A number of Thursdays ago this semester I gave my first ever excellent, perfect, no-regrets presentation. Here I am, post-shower and maybe an hour pre-presentation:
(My grandmother gifted me that gorgeous necklace, as well as most of my other really pretty necklaces. My glasses I bought online for sub-$15, which is a new-ish favorite discovery of mine, as of a few years ago. The shirt I bought in California while visiting my partner’s family (I get overwhelmed by the lights in malls and my decision-making gets tripped up). The cardigan is my favorite old cardigan. It has a huge hole in the armpit I only recently sewed up. You can’t see the armpit hole over zoom. The creatures behind me are the viruses I am studying, looming, presumably in some blood, also looming.)
Here is my set-up:
If you look closely, you can spy the following items:
My clicker, even though my presentation was over zoom. Using the clicker allowed me to sit farther away from the screen, which made for a better image of my face, and, more importantly, prevented me from fidgeting with the computer in a way that would be audible to the audience over zoom.
A lamp, for nice lighting for the presentation (otherwise I look a bit dark and distractedly don’t match the lighting on the artist’s rendition of the subjects of my presentation).
My phone, plugged in, silenced, and on airplane mode with screen timeout turned off, with a timer set for the length of my presentation.
Paper and pen, out of the way but within reach, in case anyone made any suggestions I wanted to write down.
My to-do list notebook (pink on top of the stack of books)—nearby for comfort (I take it everywhere, including bed) but out of sight.
The Relentless Moon, the third book in the Lady Astronaut series by Mary Robinette Kowal and the book I was reading at the moment, to remind me that there are nice things I enjoy I’ll get to do soon.
I took a lot of communications-focused courses at MIT. Almost all of them were about writing, which has served me extremely well. Though other classes I took did include one or two presentations, as far as I remember only one (6-unit (or half a normal course)) class actually explicitly focused on public speaking (not that I actively sought out additional public speaking educational opportunities—I didn’t), and that was 6.UAT—a course I did not fully appreciate at the time, because it was difficult for me in ways that made me uncomfortable, because public speaking made me uncomfortable, but which has turned out extremely useful for me since communication, including public speaking, has turned out to be a very important part of my job.
When I took 6.UAT I was very bad at public speaking, and I think I was still pretty bad at public speaking when the semester ended, though hopefully less bad. I remember learning to make eye contact, and not to fidget as much, and (from a particularly upsetting class where we viewed our presentations on camera) that my posture was just awful, a flaw I have improved at least a little through lots of yoga (though I imagine my posture is still awful, and I absolutely would not like to see myself on camera today either). That should tell you just about how low the bar was for me for starters.
6.UAT also taught me an extremely valuable lesson, perhaps the most valuable lesson, which I failed to actually incorporate into my presentations until just now. It is painfully simple—it almost hurts how simple it is. It is this:
✨ • ✨ • PRACTICE. • ✨ • ✨
Usually, when preparing for presentations, I focus almost entirely (or entirely) on my slide deck. I put together a silly number of slides. I make them all perfect. I memorize where they are in my presentation, including backup slides as potential responses to the many, many potential questions I’ve anticipated, which I used to fit at the end and lately, ever since I discovered hidden slides, have been slipping into their places in the narrative as hidden slides. Often, I have an epiphany about my work and generate some brand new figures specifically to add in as slides. This is probably productive for the project overall but it takes a very long time. Usually, I pull an all-nighter the night before, ostensibly to make sure my slides are ready, numerous, and perfect but actually, if I look deep into my soul, probably actually because I am usually very nervous before a presentation and have no work-life balance and a lot of trouble shutting off at night (as evidenced by me writing this blog post in bed after midnight). Then, for the actual presentation, I am exhausted, I have no concept of timing, everything takes longer than I expect, and I go over time, leaving very little room for questions and probably not a great impression overall. I almost never actually make it through all of my beautiful slides. At worst, I am preparing my slides up to the very minute before my presentation. At worst, (back when things were in person) I am late. This is my routine. This is how I am comfortable. (This is my design.)
Most of my presentations so far had been in front of a small group. Because most of our lab’s work happens in teams, I often present work to my labmates and collaborators. These presentations are largely informal, and I have gotten very comfortable with them, to the extent that I do not get nervous before them at all and prepare my slides during analysis in anticipation of presenting my work when the opportunity appears. I think I am very good at presentations during a small-group meeting. The only big change I am still working on is time management. I sometimes get less time in a meeting than expected and end up needing to go over time; I also sometimes allow too much conversation in the first half of a presentation and lose time for the second half.
I also, occasionally, present in front of the entire lab or in front of a broader but still lab-sized group of coworkers. These presentations are still a bit nervous, and I still sometimes have a lot of trouble sleeping or even disconnecting the night before. My slides are usually done, since I am mostly or entirely able to pull slides from the smaller update presentations I have already given to smaller groups of labmates. These meetings are usually an hour long, which makes time management easier, but they also invite (valuable!) input from more people, which makes time management harder. I need more practice presenting to larger groups—enough practice that I am not nervous at all and am able to be fully present to receive feedback and learn from the conversation generated by my work. Other than time management, I think I most need to work on confidently taking up space, including walking and eye contact, and figuring out something like gesturing rather than nervous awkward hand movements. (One thing I am quite happy with is that I am usually good at fielding questions, largely thanks to my massive overkill slide deck.)
Thinking back on it, I am quite happy with the amount of practice I’ve gotten presenting in different contexts in the lab. Public speaking has turned out to be so much more important than I expected when I took 6.UAT. I think I’ve gotten a lot better at it, and I am genuinely excited to keep improving: to keep growing in the contexts I already have experience in and to try on new contexts and get better and better. (And seeing the process as a valuable growth opportunity, rather than something awful I just have to get through, is already a massive step forward.)
This presentation in particular needed to go well. I was getting to present in front of an agency that funds our research, as well as PIs of other labs doing related and impactful work. I was representing our lab and I was representing the Institute. I also was worried, or in more accurate terms felt rather confidently, that it wasn’t supposed to be me, that this was a mistake, and that the people who know me would be expecting me to do rather poorly, or at the very least didn’t have particularly high expectations, which maybe gave me something to prove and at the very least made me rather desperately want to not disappoint those same people who had believed in me and given me the stage—and I really, really did not want them to regret believing in me. In other words, it was an opportunity and it was a big deal to me.
Like for larger group presentations, my slides were already largely prepared from previous presentations I had given in front of the lab and other coworkers, both in large- and small-group settings; I mostly just had to put the slides together into one coherent presentation, with a few updates in background information slides. This took longer than I expected but it didn’t take too long. I found myself done adjusting and adding slides the day before—an accident and a new record for me.
I had a whole half a day to sit with my slide deck and to practice (amazing!).
The presentation was to be eight minutes, with two minutes for questions. I was used to presenting this material in an hour-, at least half-hour-long presentation, so getting everything to fit was the main challenge. I practiced for several hours with my slides and my cell phone timer, interrupted only at one point by our building manager, who came by because we had mice. (Have mice—but at the moment they can’t seem to get past the inside of the hollow space behind the kitchen cabinet. The great benefit of this experience is that I now fully understand what authors like Neil Gaiman mean when they describe mice scratching inside the walls, and staying up late working is now that much spookier….)
I am very glad I practiced. My introduction, which I really did not have time for, initially took up three or four minutes—a full half of my allotted time. I cut it down to less than 30 seconds. Even then, I could never get through all of my slides, so I was forced to cut out most of the side paths and focus entirely on the main narrative. This was probably good for the project itself—the experience of cutting my presentation down showed me what I care about most within the wide scope of the project, and that the work was not weaker with more focus. By the end of a few hours I had the presentation down to a perfect and consistent eight minutes. I didn’t have a script, and I didn’t practice so much that my wording was the same each run-through, but I nailed down the verbal transitions that worked best at key moments when the audience could potentially get lost and identified specific slides that tempted me to go down juicy but time-consuming tangents side paths that would have been distracting and taken up too much time.
The actual presentation was very similar to my simulations. I sat in the same chair at the same place at our dining table, with my laptop the same distance from my face, and used my cell phone timer in the same way, and all went smoothly and on time. There were a few questions at the end, which were very easy to answer with the slides I had removed from the main narrative (and I was very happy to get an excuse to return to those slides). I got compliments afterward, and I got compliments from my direct supervisor and my PI, which is a very big deal for me. I don’t usually get that much positive feedback, and I certainly don’t expect positive feedback, so the experience made me very, very happy. It was a lovely confidence boost that spilled out into the rest of my work. The presentation itself and the audience’s interest in it renewed my excitement about my work, especially the project I presented on.
The ease of simulation, I think, is one of the primary nice benefits of giving a presentation over zoom. As an added benefit, the stage is (probably) a comfortable place in your home, and the audience is a small collection of faces in squares on your screen, rather than a crowd of people right in front of you. You can worry less about stage presence, or how you occupy space, or eye contact, or your weird hand motions, and you can focus more fully on the content of your presentation. Of course, parts of the usual challenges are still present—if you fidget, it will still be distracting; you need to make eye contact with your camera, if not the people in front of you; you still have a presence and your clothing and posture and voice still affect the audience’s experience of your presentation and perception of your work. Zoom also meant I did not need to travel for the presentation, which I thought was nice, though of course I cannot possibly know how many opportunities for “networking” connection with potential future collaborators and the human beings behind the names on my favorite papers and other amazing people who share my scientific interests I missed out on without the usual awkward cocktail hours or sitting next to someone or sharing an elevator—all experiences that I miss and look forward to having again someday in the future (along with speaking on an actual stage someday, which I do not expect to enjoy but which I am guessing will be a valuable growth experience).
Here is my advice on giving presentations:
Lots of pictures, minimal text. Unless you give your audience a few seconds of silence at the start of each slide, which I have never seen in an actual presentation, they are not going to be able to divide their attention between your slide and your spoken words without missing some of one or the other. Pictures are good. Figures are good. Titles and (short) labels are good. Any other information needs to justify the time it will take to process.
Provide a roadmap at the beginning of your presentation, and connect back to it as you go. One way to do this is to show a broad outline of your presentation in one of your first slides and repeat the points in the outline as slide or section titles, or echo those points verbally when you reach them. I have also seen people show their outline slide repeatedly throughout the presentation with already covered sections in grey text. I don’t like that as much. I also do not usually provide much of a roadmap and need to work on changing that.
Give your slides short, informative titles that both summarize what is on the slide and provide an idea of the relevant context or where you are in the presentation. Make sure that a person who zoned out for a minute can get caught up and place themselves by looking at the current slide.
When you present a figure, unless it is obvious (it probably isn’t), explain what each axis is, what each point represents, and the main takeaways of the figure. Most people don’t do this, which means that some fraction of the room might not understand the figure and might not feel comfortable asking, or at least might waste time trying to figure it out—any of which limits their ability to give feedback or engage in conversation and limits the value of your presentation both to them and to you.
Know what you want to get out of the meeting, and make sure you’re getting it. Literally sit down before the meeting and write down or type what you, personally, want to get out of it. Are you pitching a project? Are you asking someone for something? Are you looking for feedback? What are your priorities? Do your planned presentation and your slide deck reflect your priorities for the presentation? If conversation strays from your goals, you need to know to redirect it, which means you need to know exactly what you want.
Along the same lines, write down three or so main takeaways that you want your audience to remember. These takeaways will probably be related to your goals for the meeting. Build your narrative around those takeaways. State the takeaways explicitly—you might list them out in the end, or, especially in a shorter presentation, they might even be your roadmap slide and your title slides.
Bring a sheet of paper and a pen to write down any useful feedback or questions that you want to return to after the presentation is over.
If you are worried that you will need to redirect conversation, or that you won’t have enough time for everyone to deliver their feedback to you during the meeting, I have found it helpful to print out my figures and leave them around the room with pens or markers such that each person can reach at least one, preferably at least two (in case someone else already took one) copies (or even print one per person, though that is probably excessive). Mention at the start of your presentation that your audience can write any comments on these pages and return them to you at the end of the meeting; when you redirect conversation, invite people to write any unspoken feedback on the pages. Printed figures can make redirecting the conversation easier, both for you and for your audience. It can also help you get feedback from people who do not feel comfortable speaking in front of the entire group, and feedback that someone thought up after the particular topic had passed—and it gives people who are not engaged by your presentation something interesting to do that still achieves your goals.
Stop occasionally to ask the audience questions or solicit questions or feedback. (Pause a slightly uncomfortably long time after you ask a question to give people time to formulate their thoughts and potentially work up the courage to speak.) If you’re looking for feedback, asking for it directly will give you a better chance of getting it. Also, asking questions helps keep your audience engaged and gives you a better idea of whether or not they understand are engaged with what you are saying. (When I was TAing 6.005 (now 6.031), I learned that it is in addition important to phrase your request for feedback or questions in an inviting, open-ended way: “what feedback or questions do you have?” rather than “do you have any questions or feedback?”)
If there is something that fits naturally, it can be nice to start with or otherwise work in a relevant movie or TV clip or comic that somehow relates to your research, to make the experience more fun for everyone—and to improve your audience’s engagement with the material, make them more comfortable speaking up, and, if it’s done well, give them easier access to your key takeaways. Probably don’t do it before every single presentation, unless you want that to be your thing.
6.UAT had a lot of practice speaking assignments that you can peruse, if you’d like to try them. They are fairly varied and include a lot of different contexts—presenting with a slide deck, presenting a chalk talk (which I have not yet had to do in practice), presenting on your work, shorter persuasive pitches, presentations that are meant to connect to a lay audience, and so on.
As an aside, I have heard that acting or improv are great for improving public speaking—and one of my favorite instructors used to do theatre. I took an introductory acting class while I was at MIT, but it was absolutely not what I expected and I don’t think had much of an impact on my public speaking skills (though who knows!). One assignment I particularly remember involved all of us writhing on the floor in different directions while making loud silly sounds, literally rolling over each other and hitting the walls and rolling over each other again. The professor left the room for a long while in the middle of the exercise but we didn’t know what to do so we kept rolling. (Is there a lesson here? I don’t think there’s a lesson here.)
Some of my more corporate friends have (or had, before the pandemic) parties (I’m not kidding) where each attendee has to impromptu present (again, not kidding) on a completely unfamiliar slide deck. I don’t usually go to these parties (but I should, and I intend to when we can safely have parties again), but it seems like a great way to practice. (And how nice to look out for your friends’ public speaking skills!)
Here are some of the ways I hope to keep growing:
Knowing my priorities well enough to be flexible with time, if I get less time during a meeting than I expected.
Managing conversation to make sure that we are able to reach everything I prioritize.
Going out of my way to practice presenting to a larger group, such as at lab meeting. Presenting in front of a larger group makes me uncomfortable, but that is precisely why I should probably pursue the experience. I usually choose one-on-one or small-group mentoring over volunteer teaching opportunities, due to the massive amount of time and work that goes into preparing a lecture—but maybe I should make a point of volunteering to teach at least one or two lectures a year, perhaps on a topic that requires minimal preparation to minimize loss of research time.
Getting better at providing a visual and verbal roadmap to the audience.
Practicing presenting without a slide deck.
By far, the most important thing I’ve learned about presenting is that the priority is to convey information and have a dialogue with the audience toward some goal. Everything else—how you look, if you seem unsure or if you do not exude confidence in your own work, whether or not your explanations make sense to your audience, whether or not people zone out partway through your presentation and don’t or aren’t able to check back in—is either in service of or to the detriment of the goal. It is important to keep your priorities and your audience at the forefront, ahead of your self-esteem and your ego and your expectations. That’s not an easy thing to do. Most likely, in the end, the most important thing is the work you are presenting: your job is to give it the platform it needs in order to become whatever the world needs from it.
As an Amazon Associate I earn from qualifying purchases. The rest of this blog post includes links with my Amazon referral code. If you click one and buy something, I get up to 4% of the price as commission. You don’t have to buy these things from Amazon—actually, you don’t have to buy these things at all. You can also support me by buying merch of my art, by buying me a campground store decaf coffee, or by simply reading and enjoying. Thank you!
Here are some things you can buy, if you see them here and you like them and you want them for yourself:
My clicker, which I bought for myself and then also for my parents and for my partner. It has a nice soft texture and is pleasant to hold and easy and intuitive to use and has not failed me through multiple years of presentations. The places where I present usually have their own clicker, or an option to not use a clicker, but I like having the flexibility to move around and I quite like having my own clicker that I know I like and am familiar with and can trust not to present (hah! a pun!) me with any surprises during what is probably (by virtue of being a moment in my life) an already stressful time.
My to-do list notebook, which for 2020 is pink because the pink one was on sale when I bought it. I have been keeping my to-do lists in a dedicated notebook for I think three or four years now. It is a very pleasant ritual. The notebook itself has changed from year to year, but I have finally settled on one and I think I will be buying this exact notebook from now on. I just bought my notebook for 2021. It is still shrink-wrapped and I am excited to open it on New Year’s—my own gift to myself. I might gift-wrap it. It is blue, dark blue, like the night sky. I like it very much.
The Lady Astronaut series, consisting of The Calculating Stars, The Fated Sky, and The Relentless Moon. I like everything Mary Robinette Kowal writes. I had been looking forward to The Relentless Moon for a long time and was very excited to finally get to read it. It is a mystery story and it is extremely well-researched sci-fi and it is a very nice vacation (on the moon).
Every PhD student I talk with seems to have a different qualifying exam and a different qualifying exam experience. My department, Organismic and Evolutionary Biology at Harvard, has a very flexible and customizable quals, in line with the overall very flexible and customizable PhD program. Our qualifying exams usually happen in the second (G2) year, and consist of the following parts:
Three committee members, in addition to your advisor, one of them (not your advisor) Chair of the committee—all available at the same time, all in the same room (or zoom room). This part was trickier than I expected. The committee does not all have to be from the department, which helps. Connecting with professors I had already had excellent and productive interactions with helped. Asking for broad availability before sending out possible exam times helped. Booking the room well in advance helped (but did not end up being necessary in my case).
A written dissertation research proposal describing the work you plan to do during the rest of your PhD. I have been told that a lot of people end up deviating from the proposal. My proposal consisted entirely of projects I had already started and am committed to finishing. Even so, I am already doing work I could not have even imagined when I wrote my proposal, even though I wrote it something like seven months ago.
Three syllabi of courses you think you are qualified to teach, on varying topics and of varying levels. This is open ended and different from what I usually do and (I think) a lot of fun.
An oral exam, up to three hours long, consisting of two parts. First, you present and answer questions about your work. This part is (I think) a lot of fun. Then, the committee asks you questions, guided but not constrained by your syllabi, to find the depth (or shallowness) of your knowledge. This part is (I think) a lot harder and less fun.
I passed my quals in the spring, during my G3 year, on Monday, April 13th (like Friday the 13th but worse, because it’s a Monday). We’re required to pass sometime during the G3 year, so I just slipped under the radar. (I had also scheduled a back-up time a few weeks later in case I failed, but I did not end up needing it (!!!!).) April 13th was at the very end of the very start of the pandemic in the United States—my quals were virtual, over zoom. I had originally timed the exam to be right before my mom’s birthday and just after my dad’s and brother’s birthdays, and planned to go home to Pennsylvania right after, hopefully accomplished and with a weight off my shoulders and with full focus on family. Of course that did not happen, and I haven’t seen my family since spring break in March. Instead, I got back from my own birthday with my family over spring break in Florida to a lockdown, thinking it was temporary, and focused fully on quals prep.
I wrote my dissertation research proposal first, with three chapters covering my three in-progress projects (and one tiny transition chapter-ish section covering a relevant smaller completed project). These wound up being 1,970+510+2,245+2,628 = 7,353 words not including references and took a lot longer than I expected, largely because the writing required a lot of reading. I then compiled my syllabi. I got carried away and added far too many papers; I ended up (by request of my committee) sending another version with key papers highlighted. This sequence of events was bad, because it allowed early tasks to steal preparation time from later tasks; it was also good, because it allowed me to work on just one thing at a time, which (I think) I am better at than I am at multitasking. I give a lot of presentations at work, so my slide deck covering my research was largely already ready—which meant that in the weeks leading up to my exam I was able to focus almost entirely on reading the papers on my syllabus.
The exam itself was fine. I took it sitting on the floor between the couch and the coffee table in our living room, with my computer on the coffee table and cups and cups of water and coffee just offscreen on the floor next to me. I was very nervous leading up to the exam and didn’t sleep, which was a mistake. My presentation of my research was excellent, I think, though (not surprisingly) I was not able to get to everything I wanted to talk about and we exceeded the allotted time. The oral exam was a weaker point. I did not know the papers on my syllabus well enough to answer pointed questions about the material anywhere near as well as I would like, even though I had read every paper. I was very nervous, and made some embarrassingly dumb mistakes. In retrospect, for both the presentation and the syllabi, it would have been better to give myself less material—to go deeper into the material on the syllabi and to go less deep into my own work, at least for the presentation (not the written proposal).
When I entered the time crunch of the last few weeks left I put together a spreadsheet tracking my progress and timing of remaining work. (You update the count of papers you’ve read in the “done” columns and everything else fills in automatically.) I make a spreadsheet like this one every time I have some work to do that is both time pressured and easily quantified, which is rarely the case in grad school (except for quals prep) but was usually the case in undergrad. I started making these kinds of spreadsheets a few weeks into freshman year; my friend Mika taught me pretty much immediately after we both arrived on campus. It is motivating and reassuring and probably also a method of procrastinating. I’ve attached a version of my spreadsheet below, with Halloween set as the deadline, in case you would like to go nuts in the way I particularly like to go nuts and use it as a template or inspiration:
All in all I spent about exactly a month on full-time/overtime quals prep (pretty much quals prep and sleeping (probably not enough sleeping) and very little else) from the middle of March to the middle of April. I think it was good for me to constrain this chapter of the unending project of self-improvement and mind expansion—but if I could go back in time, I would have started compiling my syllabi and reading the papers on my syllabi during the first year of my PhD. Some of the texts on my syllabi are material I read and learned at the start of my PhD, but because I chose to also include a lot of material I wanted to know well but didn’t, there was a lot for me to read leading up to the exam and I am not satisfied with how well I absorbed some of it. Reading just one or two papers a week spread out over a year would have probably resulted in far better retention and learning, and would have allowed me to dedicate more time to getting everything I could from each paper. At the time I was intimidated by the process of putting together my syllabi, but I didn’t need to be. Organizing my favorites of the papers I was already reading into vague themes would have been a good enough start to later retrofit to the desired format.
I have been told that some students dedicate an entire semester to preparing for quals. I don’t think I would like to do that (and if the pandemic hadn’t paused my primary project I probably would have continued to try to multitask and continue working on research—which probably would have ended badly for my qualifying exam, though who knows), but focusing entirely on reading and writing for a stretch of time was very productive for me.
I learned a lot, both about my current projects while preparing my dissertation research proposal and about what kinds of work and tools are available to me in the field more broadly while preparing my syllabi. As I expected, having to write out the current and future directions of my current projects and having to read deeply enough to write every sentence with full truth and confidence forced me to gain a much, much better understanding of my own work and of the adjacent literature. What surprised me was that when I returned to my research after my qualifying exam, I returned with a lot of clarity of a sort I hadn’t had before. I knew where I was and where I was going in my current projects. I also found myself coming up with exciting new project ideas at a rate and of a quality (if I may say so myself) I hadn’t expected from myself at this stage of my career; quals definitely caused a leap in my ability to think like a scientist.
The document itself is also helpful as a compilation—I rather frequently refer back to my project proposals, my syllabi, and especially the references at the end of each project proposal. My strategy in undergrad and at the start of grad school was to do the science first, then write only when the science was done. Now I am trying something new and writing the paper as I go, and I find that so far it has made the work far more focused, informed, and efficient, and has give me a way to identify (and hopefully fix) problems and gaps in my work well before I try to build anything on them.
To sum up, here is my advice to anyone getting ready to prepare for their qualifying exam:
Start identifying and reading papers for the exam well in advance, even before you actually start officially preparing for the exam—a little at a time. Amortize as much as you can of the paper reading part of the work.
For every paper you read, put together a few sentences summarizing the key takeaways from the paper. Review your list of papers and summaries in the days leading up to the exam.
I found quals to be a great opportunity to learn things I did not know but wanted to know. You can fill your syllabi with material you know well, material you want to learn, or a mix. Consider what you want to get out of the experience and plan from there.
When scheduling the test, first ask your committee for broad swaths of time (weeks or months) that are or aren’t good and for any recurring commitments when they are always busy. Then send out a poll with specific test time options. I initially sent out a poll with five timeslots, and then when none of those worked I sent out another poll with ten additional timeslots. I had access to two of my four committee members’ calendars, which helped. I also found it helpful to allow committee members to give each time slot a score from 1 to 5 (5—extremely convenient, 3—I can make it work, 1—doesn’t work for me) rather than just saying yes/no/maybe, which made it easier to work with potential scheduling conflicts. Here is what my first scheduling form looked like:
Send out and ask your committee to reserve time for not one, but two three-hour timeslots for your exam, several weeks apart. This way, it won’t be as hard to reschedule your test on short notice if someone has an emergency or a conference or an unexpected vacation or speaking opportunity. And if you fail your test you have another one already lined up with time to prepare for it.
Don’t worry about fitting everything into your presentation. If you’re anything like me, you should make the presentation itself shorter than you think it should be—if you have more slides, then you can have plenty of hidden slides ready in case they come up in questions and discussion.
There will be questions you don’t know the answer to. Hopefully you are able to answer the shallower, easier questions before reaching something you do not know.
Have a nice, efficient stress-relief activity that doesn’t hook you into spending a lot of time on it. I almost never played video games until studying for my quals and for some reason occasionally playing Animal Crossing elevated rather than decreased my productivity, which is not something I would ever have expected.
Get plenty of sleep the nights leading up to the exam itself.
What follows is my three syllabi:
Evolutionary Perspectives on Human Disease, which is meant to be an introduction to the immune system as it appears throughout life (in humans, in animals more broadly, in plants, and in bacteria), a not very deep look at disease (infectious and otherwise) across life, and interactions between and co-evolution of infectious agents and their hosts, especially when the hosts are human (but also, briefly, when the hosts are bacteria), culminating in the evolution of the placenta.
Microbial Inhabitants and Infectious Agents of the Human Body, which is a sweeping view of past outbreaks and epidemics, culminating in the current COVID-19 pandemic, as well as short visit to some of the microbes that we more happily coexist with.
Introduction to Data Analysis Methods for Biological Inference, which covers everything from experimental design and statistical tests to multivariate models to GWAS and PCA to how sequencing works and metagenomic sequencing and genome assembly and phylogenetic trees, culminating in an exploration of how genomic sequencing can be used to track and react to infectious disease outbreaks (which is one of the things that I work on).
I tried to design the syllabi as if I were actually teaching these courses—and I would actually be very excited to teach them. They encompass, I think, most of what I know that is most relevant to my research, including a lot of things that I did not know until I put these syllabi together, found gaps in my knowledge that I was not satisfied with, and filled them. (I would also like to teach creative writing, but alas.)
You might notice that the readings include both actual papers and science journalism, in some cases science journalism about papers that are also included. (This actually came up as a question during my exam!) Including both was a very intentional choice: science journalism—specifically, Popular Science and then MIT Technology Review—was the first context in which I read about and got excited about research. I still get most of my science news from popular science journalism, especially in fields that I am curious about but am not doing research in. My hope, if I were actually teaching these courses, is that offering both research articles and popular science would
allow students who are just starting to learn about infectious disease to engage in the class, hopefully leading to increasing comfort and a transition to the primary literature as the semester goes on,
give students who are confused about or lost in a paper a way to get untangled (and teach students to seek out ways to get untangled), and
show students some of the many different ways of writing about science, and show them good (and possibly bad) examples of how to communicate both with their peers and with a broader audience.
You might also notice that I put these syllabi together in March—some of the work on COVID-19 is already out of date.
As an Amazon Associate I earn from qualifying purchases. The next few paragraphs of this blog post includes links with my Amazon referral code. If you click one and buy something, I get up to 4% of the price as commission. You don’t have to buy these books from Amazon—you can support local bookshops by buying books from Bookshop.org, or you can buy them used and donate them to or start or build a little lending library in your neighborhood, or you can not buy anything at all. You can also support me by buying merch of my art, by buying me a campground store decaf coffee, or by simply reading and enjoying. Thank you!
There are two books I reference a lot, because I like them a lot, that I highly recommend—
Regression and Other Stories (Analytical Methods for Social Research) by Andrew Gelman, Jennifer Hill, and Aki Vehtari:
We used Regression and Other Stories in OEB 201 (Introduction to experimental design and model building for ecologists and evolutionary biologists) with Professor Lizzie Wolkovich my first semester of my PhD. The class and the textbook were both extremely useful and enjoyable—definitely one of my most efficient and relevant learning experiences. Our version of the textbook was an earlier draft, spiral bound, years before it came out—we got to read it early and we got to contribute feedback that went into the final version, which I thought was a fun and special experience and a neat way to feel connected to a work that I greatly enjoyed reading. My copy is very, very dog-eared and highlighted and covered in notes and thoughts in every margin. I refer to it often whenever I need to do any modeling or think about experimental design.
Zoobiquity: The Astonishing Connection Between Human and Animal Health by Barbara Natterson-Horowitz and Kathryn Bowers:
Zoobiquity completely changed the way I think about the human experience and broadened my view of human disease—which was extremely valuable because human disease is the focus of my work. I got to be a Teaching Fellow a few years ago for three sections of HEB 1328 (Evolutionary Medicine: Comparative Perspectives on Medical, Surgical and Psychiatric Illness) with Professor Barbara Natterson-Horowitz. The lectures largely followed the book, which is nice because it means you can get a good part of the learning by reading it.
Evolutionary Perspectives on Human Disease
Immune systems, infection, and inherited disease across life.
This is a lecture-based class introducing the human immune system from a comparative perspective, along with some of the diseases our immune systems help us fight or can cause. We will learn about immune systems across life, in bacteria, plants, humans, and non-human animals—and how comparing immune systems allows us to better understand zoonotic transmission of disease. We will then look at some examples of infectious disease and inherited disease in animals and plants, and how animal parallels of human disease have helped us solve our own, human mysteries and make strides in medicine. Finally, we will look at how pathogens and their hosts impact each other’s evolution, and how human evolution has been impacted by disease.
We will meet on Tuesdays and Thursdays. Every week, you are responsible for reading your choice of two of the other listed texts closely enough to be an expert, and emailing me one generous tweet-length response to each text that you choose (≤250 words each). For the last 15 minutes of each lecture, I will display two responses on the projector and we will discuss them as a class. Highlighted texts are strongly recommended.
In lieu of a final exam, you will choose your favorite of your peers’ “tweets” that we discussed in class (not your own) and use it as a jumping-off point to write a 1,000- to 2,000-word response drawing from the texts and from class discussion.
By the end of this course, you will have a broad understanding of immune systems and disease across life, and (hopefully) the value of knowing it all.
The Immune System
Week 1: The Human Immune System
“Understanding the Immune System: How It Works,” published by the NIH in 2003 [link]
“The immune system,” published in Essays in Biochemistry in 2016 [link]
“Overview of the human immune response,” published in The Journal of Allergy and Clinical Immunology in 2006 [link]
Week 2: Bacterial Immune Systems
“The Origin of the Bacterial Immune Response,” Chapter 1 of Self and Nonself, 2012 [link]
“Systematic discovery of antiphage defense systems in the microbial pangenome,” published in Science in 2018 [link]
“Temperate Bacterial Viruses as Double-Edged Swords in Bacterial Warfare,” published in PLOS ONE in 2013 [link]
“Viruses Have Their Own Version of CRISPR,” published in The Atlantic in 2016 [link]
Week 3: Plant Immune Systems
“The plant immune system,” published in Nature in 2016 [link]
“Origin and evolution of the plant immune system,” published in New Phytologist in 2019 [link]
Week 4: Animal Immune Systems and Evolution
“Comparative Immune Systems in Animals,” published in Annual Review of Animal Biosciences in 2014 [link]
“Origin and Evolution of Adaptive Immunity,” published in Annual Review of Animal Biosciences in 2014 [link]
“Evolution of Immune Systems From Viruses and Transposable Elements,” published in Frontiers in Microbiology in 2019 [link]
Week 5: Vector Immune Systems and Zoonotic Transmission
“The Immune Responses of the Animal Hosts of West Nile Virus: A Comparison of Insects, Birds, and Mammals,” published in Frontiers in Cellular and Infection Microbiology in 2018 [link]
“Mosquito Vectors and the Globalization of Plasmodium falciparum Malaria,” published in Annual Review of Genetics in 2016 [link]
“Host phylogenetic distance drives trends in virus virulence and transmissibility across the animal-human interface,” published in Philosophical Transactions of the Royal Society B: Biological Sciences in 2019 [link]
“Surprise! British Red Squirrels Carry Leprosy,” published in The Atlantic in 2016 [link]
“Is It Possible to Predict the Next Pandemic?” published in The Atlantic in 2017 [link]
Week 6: Bats as Disease Vector
“Why Are Bats’ Immune Systems Totally Different From Any Other Mammal’s?” published in Popular Science in 2015 [link]
“Bats’ immune defenses may be why their viruses can be so deadly to people,” published in Science News in February 2020 [link]
“Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence,” published in eLife in 2019 [link]
“Dampened NLRP3-mediated inflammation in bats and implications for a special viral reservoir host,” published in Nature Microbiology in 2019 [link]
Infectious Disease Across Life
Week 7: Infectious Disease Across Life
“The Koala and the Clap: The Hidden Power of Infection,” Chapter 10 of Zoobiquity
“Plant and pathogen warfare under changing climate conditions,” published in Current Biology in 2018 [link]
“How Viruses Cooperate to Defeat CRISPR,” published in The Atlantic in 2018 [link]
“The Viruses That Eavesdrop on Their Hosts,” published in The Atlantic in 2018 [link]
Week 8: Extinctions and Mass Mortality Events
“Recent shifts in the occurrence, cause, and magnitude of animal mass mortality events,” published in PNAS in 2015 [link]
“A Starfish-Killing Disease Is Remaking the Oceans,” published in The Atlantic in 2019 [link]
“Why Did Two-Thirds of These Weird Antelope Suddenly Drop Dead?,” published in The Atlantic in 2018 [link]
“What We Can Learn From the Near-Death of the Banana,” published in Time Magazine in 2019 [link]
The Chytrid Fungus:
“Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity,” published in Science in 2019 [link]
“The Worst Disease Ever Recorded,” published in The Atlantic in 2019 [link]
“The Cascading Consequences of the Worst Disease Ever,” published in The Atlantic in February 2020 [link]
Inherited Disease Across Life
Week 9: Inherited Disease Across Life
Heart Disease:
“The Feint of Heart: Why We Pass Out,” Chapter 2 of Zoobiquity
“Scared to Death: Heart Attacks in the Wild,” Chapter 6 of Zoobiquity
Mental Health:
“Grooming Gone Wild: Pain, Pleasure, and the Origins of Self-Injury,” Chapter 8 of Zoobiquity
“Fear of Feeding: Eating Disorders in the Animal Kingdom,” Chapter 9 of Zoobiquity
“A Landmark Study on the Origins of Alcoholism,” published in The Atlantic in 2018 [link]
Cancer:
“Jews, Jaguars, and Jurassic Cancer: New Hope for an Ancient Diagnosis,” Chapter 3 of Zoobiquity
“Elephants Have a Secret Weapon Against Cancer,” published in The Atlantic in 2018 [link]
Diabetes:
“The Blind Fish That Should Have Diabetes, But Somehow Doesn’t,” published in The Atlantic in 2018 [link]
Week 10: Allergy and Autoimmune Diseases
Allergies:
“Comparative Immunology of Allergic Responses,” published in Annual Reviews in 2015 [link]
“Early life factors that affect allergy development,” published in Nature Reviews Immunology in 2017 [link]
“Pet-keeping in early life reduces the risk of allergy in a dose-dependent fashion,” published in PLOS ONE in 2018 [link]
“Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity,” published in PLOS Computational Biology in 2015 [link]
“Interactions between helminth parasites and allergy,” published in Current Opinion in Allergy and Clinical Immunology in 2009 [link]
Autoimmunity:
“Human autoimmune diseases: a comprehensive update,” published in The Journal of Internal Medicine in 2015 [link]
“Thymic tolerance as a key brake on autoimmunity,” published in Nature Immunology in 2018 [link]
“Regulatory T cells in autoimmune disease,” published in Nature Immunology in 2018 [link]
“Narcolepsy confirmed as autoimmune disease,” published in Nature News in 2013 [link]
Co-Evolution of the Human Immune System and Infectious Agents
Week 11: Co-Evolution of Microbial Pathogens and Their Hosts
“Rapid evolution of microbe-mediated protection against pathogens in a worm host,” published in The International Society for Microbial Ecology Journal in 2016 [link]
“The evolution of the host microbiome as an ecosystem on a leash,” published in Nature in 2017 [link]
“Harnessing the Power of Defensive Microbes: Evolutionary Implications in Nature and Disease Control,” published in PLOS Pathogens in 2016 [link]
“Some Microbes Have Been With Us Since Before We Existed,” published in The Atlantic in 2017 [links]
Relationships Between Bacteriophages, Bacteria, and the Human Immune System:
“Virus tricks the immune system into ignoring bacterial infections,” Nature News in 2019 [link]
“Bacteriophage trigger antiviral immunity and prevent clearance of bacterial infection,” published in Science in 2019 [link]
“We Might Absorb Billions of Viruses Every Day,” published in The Atlantic in 2017 [link]
Week 12: Human Evolution and Disease
“Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution,” published in PLOS Genetics in 2011 [link]
“Natural selection contributed to immunological differences between hunter-gatherers and agriculturalists,” published in Nature Ecology and Evolution in 2019 [link]
“How Viruses Infiltrated Our DNA and Supercharged Our Immune System,” published in The Atlantic in 2016 [link]
“Migrating microbes: what pathogens can tell us about population movements and human evolution,” published in Annals of Human Biology in 2017 [link]
Plasmodium falciparum and Sickle Cell:
“How Malaria Has Affected the Human Genome and What Human Genetics Can Teach Us about Malaria,” published in The American Journal of Human Genetics in 2005 [link]
“Sickle-cell mystery solved,” Nature News in 2011 [link]
“Hemoglobins S and C Interfere with Actin Remodeling in Plasmodium falciparum–Infected Erythrocytes,” published in Science in 2011 [link]
The Evolution of the Placenta:
“The Viruses That Made Us Human,” published by PBS in 2016 [link]
“Retroviruses and the Placenta,” published in Current Biology in 2012 [link]
“The placenta goes viral: Retroviruses control gene expression in pregnancy,” published in PLOS Biology in 2018 [link]
Microbial Inhabitants and Infectious Agents of the Human Body
Overview of common viruses, bacteria, and eukaryotes, pathogenic and not, and a history of disease outbreaks.
This class is an introduction to our neighbors in the human body: common viruses, bacteria, and eukaryotes—helpful, neutral, pathogen, or some combination of the three—that we share our bodies and our lives with, and which have profound impacts on both.
At the end of this course, you should have a broad understanding of the kinds of microbes that live in the human body and how they affect our health. You should also have a perspective and opinion on disease outbreaks throughout history, and the lessons we have hopefully learned from them. Finally, you should be able to critically read primary literature and use it to contribute to the broad conversation about human health in both speech and writing.
We meet on Mondays and Wednesdays. On Mondays, this is a lecture class, covering the texts and the topics listed below. On Wednesdays, this is a fast-paced discussion-based class. Every Wednesday meeting starts with a prescribed question, then progresses to your questions, switching topics at any ≥30-second lull in conversation.
The first week, I would like you to read all five papers. Every week after, you are responsible for reading at least two of the provided texts closely enough to be an expert, and for skimming or lightly reading at least three of the others to whatever extent is necessary for you to be able to respond to arguments and carry on intelligent conversation. In both cases, you are expected to go beyond what we cover in the Monday lecture. Come to class on Wednesday with at least three unique and interesting questions about the text(s) you choose to focus on or their implications to discuss with your colleagues. Highlighted texts are strongly recommended.
This class is a safe space. Please feel welcome to share your questions, thoughts, and opinions, even ones that seem “dumb” or “wrong.” We will work through them with empathy together as a class. To enable this atmosphere, please approach debate and discussion with empathy and enthusiasm, and remember that we are growing together and through each other. One of my favorite professors in undergrad started the semester distinguishing uncomfortable and unsafe. Fruitful discussion and growth can, at times, feel uncomfortable. If at any point this class makes you feel unsafe, let me know.
In lieu of a final exam, you will choose your favorite question proposed by a classmate (not by me and not by you) and write a 500- to 1500-word response to it drawn from the text and from class discussion. I will compile all responses into one anonymized document, and you will choose at least three classmates’ thoughts to respond to in generous tweet-length (≤250 words).
We include both scientific papers and publications from other media. I hope that every week, we will have a balance of experts in all texts in all formats, and that we start every new week more knowledgable and thoughtful than we were the week before.
Introduction
Week 1: A Bird’s-Eye View
“Introduction to Pathogens,” from Molecular Biology of the Cell, published in 2002 [link]
“Cell Biology of Infection,” from Molecular Biology of the Cell, published in 2002 [link]
“Visualizing the History of Pandemics,” published in Visual Capitalist on March 14, 2020 [link]
“The Microbiome and Human Biology,” published in Annual Review of Genomics and Human Genetics in 2017 [link]
“Highlights from studies on the gut microbiome,” published in Nature Outlook in January 2020 [link]
Neutral or Helpful Inhabitants
Week 2: The Microbiome, and Occasionally Helpful Parasites
The Microbiome:
“Man and the Microbiome: A New Theory of Everything?” published in Annual Review of Clinical Psychology in 2019 [link]
“No Vacancy: How beneficial microbes cooperate with immunity to provide colonization resistance to pathogens,” published in The Journal of Immunology in 2015 [link]
“When Poop Becomes Medicine,” published in The Atlantic in 2018 [link]
“A Probiotic Skin Cream Made With a Person’s Own Microbes,” published in The Atlantic in 2017 [link]
“The Hottest New Cancer Drugs Depend on Gut Microbes,” published in The Atlantic in 2015 [link]
“How Bacteria Could Protect Tumors From Anticancer Drugs,” published in The Atlantic in 2017 [link]
“A Tiny Tweak to Gut Bacteria Can Extend an Animal’s Life,” published in The Atlantic in 2017 [link]
Parasites:
“Friendly foes: The evolution of host protection by a parasite,” published in Evolution Letters in 2017 [link]
“Parasites inside your body could be protecting you from disease,” published in The Conversation [link]
“Helminth infection, fecundity, and age of first pregnancy in women,” published in Science in 2015 [link]
Week 3: GB Virus C, a Helpful Virus
“GB virus C: the good boy virus?” published in Trends in Microbiology in 2012 [link]
“Effect of early and late GB virus C viraemia on survival of HIV-infected individuals: a meta-analysis,” published in HIV Medicine in 2006 [link]
“GBV-C/HIV-1 coinfection is associated with low HIV-1 viral load and high CD4+ T lymphocyte count,” published in Archives of Virology in 2017 [link]
“Pegivirus avoids immune recognition but does not attenuate acute-phase disease in a macaque model of HIV infection,” published in PLOS Pathogens in 2017 [link]
“Fighting the Public Health Burden of AIDS With the Human Pegivirus,” published in American Journal of Epidemiology in May 2019 [link]
“GB Virus C Coinfections in West African Ebola Patients,” published in Journal of Virology in 2015 [link]
Harmful Inhabitants
Week 4: The Common Cold and Influenza (and why they won’t go away)
The Common Cold:
“Rhinoviruses,” Chapter 238 of Principles and Practice of Pediatric Infectious Diseases, 2018 [link]
“Human Coronaviruses,” Chapter 222 of Principles and Practice of Pediatric Infectious Diseases, 2018 [link]
“Adenoviruses,” Chapter 210 of Principles and Practice of Pediatric Infectious Diseases, 2018 [link]
“The Economic Burden of Non–Influenza-Related Viral Respiratory Tract Infection in the United States,” published in Archives of Internal Medicine in 2013 [link]
“Why Haven’t We Cured the Common Cold Yet?” published in Scientific American in 2018 [link]
Curing the Common Cold:
“Scientists think the common cold may at last be beatable,” published in STAT in 2016 [link]
“A polyvalent inactivated rhinovirus vaccine is broadly immunogenic in rhesus macaques,” published in Nature Communications in 2016 [link]
“Scientists close in on a cure for the common cold,” published in Stanford Medicine Scope in 2019 [link]
“Enterovirus pathogenesis requires the host methyltransferase SETD3,” published in Nature Microbiology in 2019 [link]
Influenza:
“Influenza Viruses,” Chapter 229 of Principles and Practice of Pediatric Infectious Diseases, 2018 [link]
“Plague genome: The Black Death decoded,” Nature News 2011 [link]
“Yersinia pestis and the plague of Justinian 541-543 AD: a genomic analysis,” published in 2014 [link]
“A draft genome of Yersinia pestis from victims of the Black Death,” published in Nature in 2011 [link]
Smallpox:
“A time transect of exomes from a Native American population before and after European contact,” published in Nature in 2016 [link]
“How Europeans brought sickness to the New World,” Science News 2015 [link]
Typhoid Mary:
“Mary Mallon (1869-1938) and the history of typhoid fever,” published in the Annals of Gastroenterology in 2013 [link]
“Typhoid Mary’s tragic tale exposed the health impacts of ‘super-spreaders’,” published in National Geographic in March 2020 [link]
“A Life in Pursuit of Health,” about Josephine Baker, published in The New York Times in 2013 [link]
And a Few Other Superspreaders:
“Extensive Transmission of Mycobacterium tuberculosis from a Child,” published in The New England Journal of Medicine in 1999 [link]
“Party Zero: How a Soirée in Connecticut Became a ‘Super Spreader,’” published in The New York Times on March 23, 2020 [link]
Week 6: Plasmodium/Malaria
“Plasmodium Species (Malaria),” Chapter 271 of Principles and Practice of Pediatric Infectious Diseases, 2018 [link]
“About Malaria,” CDC, especially “FAQs” [link], “Disease” [link], “Biology” [link], “Where Malaria Occurs” [link], and “Malaria’s Impact Worldwide” [link]
“The History of Malaria, an Ancient Disease,” by the CDC [link]
“Greater political commitment needed to eliminate malaria,” published in Infectious Diseases of Poverty in 2019 [link]
“Malaria Genomics in the Era of Eradication,” published in Cold Spring Harbor Perspectives in Medicine in 2017 [link]
How Malaria Spread to Humans and Around the World:
“Resurrection of the ancestral RH5 invasion ligand provides a molecular explanation for the origin of P. falciparum malaria in humans,” published in PLOS Biology in 2019 [link]
“Human migration and the spread of malaria parasites to the New World,” published in Nature in 2018 [link]
Acquired Immunity:
“Quantification of anti-parasite and anti-disease immunity to malaria as a function of age and exposure,” published in eLife in 2018 [link]
“Malaria: Age, exposure and immunity,” in eLife as an Insight, 2018 [link]
“Host-mediated selection impacts the diversity of Plasmodium falciparum antigens within infections,” published in Nature Communications in 2018 [link]
Week 7: Hepatitis A
“Hepatitis A Virus,” Chapter 237 of Principles and Practice of Pediatric Infectious Diseases, 2018 [link]
“Widespread outbreaks of hepatitis A across the United States,” CDC, March 2020 [link]
“Increase in Hepatitis A Virus Infections – United States, 2013-2018,” CDC, 2019 [link]
“Summary of reported hepatitis A cases linked to person-to-person outbreak, Massachusetts, April 1, 2018-March 6, 2020,” MA DPH [link]
“Forgotten but Not Gone: Learning From the Hepatitis A Outbreak and Public Health Response in San Diego,” published in Topics in Antiviral Medicine in 2019 [link]
“Molecular Genotyping of Hepatitis A Virus, California, USA, 2017–2018,” published in Emerging Infectious Diseases in 2019 [link]
“Emergence of Hepatitis A Virus Genotype IIIA during an Unprecedented Outbreak in New Hampshire, 2018-2019,” unpublished
Bathroom Access:
“An outbreak waiting to happen: Hepatitis A marches through San Diego’s homeless community,” published in STAT in 2017 [link]
“After crackdown on tent city, homeless recount Hepatitis horror stories,” published in the San Diego Union-Tribune in 2017 [link]
“Hepatitis A outbreak sparks call for L.A. to give homeless people more street toilets,” published in The Los Angeles Times in 2017 [link]
“The Politics of Going to the Bathroom,” published in The Nation in 2019 [link]
Herd Immunity and Co-Infections:
“Notes from the Field: Acute Hepatitis A Virus Infection Among Previously Vaccinated Persons with HIV Infection – Tennessee, 2018,” CDC, 2019 [link]
“Herd Immunity Likely Protected the Men Who Have Sex With Men in the Recent Hepatitis A Outbreak in San Diego, California,” published in Clinical Infectious Diseases in 2019 [link]
Week 8: HIV/AIDS
The Virus:
“Introduction to Retroviridae” Chapter 231 [link] and “Human Immunodeficiency Virus” Chapter 233 [link] of Principles and Practice of Pediatric Infectious Diseases, 2018
History:
“HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations,” published in Science in 2014 [link]
“Origins of HIV and the AIDS Pandemic,” published in Cold Spring Harbor Perspectives in Medicine in 2011 [link]
“Response to the AIDS Pandemic—A Global Health Model,” published in The New England Journal of Medicine in 2013 [link]
“The Reagan Administration’s Unearthed Response to the AIDS Crisis is Chilling,” published in Vanity Fair in 2015 [link]
“How the Media, the White House, and Everyone Else Failed AIDS Victims in the 80s,” published in VICE in 2016 [link]
“Long-term survivors of HIV/AIDS reflect on what they’ve witnessed and endured,” published on PBS in February 2020 [link]
HIV/AIDS today:
“Today’s HIV/AIDS Epidemic,” CDC Fact Sheet published in 2016 [link]
“Ending AIDS? These three places show the epidemic is far from over,” published in Science News in 2018 [link]
Curing HIV:
“Loss and Recovery of Genetic Diversity in Adapting Populations of HIV,” published in PLOS Genetics in 2014 [link]
“Second person cured of HIV is still free of active virus two years on,” in CNN on March 11, 2020 [link]
“Evidence for HIV-1 cure after CCR5Δ32/Δ32 allogeneic haemopoietic stem-cell transplantation 30 months post analytical treatment interruption: a case report,” published in The Lancet on March 10, 2020 [link]
“Sequential LASER ART and CRISPR Treatments Eliminate HIV-1 in a Subset of Infected Humanized Mice,” published in Nature Communications in 2019 [link]
Week 9: Viral Hemorrhagic Fevers: Ebola and Lassa
“Filoviruses and Arenaviruses,” Chapter 230 of Principles and Practice of Pediatric Infectious Diseases, 2018 [link]
Lessons from sequencing Ebola and Lassa:
“An Outbreak of Ebola Virus Disease in the Lassa Fever Zone,” published in The Journal of Infectious Diseases in 2016 [link]
“Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus,” published in Cell in 2015 [link]
“Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak,” published in Science in 2014 [link]
“Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone,” published in Cell in 2015 [link]
“Ebola Virus Epidemiology and Evolution in Nigeria,” published in The Journal of Infectious Diseases in 2016 [link]
“Temporal and spatial analysis of the 2014–2015 Ebola virus outbreak in West Africa,” published in Nature in 2015 [link]
“Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases,” published in Virus Evolution in 2016 [link]
“The evolution of Ebola virus: Insights from the 2013–2016 epidemic,” published in Nature in 2016 [link]
Ebola adaptations to host:
“Virus genomes reveal factors that spread and sustained the Ebola epidemic,” published in Nature in 2017 [link]
“Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic,” published in Cell in 2016 [link]
Week 10: Genomic Epidemiology and Modern Outbreak Response
“Tracking virus outbreaks in the twenty-first century,” published in Nature Microbiology in January 2020 [link]
“Precision epidemiology for infectious disease control,” published in Nature Medicine in 2019 [link]
“Real-time digital pathogen surveillance — the time is now,” published in Genome Biology in 2015 [link]
Ebola:
“Knowledge of Ebola is the weapon to fight it,” published in The Boston Globe in 2014 [link]
“Roots, Not Parachutes: Research Collaborations Combat Outbreaks,” published in Cell in 2016 [link]
“Lessons from Ebola: Improving infectious disease surveillance to inform outbreak management,” published in Science Translational Medicine in 2015 [link]
Zika and mumps:
“Combining genomics and epidemiology to track mumps virus transmission in the United States,” published in PLoS Biology in February 2020 [link]
“Zika virus evolution and spread in the Americas,” published in Nature in 2017 [link]
“Genomic epidemiology reveals multiple introductions of Zika virus into the United States,” published in Nature in 2017 [link]
Week 11: Difficult Decisions and a Case Study in Progress: Coronavirus Outbreak Response
Genomic research:
“Data Sharing and Open Source Software Help Combat Covid-19,” published in WIRED on March 13, 2020 [link]
“Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China,” published in Cell on March 11, 2020 [link]
“Probable pangolin origin of SARS-CoV-2 associated with the COVID-19 outbreak,” to be published in Cell in March 2020 [link]
“The proximal origin of SARS-CoV-2,” published in Nature Medicine on March 17, 2020 [link]
“Why the Coronavirus Has Been So Successful,” published in The Atlantic on March 20, 2020 [link]
Social measures against disease spread:
“Impact of non-pharmaceutical interventions (NPIs) to reduce COVID19 mortality and healthcare demand,” published by the Imperial College COVID-19 Response Team on March 16, 2020 [link]
“Review of Ferguson et al ‘Impact of non-pharmaceutical interventions…’” published by New England Complex Systems Institute on March 17, 2020 [link]
“The Korean Clusters,” published in Reuters on March 3, 2020 [link]
“The U.K.’s Coronavirus ‘Herd Immunity’ Debacle,” published in The Atlantic on March 16, 2020 [link]
Governmental and organizational outbreak response; economic impact and tradeoffs:
“The 4 Key Reasons the U.S. Is So Behind on Coronavirus Testing,” published in The Atlantic on March 13, 2020 [link]
“You’re Likely to Get the Coronavirus,” published in The Atlantic in February 2020 [link]
“A fiasco in the making? As the coronavirus pandemic takes hold, we are making decisions without reliable data,” published in STAT on March 17, 2020 [link]
The Daily podcast:
“Why the U.S. Wasn’t Ready for the Coronavirus” on March 11, 2020 [link]
“Learning to Live with the Coronavirus” on March 13, 2020 [link]
“Why This Recession Will Be Different” on March 16, 2020 [link]
Week 12: Disease Surveillance in the Age of Surveillance
Influenza:
“nextflu: real-time tracking of seasonal influenza virus evolution in humans,” published in Bioinformatics in 2015 [link]
“Flu Near You: Crowdsourced Symptom Reporting Spanning 2 Influenza Seasons,” published in American Journal of Public Health in 2015 [link]
“Comparison of crowd-sourced, electronic health records based, and traditional health-care based influenza-tracking systems at multiple spatial resolutions in the United States of America,” published in BMC Infectious Diseases in 2018 [link]
Coronavirus:
“This is how the CDC is trying to forecast coronavirus’s spread,” published in MIT Technology Review on March 13, 2020 [link]
“We’re not going back to normal,” published in MIT Technology Review on March 17, 2020 [link]
“Singapore is the model for how to handle the coronavirus,” published in MIT Technology Review on March 12, 2020 [link]
“To Track Coronavirus, Israel Moves to Tap Secret Trove of Cellphone Data,” published in The New York Times on March 16, 2020 [link]
Introduction to Data Analysis Methods for Biological Inference
Seminar on experimental design, modeling, working with multiple variables, wrangling messy data, genomic sequencing, and popular techniques and tools in computational biology.
This class is an introduction to some of the tools of computational biology. We will look at statistical tests and learn how to disentangle the effects of multiple variables. We will learn how to do genome-wide association studies and principal component analysis. We will learn about how genomic sequencing works, and look at how it can be used for diagnosis or discovery of novel organisms. Finally, we will learn how to use genomic sequencing to trace disease transmission. By the end of this course, you should have the tools you need to analyze your own or publicly available data.
We meet on Tuesdays and Fridays. Tuesdays are lectures on the topics and texts listed. Highlighted texts are strongly recommended. On Fridays, we meet for an extended workshop to apply the week’s tools to publicly available data or to data that you bring with you to class (except in Week 7, when we will generate new sequence data). Before every Friday, you are responsible for writing a short proposal for the week, including what dataset you plan to analyze, what tools you plan to use for what analyses, and any hypotheses you have (≤500 words). At the end of the semester, you will choose whichever workshop was most inserting or successful for you to extend into a short final project, which you can work on alone or in a group. On the last Friday of class we will go around the room and briefly summarize our analyses and findings in an informal setting over snacks.
Week 1: Experimental Design, Statistical Tests, Data Visualization
Experimental Design:
“Experimental Design,” Chapter 7 of MIT’s 6.S085 Statistics for Research Projects course notes [link]
Statistical Tests, from the Handbook of Biological Statistics, 2014:
“Visualization of multiple alignments, phylogenies and gene family evolution,” published in Nature Methods in 2010 [link]
Notes on P-Values:
“The fickle P value generates irreproducible results,” published in Nature Methods in 2015 [link]
“Aligning statistical and scientific reasoning,” published in Science in 2016 [link]
“Measurement error and the replication crisis,” published in Science in 2017 [link]
Week 2: Modeling the Effects of a Single or Multiple Variables: Part I
Regression and Other Stories (to be published in 2020):
Chapter 5: “Background on regression modeling”
Chapter 6: “Linear regression with a single predictor”
Chapter 8: “Linear regression with multiple predictors”
Chapter 9: “Transformations and model building”
Week 3: Modeling the Effects of a Single or Multiple Variables: Part II
Regression and Other Stories (to be published in 2020):
Chapter 10: “Logistic regression”
Chapter 11: “Generalized linear models”
Chapter 14: “Missing-data imputation”
Chapter 15: “Using, evaluating, and comparing models”
Appendix A: “Six quick tips to improve your regression modeling”
Week 4: Genome-Wide Association Studies, Part I
GWAS in Action:
“10 Years of GWAS Discovery: Biology, Function, and Translation,” published in The American Journal of Human Genetics in 2017 [link]
“Benefits and limitations of genomewide association studies,” published in Nature in 2019 [link]
Understanding and Using GWAS:
“Microarrays – DNA Chips,” 2017 [link] and “DNA Microarray,” 2012 [link]
“PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses,” published in The American Journal of Human Genetics in 2007 [link]
“Methods and Tools in Genome-wide Association Studies,” Chapter 5 of Computational Cell Biology, 2018 [link]
Week 5: Genome-Wide Association Studies, Part II
“Population genetics and GWAS: A primer,” published in PLOS Biology in 2018 [link]
From Principles of Population Genetics, 2007:
Chapter 9.1: “Evolution of Genome Size and Composition”
Chapter 9.2 “Genome-Wide Patterns of Polymorphism”
Chapter 9.3: “Differences Between Species”
Chapter 10.1: “Human Polymorphism”
Chapter 10.2: “Population Genetic Inferences from Human SNPs”
Chapter 2.5: “Linkage and Linkage Disequilibrium”
Chapter 2.6: “Causes of Linkage Disequilibrium”
Chapter 10.3: “Linkage Disequilibrium across the Human Genome”
Chapter 10.7: “Seeking Signatures of Human-Specific Genetic Adaptations”
Week 6: Principal Component Analysis (PCA)
PCA in Action:
“Genes mirror geography within Europe,” published in Nature in 2008 [link]
“Spatial population genomics of the brown rat (Rattus norvegicus) in New York City,” published in Molecular Ecology in 2018 [link]
“Urban rat races: spatial population genomics of brown rats (Rattus norvegicus) compared across multiple cities,” published in Proceedings of the Royal Society B: Biological Sciences in 2018 [link]
Understanding and Using PCA:
“PCA in R Using FactoMineR: Quick Scripts and Videos,” 2017 [link]
“A Step by Step Explanation of Principal Component Analysis,” 2019 [link]
“PCA: A Practical Guide to Principal Component Analysis in R & Python,” 2016 [link]
L. A. K. 