Since we can't come together in person this year, we created this virtual graduation website to celebrate your accomplishments as Biophysics students at the University of Michigan. We are incredibly proud of you and we wish you well as you take the next steps in your journey
A message from our Program Director, Charles L. Brooks III:
Bachelor of Science
Fall 2020 & Winter 2021
Kyrillos’ (Cookie's) research projects have spanned two families of noncoding RNAs from the bacteria listeria monocytogenes. In one project, he contributed to our understanding of the unfolding mechanism of a temperature-sensing bacterial RNA. He is a co-author on a recent Biochemistry paper describing this work. Dr. Sarah Keane adds “He’s been instrumental in pushing this project in a new direction - examining the sequence/structural conservation of this RNA element across various species of listeria. Cookie is well known in both Biophysics and Chemistry as an outstanding student. His excellence in both the classroom and research lab were recently recognized with the 2021 ACS Undergraduate Award in Physical Chemistry. He has also worked with the Frank lab where he co-authored a paper describing how to use chemical shifts to inform on RNA 3D structure.”
“The people are what made the Biophysics Program so enjoyable for me. The excellent and supportive faculty provided me with the guidance I needed to develop as an individual and a scientist. Additionally, my fellow students in the program helped make my education enjoyable and made me excited to go to class every day. After I graduate, I plan on pursuing my PhD in biophysics at Yale. I am so excited to continue in the next step in my academic career and I know that I couldn't have done any of this without the incredible people in the program.” – Kyrillos Abdallah
Fumiya’s undergraduate research used molecular dynamics simulations to investigate the binding of inhibitors to a flavin-dependent hydroxylase and to test the advanced sampling methods developed by Charlie Brooks and his group. His results, in collaboration with graduate student Luis Cervantes Vasquez, and mentored by Dr. Troy Wymore, showed agreement with experimental results and will be used to further investigate this important drug target.
“I joined biophysics my sophomore year of college after meeting Kevin Wunderly, a University of Michigan biophysics alum. He taught me about what biophysics is about and introduced me to a whole new world of science that I had never heard of before. One of the aspects of the biophysics community that I appreciated so much was everyone's constant devotion to science and the willingness of everyone to help one another explore our passions. Through the variety of biophysics courses, not only did I learn so much about biophysics, but also what it means to be a good researcher, and how to be a better critical thinker. I also made connections with both students and professors that I hope will last for a lifetime. After graduation, I will be taking a couple of gap years before hopefully attending medical school. During these gap years, I hope to focus on developing myself as an individual in addition to continuing various research projects. Thank you so much biophysics!” – Fumiya Abe-Nornes
Kyle’s undergraduate thesis project used generative machine learning to develop models that can assist synthetic biologists in screening and designing novel yet functional riboswitches. Dr. Aaron Frank says, “Kyle is one of those rare students that quickly turn ideas presented in the classroom into 'I wonder if you could use this to' questions. It was one of those questions that led Kyle to his honor's thesis project. Though I served as Kyle's faculty advisor for this project, this work was primarily independent, with minimal advice for me. His final thesis was exceptional: it was well-written and -researched, thoughtful, and concise. The quality of Kyle's thesis is all the more remarkable given that most of the techniques he utilized, Python coding, biophysical modeling, machine learning, etc., were, for the most part, self-taught. Moving forward, I am genuinely excited to see how Kyle continues to leverage his curiosity and passion for science and technology to solve unmet health-related problems.”
“Deciding to major in biophysics was a great choice as a pre-med. I found it useful to learn biology in a way geared towards concepts and problem-solving. Equally as helpful were my peers, who made classes enjoyable and learning more doable. After graduation, I am pursuing an MD at Weill Cornell Medical College. I hope to maintain the friends and spirit of curiosity gained through biophysics during my life beyond U of M.” – Kyle Finos
“Fiona has been important member of the lab since she first joined in the summer of 2019. She has helped us to start a completely new research direction, developing and validating new methods to probe cholesterol concentration and activity in membranes. There have been many bumps along the way but Fiona’s energy, positivity, and ability to work in teams has helped push us through, especially this past year when the bumps seemed to grow into mountains. We admire how hard you have worked both in the lab and outside of it, and we will miss all of your stories about what really happened on campus. Congratulations Fiona! Enjoy your much deserved respite and we are excited to see what you decide to tackle next.” – Sarah Veatch
“I found my way to the Biophysics Program sophomore year. I am so thankful for the program, and, more importantly, the people involved, for giving me a wonderful, supportive community at U of M. My professors and GSIs have been instrumental in my undergraduate career, always offering encouragement, answering questions, and helping me along my journey. It’s been amazing getting to my senior year and knowing more and more people from students to professors at biophysics meetings. I am especially grateful to Dr. Sarah Veatch for welcoming me into the Veatch lab, her incredible mentorship, her continuous support, and the many opportunities provided for me to build my confidence and skills in a scientific research setting. Kathleen Wisser, Anna Gaffney, and the other Veatch lab group members have made a significant impact in my learning and growth of skills, as well, creating an amazing lab atmosphere that I have been so lucky to be a part of. Graduating in a pandemic was never expected, but this year has truly taught me how fortunate I am. It is the people, experiences, and memories that are important, so I am forever appreciative of my four years in our biophysics community. I will be taking a much needed break over the summer after 4 years of almost all 18 credit semesters. I am then applying to R&D and other industry jobs to work for a couple of years before looking into more schooling. Thank you to my family, friends, professors, GSIs, lab members, students, and my fellow graduating classmates! Forever Go Blue!” – Fiona Gaffney
Bennett Hendricks’ undergraduate research significantly contributed to the work of several postdoctoral fellows in the Walter group, studying the folding and function of riboswitches as intriguing bacterial gene regulating RNA motifs. Bennett employed single-molecule fluorescence microscopy as a unique biophysical tool to probe the dynamics of transcription factor NusA binding to a paused transcription elongation complex. Dr. Walter adds, “Bennett discovered that the 30S ribosomal subunit impairs recruitment of NusA to the transcription machinery, a novel result the Walter group plans to publish soon.”
“I'm very glad to have been a part of the biophysics community here at UM. My journey in biophysics began with attending my first biophysics club meeting during my junior year. While I came looking for free pizza, I found a genuinely welcoming community of undergrads who were extremely passionate about their research as well as all things biophysics. I decided to add a biophysics major on the spot, and I've never once regretted the decision. The commitment to excellence of the faculty and their spirit of curiosity stand out to me as highlights of the biophysics program at UM. The biophysics community has left me all the more prepared and confident as I apply to medical school, and continue pursuing research opportunities in the meantime.” – Bennett Hendricks
Varsha’s undergraduate research began in the Xu group of Biomedical Engineering, studying the effects of histotripsy, a non-invasive, non-ionizing therapeutic ultrasound technique, and improve the treatment accuracy of histotripsy in hepatic tissue. She has also worked in the Frank group, helping to build a neural network model that helps predict the tertiary structure of RNAs. Dr. Frank adds, “Varsha is a thoughtful student who enjoys a good challenge. This quality was on full display when she worked in my research group to use machine learning to predict torsion angles in RNA directly from secondary structure information. Despite the huge learning curve associated with this project, and while navigating unprecedented challenges related to the pandemic, Varsha made tremendous progress that will ultimately lead to a novel approach to solve an important biophysical challenge, namely, predicting the atomic structure of RNA.”
“I am very grateful for my experience with the biophysics program. I love the flexibility that I was offered to control my own learning. Every class I took was so unique and combined concepts from biology, physics and chemistry. I will always be very thankful to the supportive faculty of the biophysics department. They have been instrumental for my success and have helped me reach my potential. I loved being a part of this tight knit group and bonding with fellow students through our biophysics club. I will be attending the Wayne State School of Medicine starting this July. I will always remember my experiences in the biophysics program as I achieve my career goals.” – Varsha Kumar
Pujan’s undergraduate research was working on a Drosophila-centric project alongside PhD student Nigel Michki in Dr. Dawen Cai’s lab. Pujan received his training in fly dissections and immunohistochemistry and try to understand the mRNA and protein expression dynamics in the developing fly brains and picked up some bioinformatics, which enabled him to look into how some algorithms in the scRNA-seq pipeline work.
“When I got accepted to U of M, I pretty much had no idea what I wanted to major in. There were so many choices that it was impossible to choose; I almost wanted to do everything! This is why I am so thankful for having been a part of the Biophysics program here. It's such a diverse program that I almost feel like I did do everything. I met so many people with different backgrounds and interests, and the courses were relevant for so many different fields. Post-graduation, I am planning on studying medicine and, thanks to the Biophysics program, I'm feeling well prepared for the challenge.” – Pujan Moradiya
Mauricio Osuna Borges
Mauricio’s undergraduate research involved successfully applied image processing and statistical tools to analyze cell motility and oscillatory behaviors of dissociated zebrafish cells in various mechanical conditions. His excellent academic achievements have been recognized the University of Michigan Honor Roll (2019), Atlas Scholars Merit Scholarship (2017), and National Merit Hispanic Scholar (2017).
Zack’s undergraduate research used computational quantum chemistry to investigate the addition of hydroxyl radicals to aromatic molecules and how the unpaired electron distribution could be altered by the surroundings. Dr. Troy Wymore adds, “The results and his software developments are part of a manuscript in preparation by myself and Charlie Brooks describing the impact of radical mechanisms in flavin-dependent hydroxylases.”
“The Biophysics Undergraduate program was amazing, and I am truly lucky to have stumbled across it. If you would have asked me during my first two years at UofM what I was going to major in it definitely would not have been biophysics or anything close. But life has a funny way of working out like that, and I am grateful it worked out as it did. From the professors to the classes, no one can beat the Biophysics program, and I am excited to continue building on what I have learned while attending graduate school for a Master's degree this coming fall.” – Zack Rauch
Undergraduate Biophysics Minor
Doctor of Philosophy
Spring/Summer 2020 & Winter 2021
“Alex devoted his graduate research to defining the molecular 'architecture' of the human kinetochore using a novel methodology based on Forster Resonance Energy Transfer or FRET. His work revealed not only kinetochore architecture, but also how the architecture changes in response to mechanical forces and biochemical regulation. Alex's insights inspire follow-up studies that will ultimately reveal the architecture of the kinetochore and how it shapes the mechanisms of its functions in accurate chromosome segregation. Alex's work is distinguished by its creativity, meticulousness, and thoroughness. In fact, one reviewer of his recent paper summarized the manuscript thus: "This reviewer's opinion is that the study is thoughtfully designed, properly executed, and complete. No additional experiments are required." – Ajit Joglekar
“I joined the Biophysics department via PIBS in July 2014, and joined the Ajit Joglekar lab in 2015. I'm somewhat surprised I joined Ajit's lab because I came to grad school with ambitions of being a structural biologist. However, my rotation in one of the structural biology labs wasn't as satisfying as I had hoped, so I joined the lab where I had the most fun with all of the people. This was definitely a great choice because I learned that all science is interesting and exciting, especially when you are surrounded by fun people who are also excited by research. I've loved the projects I worked on in Ajit's lab. Kinetochores, chromosome segregation, and cell division are much more fascinating problems than I initially realized. I definitely did not appreciate the power of fluorescence microscopy as a research tool or all the clever ways microscopy studies can be implemented. And one of the biggest things I have learned from Ajit is to not let the challenges of science (or life) stand in the way of your ambitions.
In terms of ambitions, I have secured a post-doc position in Düsseldorf, Germany studying the development of plant roots in Dr. Guido Grossmann's lab. I don't speak German, I know next to nothing about plants, and the idea of uprooting my life to live in a foreign country far from all my friends and family generates the occasional mild case of anxiety. But it's what I want to do, so I'm doing it! New science, new experiences, and hopefully research that will contribute to a better understanding of important biological phenomena. I'm extremely excited about this next stage of my journey and very grateful for the role that the Biophysics department has played in making these ambitions possible. Auf Wiedersehen!” – Alex Kukreja
Changjiang (Desmond) Liu
“During his Ph.D., Changjiang (Desmond) Liu has studied the structure and the permeability of mammalian and bacterial membranes, developing a new approach to compute the kinetics of the permeation of molecules and nanoparticles through them. Desmond has done an impressive work combining biophysics, molecular modelling and innovative algorithms to push the boundaries in the understanding of a problem that has been the focus of research for more than 100 years. Over my career, I supervised, co-advised and met many PhD students, and without any doubts Desmond is in the top 1% for his scientific capabilities. His computational skills, scientific understandings of the problem, ability to look for alternative pathways of investigation, independence, analysis of the literature and reports of the information collected are outstanding. I have no doubts that Desmond will thrive in his next endeavors.” – Angela Violi
“I graduated from Biophysics last year. Previously I worked with Prof Angela Violi on Computational Biophysics, and now I joined Google as a software engineer. The 5 years of graduate study is not only about graduating with a PhD, but also about the research I get to do, the things I get to learn, and the awesome people I get to work with. There are times that are stressful, but it's definitely worth the time after all. I hope everyone in Biophysics will enjoy their ride as much as I do, and look forward to seeing your progress in the future!” – Changjiang (Desmond) Liu
“Chris joined my lab for a rotation the same day I started at Michigan — he’s literally been with me from day 1. I’m sure it’s not easy being in the lab of a new PI, but Chris has been a great foundation for the lab. He is scientifically adventurous, a generous and patient mentor to younger students, and is intellectually engaged with every project in the lab. He’s also been very successful. He won a poster prize at the Meeting for the Society of General Physiologists, was selected for a 15-minute talk at the Molecular Evolution Gordon Research Conference, and was a co-first authorship on our recent manuscript in Nature Communications (with more papers to come!). Chris’s next move will be an academic postdoc position. He’s got a few options, and is still deciding where he’ll go next.” – Randy Stockbridge
“In my time in the Biophysics PhD program, I've had the opportunity to make great friends, learn cool techniques, and do interesting science. I've appreciated my time in Ann Arbor and the opportunities to learn, research, and grow. Being able to join a global and a local scientific community has been incredibly rewarding. I've been lucky to come across some fascinating systems for my thesis work: two families of proteins that are rare "membrane fossils," the likely antecedents of most transporters and channels that exist today. My work combines biochemical, evolutionary, and structural approaches to understand how function changes in these families and how structural complexity arises.
I am planning to continue my work as a postdoctoral researcher (exactly where: TBD). My postdoctoral projects will combine structural and functional investigations with laboratory evolution to try to understand the forces that have shaped existing protein diversity.” – Chris Macdonald
“Jeff was an adventurous and creative scientist from the time he arrived at UM. His work focused on the collateral effects associated with drug resistance--the idea that evolving resistance to one drug might lead to increased sensitivity to a different drug. He showed (both in theory and experiment) that stochastic control theory could be used to exploit these collateral effects, steering pathogenic bacteria away from multidrug resistance. His work led to 5 publications (so far) and laid the groundwork for ongoing collaborations with UM medicine, where similar control concepts will soon be tested in clinic. After graduating, he was selected for a prestigious postdoctoral fellowship through Cleveland Clinic, where he is working to apply evolutionary principles to combat drug resistance in bacteria and cancer.” – Kevin Wood
“I had a fantastic time while at Michigan. Working with Dr. Wood was a blast and I couldn't be happier with our time and work together. While at Michigan I was surrounded by bright, passionate graduate students with diverse interests and backgrounds. Though, perhaps the thing I'll miss most is the food! Since graduating I've begun a Postdoc with Jake Scott and Chris McFarland at Cleveland Clinic and Case Western. I've been doing much of the same quantitative studies of evolution, however my model system has changed from bacteria to cancer. Graduating. moving and changing jobs during a worldwide pandemic was challenging, but Michigan prepared me well!” – Jeff Maltas
“During his PhD study, Nigel together with another student pioneered a new research direction, single-cell RNA sequencing in the Cai lab. Utilizing scRNAseq, Nigel explored the cell type heterogeneity in the developing Drosophila brain. His scientific achievements include, but not limited to 1) identifying novel molecular markers that specify distinct maturation stages and neuronal subtypes, 2) the development and commercialization of a web-based scRNA informatics analysis and visualization tool, and 3) the development and commercialization of a microfluidic-based scRNAseq platform. His contributions are recognized by several published papers and awards, which include an NIH training fellowship in microfluidics and an MTRAC award to kick-start the commercialization efforts. You can read more about Nigel in the next issue of the Featured Researchers on the Center for RNA Medicine website.” – Dawen Cai
“My first experience with Biophysics actually came in 2014 when I joined for a summer REU program, and I loved it so much I came right back for my PhD. During my time in Biophysics, I was given the opportunity to become a 'jack of all trades' by learning a wide range different techniques and skills from researchers within the department and across the university. I fell in love with trying to use those skills to develop new single-cell techniques to better understand how neurons in the brain are formed during development. I will (hopefully!) be taking a position at Genentech soon to study the opposite - how the brain fails under stressful neurodegenerative disorders.” – Nigel Michki