research proposal molecular biology example

Department of Biological Sciences

Examples of Undergraduate Research Projects

Fall 2021 projects, previous projects.

PhD projects 2024

Many of our PIs are recruiting doctoral candidates in this year's application round. Below you can find their project proposals or research descriptions. Get inspired by these to draft the research proposal for your application. Your research proposal should be longer than the summary provided here (approximately 2-3 pages) and should show some of your own input, including a title, a short background of the topic, a research question, proposed methods and references. Moreover, we encourage you to explain how you plan to include both sides of the experimental-theoretical spectrum in your project. For instance, how could laboratory experiments help support the conclusions of your bioinformatics project? Which bioinformatics tools do you plan to include in your wet laboratory project?  

[NEW] - Co-evolution of transposable element activity and host genome

[NEW] - Understanding the Distribution of Mutations along Genomes

[NEW] - Chromatin regulation in stem cells and development

[NEW] - Molecular mechanisms of genome transcription regulation & dysregulation

[NEW] - Investigating Antisense Oligonucleotide (ASO) Treatments for Neurodegenerative Diseases

[NEW] - Transcriptional condensates

[NEW] - Computational systems medicine and disease control

[NEW] - Comparative Analysis of DNA Methylome Conservation Across Species

[NEW] - Genome Regulation Department

[NEW] - Synthetic biology of long-range gene regulation

[NEW] - lncRNAs in 3D – dissecting the gene regulatory function of long non-coding RNAs 

[NEW] - Evolution of primate transcription factor genes

Mathematical modelling of cis-regulatory landscapes

[NEW] - Epigenetic mechanisms controlling cell fate decisions during the early stage of liver, pancreas and biliary tree development

[NEW] - Transcriptional Regulation Group

[NEW] - Molecular mechanisms of bacterial immunity

MCDB 196A & 196B: Proposal Guidelines

• Proposals should be 1 – 2 pages, typed with 1-inch margins, single-spaced, and 11-pt Arial font
• Title of proposed project
• Student name, UID, and email address (same one on file with the Registrar)
• Faculty research mentor’s full name, department, and email address
• The proposal should be written in your own words, reflecting your understanding of the project. If you utilize materials written by someone else, such as sections of a grant proposal or research article, make sure you cite them appropriately (include in-text citations plus a bibliography). It is a form of academic dishonesty to turn in material written by someone else without giving them proper credit.
• The intent in writing a research project proposal is to convince a review panel such as the undergraduate curriculum committee that the topic and approach are sound and have a clear relationship to previous work in the same field. Students should spend considerable time thinking about their projects, discussing their projects with their research mentors, and producing multiple drafts of the proposal since the quality of this document influences whether or not the application is approved.
• The proposed project should be appropriate in scope for a 20-week project (10 weeks in 196A plus 10 weeks in 196B) and reflect accomplishments expected by both student and faculty advisor.
• A proposal should begin with a problem statement – a clear description of the larger problem within which the research project is situated.
• A description of the project should follow. This should include a rationale for the project that incorporates existing bodies of literature (published works) that will set the project into context, showing how the proposed work builds upon previous studies. This discussion should set the stage for the hypothesis(es) to be tested. The description should incorporate specific aims explaining what you plan to accomplish and how. This section should include a succinct account of methods that will be used to generate data (how will the data be collected and subsequently analyzed?) as well as a justification for why this approach is appropriate (how does it address your hypothesis or address the research question?).
• The proposal must make clear the precise role that the student will play in the lab , including how much and what part of the data collection will be completed.
• The project should reasonably fit the research and writing components within a two-quarter framework imposed by 196A and 196B and require no less than 12 hours per week in the lab. The faculty advisor should provide an estimate of approximately how many hours per week (for the duration of one quarter) the proposed project is expected to involve. That estimate should be included in the project proposal.
• Append the project proposal to the undergraduate research application & acknowledgement form , MCD BIO 196A contract signed by faculty advisor, faculty mentor agreement with signatures from both student and faculty advisor, and submit materials to the online application form.
• Project proposals will be reviewed by departmental curriculum committee. Students will be informed of their decision within 2-3 weeks of submitting application.

NOTE: If you are submitting an MCD BIO 198A (Departmental Honors) contact to be taken along with 180A, please follow the proposal guidelines for a 198A project:  https://www.mcdb.ucla.edu/mcdb-198a-d-proposals/ .  Your proposal will be for a three-quarter project, instead of a two-quarter project.

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Browse Course Material

Course info, instructors.

• Prof. Christopher Burge
• Prof. David Sabatini
• Dr. Marilee Ogren-Balkema
• Dr. Alice Rushforth

Departments

As taught in.

• Biotechnology
• Molecular Biology

Learning Resource Types

Experimental molecular biology: biotechnology ii, scientific comm..

This course includes significant instruction in scientific communications. During the term, Dr. Marilee Ogren-Balkema presents ten lectures on a range of reading, presentation and writing topics.

Background reading

Gopen, George D., and Judith A. Swan. “ The Science of Scientific Writing .” The American Scientist 78 (1990): 550-558.

Lectures on Scientific Communications

1: Basic Scientific Communication ( PDF )

2: How to Review the Literature ( PDF )

3: How To Write a Research Proposal ( PDF )

4: Preparing Effective Oral Presentations ( PDF )

5: How to Write a Mini Literature Review ( PDF )

6: How to Write a Research Paper I: Illustrations ( PDF - 1.2 MB )

7: How to Write a Research Paper II: Results Section ( PDF )

8: How to Write a Research Paper III: Methods Section ( PDF )

9: How to Write a Research Paper IV: Introduction and Discussion ( PDF )

10: How to Write a Research Paper V: Title and Abstract ( PDF )

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Department of Molecular and Cell Biology

Genetics and Genomics

Formal “qualification” for the Ph.D. degree takes place by passing the Dissertation Proposal, a tripartite examination focused upon the student’s dissertation research plans. This exam should be taken at a point at which the student has completed most course work and has research well underway. The student should aim to complete this exam by the end of the third year of graduate study. The three parts of the exam, each of which will be evaluated separately by the full Advisory Committee are:

I. A written proposal II. A seminar presentation on the proposal III. A closed-door question and answer session with faculty

A student who demonstrates acceptable performance on all three parts of the examination, evidenced by a majority vote of the full Advisory Committee to pass on all three sections, “qualifies” for the Ph.D. degree, and continues on that track of study. A student who does not make adequate progress, evaluated by a majority vote of the Committee, may be asked by the Committee to repeat any sections of the examination to achieve a full pass. In cases of inadequate performance on the examination, the Committee may also recommend transfer to one of the Master’s of Science programs.

I. GUIDELINES FOR WRITTEN PROPOSAL PREPARATION

(For Genetics and Genomics doctoral scholars in MCB)

The written proposal has a ten page limit ( excluding references) and the following suggested sections. All figures, tables, charts, and diagrams are included in this 10-page limit. This format is based on current grant submission formats for most federal agencies, which range from 4-12 pages total, preparing the student for succinct presentation and defense of their scientific premise.

You must submit this Proposal two calendar weeks (10 business days) before the scheduled examination to each of your committee members. The thesis advisor may read and make general comments on this document prior to submission, but may not edit it. For some guidelines on writing, Helpful Hints on Scientific Writing.

Cover page: This is not included within the 10-page limitation.

It will include: Title, date of submission, date of scheduled exam, student name, committee members’ names and affiliations.

I. Significance. What are the broad implications of the research that you propose? What is its importance? The significance section should “funnel” consideration from the global to the specific project at hand. One warning: everything you mention in this section is fair game for questioning. Keep focused on the issues you identify as really important. (1/2 – one page)

II. Specific Aims/Goals. Make use of numbered, concise statements of hypotheses/questions. This will immediately focus the reader on precisely what you will be doing, and place the background in context. Keep in mind that this does not have to reflect historical chronology, but rather should present a series of logical steps. (1/2 -one page)

Sections I-II is the total content of Page 1 and cannot exceed one page.

Pages 2-10 Consist of the Following Sections:

III. Background and Preliminary Data. Provide a brief synopsis of the relevant background the reader needs to interpret your proposed research. (2 pages or less) This should not be an exhaustive literature review, but rather should highlight the background needed to place the area of research into context to understand your experimental hypotheses and approaches.

Keep in mind not all members of your committee are in the same area of research; it is critical to explain why the system/question/approaches proposed are interesting, important, and feasible.

In the preliminary data component of this section, a brief presentation of the data collected by the student in support of the approach and aims should be included. Note that considerable variation in the extent of data among students is expected, but only include data relevant to the proposal.

IV. Approach. This section is the bulk of the proposal (4-5 pages). It is a good idea to have a subsection for each hypothesis/question posed in each specific aim. In this section, you are tasked with defending why you should continue for the next 2-4 years on your project. In other words, convince your readers that this work is worthwhile, feasible and will contribute to the field.

Include the following subsections under each aim in the approach section:

A. Rationale . This is a statement of the logic behind your experiment. Include in this section any thinking that went into your hypothesis, any synthesis you might have made.

B. Experimental Plan. Include in this section the strategy you plan to use to address the hypothesis, as well as information about procedures and protocols in general terms. Your committee is more interested in the logic than in the details – reference common procedures. Focus on those aspects that are conceptual rather than technical, but be aware of any limitations of the methodology you select.

C. Interpretations and Alternative Approaches. Make sure you interpret results critically. Showing alternative meanings indicate that you have thought the problem through and are able to meet future challenges. Call attention to potential difficulties you may encounter with each approach. Propose alternatives that would circumvent possible limitations. Committee members will be aware of possible problems; convince them you can handle such circumstances.

For example:

Specific Aim 1: To…

1.A. Rationale – why do this? 1.B. Experimental Plan – how will I do this? 1.C. Interpretations and alternative approaches – what will it mean if I see X or Y? If it does not work because of the following reason…I will perform….to overcome this problem

IV. Timeline and Impact.

In this section, briefly lay out your timeline of experiments for the remainder of your thesis, including anticipated milestones such as publication submissions, conference presentations, and other seminar opportunities. Do not include courses, teaching and other duties not directly relevant to the work.

The impact statement should summarize (2-4 sentences total) what your body of work would contribute to the field, highlighting the advances it makes over existing knowledge.

II. SEMINAR PRESENTATION of PROPOSAL (see Presentation Skills )

Iii. closed door exam.

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Ph.D. Thesis Proposal

Procedures and policy guidelines, a. procedures.

The Graduate Advisory Committee (GAC) evaluates all Ph.D. Thesis Proposals. The GAC consists of at least seven (7) faculty members of the Department, and of one graduate student representative. Current GAC faculty members can be found online*.

• Graduate students must present their Thesis Proposals in the 5th or the 6th semester of their graduate studies.
• The Graduate Advisory Committee convenes twice a year to evaluate proposals (Fall and Spring).
• Proposals are usually scheduled near the end of semesters (December, May).

Before the Examination

• Graduate students must have passed (overall satisfactory) their yearly presentation in front of a Research Advisory Committee (RAC), with the more recent RAC no more than 6 months.
• Permission to present a Ph.D. Thesis Proposal is required and should be clearly stated in the most recent RAC report.
• The title of the Ph.D. Thesis Proposal must be submitted at least five (5) weeks in advance of the examination to Christine Laberge ( Christine.laberge [at] mcgill.ca ).
• The complete written Ph.D. Thesis Proposal must be submitted at least three (3) weeks in advance to Christine Laberge.
• The written proposal must be prepared and formatted as described in Appendix A  below.
• The student must prepare a twenty (20) minute oral presentation of their Ph.D. The presentation should not be longer than 20 minutes. Thesis Proposal (PowerPoint or the like) as instructed in Appendix B below.

Thesis Proposal Examination

• Examinations are done in person and should take no more than 1 hour. This is usually conducted in room 908 of the Biochemistry Department.
• Before the start of the examination, the GAC will meet without the student to review the student’s progress (RAC reports, course performances, Junior Seminar evaluation), flag any areas of concern, and discuss the written Ph.D. Thesis Proposal.
• The student will deliver a 20-minute oral presentation of their Ph.D. Thesis Proposal. The overall question period should last no longer than approximately 40 minutes.
• The meeting outcome (satisfactory, conditional, or unsatisfactory)
• Identify any areas of concern and corrective actions
• Determine any other advice to be provided to the students
• Based on the outcome, set the date of the next meeting if necessary
• The GAC Chair will summarize the examination outcome in a letter to be submitted to the graduate student and supervisor.
• Graduate students must register to the BIOC702 (Ph.D. Thesis Proposal) course.

B.  Policy on Ph.D. Thesis Proposal Procedure and Outcome

The Ph.D. Thesis Proposal examination consists of the following three (3) components:

• The written Thesis Proposal . The written proposal must be prepared and formatted as per Appendix A. Incomplete or poorly written proposals will impact the GAC’s decision and examination outcome. Failure to submit the written proposal in due time may also impact the student’s status in the program.
• The oral presentation . The oral presentation should summarize the content of the written document and be prepared as outlined in Appendix B. The student should be able to defend their Thesis Proposal based on the presentation. Presentations that are poorly prepared or that last longer than 20 minutes will impact the GAC’s decision and examination outcome.
• Answers during the question period . General competence will be assessed in the question period. Students must be able to discuss and explain presented experiments and provide details as needed. They must be able to elaborate beyond what is shown in the presentation (e.g. provide alternative questions, experiments, analyses, interpretations). They must demonstrate some general knowledge outside of their immediate research by answering connected and general questions in their research fields. Failure to demonstrate competence could impact the GAC’s decision and examination outcome.

Each component of the exam will be rated as Satisfactory , Conditional , or Unsatisfactory . The overall outcome of the Ph.D. Thesis Proposal is determined as follows:

Satisfactory

When all 3 components are rated as Satisfactory, the student will be deemed to have completed all three components and will receive a “PASS” grade on the BIOC702 course (Ph.D. thesis Proposal). The next meeting will be with a RAC at their yearly presentation.

Conditional

If one or more of the components is rated as less than Satisfactory and no more than one component is Unsatisfactory , the student will be graded as “CONDITIONAL”. In the letter submitted to the student and supervisor following the examination, the GAC will impose one or more condition and a timeline for the student to fulfill them (normally no more than 3 months). If the student fulfills the conditions set by the GAC, the student will be awarded a “ Satisfactory ”, be given a “PASS” for BIOC702, and be granted permission to continue in the program. If not, the meeting outcome will be deemed “ Unsatisfactory ”, and the procedures outlined in the following section will be followed.

Unsatisfactory

When two (2) or more components of the exam are rated as Unsatisfactory, the overall meeting outcome will be graded as “UNSATISFACTORY”. In keeping with GPS regulations**, the following consequences will result:

In the case where a student is unsuccessful at the first attempt of the exam:

• A grade of “HH – to be continued” will be recorded for BIOC702
• The student will be required to repeat the entire exam at a time determined by the GAC. As per GPS regulations, this meeting must occur not sooner than 4 months and not later than 6 months after the first meeting.
• A student who is successful in the second attempt will be deemed to have passed the exam, and will be given a “PASS” for BIOC702.

In the case where a student is unsuccessful at the second attempt of the exam:

• The student will be deemed to have failed the Ph.D. Thesis Proposal.
• A grade of “FAIL” will be entered for BIOC702 replacing the previously recorded HH. The student will be required to withdraw from the program.

Preparing and formatting the written Ph.D. Thesis Proposal

The written Ph.D. Thesis Proposal should be prepared with the oral presentation in mind. This document should properly introduce the project, justify its importance, describe your research progress to date, and propose future experiments that will overall represent an important contribution to research. The Ph.D. Thesis Proposal should feature substantial preliminary experimental work and propose future experiments . The proposed experiments should be well thought of and feasible.

• Approximately and not more than 5 pages single spaced including figures.
• Figures should be inserted in line with the text, be legible, and not exceed 1 page of total space.
• References are not included in the document’s 5 page maximum.
• The main text should provide the following:
• Central hypothesis
• Specific Aims: these could represent your proposed thesis chapters. Three (3) proposed results Chapters is common but not required. In each of your Aims, specify the short and long term objectives.
• Significance
• You can include extra pages reporting additional work that does not fit in the main Thesis Proposal. This is optional and should be clearly marked as an Appendix.
• Document must be letter size (21.25 x 27.5 cm / 8.5 x 11 inches).
• In the header on the left, indicate your name (the lab you are in).
• In the header on the right, indicate the section title (Ph.D. Thesis Proposal)
• In the footer, include the page number (center) and date (right)
• A minimum margin of 2 cm all around the page is mandatory.
• Use a font size of 12 point. Single line spacing. No condensed type or spacing.
• Each section of your document should be properly separated (e.g. skip a line between sections, use bold font for section titles, etc.)
• Figures must have legends.

As per GPS ruling:

“The work submitted for this assessment is expected to be your own. The use of technologies such as ChatGPT are prohibited and will be considered a violation of the Code of Student Conduct.”

Preparing the Ph.D. Thesis Proposal presentation

The Ph.D. Thesis Proposal presentation should summarize the written proposal. It should contain everything needed to explain and defend the project and proposed experiments. With the presentation, you should be able to convince the Examiners that the Proposal is Satisfactory . Importantly , the Ph.D. Thesis Proposal is not merely a progress report: it should also clearly propose future experiments.

Your oral presentation should last approximately 20 minutes and not more. You can choose to have questions during your presentation or only after. The question period should last no more than 40 minutes.

The presentation should:

• Properly introduce the research question and project .
• Clearly state the main hypothesis, Aims and proposed experiments.
• Include substantial preliminary experimental work. You must clearly specify who did the presented experiments. Acknowledge the contribution of others where relevant. This includes figures or data published elsewhere, which must be accompanied by a citation.
• Clearly outline future directions and propose new experiments.

Evaluation criteria

• Quality and clarity of the presentation and it’s delivery.
• Quality of responses to questions about the design, background, and potential of the project. This includes experiments already performed and those suggested as future directions.
• Quality of responses to general background questions about biochemistry and molecular biology.
• Response to criticism raised during the Research Seminar 1 (Junior) examination.
• Feasibility of the proposed experiments.

Important note

• It is the responsibility of the student to inform themselves of the Ph.D. Thesis Proposal Procedures, Policy and deadlines. Failure to comply can lead to expulsion from the program, unless strong justification is provided and confirmed in writing by the Supervisor.
• The methods adopted for examination and evaluation are specified by Departmental regulations and are in agreement with the Graduate Studies guidelines approved by the Dean of Graduate and Postdoctoral Studies, McGill University.

Quick Guidelines

Before the examination:.

• Title of the proposal submitted five weeks in advance to Christine Laberge
• Complete written proposal submitted three weeks in advance to Christine Laberge
• Up to five pages single spaced
• Describe research progress to date, and proposed (future) research for the Ph.D. thesis
• Optional extra page indicating additional work not in the main proposal may be added and must be clearly marked
• Present the background, rationale, central hypothesis, specific aims and significance
• Include short and long term objectives
• Three proposed results chapters is common but not required
• Must include substantial preliminary experimental work

Thesis Proposal Examination:

• 20 minute presentation to GAC, 40 minute discussion
• Presentation summarizes the written proposal
• Questions about the design, background and potential of the project
• Questions about general background knowledge of biochemistry and molecular biology

Evaluation Criteria:

• Presentation, background knowledge and insight into the proposed research
• Knowledge in related areas of biochemistry
• Response to criticisms raised during the Research Seminar 1
• Feasibility of the proposed experiments

Revised: April 2023

*    Graduate Advisory Committee Members (GAC)

**  Graduate Student Supervision

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Sample student biology research proposal (P. Pazos & P. Hirsch 2008)

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  Sample student biology proposal with annotations about content and writing style

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