Fall Senior Seminar Schedule and Deadlines
(Thursdays 11:00 a.m.-12:15 p.m. in ESTE 2131)
Your regular attendance at senior seminar discussions and workshops is expected. Meetings will be held on Thursdays from 11:00 AM – 12:15 PM in ESTE 2131. The site we will use for senior thesis is the following: UBER MOBI Senior Thesis PO FA2025 & SP2026. Please do not use the individual MOBI194 or MOBI191 sections, for example: PO MOBI 194A.9 where the #9 is a particular section that indicates the professor that is your thesis advisor. You may see these sites but we will not be using them.
Week 1 Discussion: Orientation (Thursday, August 28)
We will discuss class outline, goals, requirements, and deadlines, and other important business. Students will share with classmates their preliminary project interests. 11 AM, ESTE 2131. Students need to start working on Unit 1 (found on the research and planning section of our Canvas site).
Thesis Contract Due Friday, August 29 by 11:59 p.m.
Complete the senior Exercise Contract, indicate type of thesis you enrolled in (experimental or grant proposal) and list the general topic you plan to study. You can download the contract and then submit it by going to the Molecular Biology contract Assignment on our Canvas site : UBER MOBI Senior Thesis PO FA2025 & SP2026.
Week 2 Discussion: What Is a Literature Review? (Thursday, September 4)
Students should have completed Unit 1 before this discussion. Students need to start working on Unit 2.
Week 3 Workshop: How to do an Oral Presentation and Research Note Taking Strategies (Thursday, September 11)
An introduction to talking about your science. Professor running session: Negritto, 11 am, ESTE 2131. And discussion on research note taking strategies. Students should have completed Unit 2 before this discussion. Students need to start working on Unit 3.
Week 4 Workshop 2: Searching the Literature and Citation Management (TBD)
Katie Kohn, Ph.D., STEM librarian at 11:00 am. Room TBD. Students should also complete by this date Unit 3.
•Submit Annotated Bibliography (Friday, September 26)
Deadline: 11:59 p.m Friday September 26. Submit an annotated bibliography of at least 10 references on your senior thesis topic by uploading into the Annotated Bibliography Assignment site on the Canvas Molecular Biology Senior Thesis master site: UBER MOBI Senior Thesis PO FA2025 & SP2026. 10 annotated references (primary or secondary scientific papers) that are relevant to your literature review. You will need references that:
- Provide context for your question and your proposed experiments.
- Provide support for any claims you make.
- Provide support that the question you are asking is an important and unanswered one
- Help you develop your experimental approach (perhaps a similar study was done?)
For your citations use a citation format suggested by your primary thesis advisor.
Weeks 5 thru 9: First Oral Presentations (Thursdays October 2, 9, and 16).
Schedule of presentations to be determined in class.
The purpose of this exercise is to provide the student an early opportunity to communicate orally an overview of their thesis project – the major question being asked and how the question will be addressed. The target audience for this presentation is any faculty member in the Molecular Biology Program – someone who has a degree in biology or chemistry but is not necessarily an expert in your field.
Students will give a brief (~8-10 minutes, suggested no more than 7 PowerPoint slides) introduction to their project. This is an opportunity to share with the MolBio faculty and your peers the project that you are undertaking for the year. This presentation should focus on your literature review and background research, rather than on experimental work that has been done or is planned. The goal is to present the context for the experiments that will be proposed or reported on in the 2nd presentation at the start of the Spring Semester. Relevant information for preparing presentations will be discussed in class and can be found in Unit 5 and Unit 6 (found in the Presentations section in Canvas.)
**Students should coordinate with thesis advisors when signing up for a presentation time to ensure advisors are able to attend the talk. **
Students must submit the final version of their presentation file by uploading into the First Presentation Assignment site on the Canvas Molecular Biology Senior Thesis master site: UBER MOBI Senior Thesis PO FA2025 & SP2026 by 8:00 a.m. the day of their presentation.
All students are expected to attend the presentations and provide anonymous feedback to the speaker via a survey that will be administered after each presentation.
During these weeks that we have presentations you should work on Unit 4: Outline of your literature review. You will need to formally submit an outline of your literature review on October 31 by 11:59 pm. On Thursday October 30 you will be sharing a draft of your Literature Review Outlines with each other in small groups during class. Feedback received during class will help thesis authors review and revise their outline before formally submitting by 11:59 pm on October 31. Students should have Unit 4 (found in the Write Your Lit Review section of Canvas) completed before October 30.
Friday, October 10 — Mid-Semester Evaluation
(Experimental and Grant proposal)
Experimental & Grant Proposal theses: By October 10, students must meet with their thesis advisor to receive feedback on their thesis progress (see Mid-Semester Evaluation Form at the end of this document). If the student is not meeting the requirements for the Molecular Biology thesis, they will have until the end of the semester to remedy the concerns outlined in the evaluation.
Experimental theses: If you decide to withdraw from MOBI194A (by the October 16 drop deadline), you will receive no credit (NC) for the Fall semester. You must sign up for a Grant Proposal Thesis in Molecular Biology (MOBI191B) in the Spring semester (0.5 credit).
Week 10 Discussion (Thursday, October 30): Sharing Progress on Literature Review Outlines.
Students will informally present their progress on their project by sharing a draft of their Literature Review Outline with each other in small groups. This feedback will help thesis authors review and revise their outline before formally submitting it at 11:59 pm on Friday October 31. Students should complete Unit 4 (found in the Write Your Lit Review section in Canvas) before this discussion.
Submit Literature Review Outline (Friday, October 31)
Due date: 11:59 pm, Friday October 31, 2025. Upload document into the Literature Review Outline Assignment site on the Canvas Molecular Biology Senior Thesis master site: UBER MOBI Senior Thesis PO FA2025 & SP2026. Need to continue working on the writing of your Literature Review since you need to have a draft by November 13 for peer review.
Weeks 11 Workshop 3: Scientific writing, figures/figure legends (Thursday, November 6)
We will go over tips on scientific writing, making your own figures and guidelines on writing figure legends. (Suggestion: make sure you started working on Unit 7 which needs you to have a draft of your literature review done by week 12)
Week 12 Discussion: Peer Review (Thursday, November 13)
We will discuss the process of Peer Review in the context of scientific research as well as in the context of the thesis exercise. Students should complete the writing of the literature review by this date. Unit 7 (found in the Write Your Lit Review section of Canvas) explains and guides you on how to give feedback on your classmates Literature reviews.
Submit a Draft of Your Literature Review for Peer Review (Thursday, November 13)
Due Date: 11:59 pm, Thursday, November 13, 2025 (electronic copy uploaded to the Draft of Literature Review for Peer review Assignment on the Canvas site: UBER MOBI Senior Thesis PO FA2025 & SP2026)
Thesis authors submit a complete draft of their Literature Review, which will then be read by two of their classmates, who will provide feedback. This process is meant to give feedback such that a thesis author can review and make edits to their Literature Review before submitting it for formal evaluation. While this draft will not be formally assessed, it is respectful and appropriate to submit a draft of your Literature Review that is in a fairly complete state - that is, it is worth your classmate’s time and energy to read it and give you feedback.
Submit your feedback on the Literature Reviews written by two of your Peers (Thursday, November 20)
Due Date: 11:59 pm, Thursday, Nov 20, 2025, (electronic copies, uploaded to the Feedback on Literature Review Assignment on the Canvas site: UBER MOBI Senior Thesis PO FA2025 & SP2026))
The Thesis Coordinator (Prof Negritto) will assign you two classmates and will email the Literature Review drafts to you by 11:59 pm on November 13. Read these reviews and submit a document containing your thoughtful feedback to Feedback on Literature Review Assignment on the Canvas site by November 20. Prof Negritto will distribute your feedback to your peers. Guidelines for how to give effective feedback can be found in Unit 7 on Canvas.
Submit your Final Fall Semester Progress Report (Wednesday, December 3)
Due Date: 11:59 pm, Wednesday, December 3, 2025, (electronic copy, uploaded to the Final Fall semester Progress Report Assignment on the Canvas site: UBER MOBI Senior Thesis PO FA2025 & SP2026).
This document includes the literature review that includes revisions based on feedback received, with one additional section:
- For experimental theses: highlight main results in outline/bullet point form. If analyzed data are available, they may be included either as figures with figure legends, or tables with appropriate footnotes.
- For grant proposal theses: list of Specific Aims with brief explanation (see examples in Canvas Resources folder – Liu Specific Aims and Sazinsky Specific Aims)
Consult with your primary thesis advisor on expectations for this final section.
Your Fall semester grade takes into consideration the progress report, oral presentation, feedback provided to other students, information literacy skills, and work you have accomplished towards your project (for experimental theses).
For experimental theses: A passing grade is required to register for Experimental Senior Thesis, MOBI194B, in the Spring semester. If a passing grade is not accomplished you must sign up for a Grant Proposal Thesis in Molecular Biology, MOBI191, in the Spring semester.
Spring Senior Seminar Schedule and Deadlines, 2026
(there is no scheduled class meeting time in the spring)
Fridays January 30, February 6, and 13 (these dates are tentative) 2026 — Oral Presentations
(Experimental and Grant Proposal theses)
This is the first opportunity you have to introduce in depth your thesis project. What is the major question you are addressing? Why is it important to address it and how are you planning on addressing it? You should present the nature and significance of the problem you are addressing and give extensive background information on what is already known in this area of research and what experimental approaches you plan on using to address this question. Remember to take into consideration the guidelines and tips given to you on how to give a successful oral presentation. Your presentation will be 8–10 minutes, plus 5 minutes for questions. Everyone is expected to attend the talks given by their classmates, to provide feedback, and to ask questions.
Students must submit the final version of their presentation file by uploading into the Second Presentation Assignment site on the Canvas Molecular Biology Senior Thesis master site: UBER MOBI Senior Thesis PO FA2025 & SP2026.by 8:00 a.m. the day of their presentation.
Submit Research Progress Report II by Friday February 20, 2026
Experimental: Add Materials and Methods section to the Research Progress Report I and revise Introduction, Figures and Figure legends with comments received.
Grant proposal: Define Specific Aims and, in outline format, propose experiments to address Specific Aims.
In outline format, identify the experiments and appropriate controls you will propose to address the Specific Aims. Clearly outline what are the possible results and how these will refute or confirm your hypothesis.
Deadline: by 5 PM electronic copy uploaded to the Research Progress Report II Assignment in the UBER MOBI Senior Thesis PO FA2025 & SP2026 Canvas site
Submit Exp. Approaches — Grant Proposals, Friday February 27, 2026
Grant proposal: Work on defining in detail the experimental approach you will be taking to address your specific aims. You must include an explicit description of the materials and methods used in each of the experiments you propose. This need not be as detailed as the Materials and Methods section of most published papers. Rather, you should clearly describe what you will be doing, what is the theoretical basis for major experimental procedures, and what specifically is required to undertake each procedure. Additionally, you need to clearly describe how you will obtain or make whatever specialized reagents, probes, antibodies, etc., that are required for the procedures you propose.
Deadline: submit by 5 PM electronic copy uploaded to the Grant Proposal – exp approaches Assignment in the UBER MOBI Senior Thesis PO FA2025 & SP2026 Canvas site.
Friday March 27, 2026 - Submission of Thesis
(Experimental and Grant proposal theses)
Deadline: On or before this date submit an electronic version of a complete Thesis, Experimental or Grant Proposal, to the MOBI Thesis First version Assignment on the Canvas site: UBER MOBI Senior Thesis PO FA2025 & SP2026.
Note that this first version must be a finished piece of work, not a "rough draft." A graded copy with the comments and suggestions of your advisers will be returned to you no later than ten days after submission (April 6). You are highly encouraged to incorporate the suggestions you have been receiving up to date from your advisers into the final version. The grade received on the first version will be taken into consideration when determining your final grade.
Monday April 6, 2026
(Experimental and Grant proposal theses)
Return of thesis with comments and suggestions. Each of the readers will comment extensively; it is up to the student to obtain and request the input from thesis advisors.
Thursday April 23 and Friday April 24, 2026 – Final Thesis Presentation in the Senior Molecular Biology Symposium (an extra presentation date may be added).
(Experimental and Grant proposal theses)
Monday May 4, 2026: Final Thesis due (Research Report and Grant Proposal) theses
(Experimental and Grant proposal theses)
Submit on or before this date by NOON an electronic version of a complete revised final Thesis, Experimental or Grant Proposal, to the MOBI Thesis Final Assignment on the Canvas site: UBER MOBI Senior Thesis PO FA2025 & SP2026.
- Submit to professor Negritto 3 hard copies of the final, revised version of your Research Report (senior thesis) (binding is optional but highly encouraged, the molecular biology program will cover the binding of your thesis at Pomona Duplicating services. Binding, NOT printing).
- Fill out exit survey, having on hand a current Curriculum vitae will help you be able to answer questions more quickly. The exit survey will be taken online thru Qualtrics. At the end of your senior year you will receive a link to the survey.
- Submit Electronic versions of your final presentation to Final Oral Presentation Assignment and Research Report (Senior Thesis) or Grant Proposal submitted to MOBI Final Thesis Assignment site in the Molecular Biology Senior Thesis master site (UBER MOBI Senior Thesis PO FA2025 & SP2026.)