Dr. Stopfer, at last!

On January 26, 2021 I finally defended my thesis dissertation at MIT and earned my PhD! In many ways it was not the day I expected. I expected a full auditorium at the Koch Institute, popping champagne with my lab, dinner with family and friends, and being able to hug all the people that supported me on this journey. 

Because of COVID 19, my defense was virtual and I presented my slides from my studio apartment. Still, I was lucky that over 150 people could tune in via Zoom and watch my defense live. After the dissertation my labmates (past and present) made the day as special as possible by decorating the lab, giving me a sweet scrapbook of all the photos and stories from my time in the lab, and popping champagne with me from afar. They even made a custom zoom background in honor of my thesis work: hip hip(MHC), hooray! The flooding of congratulations and messages of support from my friends, family, and colleagues made the day so wonderful but bittersweet. 

Dr. Stopfer, at last!

My labmates know me too well! Champagne and a champagne balloon!

Science for Anyone!

I think one small way we can start to improve diversity in STEM and academia, as well as to continue educating the public about science, is to make the “ivory tower” of academia more accessible.

As a result, I made a two minute video explaining the motivation for my recent publication on quantitative immunopeptidomics to better communicate to my family, friends, and beyond the work I have been doing throughout my PhD.

With the lab still shut down for COVID-19, I figured it was time to spend a little time on a passion project. Enjoy!

2019 BE Departmental Retreat

Targeting the targets: 
high density monitoring of signaling pathways in phosphoproteomics

Each year, the Biological Engineering department at MIT holds a retreat primarily for graduate community and faculty. The retreat is comprised of short 10 minute talks from graduate students and post-docs, as well a a keynote speaker, panel, and poster sessions, and a state of the department talk by the graduate leadership.

I remember older students giving talks at the retreat in October of my first year. They seemed so accomplished, so knowledgable. I wondered if I’d ever do anything worthy of sharing… time flies! This year I was selected to speak, and I chose to present a shortened version of the work with Thermo Scientific on targeted tyrosine phosphorylation mass spectrometry methods.

It was challenging to adapt a talk I had crafted for a mass spectrometry technical audience to a general bioengineering audience, with only 7 minutes! I ended up spending very little time on background and methodology, providing the bare minimum information required to motivate the project. Instead I highlighted the story of how the project began, what the results mean in a biological context, and why we are excited by the results.

It was such a privilege to share this work with my talented peers in bioengineering!

Thermo Scientific Mass Spec Users’ Meeting

Real-time, High-density Monitoring of pTyr Signaling Targets in Human Tumors using SureQuant Heavy Peptide Triggered Targeted Quantitation

I was fortunate enough to be able to present our collaborative work using the SureQuant method and the new Exploris 480 Orbitrap Mass Spectrometer at the 2019 Thermo Scientific Mass Spec Users’ Meeting in Somerset, New Jersey.

Presenting at the Palace at Somerset Park, NJ Mass Spec Users’ Meeting

This work leverages the SureQuant internal standard parallel reaction monitoring (IS-PRM) method built into the Exploris. We use SureQuant to selectively monitor 350 unique tyrosine phosphorylation sites to profile the tyrosine phosphorylation signaling networks in 30 human colon cancer samples. This work reveals the unique tyrosine signatures among patients, and suggests targets for therapy by looking for enrichment of tyrosine mediated signaling networks.

SureQuant workflow for IS-PRM tyrosine phosphorylation profiling

The work was presented at the users’ meetings in Cambridge by my advisor, Forest White and by my colleauge Cameron Flower in New York as well. Many thanks to our collaborators at Thermo Scientific, especially Aaron Gajadhar who worked with us on this exciting, cutting edge project, as well as Adreas Huhmer for inviting me to present, and the organizing team of the 2019 Mass Spec Users meetings. What an opportunity to connect with the northeast mass spec community!

2020 Siebel Scholar

This fall, I was among 93 students named a member of the 2020 cohort of Siebel Scholars hailing from the world’s top graduate programs in bioengineering, business, computer science, and energy science. Of the 96, 16 were from MIT, 5 of which were from my department of Bioengineering.

Siebel scholars are honored for their academic achievements, leadership, and commitments to addressing crucial global challenges.

Siebel Scholars each receive an award of $35,000 to cover their final year of study from the Thomas and Stacy Siebel Foundation. In addition, we join a community of more than 1,400 past Siebel Scholars, including about 260 from MIT. I am so grateful to be recognized among such an accomplished group of peers, and look forward to connecting with the community of Siebel Scholars at the upcoming Siebel Scholars Conference, and throughout my career!

MIT news article
Siebel Scholars news article

HUPO 2019, Adelaide

High-density Monitoring of pTyr Signaling Targets in Human Tumors Using Heavy Peptide Triggered 
Targeted Quantitation
Poster presentation at 2019 Hupo in Adelaide

This year, I was asked to present at the 2019 18th Human Proteome Organization World Congress (HUPO) in Adelaide, Australia. I presented alongside Thermo Scientific on using the SureQuant method for targeted monitoring of tyrosine phosphorylation (pTyr) signaling in human colon tumors. This was during a lunch session, so the SureQuant internal standard parallel reaction monitoring (IS-PRM) based method was first introduced along with commercial applications such as the AKT/mTOR targeted kit, along with the new instruments and their advanced capabilities for targeted mass spectrometry. 

I presented on a custom application of the method, targeted 350 unique tyrosine phosphorylation sites with the SureQuant acquisition method. Data driven acquisition (DDA) methods commonly used for quantitative tyrosine phosphorylation analyses in our group suffer from poor run-to-run overlap, therefore using a high accuracy, high reproducible method like SureQuant lets us profile the signaling networks across many samples while minimizing missing values. 

The journey was long (12h + 14h flights), but I had an incredible time. The food was unbelievable, the weather was perfect, and I may or may not have started exploring post-doc opportunities in Australia…!

Australia Travels in Adelaide and Sydney

Evolution of the MIT Grad Blog

The blog helped me regain a voice, and I didn’t want it to end

Understanding what graduate student life is like at MIT is challenging for an outsider. Before I arrived, I had preconceived notions about what the student body would be like: ultra-nerdy kids that participated in hackathons on the weekend and probably couldn’t chug a beer. While admittedly some of these stereotypes are true, I now embody some of them myself (I spent last Friday night checking out a friend’s virtual reality setup instead of hitting up a bar…ha!)

This blog was started in order to provide a window into the real MIT grad life. The objective was to provide prospective students with diverse perspectives on what being an MIT student is really like: the good, the bad, and the ugly. It’s not just shiny lab equipment and high impact publications. It’s a grind. My work with this blog is tangled in my personal and professional challenges. It has been a big part of helping me find my place in grad school, and I’d be remiss to sugarcoat my experience; that’s not the point of the blog. So, here is my story on how this blog came to be, honest and unfiltered.

Over IAP, a period of time in January where MIT students can take a short class of interest, I registered to take a three-day blog writing workshop. The workshop required each student to write two pieces for publication on the new “grad admissions blog” site, an experiment modeled after the popular undergraduate admissions blog. I excitedly signed up in October, dropped out when I’d lost my confidence and energy in November, and hesitantly rejoined in December. Those were some of the hardest months I’ve ever experienced.

I started graduate school as a bold, goofy, and highly opinionated individual. There are many people who will talk about having “imposter syndrome” at MIT, the idea that everyone feels like an imposter that somehow managed to slip through the cracks to get into MIT. I have to admit, I had moments of feeling insecure, but broadly, I felt I deserved to be here. Sure, finding a lab was stressful and the coursework was challenging, but it wasn’t anything I couldn’t handle. Somehow, that changed the summer after my first year. Maybe it was being new in a lab doing things I didn’t know much about— that was intimidating. Perhaps it was getting my scientific ideas rejected. Maybe it was more personal, having someone tell me I was not well liked in my department. That I had a polarizing personality. That I was un-relatable because of where I come from. Most likely, it was a combination, and that led to anxiety, which I am only now starting to get under control.

I guess what I’m saying is that I felt both lost and empty when I started on this blogging adventure. Showing up to the first day felt like the hardest task. I was having trouble even getting out of bed and remembering to eat, so the thought of having deadlines and reading critiques of my writing was terrifying.

When I started writing the first day, I started to feel a little freer. I cracked a few smiles. Was I laughing? My legs felt less heavy as I walked through my day. I stayed up late with a cup of mint tea on my nightstand, writing, editing, and revising my pieces. The blog workshop gave me purpose, a voice, and a platform to express myself during the time I felt the most disoriented. In retrospect, the timing couldn’t have been better. See, I’ve always loved writing, but somewhere along the way, that passion fell out of the moving van as I progressed through my early 20’s. No room for dance, theatre, poetry, or creative writing. My schedule was already full from science, studying, and tailgating Wisconsin football games. But now, here I was, staving off anxiety through my keyboard. When the workshop ended and there was no system in place to continue blogging, I was disappointed. I had so many ideas, but beyond that, I was finding writing to be so therapeutic that I didn’t want it to end.

During a lunch with the former Dean of Engineering, now Vice Chancellor of MIT, the IAP bloggers reflected on the blogging experience and I was excited to learn that others also wanted to keep writing. There was no plan in place to continue the blog, so I drafted a proposal to create an editorial board of students that could continue running the blog autonomously. The Dean approved. Now, six of the original bloggers, including myself, serve on the editorial board. Having this blog as an outlet to express my thoughts and experiences at MIT has been a powerful part of helping me re-stabilize after a difficult period in my life. I always thought the hardest part of grad school would be the science, but I’ve found it to be the opposite. It’s staying sane. It’s finding balance. It’s discovering how you want to spend all the rest of your time (whatever small amount that may be), and making it count.

This blog continues to be an experiment. As an editorial board, we organize workshops, edit pieces, manage and post the blog content, and develop resources to help teach others what makes a compelling blog post. It has been fun to work with fellow creative minds as we turn the grad admissions blog into an autonomous, student-run platform. We learn as we go, but we are proud to help provide diverse perspectives for current and prospective students on all aspects of graduate and MIT life. We hope to add new voices to our roster by hosting another workshop during IAP. If you are interested, keep an eye out for the application in the fall.

*I am no longer an editor of the MIT Graduate Admissions blog, but you can find more information about the blog and upcoming workshops here.

Originally posted on the MIT Graduate Admissions Blog.

MIT News story.

Feature on GLiMPSE Podcast

GLiMPSE is a podcast featuring the science and the people working on it at MIT. In this episode, I talk with founder and producer Alex Albanese about improving the transparency of MIT grad school applications, the engineering genius of Laos rice paddies, and the pressure to “dress down” in science.

S2E3: Lauren Stopfer – Everything you Need to Know about MIT Grad School!

Check out the episode!

Publicized via MIT Bioengineering news article.

Dressing Down for Success

A fashion conscious female navigating the judgement of her peers

What you need to know about me: I am a 25 year old white female, 5’5”, with long legs and a burst of tangled brown curly hair. I have more Lululemon leggings than pairs of jeans, and I prefer wine to beer. I listen to NPR and the Chainsmokers, and love any season of the Real Housewives (except Miami, that was a flop).

I probably sound insufferable. And basic. Afterall, I’m writing this sipping out of my S’well water bottle wrapped in a blanket scarf.

What you also need to know about me: I’m a Biological Engineering PhD student at the Massachusetts Institute of Technology, researching the interplay between immunotherapy and kinase inhibitors and how the signaling dynamics of these therapeutics contribute to drug resistance mechanisms in melanoma.

“Whoa… didn’t see that one coming.”

I get that a lot these days. I don’t “look” like a stereotypical PhD student. I didn’t “look” like a biomedical engineering student in college.

In high school I thought that being a well-spoken, put-together female in engineering would be a positive. Quickly, my naïve outlook dissipated when I started college at the University of Wisconsin, Madison. I joined a sorority with a reputation of being blonde and bitchy, and wore Kappa Kappa Gamma branded apparel to class regularly. My classmates would first assume I wasn’t very bright until I proved myself otherwise. The men who worked in the machine shop made snide comments about my being a “stupid sorority girl” when I asked for help operating the lathe. A design project team asked me to come up with the cute logo for our project while they built it in the shop without me. I was the only female in my Mechanics of Materials class, and nobody wanted to be my partner for the final project so I did it alone. Ironically, guys in the class would come up to me at bars in later years remembering me as the girl from ME418 and ask for my phone number.

… you could’ve had my number if you’d been my PROJECT PARTNER! Sigh.

Let’s face it, being a woman in the STEM fields is tough. I could write for pages on the general adversities women face, but that’s already out there. What I want to talk about is something a little different. Something that’s kind of awkward to put down in writing. I care about how I look, follow fashion trends, and strive to look my best (most) days of the week. And, I think I’m treated differently because of it. Here’s an anecdote.

During the fall of my sophomore year I was excited about the prospect of getting an internship. Now this was an opportunity where I could really shine. I think I’m skilled at communicating, networking, and planned to really “turn on the charm” in this male-dominated career fair. I’ll look put together and professional, but (of course) still fashionable.

I handed out my resume to anyone who would take it at the Fall Engineering Career fair with little luck. I passed it to a young man from Baxter Healthcare, and as we chatted I learned he used to work in the research lab next door. We had a nice conversation, and he moved my application onto the next round and invited me to the company info session.

I attended later that evening, in a black shift dress with tights and two-inch heels. Two inches was a conservative heel height for me back in my Kappa Kappa Gamma days, if you need some context. I don’t remember much from the session besides a bland PowerPoint deck, disconcertingly soft oatmeal cookies, and a recruiter whom I’ll call “J.”

J. was an average man of medium height and medium build, who heavily emphasized the focus on diversity and ethics at Baxter Healthcare. “This was cool,” I thought. “They care about diversity, I’m diverse. Maybe I’ll get lucky.”

We ended the session with a trivia Q&A about Baxter. I shyly raised my hand on each question but was outreached by more aggressive men from my department for all the cool prizes. I left with a consolation pizza cutter with the Baxter logo plastered on top. I lived in my sorority house and we had two chefs so I didn’t really need a pizza cutter, but I tossed it in my backpack thinking that maybe someday this will be a cool reminder of my first internship. My interview was the next morning, so I headed home to plan my outfit.

I arrived for my interview wearing a grey tweed two-piece skirt suit with a black applique on the left shoulder. I was feeling confident so I opted for my  two-and-a-half inch patent leather t-strap pumps. Remember, that was me being “heel height” conservative. Designer handbag and leather portfolio in hand, I clicked into the interview suites. J. ended up being my interviewer, and I handed him my resume. He held it up, but seemingly looked through it at my face, my two-piece tweed suit, my handbag, my heels.

“Why would a girl who looks like you think she was qualified to design catheter bags?”

Pause here. If you aren’t shocked, please re-read that line again.

His comment was deeply unsettling for two reasons.

  1. What do you mean by “a girl who looks like me?” He didn’t look at my qualifications, my grades, my research and design experience. He didn’t notice that I was fluent in the computer programs Baxter uses, or that I had won a top scholarship for my department. All he saw was my physical appearance, and apparently, I looked like I didn’t know what I was doing.
  2. J., I implore you, What exactly does someone qualified to design catheter bags even look like?!

At that point, he told me I was unqualified for the position, and asked me to leave his office.

I was shaken, and what I did next I am still embarrassed about to this day. I went home that night and wrote J. from Baxter Healthcare an email, thanking him for his time and consideration.

(Even though it was more like two minutes of his time and complete lack consideration).

Surprise, he didn’t respond.
Surprise, I didn’t get the job.

Maybe Biomedical Engineering wasn’t the right field for me, maybe I was underqualified. I spent the night researching other majors I could transfer into and still graduate on time. Unfortunately for me there weren’t any other majors. I was too far along, so I decided to stick with my choice. It was shortly after that I found Dr. Pamela Kreeger’s research lab, where I finally felt like I wasn’t being judged for my appearance. Dr. Kreeger was a well-dressed, sassy woman, and she gave me the encouragement, support, and tough love I needed when I was feeling discriminated against. It was with her encouragement I decided to apply graduate school, and with even more support that I shot for the moon and applied to MIT.

I’d like to say that everything got better when I moved to Cambridge, but I’d be lying. I’m still judged on my appearance, by both female and male coworkers. I show up on a Saturday in sweatpants and a sweatshirt with no makeup and am greeted with, “rough night?” I wear a dress and suede booties on a Wednesday and hear “whoa, what are you all dressed up for?” One time I wore a choker and a guy from my lab asked me why I was wearing a dog collar. Have you not seen Kendall Jenner’s Instagram? Chokers are (were) in!

These are of course microagressions I can ignore, but it is frustrating. A colleague recently shared a satirical article with me where a woman jokes that for the reasonable price of a $5.00 drugstore lipstick, she can transform herself into someone who is no longer taken seriously by male colleagues! I felt like she wrote that piece for me. PREACH.

I think there is a lot of societal pressure to dress a certain way in science. To not appear too girly in a field of cisgender males. Not just professionally, but even as a grad student walking around in lab or presenting at a poster session. We are more approachable if we “dress down.” I look “bitchy” if I wear heeled shoes.  Dressing to be taken seriously in this field exploits a more obscure field of sexism where if we are too feminine, we must be too concerned with our appearance to also be intelligent. That we value “style over substance”. As if the 10 minutes in the morning I spend putting on makeup is 10 minutes I should be spending curing cancer.

I found this 1998 article published in Science where a man and his wife take out a recent female PhD graduate to find outfits to interview in. It’s hilariously outdated from a fashion prospective, but some of the tips probably aren’t. The author suggests finding a basic blue suit with a white undershirt “because nobody hates white.” Other tips are no dangling earrings, and no jewelry except a wedding ring. So basically, dress like a man. I guess that was my first mistake with Baxter…

The article ends with a truly unsettling statement: “When someone looks at your résumé and sees Ph.D. after your name, their mental image of you may not be flattering!” …Why? Why is that the first assumption?

Look, I’ve been guilty of judging other women for what they are wearing too. It is ingrained in me. I woman down the hall from my office always has impeccable eye makeup on and knee-high heeled boots. She looks fabulous, but at first my reaction was “whoa… why get so dressed up for work?”

I’m a victim of my own complaint. So what do we do?

Embracing who you are. You’re not just a scientist, you’re also a woman. This attitude will help change the culture of academic science for future generations. Personally, I need to check myself on judging other women. But beyond that, I’m not sure. Last year, some women in my department created a group to start conversations about this and other topics that apply to being minority genders in science. We discussed productive ways to talk about these issues, inform ourselves and others, and make change. Unfortunately, and I’m partially to blame, nothing concrete happened. We all find ourselves busy with lab work, social lives, and other things.  These are excuses. We have to keep the conversation going.

Last night, I got home from a long day at lab and kicked off my suede booties. I threw a pizza in the oven and cut it into slices with my Baxter pizza cutter. I have a nicer pizza cutter at my apartment, but I won’t use it. I want to  use the plastic Baxter one and think of J. I think of him telling me I don’t look like an engineer. I don’t look like a scientist. Well, maybe I’m not designing catheter bags, J., but look where I am now.

Originally published on the MIT Graduate Admissions Blog

Out of the lab, into the Rice Paddy

A reflection on engineering principles observed on an adventure in Laos

I’ll pose this question to the MIT and scientific community: how would you identify and separate healthy rice grains from empty or insect-damaged grains to feed to the chickens? As MIT graduate students, we’d probably over-engineer this. Is there some protein in the healthy grain I can image for? I’m a mass spectrometrist, so I’d probably find something to mass spec because heck, why not! We could send it out for sequencing, too – isn’t that a thing, to sequence everything these days? (Or to put it colloquially, sequence the shit out of it).  Maybe we should just re-engineer the rice altogether. What other buzzwords can I throw in here to convince you I know what I’m talking about? Scanning electron microscopes. GWAS hits. Machine learning. Expansion microscopy. Self-organizing maps. Microfluidics. Small molecule screening. DNA ORIGAMI. That’s it. DNA origami.

Guess how rural Laotian farmers solve this question? Water, salt, and an egg.

After I proposed my thesis at the end of July, I set off as a new PhD candidate to explore a new part of the world. Of the places I traveled, Laos was by far the least “touristy” country, and also noticeably the poorest. Despite that, Laos lived up to its slogan of being “simply beautiful.” We stayed in a picturesque bungalow in the middle of a rice paddy in Vang Vieng, and when we arrived at the hotel in Luang Prabang, our second stop in Laos, I chatted with the concierge about “must do” activities. A tour of the Living Land Company’s rice farms came highly recommended, but I decided to go because of a photo in their brochure of Susan: Susan the water buffalo.

When we showed up for our half-day adventure, I found out Susan had moved on to greener pastures, and the young Rudolph would be accompanying us in the rice fields today. I spotted him across the patty- he was pink. Are water buffalos usually pink? Susan was not pink. Our guide, Long Li, told me that I’d get to meet him later. I put on the conical straw hat (it’s tradition) and waded into the rice paddy, feet sticking in the mud. Today, I was going to plant some rice, harvest it, maybe eat it? Hopefully eat it.

The Living Land Company was designed in response to the destructive farming methods occurring throughout Laos, methods that result in barren, inarable land. It teaches local farmers organic, sustainable farming techniques, and also provides scholarships and on-site training to college students studying agriculture in Luang Prabang. Long was one of those students. He taught us the thirteen steps of rice farming by hand, no modern machinery needed. We learned about germinating, planting, ploughing, harvesting, threshing, winnowing, and processing rice. What struck me most about the experience was the simplicity and elegance of the methods used. Nothing fancy, nothing expensive. All the tools were made from straw, rock, wood, clay, water, and human energy.

My favorite step in the rice farming process was how seeds are selected for germination. Empty and damaged grains weigh less than healthy grains, so salt is added to a bowl of fresh water until a chicken egg floats. Grains that float in the water are damaged, so they are removed and fed to the chickens. Nothing is wasted.   

A similar technique is used to remove empty grains in the harvesting process. By fanning the grains with a straw paddle, you blow away the chaff and empty grains. A fancy machine isn’t necessary.


While I appreciated all the ingeniously simple examples of engineering around the farm, the best part of the trip was meeting Rudolph and plowing a rice patty with him. Rudolph trudged through the mud as I tried to steer the plow, without much success. Rudolph was supposed to respond to “stop” and “go” commands in Lao (my Lao was admittedly poor), but he seemed to be doing whatever he pleased (how do you say, “Rudolph, please give me three seconds to collect my balance” in Lao?). Sweating and caked in mud, I hopped out of the paddy. Susan probably would’ve been a better listener.

Plowing the rice paddy with Rudolph

My morning at the Living Life Company left me reflecting on the differences between the simple tools used for the involved task of farming rice, and the expensive, top-of-the-line gadgets I have access to at MIT. When I first arrived at MIT, I was in awe of the resources at MIT compared to my undergraduate institution. I remember being dumbfounded that you could simply buy cell culture media. In my prior lab, we made it by combining several powders, adjusting the pH, and filtering it. Now, I just run into the cold room and grab a bottle. It has become my new normal. This institution provides us with access to unparalleled opportunities, and my day at the farm reminded me of that. While I’m probably not going to start whittling my own pipettes from tree branches (a process that would be both challenging and unsterile), I am aiming, to be more conscious about how I use the tools I have: to be less wasteful, to think my experiments through before haphazardly trying something, but not to beat myself up when something doesn’t work (like when three $1,000 experiments failed in a single day last month). It’s a balance. Long Li and Rudolph reminded me of that.

Oh, and the sticky rice was exceptional.

Originally published on the MIT Graduate Admissions Blog

Planting the germinated rice stalks, one by one.
Grinding the rice into rice flour
Hitting the dried rice stalks against a board to knock the grains off the stalk
Walking into the Rice Paddy behind our guide, Long
Weaving baskets, paddles, strainers, and hats from bamboo grown on the farm.
Rudolph selfie 🙂