People

Folks in the lab

Joe Walker (PI)

My name is Joe Walker faculty webpage here. I received my BS from Purdue University in 2012, my Master’s degree from Purdue in 2014 (because who doesn’t want to stay in beautiful West Lafayette, Indiana), and my Ph.D. from the University of Michigan in 2018. I then went to the University of Cambridge as a research associate until 2021. Now I’m a faculty member who has the privilege of working with the folks listed on this page. Also, on the rare occasion that I remember to update the website, I mostly edit the pages in vim without a grammar or spellchecker, so apologies to anyone who notces those mistkes.

Postdoc

Karolis Ramanauskas

Karolis earned his Ph.D. from UIC in 2022. He is the lab’s go to point of contact for anything related to biology or programming. He’s a computational molecular biologist with an in-depth knowledge of plant genomics. Pretty much the only thing Karolis seems to have trouble with is remembering Eric’s name. Karolis single handedly wrote a new tree viewer in Rust that has been a huge help to the lab. You can find it here. He has some level of involvement in most of the ongoing projects in the lab and facilitates pretty much all aspects of day to day operation. In his free time, he designs and maintains open-source software such as kakapo. Karolis updates his website less often than me, which you can find here.

Graduate Students

Alexa Tyszka

Alexa is a fifth-year Ph.D. candidate whose research focuses on developing new methods for obtaining transcriptomes from unpreserved tissue and studying how they may be used for transcriptomics. She’s been pretty prolific in this area, helping with this paper and authors this perspective piece and this study. Alexa completed her undergraduate degree in 2021 from UIC and joined the lab right as it started. She has received the GRFP, the UIC research award, and the UIC graduate teaching award. You can check out her website here and her google scholar here.

Eric Bretz

Eric is a second-year Ph.D. student whose research is focused on computational methods to clean up genomic data, specifically filtering out chimeras. Eric joined the Marines out of high school, then after his service, completed his undergraduate degree at UIC in 2020. He was a postbacc with Dr. Andrea McGinley Bassett for a year before deciding to join the lab. Despite only being in his second year, he has already co-first authored a paper and would have presented his work at Botany 2023 if he didn’t have his luggage accidentally sent to Denver instead of Boise. He has quickly picked up several programming languages. You can find his website here, his linked in here and his google scholar here.

Holly Robertson

Holly is externally co-supervised by the lab and based in Cambridge in the lab of Edwige Moyroud, my fantastic postdoc advisor. They completed their undergraduate at the University of Cambridge and finished a Part II project on phylogenetic conflict under the supervision of myself and Edwige Moyroud. Holly later completed a Part III project at the Sanger Institute, working on genomics. They are now back to studying conflict, addressing it in both Carnivorous plants and Hibiscus.

Oluwatomi Jacobs

Tomi is a first-year Ph.D. student learning the ways of UIC and developing her thesis. Tomi completed her undergraduate degree at the University of Ilorin, a Master’s degree at Delaware State University, and a Thomas Wyatt Turner Fellow at Cornell University. You can find her github here, her linked in here and her google scholar here.

Shawn Arreguin

Shawn is a first-year Ph.D. student who is co-advised with Dr. Mary Ashley. He is working on developing his thesis, with a broad interest in urban ecosystems. Shawn completed his undergraduate degree at the University of Illinois Urbana-Champaign.

Timi Okeseni

Jess Zhang

Postbaccs

Linda Mansour

Linda has been working in the lab since the fall of 2023 and luckily Linda has continued in the lab as a Postbacc to gain experience and develop a sense of what being a graduate student is like. Linda is an awesome programmer and has been working on developing programs that use LLMs to help navigate databases such as NCBI. You can follow her work here. Her undergraduate work focused on analyzing next-generation sequencing data and the quality of the reads that are produced and she contributed to this study here.

Undergraduate Students

Jordan Kressman

Jordan Is a senior biological sciences major assisting Tomi Jacobs and Shawn Arreguin with their respective research. She spent her first two years of undergrad studies at Temple University in Philadelphia before transferring to UIC in Fall of 2024. Lately, Jordan has been doing a little bit of everything phylotrascriptomics related. She’s rapidly learned the basics of the methods and how to process transcriptomes as she has worked with Tomi on analyzing Ice Plant data.

Former Lab Members

Miles Woodcock-Girard

Miles was with us for a little over two years and after finishing his undergrad degree in Biomedical Engineering, he moved on to the Drew Lab for grad school. In lab he developed a C++ package to efficiently and thoroughly process short-read data in transcriptomes. Click here to check it out and the publication here.

Alexandra Siek

Alex worked in the lab as a BIOS391 student. Her project focused on transcriptome assembly and what we can do with the different programs. Alex also worked on a side project for automatically labeling phylogenetic trees with their NCBI taxonomy.

Renée King

Renée completed her undergraduate thesis project in the lab. She analyzed how the quality of the sequencing has changed over time and what implications that may have.

Vaishnavi Vanamala

Vivi worked on her BME 398 project in the lab, developing Python programs to summarize and manipulate phylogenetic trees.

Pratiti Bandyopadhyay

Pratiti was an undergraduate student in the lab who completed her senior thesis with us. Her research focused on applying computational methods to the Caryophyllales. Pratiti then completed the postbacc program in this lab along with the lab of Dr. Alex Shingleton and is now pursuing her graduate degree at the University of Zurich.

Josh Lee

Josh completed his honors capstone project, studying the phylogenetic signal associated with dentition in primates. He has now graduated and is on his way to becoming a dentist, so sadly, I’ll probably never see him again.