Lingyu Wang

I’m highly interested in all kinds of sequencing technologies, their applications and the data analysis.

Current Projects

In the Wray lab, one the my major projects is to study the gene regulation divergence in two closely related species of sea urchins, Heliocidaris tuberculata and Heliocidaris erythrogramma. The two species are only about 5 million years divergent but their developmental modes and life history modes are extremely different. In this study, I am analyzing the mRNA-seq data generated by Dr. Rudolf Raff and a previous lab member, Dr. Jennifer Israel, to investigate allele-specific expression of the hybrid embryos of the two species. The results can reveal whether the gene regulation divergence between the two parental species are caused by trans– or cis-regulatory changes, or the combination of the two types. 

I’m also working on the de novo genome sequencing and annotation of three species of sea urchins: Lytechinus variegatusH. tuberculata and H. erythrogramma. These resulting genomes and their annotations will provide valuable reference information, especially for mRNA-seq and ATAC-seq studies in the future.

I’m also excited to participate in the Malaria project. It’s a great opportunity for me to learn how to analyze the PacBio single-molecule long-read sequencing data and study the evolution of Plasmodium vivax.

Another fun project is to study the transcriptome of sea urchin embryos where the gene Snail and Twist are knocked down separately, leading to inhibition of the processes of epithelial–mesenchymal transition (EMT) and mesenchymal–epithelial transition (MET). This is a collaborative project done with people in the McClay Lab.

Past experiences

I did my PhD at University of Miami and my mentor was Dr. Athula Wikramanayake. I was fascinated by the embryonic polarity formation. I worked on the identification and characterization of proteins and RNAs involving in the initial anterior-posterior axis formation and maintenance in the sea urchin eggs and embryos using endogenous protein CoIP followed by mass spectrometry and RNA-seq. This is where I began my bioinformatics journey. 

I like to collaborate with people. I have worked with chemists, because sea urchin embryos, as a versatile model,  can be used to test the toxicity of newly synthesized nanoparticles. My research is not limited to sea urchin. It’s  fun to work with other labs to analyze transcriptome data from multiple organisms: Xenopus, zebrafish, sponges, and even pea aphid and its endosybiont!

I’m very grateful for these three experiences during my PhD that have made me to get where I am:

1. Independently design and perform my first RNA-seq project, learn the data analysis from scratch and learn it the hard way. I super appreciate the maximum freedom Dr. Wikramanayake had gave me for me to develop my project the way I like. It is the most valuable project for me.

2. The MSU NGS Summer course organized by Dr. Titus Browne (now is ANGUS: Analyzing High Throughput Sequencing Data at UC Davis). It was extremely helpful for me to get a general idea of this field before I started my own analysis. It also provided A LOT of useful resources for my future work.

3. The Visiting Scientist Program in the Regev Lab at the Broad Institute. After that trip I completely understood one particular concept–among many other gains–batch effect. It was helpful for me to understand the nature of my data, to explain this effect to biologists and to study how to control it in the analysis. Ultimately, I was able to establish a couple of collaborations just based on that. Moreover, the experience of working with the leading scientists in the Regev lab inspires me to moving forward all the time.

Google Scholar Page:
WeChat: cellcreator

Something else

Outside of my work and my family, I have little time. But when a free moment comes, I do have a few hobbies:

I played an enormous amount of soccer growing up. That’s also one reason why I loved living in Miami before, because you can play soccer all year around as long as there’s no hurricane.