My Journey to Graduate School

Today is my first ~official~ day as an Assistant Professor at Vassar College so I’ve spent a bit of time reflecting on how I got here. I did an overview of my career path for my friends and family on Instagram but I think there are academic aspects of this story that could be useful to PIs and trainees alike.

I'm going to start at the very beginning - I grew up on a farm. Today my family farms corn, soybeans, and wheat. For most of my life we had a sizeable herd of beef cattle. For many generations, my family has worked as farmers and ranchers and cowboys. I credit this with both my interest in science and my commitment to hard work. In my family, we talked about how plants grow and why we use fertilizers, I watched cows and cats and dogs have babies and grow up. When we asked a question, we were encouraged to explore it even if my parents didn't know the answer. They even let me grow soybeans in their bedroom for a science fair project.

Rebecca and her brother and sister sit at the top of the stairs but outside the cab of a John Deere combine.

My parents didn't graduate from college but it was always clear that they hoped I would. I could go to "whatever college I could get paid for." I don't remember ever being told I couldn't do math or science. I remember plenty of surprise from teachers and other parents that I wanted to continue to math or science when I was the only or one of just a few girls and some skepticism that I would continue to do well but mostly I remember support.

Rebecca standing in front of a large tri-fold style board displaying her science fair project. The title on the board reads “How do Coke products affect your blood sugar?”

After attending some well resourced schools, I finished high school at a small school with a large contingent of Indigenous students and a high percentage of students on free or reduced lunch. There were 100 people in my graduating class so even though I had only been there 3 years, I knew everyone. I tell you this not to say that I came from a disadvantaged background; instead, I tell you this to highlight that opportunity comes in many forms. My high school did not have an AP Bio class, but our biology teacher sacrificed a lot of her personal time to prepare us to take the AP Bio exam. I had teachers who fought to implement or maintain the AP classes we did have. When I qualified for the state science fair and the school didn’t have money budgeted to support us, parents and teachers came together to figure out how to get me and the other qualifiers there.

During high school I worked at a small, hometown pharmacy. Answering the phone, ringing up clients, and stocking the shelves was a great job but it also gave me an application for the biology and chemistry I was learning at school. On slow days the pharmacist would pull out the drug info sheets and we would talk about drug mechanisms of action. I was often surprised at how little we knew about how drugs work.

So when I graduated high school I knew I liked biology and chemistry and it would be cool to learn more about medicines. Off I went to the University of Tulsa to major in biochemistry with the intention of going to pharmacy school.

But once I got to college I had a friend who was working in a biochem research lab and she invited me to come work with her. After a few afternoons in the lab, I was hooked and I have been in the research lab ever since. This happened during my first semester of undergrad, did I really understand everything that was happening? Absolutely not. But Dr. Robert Sheaff was very patient and spent a lot of time outlining experiments and talking with me about how to relate our project to whatever I was learning in class. In fact, I often use lessons as a student with Dr. Sheaff to inform my own mentoring techniques. By junior year I had my own project and was mentoring other students. At the same time I started TAing for Dr. Gordon Purser for a computational based lab course. So as a junior in college I realized I wanted to keep doing research and I wanted to stay in the classroom. When I was choosing college I knew that the small class sizes and the relationships I could develop with faculty seemed like something that would be useful to me but I never could have imagined how important it would be for my career.

Rebecca and her friend Ashley stand in front of a sink while disassembling a SDS-PAGE apparatus.

Rebecca stands in front of a gray wall on which a poster displaying scientific data is hung.

Then, I vividly remember the day Dr. Sheaff said "you know you can get paid to go to graduate school right?" At this point I had been to ACS National meetings and I was well on the way to completing my project so my name could be on a manuscript but I didn’t know how to apply to graduate school, how to move several states away. When I went to my first ACS meeting, it was the first time I had flown since I was a baby. I had been to maybe 7 states in my life, all right around Oklahoma. A lot of time I didn’t really know what I was doing, I just went a long with what my mentors said I needed to do. I absolutely would not have made it to graduate school if it had not been for all of the mentoring and support I received at TU. If you are mentoring a student, don't be afraid to take a student their first year and don't be afraid to take a student to a conference. It might be the thing that changes their life.

After listening to Dr. Sheaff describe graduate school, I decided to apply. I knew I had some solid backup options in Oklahoma so I decided to apply to top PhD programs. I had no idea where to start but Dr. Sheaff had advised us to start with considering where we wanted to live. I saw this an opportunity to try out a new place so I picked the east coast. I applied at schools up and down the eastern seaboard and a few places a little closer to home. But even then, I had a ton of options. At the time I thought I was interested in doing cancer biology research that took a biochemical approach so I looked up the schools with the top cancer biology programs. I also asked my professors for suggestions and considered if there were faculty with projects that sounded interesting. I ended up not applying at the actual top cancer biology programs but programs a little further down the list that were probably a better fit for me. I spent my Thanksgiving break completing applications. I was thrilled to get interviews and then acceptances at most of the schools. I’ll save the whole story of interviewing for another day but I ended up choosing between Vanderbilt and the University of North Carolina at Chapel Hill. I truly think both are amazing PhD programs but I am so glad I ended up at UNC. I found a supportive community through the IMSD program, interesting research, and a great place to live.

How I Stay Up to Date on New Publications

Throughout graduate school and my postdoc I have worked on refining a system for staying up to date on new publications and relevant literature that works for me. This is an evolving system and will mostly certainly change as my job changes, but I want to take some time to share my process.

Please keep in mind, it is almost impossible to see everything that is published that is relevant to your work and it is definitely impossible to read everything you might be interested in. You have to decide what is most important to you and how reading the literature fits into your schedule!

Part 1: How I Find Relevant Publications

1. Use your My NCBI account to set up alerts for newly published articles from specific people and on specific topics of interest.

• To create your account follow the “Sign in to NCBI” link at the top right of https://www.ncbi.nlm.nih.gov/

• Once you are signed into your account you can create “saved searches.” For instance, if you search PubMed for Rebecca M Pollet, once you get to the results page there will be an option to “Create alert” under the search bar. Once there you can select the options that work best for you.

I suggest using the option to add additional text if you are creating an alert for an individual that you don’t interact with often- for instance, when I meet a person at a conference that is doing work I am interested in I may create a saved search for their work. In the optional text box I’ll add information about when and where I met that person and what about their work I’m interested in. Then when I get the email I can scan the new work more quickly to decide if I’m interested in it and, if I want to reach out to the person about the work, I don’t have to think back to when and where I met them.

• Here are some examples of saved searches I have set up:

  • People I have worked with including my PhD advisor and most of the people in my PhD and postdoc labs

  • People who work on similar topics to me and who I see at conferences

  • People whose work is more distantly related to my own but that might serve as good mentors

  • Specific topic searches- I have a search for “bacterial beta-glucuronidase” to capture papers related to my PhD work.

  • Broad topic searches-I have a search for “glycoside hydrolase” to give me a general sense of the work happening in this area. It is rare that I read many of these papers in depth but skimming the abstracts gives me a sense for what the field is interested in and makes sure I don’t miss the big papers.

2. Table of Contents e-mails from specific journals (or RSS feeds if that’s more your thing)

How you set this up for each journal is a little different and can be frustrating to actually set up, especially because you often have to create a new account but once you have it going, hopefully you won’t have to change it.

Choosing which journals to get emails from can be difficult. Remember, you should get the most important papers for your work from the NCBI searches so the benefit of getting this information from journals is to stay up to date on more broad topics/fields and to get a sense of what kind of articles get published in different journals. Journals like Science and Nature will mostly give you insight on what the broader scientific community is talking about and may introduce you to new techniques you could apply to your research but I try not to spend too much time going through these emails. Journals that are more specific to your field are more likely to be useful; to get a sense of this, ask people in your field where they most commonly publish and what journals are considered top for the field.

Keep in mind that in today’s digital publishing, the papers included in these table of contents emails are likely to have been released digitally several weeks earlier so if it is truly a paper of interest you may get it faster through the NCBI searches. Additionally, many journals release new volumes once a month or every two weeks and these releases are staggered across the journals so even if you sign up to get table of contents from many journals, you aren’t going to looking through all of them every week.

I don’t have a complete list of journals I receive emails from but here are most of them:

• Nature

• Nature Communications 

• Nature Structural & Molecular Biology

• Science

• Cell Host & Microbe

• Journal of Bacteriology

• mBio

• Molecular and Cellular Biology

• mSphere

• Acta Crystallographica Section D

• Acta Crystallographica Section F

3. Publication aggregator sites

Across different fields people have created RSS feeds and blogs to aggregate new publications. Academic twitter is a great way to find these resources. The only resource like this that I use is Microbiome Digest- microbiomedigest.com. This resource was started by Elisabeth Bik in 2014 just as the microbiome field was starting to take off. For many years she compiled the daily blog posts alone and now she has assembled a team to help her compile links to newly published microbiome related papers. This includes work on human microbiome, non-human microbiome, general microbiology, and some general science trends. While most of the content is newly published, peer-reviewed articles, it does include pre-prints and some general/popular press articles. This resource has helped me understand the microbiome field so much and I’m incredibly thankful to Elisabeth for organizing this for the good of the community.

4. Academic Twitter, journal clubs, sharing papers with peers, etc

It would be disingenuous of me if I failed to mention that scientific communities in which I choose to associate are a huge source of staying up to date on publications in my field. I try to share interesting and important articles with people as I find them, particularly if they aren’t in big name journals and therefore aren’t something the person is likely to see or if it is helpful for me to discuss the paper with someone. I hope that by sharing papers in this way I can help create a community around me that values spending time reading and discussing literature, so I am always happy to get a paper alert from you!

Part 2: Managing the stream of new publications

Once you have set up all these email alerts they can become very distracting- you’re in the middle of writing but oh look, an email from a journal just came so I better go check if there are any new papers I should incorporate into my paper! Again, this is 100% something that you must find what works for you, but this is my current system to streamline reviewing new publications and minimal distractions:

1. Managing the email alerts

I have all email alerts go to my personal Gmail account so that I don’t have to change the alerts when I change jobs and potentially loose access to email accounts. I also have a filter set up for each email alert that makes that email skip my inbox and moves the email to a “Lit Review” folder in my account. This means I’m not constantly getting distracted by new alerts and can choose when to look at this. Like setting up the email alerts, setting up the filters can be a tedious since you may have to create a separate filter for each journal depending on what email address they come from. Luckily all NCBI alerts come from the same email address so a single filter will take care of all of those. A quick google search should get you the instructions on how to set up a filter for your email provider or I’m happy to help you with Gmail!  

2. Scheduling time to review email alerts and check Microbiome Digest

At different times I have tried doing these reviews with different frequencies, at one point I was checking Microbiome Digest every day before I left work, but right now I review all of this once a week, usually on Friday. I am trying to structure my time and follow the NCFDD Sunday Meeting format of planning out my time so right now I have a recurring, 1-hour event on my calendar every Friday afternoon to review new publications. If I set down undistracted, I really can get through all my alerts in about an hour. This is not reading papers; this is reviewing the publications and picking out what is important to me! Here’s my system:

• Skim through each email alert and Microbiome Digest blog post using the article title to decide what might be interesting or useful for me to read. When something looks interesting, I open it in a new tab.

• Review your new open tabs. I usually go through this process for each email alert one at a time, rather than having 50 open tabs to go back through. For each open tab or interesting paper, I start by skimming the abstract. From the abstract I can usually break the articles into 3 categories:

  1. I the abstract and don’t need the details. I can close this tab immediately.

  2. Interesting but I don’t need to read the paper in detail. Depending on my schedule for the day sometimes that usually means I skim the paper right then, maybe just looking at figures or reading the discussion. This is most common for papers that aren’t actually in my field but represent major advances that I want to be aware of. Reading News and Views type articles that summarize a paper can also help with this when I want to know about a study without spending time understanding it deeply. If I don’t have time to skim the paper right then, I may leave the tab open with hopes of reading it later but, let’s be honest, a lot of time that doesn’t happen before the tab gets closed and that’s ok.

  3. Papers that I need to read deeply. These are the important ones! I’ll give more detail on this in Part 3 but at this point, the important thing is to add these papers to my “to read” list since it is unlikely I have time to fully read the paper right now.

Part 3: Dealing with the Important Papers

Like I said at the beginning, it is likely impossible to read everything you want and get other things done. I have a paper on my to-read list that could be important for one of my side projects that has been there for almost 2 years…but it’s a side project that I’m not focusing on so it’s just staying there for now. Again, this is my approach, it’s not perfect and others will have different opinions.

My to-read list- I maintain this in a Google Spreadsheet that you can view here. The reading list is mostly just the title of the paper and the link. I have an urgency/rank column so I can note if it’s for a specific project or if I think I should read that paper next but for the most part I’m just dumping papers in here in the order that I find them and then when I have time to read I skim through to find one I’m up for reading at the time. Or I’ll remember a paper I wanted read, not be able to find it in my reference manager and find it in this list.

I’m constantly trying to figure out how to fit actually reading these papers into my schedule. There have been some discussions about this on Twitter and some people have strong feelings, this might be a good thing to ask your PI and other mentors. Right now, my goal is to spend 30 minutes reading papers, 3 times a week. I roughly schedule this time in each week (I have repeating events on my calendar) and somewhat adhere to that but it doesn’t mean that time is reading these new papers. Sometimes that is reading a paper for journal club, most of the time right now that time is re-reading a paper so I can cite it in what I am currently writing. But it at least helps me make reading some papers a priority and I fit in these new papers as I can.

Tracking what I am reading- in 2018 I was inspired by Auriel Fournier to track what I am reading. In the additional tabs in my Manuscript Reading List spreadsheet you can see what I’m tracking. The biggest thing is that despite having much higher goals, I read about 60 papers in both 2018 and 2019. If you scroll down to the bottom you can see I’m tracking the number of women first authors, women corresponding authors, and the percent of papers I read that are from US-based institutions. I’m not necessarily doing anything to change these statistics since women corresponding authors are likely limited by the number of women PIs but I have added some non-US based people to my NCBI email alerts and am always trying to think about how to cite more women. I am interested to see if and how these change over time though! The major advantage of this is many of these papers I add to my reference manager but not all of them, so sometimes I remember reading a paper and these lists are a good way to go back and find them.

I hope this is helpful to you forming your own plan and I’d love to hear your approaches!