations in six month’s time.
Dissertation Research Committee:
(1) _____________________________ (2) _____________________________
(Chairperson) (Advisor)
(3) _____________________________ (4) ____________________________
(Second inside member - optional) (Outside member)
(5) _____________________________
(Second outside member - optional)
This committee must meet at least once per year to monitor the progress of the dissertation research. The
Chairperson is responsible for summarizing the proceedings of these meetings and submitting the report to the Program
office (Room 130 Life Sciences, SUNY Stony Brook, Stony Brook, NY 11794-5222).
