Featured Researcher: Simone Spandau '23

About the Student Researcher

Major

BS Computational Biology

What's your research story?

I am a senior in the Computational Biology program, and I currently conduct research in two different labs.

In Dr. Yan Sun's lab at the Department of Microbiology, Immunology, and Virology, URMC, I created a pipeline to analyze single cell RNA seq data to study the mechanisms for Covid19 defective viral genomes' generation and their relationship with the host's immune system. Defective viral genomes are truncated viral RNA that accumulates from recombination events after the viral genome was entered the host's cells. They are missing the transcriptional regulatory sequence, so they are unable to produce functional viral particles from the viral mRNA. My PI's past work on other viruses has shown that some defective viral genomes can stimulate an immune response. My work is included in Dr. Sun's paper "Analysis of SARS-CoV2 Defective Viral Genomes," along with several other students' analyses of RNA seq data. This paper is currently in review at mBio.

I recently began working on a research project for Dr. John Werren's lab at the school of Arts and Sciences. I am exploring various clustering algorithms and gene enrichment methods to test if proteins' with similar evolutionary rates share biological functions and pathways. Dr. Werren is currently looking for more undergraduate students to take on various projects related to his ERC (evolutionary rate correlation) pipeline, which characterizes pairs of proteins based on their similar evolutionary rates.

How did you initially secure your research position?

I secured my position at the Sun lab by cold emailing several PI's at the medical center, the school of Arts and Sciences, and neighboring institutions after reading about their research. I had asked to discuss various research projects that I had an interest in studying. It is very important to actually read about a lab's research before meeting with one of their members in order to show that you actually are interested in their projects and not just looking for experience. PIs look for students that will commit to their projects, hopefully long term, as this will aid them in producing more papers. I reached out to around 20 labs before hearing back from any PIs that had room for an undergraduate student. I was the most excited about Dr. Sun's research, because I wanted to be involved in Covid19 related research. After conducting research for Dr. Sun for a year, she hired me as her laboratory technician. I order supplies and manage inventory. My research is compensated via course credit.

I secured my research position at Dr. Werren's lab after he had sent out interest forms through the UPBM weekly emails. I read about their projects, filled out the interest form which asked for relevant coursework and what projects in the lab interested me. I then had an interview, after which I was offered the position for which I would receive course credit.

Departments/programs of research

Yan Sun, PhD, Department of Microbiology, Immunology and Virology, URMC

John Werren, PhD, Department of Biology, School of Arts & Sciences, University of Rochester

Any research presentations, awards, or publications?

I have presented my Covid research at the UofR Undergraduate Research Expose (Spring 2022), and at the Microbiology, Immunology and Virology Department retreat (Summer 2022).

https://pubmed.ncbi.nlm.nih.gov/36172120/

https://www.linkedin.com/in/simone-spandau/

Can you share some "lessons learned" as a result of your undergraduate research experience?

Conducting quality research takes practice and patience. You will likely experience at some point inconclusive results from an experiment or analysis. Just because your experiment didn't confirm your hypothesis does not mean the results are insignificant with regard to better understanding your subject of interest.

What advice can you share with new undergraduate researchers?

If you don't get a position in a lab, you must keep looking as you will eventually find the lab that suits your interests, even if it is not the one that you expected.