Policies and Procedures of the Cell and Molecular Biology Graduate Program (CMB)

Approved by vote of the CMB Faculty June 3, 2024

Contents

ADMISSION.. 2

INTERNATIONAL STUDENT APPLICATIONS. 2

TRANSFER FROM MS TO PHD PROGRAM… 2

TRANSFER TO CMB FROM OTHER GRADUATE PROGRAMS AT CSU.. 2

TRANSFER OF CREDIT. 3

SELECTION OF ADVISOR AND GRADUATE COMMITTEE. 3

ANNUAL MEETING WITH GRADUATE ADVISORY COMMITTEE (GAC). 4

LABORATORY ROTATIONS FOR FIRST YEAR STUDENTS. 4

DIRECT RECRUITMENT INTO LABORATORIES. 5

STANDARDS OF PERFORMANCE. 5

GRADUATE ASSISTANTSHIPS. 6

GRADUATION REQUIREMENTS. 6

CONTINUOUS REGISTRATION.. 7

DIVERSITY AND INCLUSION.. 7

COURSES REQUIRED FOR THE MS DEGREE. 7

COURSES REQUIRED FOR THE PhD DEGREE. 8

COURSES REQUIRED FOR THE CANCER BIOLOGY SPECIALIZATION.. 8

ETHICS, TOPICS, STATISTICS & WRITING ELECTIVES. 9

CMB PREFIX COURSES. 10

OTHER ELECTIVES. 11

SAMPLE CURRICULUM – MS 15

SAMPLE CURRICULUM – PhD 16

EXAMINATIONS. 17

PUBLICATIONS. 21

STUDENT APPEALS OF GRADING DECISIONS. 21

Admission

The admission requirements of the Cell and Molecular Biology Graduate Degree Program (CMB Program) include a bachelor’s degree in any of the biological, biochemical, or physical sciences. The university requirements for admission to graduate school apply. Coursework including organic chemistry, physics, mathematics (including calculus), biochemistry, coding, cell biology, microbiology, developmental biology, immunology, genetics, physical chemistry, analytical chemistry, biophysics, physiology, and anatomy may be considered in evaluation for admission as well as research experience, and presentations. Promising students who are under-prepared for core CMB coursework may be accepted into the program provided all deficiencies are corrected during the first year. This may be accomplished by passing a background examination, by taking appropriate undergraduate courses, or by successfully completing graduate level courses that require the undergraduate courses as prerequisites. Applications are evaluated by the Admissions Committee and recommendations for admission are forwarded to the Program Director for final decision. Unofficial transcripts are sufficient for review, but official transcripts must be provided before admission.

Students are admitted as graduate teaching assistants (GTA), as graduate research assistants (GRA) or, if they have governmental or other form of fellowship support, as pre-doctoral fellows

International Student Applications

The CMB Program is also committed to educate students from foreign countries, particularly those from developing countries. Foreign student applicants must meet the same admission requirements as United States applicants. In addition, they must show evidence of competence in the written and spoken English language as evidenced by a TOEFL score of 80 (internet-based), 550 (paper-based) or higher. An IELTS score of 6.5 or above, or a PTE Academic Score of 58 or above or Duolingo with a minimum score of 120 are also acceptable. Alternatively, applicants can complete the Intensive English Program Level 3 at CSU.

Transfer from MS to PhD Program

Students who have been admitted to the MS Program may apply to enter the PhD program with or without first completing their MS degree. To be considered, students should provide the Program Director with the following:

· Two letters of recommendation from CSU Faculty Members (one can be from the advisor)

· A personal statement describing how a PhD fits into their career goals and what qualities they possess that will allow them to be successful in a PhD program.

· CSU Unofficial Transcript

· A statement from the PhD advisor describing how the student’s stipend and research project will be supported.

These documents along with the student’s original application to the program will be forwarded to the Admissions Committee for evaluation. The committee may also interview the student in person. If the application is deemed acceptable, the student, Department Head, CMB Director and advisor must sign a letter describing the new commitment that the advisor and department are making to the student, prior to submission of the GS7 form that completes the transfer into the PhD program.

Transfer to CMB from Other Graduate Programs at CSU

Students from other programs (such as Molecular, Cellular & Integrative Neurosciences, or the DVM Pathology PhD program) may transfer into the CMB program after the first year of their graduate studies. On rare occasions, transfers may also be considered at a later point in the degree. In most cases these students will be directly admitted into a laboratory as a GRA. Students wishing to transfer into CMB must provide the following:

· Two letters of recommendation from CSU Faculty Members (one can be from the advisor)

· A personal statement describing how a PhD or MS in Cell & Molecular Biology fits into their career goals and what qualities they possess that will allow them to be successful.

· CSU Unofficial Transcript

· A statement from the advisor describing how the student’s stipend and research project will be supported.

These documents along with the student’s original application to the University (which includes UG transcripts) will be forwarded to the Admissions Committee for evaluation. The committee may also interview the student in person. If the application is deemed acceptable, the student, Department Head, CMB Director and advisor must sign a letter describing the commitment that the advisor and department are making to the student, prior to completion of the GS7 form that completes the transfer into the CMB program.

Transfer of Credit

Students completing an MS degree at another institution prior to entering the PhD program may transfer up to 30 credits as specified in the Graduate Bulletin. Students completing an MS degree at CSU and then immediately entering the PhD program may potentially transfer a higher number of credits with the approval of their GAC. In each case, all transferred credits must be approved by their GAC. In addition, students must continue to participate in CM792 and CM793 once per year until they graduate.

Selection of Advisor and Graduate Committee

The Program Director with input from the Academic Committee will advise students concerning course work during the first year. If a student is admitted as a GRA with direct support from a faculty member, the faculty member will serve as the advisor and co-advise on course selection. After registering, a graduate student must obtain approval from the Academic Committee or their advisor before adding or dropping a course. Students receiving support from the CMB Program or from fellowships generally rotate through three laboratories of their choice during their first two semesters in residence. This experience will allow them to become familiar with potential thesis projects and with several faculty members in their area of interest.

Final selection of an advisor should be made by the end of the second semester following enrollment but must be made by the end of the first calendar year. The Advisor, their Department Head, the student and the CMB Program Director will sign a letter describing the commitment that the Department and Advisor are making to the student prior to the student joining a lab.

The advisor and student shall select a Graduate Advisory Committee (GAC) that has expertise relevant to the major areas of the student’s graduate study. A minimum of 3 members is required for M.S. degree candidates and 4 committee members for Ph.D. degree candidates, at least two (M.S.) and three (Ph.D.) of the committee members must be members of the CMB faculty. In addition, the Graduate School requires the appointment of an outside member. This member must be a faculty member whose primary appointment is outside the home department of the student’s advisor. Faculty from outside of the University may also be appointed to committees (see the CMB Program Code for details). The CMB Program Director and/or Academic Committee may require changes to the committee structure or request justification prior to approving the GS6. This may be necessary to address, for example, conflicts of interest (e.g. committee members have a marital or mentor/mentee relationship) or perceived lack of relevant expertise. The development of a formal plan of course work and research activities is the responsibility of the GAC.

The GAC should be selected and meet within three months of selecting an advisor to prepare the formal plan of study (Form GS 6, Program of Study). Subsequently, this committee should meet annually, or more frequently if necessary, to advise a student and to submit an evaluation of the student’s progress in completing their academic requirements and thesis research.

The procedures required for graduation are detailed by the Graduate School in the Graduate and Professional Bulletin.

Annual Meeting with Graduate Advisory Committee (GAC)

Annual Performance Evaluation by Graduate Advisory Committee

To assist in the evaluation of a student’s progress in research, each student must meet annually with their Graduate Advisory Committee (GAC). This annual evaluation will consist of the following:

1. Completion of the progress report form. This form can be found on the CMB website and should be initiated at the time of the first GAC meeting and updated annually. Part 1 comprises sections describing progress in courses, professional development, teaching, mentoring, presentation skills and outreach. In Parts 2 and 3, the student and advisor are each asked to assess the student’s development and progress. In part 4 the student should summarize their research progress. The first research summary should be prepared at the time of the first GAC meeting and should describe the student’s future research goals. Subsequent research reports should briefly summarize the goals of the research and the progress made since the previous meeting with the Graduate Advisory Committee. The progress report must be distributed to the members of the Advisory committee at least one week before the scheduled meeting of the committee. The GAC are asked to sign the progress report and a copy should be provided to the CMB coordinator within one week of its completion. Students beyond their first year who fail to submit an annual progress report to the CMB program coordinator by February 1st each year will have a hold placed on their registration for the fall semester and will be required to petition the CMB Academic Committee to get the hold removed.

2. A research seminar in CM 793. Students are required to enroll once per year in CM 793 starting in their first year and present a seminar in this course describing their progress in research starting their second year. Students should inform their committee well in advance of the date of their scheduled seminar and strongly encourage members of their GAC to attend. Optimally, students should give their written progress report to their committee a week prior to their research seminar and a meeting should be scheduled within two weeks after the seminar to clarify questions raised by the progress report and the seminar, and to solicit guidance and suggestions from the GAC concerning goals, methods, and evaluation of the research. The GAC members may evaluate the presentation as part of the progress report.

Laboratory Rotations for First Year Students

The advisor-student relationship is unique, and it is the mutual strength, respect, and stimulus of this relationship that promotes scientific achievement. First-year Ph.D. students who receive support from the CMB Program generally complete three laboratory rotations during the first two semesters in residence. The aim of this program is to introduce students to a variety of research approaches, techniques, and projects, and to aid students in choosing an advisor for their dissertation research. The goal of each rotation is to allow the student to accomplish some research and to experience the culture of the laboratory. Students are expected to attend group meetings of the laboratories through which they rotate and complete some original research while learning the techniques and approaches of different disciplines. At the end of each rotation the student should meet with the advisor to discuss their performance and the advisor will complete a Rotation Report that will be shared with the student and the CMB Program Manager and will be used to determine satisfactory performance for grading of Independent Study (CM595/795) credits. The Rotation Report form can be found on the CMB website and must be submitted to the Director within one week of completing a rotation.

Entering students will participate in an orientation during the week prior to the first day of classes. The orientation will provide students with information on the breadth of research conducted by faculty in the program and faculty who are willing to provide laboratory rotations. Students will submit a list of their preferred rotations. Matches will be made in consultation with the Academic Committee and/or Program Director. Students will begin the first rotation in August and the second rotation in October. The third rotation begins in early January. The selection of an advisor should occur shortly after Spring break. This allows the student maximum flexibility in making their final choice of advisor. In the unlikely event that a student has not found a good match they may complete a fourth rotation before the end of the Spring semester. After this time students who have not found a lab may approach additional faculty for further rotations but cannot rely on the CMB Program for stipend support. A student who has not found an advisor by the start of the Fall semester following admission risks dismissal from the CMB program due to inability to make progress on the research portion of their studies.

In consultation with the Director or Academic Committee, Ph.D. students should register for a variable number of CM795 credits (Independent Study) for these lab rotations. Support in selecting an advisor and resources for success in graduate school are shared in CM510: Intro to Cell & Molecular Biology.

Direct Recruitment into Laboratories

Faculty will be allowed to recruit incoming students directly to their laboratories to immediately begin work on a thesis or dissertation project. Such students must be approved for admission into the CMB program by the Admissions Committee and the Graduate School and must be supported by funds other than those of the CMB Program, generally in the form of a teaching or research assistantship or fellowship. The Admissions Committee must approve the advisor’s plan to support the student’s stipend and research project prior to admission of the student. Such students will not participate in rotations.

Standards of Performance

The academic and research performance of each student is evaluated annually by the student’s Graduate Advisory Committee (GAC) and the advisor, and the signed progress report must be submitted to the CMB Program to be put in the student’s file. Unsatisfactory performance in course work, laboratory rotations, or research is grounds for probation or dismissal from the CMB program following Graduate School guidelines. In course work, an unsatisfactory performance is based upon grade point average. For laboratory rotation and research, unsatisfactory grades are assigned based upon a comparison with the performance of successful students in similar disciplines. This requirement is to assure that students are making adequate progress and that failure to progress satisfactorily is addressed expeditiously. Following a committee meeting the GAC may recommend that the advisor enter a grade of U for research credits, or the committee may provide a letter describing unsatisfactory progress which can be shared with the CMB Academic Committee and the Dean of the Graduate School. A student in this position will be required to hold another committee meeting after four months which will be attended by a member of the Academic Committee. If there is no improvement the GAC may recommend to the Graduate School that the student be dismissed from the program. Each student must maintain a cumulative Grade Point Average (GPA) of at least 3.00 in all didactic course work taken during their graduate program at Colorado State University, achieve a B or higher in all core courses and receive satisfactory grades in Independent Study and Thesis Research courses. After a second semester in which a student fails to attain a cumulative average of 3.00 or receives unsatisfactory grades in research/independent study, they will be dismissed in accordance with Graduate School procedures. Any exception must be initiated by the student in the form of a petition to the student’s GAC, or the CMB Director, if no GAC has been established. The advisor or the director may then appeal to the Dean of the Graduate School for reinstatement.

After completing 3 years in the MS program or 6 years in the PhD program, students must formulate a written plan for completion including a timeline that should be reviewed by the Program and their GAC. At any time after this point the CMB Director may call a meeting of the GAC to review the student’s progress and performance. This meeting and any subsequent meetings may be attended by the CMB Director or a member of the CMB Executive or Academic Committee.

Any time that a student experiences an event or issue that impacts their ability to make progress on their degree for more than 3 months, they should notify the CMB Program Manager or Director as well as their advisor. The information will be kept confidential but will allow the Program to intervene and provide support and guidance.

Graduate Assistantships

Graduate Assistantships may be awarded to students who enter with a GPA of 3.00 or above, and occasionally to students with slightly lower GPAs who have demonstrated their ability to be successful in graduate study in other ways. Graduate Teaching Assistantships are awarded on a competitive basis. Any student holding a Graduate Assistantship and failing to maintain a cumulative GPA of 3.00 risks losing such support until raising their cumulative GPA to 3.00 or above. Students entering with a GPA of below 3.00 must attain a GPA of 3.0 in their first semester to retain their assistantship in the second semester.

Students entering with support as a Graduate Teaching Assistant from the CMB Program receive a monthly stipend at least equivalent to either that provided to first year LIFE GTAs through the College of Natural Sciences ($2,471 per month in 2024) or the minimum stipend set by the Graduate School, whichever is higher. Stipend is base-funded, and tuition is provided by the GTA/GSA Base Tuition Program. Alternative and subsequent support for graduate students is provided through diverse sources, including fellowships, research grants awarded to faculty members, and GTAships from various departments that utilize different guidelines. However, the goal of the CMB Program is that all students should receive a stipend of at least that set for the LIFE GTAs, or the level set by the departmental program of their advisor if it is greater than the LIFE GTA stipend. Students appointed as assistants (GRA/GTA/GRA-PD) also receive a contribution to fees. In 2024/25 75% of fees will be covered and in subsequent years 100% of fees will be covered.

The Graduate School provides a health insurance contribution to help offset the cost of health insurance to graduate assistants who meet all of the following criteria each fall and/or spring semester:

• appointed to a 25% (10 hours per week) or more assistantship (GTA, GRA, GSA) by the end of the regular add/drop period in either fall or spring semester or both,

• enrolled in CSU health insurance, and

• enrolled in 5 or more resident-instruction credits (Audits, Continuous Registration, and CSU Online credits do not meet the Resident Instruction enrollment criteria for this policy). Students who have been advanced to candidacy and are appointed to a graduate research assistantship are expected to devote a full-time effort to their research. It is the responsibility of the advisor to designate the workload. Graduate Assistants are considered temporary employees by the University and, as such, do not earn vacation time. The general CMB Program leave policy is two weeks per year for all Graduate Assistants, subject to approval of their advisor.

Conflict Resolution

While CMB endeavors to support students in selecting an appropriate mentor through rotations and/or advising early on in their graduate career, mentor/mentee conflicts do still occur. The CMB Program Director and other members of the CMB leadership team are available to mediate and advise both parties. Faculty and students may also contact the Student Resolution Center and are encouraged to engage in formal mentorship training such as the Mentor Well training offered through the Graduate School.

In the unlikely event that the student and their advisor are unable to resolve their differences, the student may change advisors, and the CMB Program will provide advice on how to go about this. However, the student should be aware that the former advisor has no obligation to support the student as a Graduate Assistant during their transition, and the CMB Program generally has no funds to provide transitional stipend/tuition support.

Graduation Requirements

The graduation requirements will in general follow those outlined in the current Graduate and Professional Bulletin. During the two years, M.S. and Ph.D. candidates are expected to complete graduate courses in Molecular Regulation of Cell Function (BC565) or Molecular Genetics (BC 563) as well as CM510 (Introduction to CMB) and CM544 (Reproducible Biomedical Research Methods). All students must enroll in graduate seminar (CM 793, Fall), in which each student presents their thesis research, and CMB Seminar (CM792, Spring) in which invited speakers present their research. These two seminar courses aim to create community within the program and allow the program to evaluate student progress. Every CMB student must enroll in these courses once each year Appropriate courses to complete the elective requirements for Cell & Molecular Biology, Ethics, Statistics and Writing, along with additional courses appropriate for the planned thesis research, may be established by the Graduate Advisory Committee and should ideally be completed

before the preliminary exam.

To advance to candidacy for the Ph.D. degree, students are required to pass a preliminary examination administered by the student’s Graduate Advisory Committee according to the procedures described in the Preliminary Examination section of this booklet and in the Graduate and Professional Bulletin. The plan A M.S. degree in Cell and Molecular Biology is a research- oriented degree, so the Plan A Master’s thesis must be based upon laboratory research. The M.S. degree is not a prerequisite for the Ph.D. degree.

The completion of a thesis is necessary for both the M.S. (Plan A) and Ph.D. degrees. Each candidate is required to present a formal seminar summarizing their research and to pass a formal thesis defense administered by the Graduate Advisory Committee. In special cases a Plan B M.S. degree may be awarded. The Plan B M.S. degree does not require a thesis but does require a written report on a topic approved by the GAC and an oral exam. The final corrected and approved thesis must be submitted to the Graduate School within 1 semester of the thesis defense. Any exception must be initiated by the student in the form of a petition to the student’s Graduate Advisory Committee. If the thesis is not submitted in this time frame, the student will be considered to be making unsatisfactory progress towards the degree. After two semesters, the GAC may recommend to the Graduate School that the student be dismissed from the program with no degree.

Continuous Registration

During periods where a student is not utilizing University Resources (other than library and computing resources) they may enroll in Continuous Registration (CR). Examples of appropriate use of CR include medical or family leave, internships, and reaching the point of writing the dissertation full time. In each of these cases, CR must be approved by the advisor and the GAC, and the request must be accompanied by a plan for completion of the degree. The form for CR approval will be provided by the CMB Program Manager upon request and is specific to CMB. It must be completed for the 1st, 4th, and 8th semester of CR and signed by the student’s entire GAC. In general, students should require a maximum of 2 consecutive semesters of CR. CR may be used for the summer semester without approval when the student is planning to graduate during the summer. At all other times students should register for Independent Study or Dissertation Credits that reflect the time being spent in the laboratory (3hr per credit per week). Further details on CR can be found in the Graduate and Professional Bulletin.

Diversity and Inclusion

The CMB Program recognizes that each student has a unique set of merits, experiences and challenges and we value this diversity. The Program is committed to giving every student the best possible chance for success. With this in mind, members of the Academic and/or Executive Committee will work with individual students and their advisors to map out alternative paths to graduation if they find they cannot easily fit into the traditional path.

Courses Required for the MS Degree

The M.S. degree requires 12 credits of upper level (500 or above) didactic course work. A total of 30CR are required.

Course NumberTitleCredits
CM 510introduction to Cell & Molecular Biology1
CM 544 / MIP 544Reproducible Biomedical Research Methods3
CM 792  Cell and Molecular Biology Seminar11-4
CM 793Graduate Seminar11-4
Select one course from the following
BC 563Molecular Genetics 4
BC 565Molecular Regulation of Cell Function
4
Independent Study & Dissertation
CM 595Independent Study2 1-17
CM 699Thesis2,4 1-17
Ethics Elective (see list below)1-3
CMB Electives3 (see list below) 8
Total Credits30

1* Seminar (CM 792 and CM 793) must be taken every year

2* Students must complete at least one credit from each CM 595 and CM 699 and select enough independent study, dissertation, seminar, and other elective courses to bring the program total to a minimum of 30 CR, with approval of graduate advisory committee.

3* Course selection depends on each student’s focus within Cell & Molecular Biology and must be approved by the student’s graduate advisory committee.

4* Plan B MS does not require thesis credits.

Courses Required for the PhD

Course NumberTitleCredits
CM 510introduction to Cell & Molecular Biology1
CM 544 / MIP 544Reproducible Biomedical Research Methods3
CM 792Cell and Molecular Biology Seminar1   4-10
CM 793Graduate Seminar14-10
Select one course from the following
BC 563Molecular Genetics 4
BC 565Molecular Regulation of Cell Function 4
Independent Study & Dissertation (minimum of 6 CR)6-30
CM 795Independent Study2 
CM 799Dissertation2
Ethics Elective (see list below)1
Statistics Elective (see list below)1
Topics Elective (see list below) 3
Writing Elective (see list below) 1
CMB Electives3 (see list below)3
Optional: MS degree CR (maximum 30 may be applied) 30
Total Credits72

1* Seminar (CM 792 and CM 793) must be taken every year.

2* Students must complete at least one credit from each CM 795 and CM 799 and select enough independent study, dissertation, seminar, and other elective courses to bring the program total to a minimum of 72 CR, with approval of graduate advisory committee.

3* Course selection depends on each student’s focus within Cell & Molecular Biology and must be approved by the student’s graduate advisory committee.

Courses Required for the Cancer Biology Specialization

CMB students may elect to specialize in Cancer Biology which leads to a Specialization noted on their transcript. At least five credits must be selected from courses below:

CourseTitleCredits
ERHS 611Cancer Genetics2
ERHS 510Cancer Biology3
VS 718Cancer Biology Clinical Practicum2
ERHS 733Environmental Carcinogenesis3

In addition, students specializing in Cancer Biology may satisfy the CM792 seminar requirement by attending Clinical Oncology Seminar/Journal Club.

Any variation from the required courses must be approved by the Academic Committee and the student’s Graduate Advisory Committee. Requests for course substitutions or omissions must be submitted to the Academic Committee by the student in writing. Each graduate student must present a seminar of their work before graduating.

It is the responsibility of each graduate student to know and meet all requirements of the Graduate School. These are listed in the Colorado State University Graduate and Professional Bulletin, Handbook on Graduate Study, and Guidelines for Graduate Advising and Committee Service. The latter two publications will be sent to students during the first term they are registered.

Elective Courses

These lists are not exhaustive. Other courses may be appropriate to fulfill these requirements but should be approved through the CMB Program Office.

Ethics Electives (3 CR):

CourseTitleCredits
BC 601Responsible Conduct in Biochemistry 1
GRAD 544Ethical Conduct of Research1
MIP 554Research Policies & Regulations 1
NSCI 575 / GRAD 575Ethical Issues in Big Data Research11

1* Preferred Course

Topics Electives (1 CR):

CourseTitleCredits
CM 700Critical Analysis of the Literature11
BMS 796A / NB 796CGroup Study: Topics in Neuroscience1-4
BMS 796B Groups Study: Cardiopulmonary Physiology1-18
BMS 796CGroup Study: Reproductive Physiology1-18
BSPM 502BTopics in Plant Pathology: Plant Bacteriology  1
CHEM 651BSpecial Topics in Chemistry: Inorganic Chemistry1-4
FSHN 650ARecent Developments in Human Nutrition: Topics in Community Nutrition  2
FSHN 650BRecent Developments in Human Nutrition: Carbohydrates, Lipids, and Energy 2
FSHN 650CRecent Developments in Human Nutrition: Genomic, Proteomics, and Metabolomics  2
MIP 700Topics in Microbiology, Immunology & Pathology1
SOCR 730Topics in Plant Breeding & Genetics1

1* Preferred Course, if you are not taking CM 700, select a substitute with consultation of your advisor.

Statistics Electives (3 CR):

CourseTitleCredits
ERHS 535R Programming for Research3
ERHS 537AR Programming: Research I1
ERHS 537BR Programming: Research II2
ERHS 544 / STAT 544Biostatistical Methods for Quantitative Data3
STAR 501Data Wrangling / Visualization for Researchers2
STAR 502Multivariate Analysis for Researchers4
STAR 511Design and Data Analysis for Researchers I4
STAR 512Design and Data Analysis for Researchers II4
STAR 513Regression Models for Researchers2
STAR 514Experimental Design / Analysis for Researchers2
STAR 531Generalized Regression Models for Researchers2
STAR 532Mixed Models for Researchers2
STAR 534Machine Learning for Researchers2
STAT 540Data Analysis & Regression4
VS 562Applied Data Analysis3
VS 733Advanced Veterinary Epidemiology4

Writing Electives (1 CR):

CourseTitleCredits
BC 701Grant Proposal Writing & Reviewing1
BSPM 530 / SOCR 530Scientific Writing1
BZ 544Presenting Research in Biology2
HES 700Professional Skills in Bioenergetics3
MIP 643Grant Writing for Microbiology / Pathology1
MIP 666Writing Scientific Manuscripts3
NB 771Writing, Submitting, and Reviewing Grants1

Cell & Molecular Biology Electives (3 CR):

Course NumberTitleCredits
AB 511Microbiome of Plant Systems3
ANEQ 505Microbiome of Animal Systmes3
ANEQ 545Molecular Methods in Animal Genetics 3
ANEQ 575Computational Biology in Animal Breeding3
BC 511Structural Biology I4
BC 563Molecular Genetics
BC 565Molecular Regulation of Cell Function4
BC 571Quantitative Biochemistry1
BC 611Structural Biology II2
BC 663Gene Expression2
BC 665AAdvanced Topics in Cell Regulation: Microscopic Methods 2
BZ 565/MIP 565Next Gen Sequencing Platform/Libraries1
BIOM 533/CIVE 533Biomolecular Tools for Engineers3
BMS 500Mammalian Physiology I4
BMS 501Mammalian Physiology II4
BZ 570Molecular Aspects of Plant Development3
BZ 576/BZ 476Genetics of Model Organisms4
CBE 560Engineering of Protein Expression Systems3
DSCI 511Genomics Data Analysis in Python2
DSCI 512RNA-Sequencing Data Analysis1
MIP 530Advanced Molecular Virology4
MIP 543RNA Biology3
MIP 670Molecular Immunology and Immunogenetics3
MIP 730/ERHS 730Principles of Flow Cytometry & Cell Sorting2
NB 503/BMS 503Developmental Neurobiology3
NB 501Cellular and Molecular Neurophysiology2

Graduate Certificate In Microbiome Science & Engineering

The Microbiome Science & Engineering certificate provides a foundation in the concepts and methods of microbiome science and engineering and provides perspectives on the applications of those fundamentals to a range of topics in environmental, animal and human, plant, and industrial contexts. Coursework can also count towards degree requirements.

Course NumberCourse NameCredits
Select one course from the following:
AB 511Microbiome of Plant Systems3
ANEQ 505Microbiome of Animal Systems3
Select a minimum of 6 credits from the following with at least one course (not previously taken) from each Group.
Group A. Experimental Methods and Data Analysis
AB 511Microbiome of Plant Systems3
ANEQ 505Microbiome of Animal Systems3
CIVE 533 / BIOM 533Biomolecular Tools for Engineers3
MIP 545Microbial Metagenomics/Genomics Data Analysis2
MIP 565/BZ 565Next Generation Sequencing Platform/Libraries1
MIP 570Functional Genomics3
SOCR 545Current Methods in Microbial Genomics2
Group B: Microbiomes in Context
AB 511Microbiome of Plant Systems3
ANEQ 505Microbiome of Animal Systems3
FSHN 650CRecent Developments in Human Nutrition: Genomic, Proteomics, and Metabolomics 2
FTEC 578/HORT 578Phytochemicals and Probiotics for Health3
Program Total Credits: 9

A number of graduate certificates are offered at CSU. Many CMB students take the Graduate Certificate in Data Analysis through the Statistics Department.

CMB students are encouraged to work towards a Graduate Teaching Certificate through The Institute for Learning and Teaching (TILT) to demonstrate their commitment to college teaching. This is a free non-transcripted certificate and the coursework does not generally count towards degree requirements.

CMB Prefix Courses

CourseTitleCredits
FALL
CM 510Introduction to Cell & Molecular Biology1
CM 544Reproducible Biomedical Research Methods 3
CM 595Independent Study (MS)variable
CM 699Thesis (MS)variable
CM 700Critical Analysis of the Literature1
CM 784Supervised College Teachingvariable
CM 793Graduate Seminar1
CM 795Independent Study (PhD)variable
CM 799Dissertation (PhD)variable
SPRING
CM 515Computational Cell & Molecular Biology2
CM 595Independent Studyvariable
CM 640Creative Science Writing3
CM 699Thesis (MS)variable
CM 784Supervised College Teachingvariable
CM 792Cell & Molecular Biology Seminar 1
CM 795Independent Study (PhD)variable
CM 799Dissertation (PhD)variable

Sample Curriculum – MS

This is based on a Plan A – M.S. degree requiring a thesis. It may be possible to complete the requirements in fewer than four semesters. A Plan A Masters degree requires 30 credits of which 12 credits are at the 500 level or above in regular course work.

First Semester

Course NumberTitleCredits
CM 510Introduction to Cell & Molecular Biology1
CM 793Graduate Seminar1
CM 544Reproducible Biomedical Research Methods3
BC 563Molecular Genetics (or CMB elective)4
CM 595Independent Studyvariable
Second Semester

Course NumberTitleCredits
BC 565Molecular Regulation of Cell Function
4
CM 792  Cell and Molecular Biology Seminar   1
Ethics Elective1
CM 595Independent StudyVariable
Third Semester

Course NumberTitleCredits
CM 793  Graduate Seminar1
CM 699Dissertation (or Independent Study)Variable
Electives (including CMB electives)Variable
Fourth Semester

Course NumberTitleCredits
CM 699DissertationVariable
CM 792 Cell & Molecular Biology Seminar1
Electives (including CMB electives)variable

Sample Curriculum – PhD

A Ph.D. degree requires 72 credits of which 37 credits are at the 500 level or above in regular course work.

First Semester

Course NumberTitleCredits
CM 510introduction to Cell & Molecular Biology1
CM 793Graduate Seminar1
CM 544Reproducible Biomedical Research Methods3 (can be taken in 3rd semester)
BC 563Molecular Genetics (or other CMB elective)3-4
CM 795Independent Study credits to fill schedule variable
Second Semester

Course NumberTitleCredits
BC 565Molecular Regulation of Cell Function (or other CMB elective)3-4
CM 792  Cell and Molecular Biology Seminar   1
CM 795Independent Study credits to fill schedulevariable
CM 515Computational Cell & Molecular Biology (optional)2
Ethics Elective1
Third Semester

Course NumberTitleCredits
CM 793Graduate Seminar1
CM 795Independent Studyvariable
CM 700Critical Analysis of the Literature1
Writing Elective1-3
Statistics Elective3-4
Other ElectivesVariable
Fourth Semester

Course NumberTitleCredits
CM 792CMB Seminar1
CM 795Independent StudyVariable
ElectivesVariable
Beyond the 2nd Year

CM793 and CM792 should be taken every year in the fall and spring semester respectively.
CM799 Dissertation should be used for the last semester, while writing the dissertation.

The above curriculum is approved through the University as of Fall 2024.

Examinations

See the current Graduate and Professional Bulletin for details concerning administration of examinations and requirements for submitting specific forms to the Graduate School Office including graduation requirements.

Students are required to pass a comprehensive preliminary examination for admission to candidacy for the PhD. This examination consists of preparation of a written research proposal and an oral exam which covers the candidate’s entire program of study. This document provides guidelines to be used by the student and the student’s graduate committee during preparation for, and administration of, the examination.

Final M.S. Examination – The final examination will be oral and is conducted by the student’s Graduate Advisory Committee that is chaired by their advisor. The examination for Plan “A” is primarily a defense of the student’s thesis. The examination for Plan “B” is based upon the completed course work and the topic selected for the final report due under Plan “B”. A copy of the thesis/report must be circulated to the student’s Graduate Committee at least two weeks before the final examination. All CMB faculty and students are invited to attend. The graduate student has the responsibility to check with each committee member in order to schedule a suitable time and place for the oral examination, and to inform the CMB Administrative Assistant so that the CMB faculty can be notified at least two weeks in advance of the examination.

Preliminary Examination for Ph.D. Degree – Students are required to pass a comprehensive preliminary examination for admission to candidacy for the PhD. This examination consists of preparation of a written research proposal and an oral exam which covers the candidate’s entire program of study. This document provides guidelines to be used by the student and the student’s graduate committee during preparation for, and administration of, the examination.

Timing

The comprehensive preliminary exam is to be administered by the end of the 5th semester in the graduate program (Fall semester of 3rd year) by which time the student should have completed all the required classes. Failure to comply with this requirement will result in the CMB Graduate Education Office placing a hold on registration. Exceptions may be made in extraordinary circumstances but must be approved by the CMB Academic Committee and the CMB Program Director. The student is responsible for notifying the CMB Program Office of intent to hold the examination. In addition, the student will provide the CMB Program Office with documentation (copies of the GS16 form, the proposal and the examiners’ evaluation) upon completion of the exam, regardless of the outcome.

A summary of the examination process is provided below:

Early Fall Semester of Second yearAll Second year students should attend a Preliminary Exam Information Meeting during which the format and timing of the CMB Preliminary Exam will be discussed.
Fall or Spring Semester of Second yearThe student should prepare a research proposal on their own project, either as part of a grant writing class and/or in close collaboration with the primary advisor. This document does not need to contain an independent Specific Aim (see below) and it is not expected to be in its final, defendable form.

This proposal should be shared with the examination committee at least one week ahead of a Pre-Exam Committee Meeting along with a copy of the “Guidelines for the Comprehensive Preliminary Exam”(this document).
Spring / Summer of Second year or Early Fall of Third yearA Pre-Exam Committee Meeting should be held at which the research proposal will be approved / discussed. An independent Specific Aim does not need to be included at this point. In addition, the chair of the committee (not the advisor) and date of the exam will be finalized. This committee meeting may also double as the student’s annual committee meeting. The CMB Office should be notified of intent to take the examination, the planned date and the chair of the committee (see attached form).
Seven weeks prior to the exam (and before the last week in October)The student should provide the examination committee with a one page document describing the Specific Aims of their proposal, including one Aim developed independently.
Six weeks prior to the examThe committee chair should provide comments on the specific aims to the student (by email).
Four weeks prior to the examAny revisions to the Specific Aims should be approved by the examination committee (by email). The student should allow two to three weeks of full-time effort to complete the proposal.
One week prior to the examThe final proposal should be handed to each committee member for evaluation, along with a copy of the preliminary examination evaluation form.
Day of the Exam (must be completed by end of Fall semester in the Third year)Student and committee meet for the oral examination. Committee members provide their written evaluation forms to the chair after the exam.
Within two days after the examThe original, signed GS16 form must be submitted to the Graduate School. Copies of GS16 and the proposal will be provided to the CMB Office. Copies may be electronic.
Within one week after the examThe chair of the committee will provide the student, other committee members and the CMB office with a summary statement describing the student’s performance in the examination.

Preliminary Exam Information Meeting

During the fall semester, all second year CMB students should attend an information meeting during which the format and timing of the CMB preliminary exam will be discussed.

Preparation

In order to pass the preliminary exam, the student must be able to independently formulate a hypothesis and design experiments to test this hypothesis. In addition, the student needs to be able to convey their ideas concisely and coherently to the examiners both orally and on paper. To develop these skills prior to the examination the student should prepare a research proposal (Thesis Proposal) on their own project in collaboration with the primary advisor and/or as part of a grant writing class. This proposal should be shared with the examination committee prior to the Pre-Exam Meeting to allow them to evaluate whether the student is adequately prepared for the examination and familiarize themselves with the student’s research area.

Pre-Examination Committee Meeting

Once the student has completed the Thesis Proposal on their own research and it has been approved by the primary advisor and/or received a passing grade in a grant writing class, they should arrange the Pre-Examination Committee Meeting. This committee meeting may also serve as the student’s annual committee meeting and all committee members should be present. In addition, the CMB Program Director (or Chair of the CMB Academic Committee) may be invited to attend this meeting in order to describe the CMB Preliminary Exam and the purpose of the meeting to the Committee. The purpose of the Pre-Exam Meeting is:

To Approve the Thesis Proposal. The committee should determine whether the Thesis Proposal meets expectations and demonstrates that the student is ready for the Preliminary Examination. The student may present the proposal orally as part of CM793 Seminar or during the committee meeting, if desired. If the proposal does not meet expectations, the committee should provide detailed guidance as to what is needed to bring it up to standard.

To Select a Chair of the Examination Committee. The chair will communicate directly with the student during preparation of the independent proposal and provide a comprehensive written evaluation after the examination. The chair may not be the major advisor or co-advisor although these individuals are permitted to participate in the exam as regular committee members.

If the advisor will not participate in the examination another CMB faculty member may substitute for the purposes of the examination only. Any substitution should be pre-approved by the CMB Program Office through the pre-exam form, to ensure the altered committee meets CMB requirements. The advisor should then inform the Graduate School of the substitution in writing at least two weeks before the exam, providing the name and CSU ID number of the student, the date of the examination and the name and CSUID number of the substituting faculty member. After the examination has occurred, the CMB Program Manager will initiate the GS16 Preliminary Exam Form, to ensure the exam committee is listed correctly. In cases where the advisor is substituted, they may no longer actively participate in the examination or vote on pass/fail but they may observe.

To Establish Acceptable Practices during the Writing Process. Although the primary advisor may NOT collaborate with the student on the independent Specific Aim of the final proposal, the committee may specify whether this part can be discussed with peers, whether the student may obtain assistance with English language editing (this should generally only be considered for those students with English as a second language) and may also provide a list of acceptable topics.

To Determine a Date and Time for the Examination. The decisions made at this meeting should be documented on the Pre-Examination Form and the student should provide the CMB Office with a copy.

Format of the Proposal

The Thesis Proposal, including an independent Specific Aim, should be in the format of an NIH F30/F31 application and use the template provided on the CMB Program Website. The entire document should not exceed 8 single-spaced pages including 1 single-spaced page allocated to the Specific Aims. Margins should be no less than 0.5” and the font should be no smaller than 11pt Arial. The main proposal should be divided into Significance and Approach sections. Figures should be embedded in the text and have a font size of no smaller than 8 pt. Use of color figures is acceptable and encouraged. References are not included in the page limit. If a grant writing course specifies a different format for the Thesis Research Proposal, then that format is acceptable for that document, but the Proposal should still follow the guidelines outlined above. Additional required parts of the proposal are (i) Respective Contributions (0.5 page), (ii) Authentication of Key Biological and/or Chemical Resources (up to 1page) and (iii) Data Management Plan (up to 1page).


Preparation of the Independent Specific Aim of the Proposal

The independent Specific Aim of the proposal should be prepared by the student, without discussion of the approach or hypothesis with the adviser(s). The student should rely on the literature and their own background knowledge to develop a strong, original hypothesis and design an experimental approach to test it. Potential pitfalls and alternative approaches should be considered, and the techniques proposed should be appropriate and state-of-the-art. The experimental approach should rely mainly on techniques other than those the student routinely uses in their own research. For example, if the student’s research project extensively utilizes ELISA assays and flow cytometry, these types of assays may not form the bulk of the experiments in the independent specific aim, although they need not be completely avoided. Additional guidelines are provided on the CMB Program Website.

The proposal should be written in English. Students who feel they are deficient in their written language skills are encouraged to consult the CSU Writing Center for assistance. Students are also cautioned that the proposal should be an original, independently prepared document. Plagiarism of ideas or inappropriate use of passages from published documents (including proposals from the adviser’s lab) will result in immediate dismissal from the PhD program.

Evaluation of the Specific Aims

The committee or advisor may provide the student with a list of four or five acceptable areas of study if they wish but experimental approaches and specific problems to be addressed within the independent aim should not be discussed. The committee is asked to evaluate the Specific Aims before the student prepares the main proposal. Comments and suggestions should be communicated to the student by email ~6 weeks prior to the oral examination. In particular, the committee should:

i. Evaluate whether the independent Specific Aim is relevant and within the realm of their own area of expertise. For example, a student working on replication of HIV-1 could propose to investigate a divergent aspect of the cell biology of this virus. The committee is encouraged to use their discretion to determine whether the independent aim is appropriate. Finally, the independent aim of the proposal should not overlap significantly with other projects in the laboratory of their major adviser. In general, the subject matter of the proposal should be close enough to the student’s own area that the knowledge garnered will enhance the student’s understanding of their own research.

ii. Give the student guidance regarding the scope of the specific aims and make suggestions that could help focus the proposal. For example, if the student proposes too broad a study the committee members could suggest which parts should be discarded and which expanded.

The committee should not overtly suggest better experimental approaches or better hypotheses; although it is acceptable to ask that the student formulate another hypothesis and develop a new specific aim if those submitted are considered unacceptable.

 The Examination

At the start of the oral examination the student will give a ~20min presentation covering the material in the proposal. The committee will then question the student to determine how well they understand the literature in their chosen field of study as well as the background information relevant to the written proposal. The committee will also test the student’s ability to think creatively and communicate their ideas orally. In addition to the material presented in the proposal, the student can expect to be questioned on material taught in BC563 and/or BC565 or other graduate classes they have completed, as well as on material they presented in the Thesis Proposal. The CMB Program Director or Associate Director may be invited to attend the Preliminary Exam as an impartial observer and in an advisory capacity.

Note that the examination will be administered by the examination chair, which should not be the advisor. The chair is responsible for compiling examiner comments and completing the final evaluation form.

Overall Evaluation

An evaluation form is provided on the CMB Graduate Program Website. The independent proposal should not be evaluated as if it were being considered for funding. One goal of the preliminary exam is to ascertain whether the student understands their chosen field of study sufficiently that they can formulate an interesting and original hypothesis and develop a means to test it. The exam also tests the student’s ability to communicate their ideas effectively orally and on paper. The written proposal, the oral presentation and the student’s performance in the questioning period will all be evaluated.

Failing the Examination

The student must pass both the written and oral parts of the examination to pass the preliminary exam. If performance in either portion is inadequate, the student fails the examination. In this case, if the committee agrees, the exam may be administered a second time no sooner than two months and no later than 1 year from the date of the original examination. The requirements to pass the second exam should be clearly defined by the committee and may include rewriting the proposal, taking additional classes and/or repeating the oral defense. If the student fails the second examination they will be immediately dismissed from the Ph.D. program.

Final PhD Examination: The final examination will be oral and is conducted by the student’s Graduate Advisory Committee, chaired by their advisor. The examination is primarily a defense of the student’s thesis. A copy of the thesis must be circulated to the student’s GAC at least two weeks before the final examination. All CMB faculty and students are invited to attend. The graduate student has the responsibility to check with each committee member to schedule a suitable time and place for the oral examination, and to inform the CMB Program Manager so that the CMB faculty can be notified at least two weeks in advance of the examination. All committee members must participate in the examination either in person or remotely. If a committee member is unable to participate, the exam should be postponed, or the missing member can be replaced for the purposes of the exam. Approval can be obtained by contacting the Graduate School.

Thesis/Dissertation Format:

The thesis or dissertation must be formatted according to the Graduate School guidelines. The CMB Program does not have any required content or format. It is largely up to the student’s Advisory Committee to determine the requirements.

Publications

Presentation of research results is an important aspect of graduate education. Ph.D. candidates must prepare and submit a manuscript for publication in a peer-reviewed scientific journal with the student as first author. The CMB Program should be noted as the student’s affiliation in all publications.

Student Appeals of Grading Decisions

Faculty members are responsible for clearly stating the instructional objectives of the course at the beginning of each term and for evaluating student achievement in a manner consistent with these objectives. Students are responsible for meeting standards of academic performance established for each course in which they are enrolled. Faculty members and instructors are responsible for determining and assigning final course grades. Graded examinations, papers and other materials used as a basis for evaluating a student’s achievement will be available to the student for inspection and discussion. Students may appeal faculty grading decisions through the mechanism described in the Code of the CMB Program, which is in line with procedures described in Section I.7 of the Faculty Manual.

 

Approved by vote of the CMB Faculty June 3, 2024

Last Updated July 5, 2024