Our awesome undergraduate students had a great time in the summer! Several of them presented at the Summer Undergraduate Research Conference at the University of Iowa, including Zoe and Seren (REU student in the Neiman lab, working with Zoe on the experimental evolution project), Jess, who worked with Emily on the divergent response to phosphate limitation across yeasts, and finally Kelsey, who worked with Baylee on optimizing the ChIP assay for Pho4 orthologs.

Congratulations to Jinye, who successfully defended her PhD thesis titled “Evolution of Acquired Stress Resistance in an Opportunistic Yeast Pathogen”

Congratulations to Hanxi, who successfully defended her MS thesis titled “Divergence of Acquired Stress Resistance Among Yeast Species and Establishing a Flow Cytometry-based Assay for Post-Stress Survival Quantification”.

Bin helped an undergraduate team address a statistical question in their micropublication. The biological question was whether crayfish recognize themselves in the mirror! It was a lot of fun discussing the phenomenon and working out the stats behind their analysis. Proud to be part of the team. The publication is now online: publisher’s website. The student authors are Stephanie Rocca and Danielle Saldana. Danielle was a student in my Bioinformatics for Beginners course. Their study was part of the Animal Behavior Laboratory taught by Olga Miakotina and Dan Eberl in our department.

Our Pho4 evolution paper is on biorxiv! Read it here or a synopsis in this twitter thread. Lindsey Snyder is the leading author, with help from multiple lab members, including Emily, Jia, Jinye, Tom, as well as Nick Schnicker at the Protein and Crystallography Facility at the University of Iowa. We also collaborated with Raluca Gordan’s lab at Duke, who helped us conduct Protein Binding Microarray experiments (Thanks Yuning and Wei!). Lastly, Xu Zhou started this work when he was a graduate student in the O’Shea lab. How time flies! We are working hard to get this work published in a journal!

We gathered at the Texas Roadhouse for a nice dinner. It was both to celebrate the end of the semester, and, with bitter-sweetness, see off several members, who are leaving the lab for their next steps. Our first minted Ph.D., Lindsey Snyder, will be moving to Cambridge, MA and hopefully will be joining an exciting biotech venture soon! Cole is going to graduate and join the Pathogbiology graduate program at UIUC as a MS student this fall. Anthony is going to start as a postdoctoral researcher in the USDA National Center for Agricultural Utilization Research in Illinois, with a career path to become a group leader at the institution. Lastly, Jinye and Hanxi are going to defense this summer. Hanxi will be joining the Chemical and Systems Biology graduate program at Stanford, and will be away during the summer. So, this is also a fareware party for them. Good luck all the GRE’ers! Proud of all of you and keep in touch!

First Ph.D. minted from the GRE lab! Lindsey Snyder successfully defended her thesis on “Evolution of stress response regulators and adhesin genes in pathogenic yeast”. Lindsey has had a productive Ph.D. training, with one co-first and one co-second author publications, and a first-author publication being submitted right now. Her broad skillsets, including biochemistry, genetics and flow cytometry, her ability to work with others and her devotion to mentoring new members make her invaluable to the lab. We will all miss her after she leaves!

Our awesome undergraduate researcher Jessica Miller presents a poster on her work on the polyphosphate quantification in diverse yeast species at the Spring Undergraduate Research Conference. The poster drew a lot of attention, and highlights a new direction we are diving into - how different species decide on nutrient storage and growth strategies. Other members who contributed to this work include Emily O’Brien, Varshu Saravanakumar and Chris Youngstrom.

Happy birthday Emily! And, we missed Jinye’s birthday in March this year. But it’s never too late to say Happy Birthday, Emily and Jinye!

Our awesome member (terrific undergraduate student mentor), Dr. Chris Youngstrom, is going to move to his next position as a scientist and postdoctoral researcher in his Ph.D. field - plants! He won’t be moving very far (Ames, IA). We wish him all the best. Hope to see you when you visit back at Iowa City!

Our Acquired Stress Resistance paper is now online at PLOS Pathogen’s website. First author Jinye Liang will be presenting this work at the upcoming The Allied Genetics Conference as a platform talk! You can also read about our work in this twitter thread, or from this great news story on our findings from Iowa Now, expertly written for non-experts by Richard Lewis.

The lab went for a skating party at the Coralridge mall rink at the end of the semester. We are a very nice bunch, as old timers helped newbies learn the trick. It was really fun! We went for bubble tea afterwards. Not my favorite bubble tea place, but the warmth of the gathering was the point!

We continued our tradition of going for a lab lunch before Thanksgiving. This year we were joined by Agnes, a second grader and who didn’t have school that day. We went to her favorite lunch place, Z’Mariks Noodle Cafe. She goes there almost every Saturday and loves it!

Excited to share that our Acquired stress resistant story is now accepted at PLOS Pathogen. We will post a link and a synopsis very soon. This work is started and almostly entirely accomplished by our wonderful graduate student Jinye Liang, with help from other lab members including Lindsey Snyder, Hanxi Tang and Chris Youngstrom. Congratulations to the team!

Happy birthday Varshu! It is always nice gathering for these happy moments!

Congratulations to our fantastic graduate students, Lindsey and Jinye, both of whom were awarded the highly competitive Ballard Seashore Dissertation Fellowship by the Graduate College. Well deserved and very proud!

It has been a very busy and productive summer for the GRE lab. First, it was Cole and Ava’s poster presentations at the Summer Undergraduate Research Conference (SURF). Before the end of the REU program, the lab also organized a potlock (we miss you, Ava!). Lindsey, Emily and Baylee went to the Summer Symposium at the Penn State University, on the topic of “Chromatin and Regulation of Gene Expression”. All three presented their work and got a lot of feedback. Last but not least, Cole, Varshu, Hanxi and myself went to UIUC to join the Midwest Neglected Infectious Disease conference, where we made lots of friends! Summer is too short, as always…

Welcome to Anthony Pannullo, who joined us in March of 2023 as a postdoctoral scholar. Anthony completed a highly productive Ph.D. with Craig Ellemeier in the Microbiology and Immunology Department, Carver College of Medicine at the University of Iowa. He studied the pathogenesis of Clostridium difficile, a cause of colitis and a great threat to human health. After joining our lab, Anthony is actively applying his skills and learning new tricks with yeasts to better understand the interaction between host macrophages and yeast pathogens. Also joining the lab recently is Ava Gabrys, who came to us from the Penn State University, where she is currently an undergraduate students. She is part of the Interdisciplinary Evolutionary Sciences Research Experiment for Undergraduate (REU) program. In our lab, she is applying her awesome bioinformatic skills to expand our adhesin evolution study to the Als family. She is also learning cloning and protein techniques to characterize a chimeric Hil adhesin construct we built. Last but not least, Baylee Bruce joined the lab as a new graduate student. She is in the Interdisciplinary Graduate Program in Genetics, the same as Lindsey. Welcome!

After several rounds of revisions, our adhesin paper is now in print in GENETICS (link). Thanks and congratulations to everyone involved, Dr. Rachel Smoak, Lindsey Snyder and Dr. Jan Fassler. Also thanks to many friends and colleagues who read / heard the story and provided critical feedback. Three reviewers and the editor at Genetics all made a significant contribution to our final product. Our paper is featured in the April issue of Genetics and Richard Lewis at Iowa Now wrote a great news story on our findings (read it here).

Happy birthday Emily! This time we got the cake from the awesome Molly’s Cupcake in Iowa City downtown. They did a fantastic job and we all enjoyed the sweets and the time together.

Congratulations to Lindsey for being awarded the Graduate College’s Summer Fellowship. Lindsey is working hard towards her second first/co-first author paper on Pho4 transcription factor evolution. Stay tuned!

Happy birthday Jinye! Bin really wanted to do experiments (since he spent a lot of his time now writing..). So he decided to make a chiffon cake decorated with homemade blueberry sauce and whipped cream. The lab had a nice time together.

We went for a nice lunch gathering at the Heirloom Cafe. Without the usual student crowd, the place is warm and cozy. Great food and company!

The GRE lab had a good summer, with several new undergraduate students joining us, including Sarai, who came to us from U of Texas at Permian Basin and is here for the Interdisciplinary Evolutionary Biology REU program. Also here is Sierra, who is a high school senior and with us as an intern. We also had a nice ice-cream social, where we welcomed our new rotation graduate students, Lucretia and Chase.

Bin was invited to give a talk on our recent adhesin paper at the SMBE satellite meeting on the Evolution of Fungal Pathogens. The talk went well and attracted many interests. The conference was held in the old Quebec City, which is a great place to visit!

Congratulations to Jinye for being awarded the Graduate College’s Summer Fellowship. Jinye is planning to use this award to finish up her first manuscript on the exciting acquired stress resistance project. Stay tuned!

GRE lab’s first preprint is online! Read it here or a synopsis in this twitter thread. This work started as a student project for the 2019 Bioinformatics course I co-taught with Dr. Jan Fassler (who is co-corresponding author on this manuscript). In this course we ask the students to apply the tools they learned to conduct new research on a protein family from a species whose genome was recently released. In the 2019 course, the theme genome is that of C. auris. Two of the star students in that class, Rachel Smoak from the Civil and Environmental Engineering program and Lindsey Snyder from our lab bravely delved into the unknown world of fungal adhesins. Their discoveries were exciting enough that we decided to spend another year and half to develop it further. And this is our product! Thanks to this fortuitous encounter with fungal adhesins, we are now actively looking into connections between stress in the host and cell wall alterations in both C. auris and our favorite species C. glabrata.

After a busy semester is finally over, we decided to have a small get-together at Bread Garden, both to celebrate the end of the semester and the isolation imposed by the pandemic, and also to send off some of our lab members with a mixture of pride and sadness: Jia has graduated with honor and distinction from the university and will start her graduate school in MIT Biology this fall. Also graduating from the college are Emily and Diandian. Emily will stay in the lab as a research assistant (Yah!) and Diandian will also continue to work in the lab in the summer. In the meantime, our wonderful high school interns, Ananya and Peter, have both graduated from their high schools and will go off to their dream schools this fall – Oxford in UK for Ananya and UCSD in California for Peter. We will surely miss all of you, best wishes and good luck!

Delayed welcome to Peter Chen, who joined us back in January of 2021 as a high school intern. He has been learning and applying Python skills to look at amino acid composition differences between orthologous TFs. Also warm welcome to Vivek Kumar Srivastava, who joined us from his home country of India as a postdoctoral researcher. Vivek has got his Ph.D. in the lab of Dr. Rupinder Kaur, whose work on C. glabrata has been inspiring for me. Vivek will be working on a few projects including the evolution of oxidative stress response between related yeast species with different pathogenic potentials.

Congratulations to Jinye for being awarded the Graduate College’s Post-Comprehensive Fellowship. The competition for this fellowship is especially strong this year, with many more applications than normal. Jinye was nominated by the Integrated Biology Graduate Program housed in the Biology Department and we are proud for her winning the fellowship! (picture credit: snack bought by the awardee herself)

Congratulations to Jia for her successful graduate school application this year! Among the many top programs that she got the offer from, she has decided to accept and join the MIT Biology Graduate Program. We are so proud of you!

A postdoc position is availabe in the GRE lab. Come and join us to discover how stress response networks evolved between free-living and commensal yeasts using a combination of biochemistry, molecular and functional genomics! See here for details. Update 2020-11-14 This position is now filled.

As a response to the pandemic-forced lab shut-down, we organized a programming bootcamp over the summer, where half the lab followed the CodeHS’s Python course, and the other half followed Udacity’s Data Analysis with R course (thanks to the recommendation by Pleuni Pennings). We also had a new member – Ananya, who joined us as a high school intern and has been amazing! After finishing the courses, I assigned real research problems to both groups. In the past two weeks, both teams reported their results at the lab meeting. Moreove, to make our research accessible and reproducible, both teams’ results are on github. Team 1 (Erin, Jia); Team 2 (Amanda, Ananya). Proud of our students!

Excited to announce that we were awarded our first NIH grant, an R35 (Maximizing Investigator’s Research Award) titled “Evolution of Stress Response Gene Regulatory Networks in a Commensal and Opportunistic Yeast Pathogen”! To be honest, my feeling is more relief than excitement, because, I can finally focus on my research now! Will be recruiting a postdoc soon.

The past four months have been surreal, with labs closed and classes moved online. However, even amidst this pandemic, we do have some exciting achievements to celebrate. Let’s put them in order! First, our undergraduate researcher Jia won both the College of Liberal Arts and Sciences Kenneth J. and Sharon L. (Reisch) Erickson Scholarship and (!) the Biology Department Clifford W. Hesseltine Award for Academic Excellence. Next, both Erin and Jia again, were awarded the 2020 Summer Fellowship by the Iowa Center for Undergraduate Research, for which they are deeply buried in a computational project (which was not our original plan, but it is working really well!). Amanda put in a strong application for the 2020 academic year research fellowship by the same center, whose result will be announced later. Erin also won the Latham Science Engagement Fellowship, for which she will engage in science communication through a course and an independent project. We need more science communicators like you, Erin! Now to the graduate students side: Jinye was awarded the Biology Department summer graduate research fellowship. Meanwhile, Lindsey put in a really strong application for her renewal of the T32 grant. Although it was not selected in the end, I’m really proud of her work and I’m sure she is going to do great in the coming years! Oh, what a lab!

We are welcoming three new members joining the lab, Amanda Caraballo, Daniel Ikobar and Erin Smith.

Tom started as a senior RA in our lab after plenty of research experience from the Prahlad lab. We were lucky to have him and he has helped jump start the BioLayer Interferometry experiments. Now he is on to his dream trip – a solo drive through Canada to Alaska – before he starts his medical school here at UIowa. Good luck, Tom! We always welcome you come back to visit!

The GRE lab has had a great semester. Now it’s time to relax and enjoy the summer (finally)! Here we are in the City Park shelter #11. In the picture are: (front) Abhi, Jinye, Jia; (back) Yann (special guest), Lindsey, Zoheb, Kyle, Tom, Bin; (top) Agnes (special guest).

Welcome Lindsey Snyder to join our lab. Lindsey is a first year Interdisciplinary Graduate Programs in Genetics student. During her undergraduate research in the University of Idaho, she has got a solid training in microbiology and molecular biology. She rotated in our lab last fall and we are thrilled to have her officially join the lab. She will work on Pho4 protein evolution, taking advantage of the additional skills in CRISPR and computational biochemistry she gained during her other two rotations. Welcome Lindsey!

Congratulations to Jia Zhao for winning two prestigeous awards from the Biology Department. The first one is the Clifford W. Hesseltine Scholarship in Biology, which recognizes one Biology or Biomedical Sciences student of sophomore or junior undertaking laboratory research and have a strong academic record (GPA > 3.5). She was also accepted into the Iowa Biosciences Academy (IBA),an NIH-funded program that supports the academic and personal success of University of Iowa students interested in pursuing a Ph.D. Well done Jia, proud of your achievement!

Everytime I read a paper or listen to a talk that includes plethora of gels, and each time I see other people play with the HPLC and columns, I thought I would never do those things – I’m an evolutionary geneticist after all, or so I believed, until… now we are officially purifying protein from E. coli. I know it’s trivial for many people, but I’m really proud of what we achieved. Kudos to the heros, Tom Cassier and Kyle Malcolm.

Welcome Tom Cassier to join our lab. Tom came to us with a solid research background in Veena Prahlad’s lab from our department. He will stay with us until the end of May, during which time he will work on recombinant TF purification, BioLayer Interferometry, and will help with a number of lab maintenance tasks. After that, he will go on a solo trip and then, start his medical school at the University of Iowa.

Warm welcome to the newest members of the lab: Abhishiktha Godthi is a first year iBio graduate student and Diandian Tang is a junior UI undergrad. Check out their profiles in the Team/Join page. We are sad to say goodbye to Joe Wisniewski, who has been one of the earliest members of the lab and has helped the lab in many ways, including being the safety and MSDS tzar and working on the Pho4 target validation project. Good luck Joe, you will be an awesome doctor!

This is probably the peak size of the GRE lab, as we luckily have two rotation students joining us in addition to our summer crew. From left to right: Weilong (Jesse) Liu (undergrad assistant), Abhi Godthi (iBio rotation student), Jinye Liang (iBio graduate student), Lindsey Snyder (Genetics rotation student), Jia Zhao (sophomore), Carl Skoog (junior), Bin He, Zoheb Khan (senior), Joe Wisniewski (senior), Kyle Malcolm (senior). Thanks again to our awesome photographer, Steve Kehoe at the admin office of Biology Department!

These are the awesome students who were brave enough to join a new PI’s lab. From left to right: Ian Wallace(rising sophomore from U of Minn), Jinye Liang (1st year iBio graduate student), Kyle Malcolm (rising senior of UI), Jia Zhao (rising sophomore of UI), Bin He (yup, that dude), Carl Skoog (rising junior of UI), Zoheb Khan (rising senior of UI). Joe Wisniewski, who is also a rising senior of UI, couldn’t join us because he is back home in Illinois. Lastly, big thanks to our awesome photographer, Steve Kehoe at the admin office of Biology Department!

Carl (right) and Kyle (middle) from Team 1 presented their latest understanding about transcription factor cooperativity at the Summer Undergraduate Research Conference. We had a lot of fun explaining our ideas to the audience, which include both fellow undergrad researchers as well as cool faculties from our own department!

I’m excited to have six talented undergrad students and a high school intern to join me for the first summer of research. Gabi Mumm, Joe Wisniewski, Kyle Malcolm, Carl Skoog and Zoheb Khan are from U of Iowa and Ian Wallace is from U of Minnesota. Noah Bullwinkle is from the Iowa City’s City High. We are going to form two teams: Team 1 is the TF protein evolution task force, while Team 2 will investigate the target genes of the TF (C. glabrata Pho4). Stay tuned for our first batch of results!

Today is my first day on the job. Excited to join a great group of faculty, students, staff!