Schumer lab:Grad program
Overview
Here is some information compiled to help make the degree progress process as smooth as possible!
- A Stanford requirement is that you take 3 units with 4 faculty. One of those sets of units will be your first year seminar class with Marc, another will be units you take for research credit with Molly. Since you have to teach twice, it is super important that you make sure to record these units with **other** faculty that are not Marc or Molly
- This is not an issue if you are also taking additional courses
- Many forms you will need at different stages are available on the Biology department website here: https://biology.stanford.edu/academics/phd-program/requirements-forms
Courses
Note: Taking the full version of a course is usually the best way to learn the material. But if the workload seems like too much, you can usually audit and be exposed to the material with much less effort.
Compiled here is a list of classes that members of the lab have taken and any relevant information:
- BIO105A/B: Ecology and Natural History of Jasper Ridge Biological Preserve with Rodolfo Dirzo and Jorge Ramos
- A two-quarter field-based course that takes place one afternoon per week at Jasper Ridge (transportation is provided)
- Each week centers on a different aspect of Jasper Ridge: geology, soils, plants, trophic and community ecology, mammals, herpetofauna, fishes, plus research history and archaeology
- Students propose and carry out a small independent research project in the Ridge, then present their findings at the end of the second quarter.
- Completing both quarters certifies you as a Jasper Ridge docent, which gives you free access to the Ridge and the ability to bring others on hikes there.
- Good for those looking for inspiration on local research projects, or who want to be more connected to Bay Area nature.
- BIOE 204: Genetic and Epigenetic Engineering (2 Units)
- A useful course that constitutes weekly literature review.
- Topics include: gene editing using transposases, integrases and nucleases, gene regulation with a focus on transcriptional control, chromatin-mediated epigenetic regulation, and epigenetic editing.
- Each week builds upon the previous one and ties together nicely, culminating with a final project.
- Good for those looking to learn more about epigenetic engineering, as well as python and computer modeling.
- Lacra Bintu is a wonderful professor, very approachable and nice
- BIO 208: Spanish in Science/Science in Spanish with Rodolfo Dirzo (2 units)
- Lecture/discussion based class where you how to speak about science in Spanish
- Fairly informal class, few assignments
- Useful for learning a lot of science-specific vocabulary in Spanish
- Recommended that you have a conversational level of Spanish fluency before taking this class
- BIO 287A: Advanced Topics in Mathematical Evolutionary Biology with Noah Rosenberg
- A mostly peer-taught seminar course: each lecture is given by a student and is based around an important paper in theoretical biology
- Your responsibility in the course is to read one paper in enough depth to present it to the rest of the class, and to read the papers others choose in enough depth to follow along
- The course ends with a final paper in the same style as the presentations: pick a paper and explain its main insights, plus what makes it important to the field.
- Can be rough depending on the particular papers that people pick, but is in forcing you to go in-depth on the math that underlies the field, and that you would probably skim over if you were reading papers in another context.
- BIO 296: Teaching and Learning in Biology with Jamie Imam
- A weekly workshop class designed to help students be more effective teachers and TAs
- Through in-class activities and light homework assignments, learn techniques for communicating clearly, keeping all students engaged, and continually improving your classroom.
- Recommended to take at the same time as your first TAship, as many of the class activities are meant to be brought into the classroom where you're teaching.
- BIO 302-304: Current Topics and Concepts in Population Biology, Ecology, and Evolution with Marc Feldman and Larry Bond
- AKA Professor Parade AKA Pizza Party
- A weekly seminar featuring a professor or an outside academic who happens to be visiting the department that day. Also featuring pizza.
- Good socializing and free food, no responsibilities except skimming the paper that the speaker may or may not recommend.
- BIO 313: Ethics in the Anthropocene with Liz Hadly
- A weekly ethics seminar with a focus on topics relevant to ecology, evolution, and conservation biology
- Subjects include different ways of deciding what has value, what is right and wrong, and who gets to set the standards for society
- Students are only responsible for doing the readings and being ready to discuss them in class.
- Seems to be slightly more of a time-commitment than the CMOB-oriented ethics class (since that one is only one day), but is more relevant to issues outside of research misconduct and lab animal welfare.
- BIO 386: Conservation and Population Genomics with Liz Hadly and Stephen Palumbi
- A weekly seminar centered discussing subjects relevant to conservation biology and genomics.
- Students work in small groups to prepare a presentation about a topic of their choosing, choose papers relevant to the subject for everyone to read, then present for half the class before leading a discussion on the topic.
- Relatively low-commitment and a good way to be exposed to a wide variety of subdisciplines related to conservation.
- BIOS 221: Modern Statistics for Modern Biology with Susan Holmes (and sometimes Wolfgang Hüber)
- A hands-on crash course in the methods commonly used in biology publications today.
- Structured around Susan's awesome statistics textbook of the same name, which is available free online: https://web.stanford.edu/class/bios221/book/
- Responsibilities include weekly lectures and R labs (no grades, just exercises), plus a self-directed final project in which you analyze a real biological dataset using one or more of the ideas discussed in class.
- Highly recommended for an overview of differential expression analyses, mixed models, clustering, machine learning, etc. with the chance to say how they're implemented in R
- BIOS 227: Mass Spectrometry and Proteomics: Opening the Black Box with Parag Mallick and Sharon Pitteri
- A mini-course covering the fundamentals of proteomics and mass spectrometry
- Subjects include mass spectrometry instruments and sample preparation, data processing, protein identification, quantitation, and other new applications
- Responsibilities include lectures three days a week, plus (ungraded) labs, and a final presentation on a proteomics paper of your choosing
- A nice proteomics crash course with two very effective instructors, but with big time commitments for the two weeks that it takes place
- BIOS 267: Proteomics, Protein Interaction Maps, and Systems Biology with Peter Jackson
- A mini-course centered on proteomics as it applies to the study of protein-protein interactions (PPI) and systems biology
- Subjects include mass spectrometry techniques, molecular and computational tools for detecting and visualizing PPI, and applications to biomedicine
- Only assignment was a very open-ended final project visualizing a PPI dataset in Cytoscape to form a hypothesis and devise a rough experiment to address it.
- Lectures are pretty disorganized, but I did learn something about PPI and Cytoscape that has helped me since
- Low commitment for a mini-course, but the fact that involves no work means you don't get much out of it
- CME 193: Introduction to Scientific Python with Anjan Dwaraknath and Arun Jambulapati
- A workshop course teaching basic Python in a STEM context
- Subjects include a brief review of programming fundamentals (variables, control flow, etc.), object-oriented programming, data science in Pandas, plotting, and machine learning basics
- Probably ideal for those with some programming experience but who want practice in Python; a steep learning curve for those with no programming experience, but doable; experienced Python programmers will probably be bored
- GENE 211: Genomics with Gavin Sherlock and Michael Cherry (3 units)
- A hands-on introduction to the field of genomics with lectures, paper discussions, and labs
- Topics include the molecular biology and engineering of dominant sequencing platforms, assembly algorithms, genome browsers, and biological applications
- Problem sets teach how to manipulate genomic data through Python (some prior experience recommended) and web interfaces
- GENE 220: Introduction to Genetics, Ethics, and Society with Roshni Patel, Rachel Ungar, Julie Baker, Daphne Martschenko (instructors likely have changed since 2023) (1 unit)
- Class that takes a discussion-based approach to ethics and controversies of genetic studies
- Learn about the history of eugenics in general and at Stanford, including a trip to Green library archives to see primary sources
- Useful for learning how to engage with hard conversations about genetics/eugenics
Courses that lab members have not taken but have heard good things about:
- BIO 202: Ecological Statistics with Leslie Decker and Tad Fukami
- BIO 305: Managing your PhD with Fio Micheli and Jose Dinneny
Yearly requirements
- Make sure to complete your IDP with Molly each year and submit it on GST
- Make sure you are signing up for research credits as needed to accumulate 135 units by your fourth year. Talk to Student Services about your plan for this
First year requirements - EcoEvo
- First year committee meeting
You will have a meeting with your committee at the beginning of your first year to plan your first year courses and requirements. Lorena will assign your first year committee but please check in with Molly if it hasn't been set up by early October of your first year.
- First year paper
Your first year paper describes your progress on a research project or is a literature review. Examples of proposals completed by lab members can be found here:
~/Swordtail\ Dropbox/Schumer_lab_resources/Shared_lab_resources/Example_First_Year_Requirements/
Two faculty members will need to review your first year paper and complete a form to be submitted to Student Services. One of these faculty members can be Molly. The faculty members who review your first year paper can be the same or different as the ones who review your first year talk.
- First year talk
Your first year talk is a research update or a description of your research plans. Examles of first year talks given by lab members can be found here:
~/Swordtail\ Dropbox/Schumer_lab_resources/Shared_lab_resources/Example_First_Year_Requirements/
Two faculty members (one can be Molly) will need to view your talk and submit a form to student services. The talk can be a regular lab meeting for our lab, another lab, or another speaking venue (e.g. EcoEvo lunch)
First year requirements - CMOB
CMOB students are typically completing rotations during their first year and don't join the lab until their second year. We still need to build out this resource section!
Required Courses:
- A quick note: The department is fairly flexible, so you can arrange to take required courses the year after if you have a really cool course that you want to take instead that's only offered certain times**
- BIOS 200: Foundations in Experimental Biology (5 units)
- This is a required course for fall term and is composed of two 3-week cycles. The first cycle is focussed on grant writing and requires you to submit for an NSF GRFP, if eligible. The second cycle is focussed on presentations and you give a mini presentation on a topic to a small group.
- Attendance is mandatory and they are strict about the number of classes you miss
- Heavy workload during the first half, when you have to apply for the NSF GRFP
- BIO 301: Frontiers in Biology (1-3 units)
- This is another required course for fall term.
- Each week you attend seminar and take notes on the presentation. You also meet weekly to discuss scientific papers from different people in the department. During class time, you go over the papers and then get to talk to the professor at the end of class and ask them questions about their paper, research, and scientific journey.
- A very cool course that helps you learn to analyze papers more critically and introduces you to a bunch of different research topics and options for your rotations.
- Low work load
- BIO 165: Quantitative Approaches in Modern Biology (3 Units)
- This is a required course for winter term.
- This course explores the quantitative basis of major cellular processes and their coordination to form a cohesive physiological entity that is capable of rapid growth and acclimation to changing environments
- Weekly lectures and dry labs
- Heavy workload, depending on your coding experience, but they are reworking the class
- BIO 312: Responsible Conduct in Cellular and Molecular Biology (1 unit)
- This is a required course for spring term.
- Selected faculty will lead discussion of topics related to responsible conduct of research and ethics, such as conflict of interest, authorship, collaborative research, and data management.
- Attendance is required, but there is no additional work outside of class.
Two additional courses are required that fall under "cell and molecular biology" broadly. They can be mini courses or full courses.
TAing:
- You are required to TA twice during your program and typically most people do the first TAship during their first year. This is a heavy workload so it is important to plan your rotations wisely around TAing, or plan to work very hard during that quarter. Most PIs are aware of the heavy workload of TAing and will work with you to plan your rotation so you can still have a productive time.
Quals
For EcoEvo you are expected to prepare the following:
- 40-50 minute presentation of your dissertation plan and preliminary results. Be prepared to be stopped for questions, the whole presentation with questions will take about two hours.
Schedule at least one practice with Molly and at least one practice with the lab
- A written document describing your plan for each chapter. This should include 3-4 chapters, each expected to result in a publication.
Plan to have this written document completed >1 month before your qualifying exam. Molly will give you multiple rounds of comments. You should also schedule one-on-one meetings with each member of your committee ~2 weeks before your qualifying exam and send them this document a few days before. This way you will be able to incorporate their feedback before your exam.
- After your exam your committee needs to fill out and submit this form to Student Services: https://drive.google.com/file/d/1g4G0KujkBX5clFEaSAiEMR74EwVTP0pP/view
- You will also need to complete this form, get it signed by Molly, and submit it to Student Services: https://drive.google.com/file/d/16VV3KSILEr_zgej-PbX3Y6AKCR0O21kR/view
There are example qualifying exam proposals and presentations in Dropbox, check them out:
~/Swordtail\ Dropbox/Schumer_lab_resources/Shared_lab_resources/Example_quals_proposals
For CMOB you are expected to prepare the following:
1. Written dissertation proposal that outlines the student’s projected dissertation research (November 1st) 2. Oral defense of the dissertation proposal (November 15th)
- One exception to these deadlines would be for students TAing a fall core course (e.g., BIO83) who are allowed to defer the qualification exam to the winter of the same academic year.
- Dissertation Proposal Committee Responsibilities and Proposal Guidelines
Students are required to organize a committee that consists of their advisor, at least one other Biology Department faculty and two other members. At leat one of these members must be from outside the Biology Department. Faculty may be emeritus at the time of the exam.
- Guidelines for the Written 10-page dissertation proposal:
- Introduction and specific aims (~1 page)
a) Describe the broad significance of the research topic. b) Describe the gap in knowledge that hinders our understanding of the research topic. c) State your hypothesis (or goal, if not hypothesis driven) that will fill the previously stated gap in knowledge. d) State your specific aims that will directly address your stated hypothesis (or goal, if not hypothesis driven). Include a brief overview of the experimental design. e) Describe the beneficial outcomes upon completion of your proposed research. Remember to include broad significance to the research field.
- Background and significance
- Preliminary data (if available)
a. Preliminary data should be included if relevant but is not required. b. This can be included before the research design or as each aim is proposed.
- Overview and research design for each aim
a. Detailed experimental plan i. Include plan for rigor and reproducibility, such as: 1. Authentication of key reagents and methods 2. Thorough and transparent data collection and documentation b. Statistical considerations (sample size, significance tests, power calculations, error propagation, outliers, replicates, etc) c. Possible anticipated results d. Limitations/contingency plans
- Oral Exam
The oral exam must be scheduled for a minimum of 90 minutes. Oral examiners may ask questions at any point of the presentation. The committee will question the student until consensus by committee is reached or maximum time (90 min) is reached.
- Note that the oral qualifying exam is not a seminar—it is an evaluation of the student’s ability to:
● Summarize the field of study, including past and current work from others ● Generate a working hypothesis ● Develop project goals ● Design logical experiments ● Draw conclusions and adapt hypotheses depending on results
Yearly Committee Meetings
- After your Quals, you are required to have a yearly (twice yearly starting fifth year) meeting with a committee of 3-5 faculty to discuss your progress towards graduation
- Be sure to schedule 2 hours for your committee meeting, 1 hour is not enough for a presentation on your progress and meaningful feedback from your committee
- Pinning down multiple faculty for multiple hours is nearly impossible, so reach out months in advance!
- You are (loosely) required to submit your committee meeting form to Student Services by May 15 (form available on the Biology website)
Reading committee & Defense
- Your reading committee must include four faculty (including Molly)
- You can have external people (non-University) on your reading committee, but you need to fill out a form that you can get from the Student Services office and send in the external member's CV
- For your actual defense you will need a 5th person outside of the department. This is often difficult to arrange so start thinking about and asking people it early!
- People in Biology frequently ask faculty in Genetics but it can be any non-Biology department
Small Grants and Fellowships for Research
Suzanne Ou (defended in Spring 2023) compiled the following list of small grants and fellowships for research:
https://docs.google.com/spreadsheets/d/1lTu2V1cbHpLBumRe0atcxPMjUKX8jSyQNO3JWK_jVgI/edit?usp=sharing
The list is now maintained by crowdsourcing, so if you find any broken links or inaccurate information, please feel free to correct it!
Other important info
- Once you advance to candidacy you have a 3.5 year window to graduate from the program
- You are entitled to up to 8 quarters of leave of absence, which do not count towards your graduation timeline
Q. What resources are available specifically for mental health co-pays?
- Biosciences Mental Health Support Program https://oge.stanford.edu/mental-health-support/
Q. How much is the compensation for an additional TAship, beyond the required 2 courses? (as of June 2023)
- $13,914 TOTAL per quarter for 100+ upper division courses
- $15,774 TOTAL per quarter for 40s, 60s, 80s core lower division courses
- The H&S standard salary for 22-23 is $12,054 per quarter
- External fellowships can impact TA funding and please contact Student Services directly for more information about your TAship if you are on a fellowship.
Q. What financial support is available for conference travel?
- OGE Biosciences Travel Grant https://oge.stanford.edu/financial/travel-grant-program/
- Ecology/Evolution travel grant announced each summer via eco/evo listserv
- Each lab may have a different policy on supporting conference travel and the number of conferences per year.
- If you’re interested in borrowing a portable travel poster tube with a strap, please see Student Services
- As a reminder, a resource for any unanticipated expenses is the Emergency Grant in Aid. More information below for funding options for graduate students.
