GSF Spotlight: Eddie Ruiz, Genetics & Genomics PhD student

Edward Ruiz, a 2023 Hariri Institute Graduate Student Fellow and GPGG PhD student, is working in the Dries Lab on new approaches in the emerging research area of spatial omics.

Applying experimental and computational methods to improve systematic understanding of tissue and tumor biology

By Chloe Wojtanik, Hariri Institute for Computing

When Edward C. (“Eddie”)  Ruiz, a third-year Genetics & Genomics PhD student, was asked to share what he’s most excited to accomplish during his time at the Hariri Institute, he simply said with a smile, “helping others learn.” Ruiz has always gravitated towards helping people, and this mindset has inspired his research focus at Boston University. 

Ruiz is a 2023 Hariri Institute Graduate Student Fellow (GSF), advised by Ruben Dries, PhD, whose research applies experimental and computational methods to improve systematic understanding of tissue and tumor biology.  In the Dries Lab, Ruiz’ research involves RNA processing (a field of biology concerned with RNA molecules e.g. alternative splicing), machine learning, and an emerging research area called spatial omics, which employs diverse technologies and computational methods to measure the molecular characteristics of cells (e.g. RNA, DNA, proteins, etc) within a tissue sample.

“Spatial omics is a really exciting field,” says Ruiz. “The ability to analyze cells in tissues and map their locations in the tissue is important for understanding tissue biology and disease pathology. It has the potential to reveal new insights on why special cell types or tissues function a certain way, or how cancers develop. However, one of the challenges is that different spatial technologies provide different readouts  and they often do this at different resolutions.” 

This poses a challenge to scientists who are trying to study tissues at the highest resolution possible to make clinical decisions or study rare cells in tissues. “It’s like taking a picture at 144 pixel resolution versus 4K resolution,” Ruiz says. “When analyzing spatial omics data micro (e.g. subcellular) and macro (e.g. multi-cellular) patterns of tissue biology are more or less apparent depending on the technology that you use and the methods you analyze this data with. So it’s important to enable researchers to derive these insights from their data, to get the most complete picture of their tissues.”

The Dries Lab developed Giotto Suite, an open-source software package that provides data structures and computational methods for comprehensive analysis and visualization of spatial omics data, to address these problems. Ruiz is working on developing  Giotto Suite as part of  a project called “Multi-resolution and Multi-modal Data Structures for Integrative Spatial Omics Analysis,”  which aims to harmonize data structures for processing, integrating and jointly analyzing virtually all spatial omics datasets. This research project received a prestigious award earlier this year from the Chan-Zuckerberg Initiative to support essential open source software used in the biomedical research community.  

Ruiz is also working on addressing another major challenge in the spatial omics field: analyzing large spatial omics datasets without the need for expensive computational infrastructure. “The size of these spatial datasets pose a major challenge to researchers because existing computational methods were designed to work with smaller datasets and often do not work with the latest spatial omics datasets, which are ten or hundred times bigger in size. So new approaches for representing these data are required that are more scalable and accessible to researchers.” Ruiz is actively working on a new software package that he plans to publish later this semester and will be presenting at the Boston University Department of Medicine Evans Day symposium later this October.

In addition, Ruiz shared that learning about best practices for analyzing spatial data has been one of the most exciting parts of his research so far. “Methods for analyzing spatial data have been largely pioneered by the geospatial field and we are still figuring out how best to implement these methods with spatial omics data.” To learn more about spatial analysis methods, Ruiz was awarded a scholarship to attend the University of Washington Summer Institutes in Summer 2023 where he took several courses related to statistics and spatial data analysis. “The experience was very helpful and I enjoyed being able to learn from so many different researchers across the world,” says Ruiz.

When asked what first got him interested in spatial omics, Ruiz circled back to his undergraduate years at the University of Wisconsin-Madison. Like many young STEM students, Ruiz was trying to find labs he could participate in to give himself more experience and exposure. With the help of a work-study grant, he happened to get involved in a stem cell research lab during his first year, which he slowly  fell in love with. 

“When I started, my job in the lab  was really basic, like maintaining the lab equipment, but I was excited to go every time and learn what people in the lab were doing,” says Ruiz. “Gaining experience on how technology and research were being used to improve patient lives really drove me. I worked in my first lab  for all four years of my undergrad  and was able to gain a lot of exposure to stem cell research . This experience made me interested in focusing on  stem cells more and today remains a part of my other major research project focusing on human blood stem cells and the niche that support their development in the fetal liver.”

Ruiz says he feels a responsibility to help guide other students towards learning about computational research methods and open source software development . “ I am very honored to be chosen as a Hariri Institute GSF, and one of the first at the BU Medical Center. I know how hard it can be to learn about computational methods, especially if you come from a ‘wet lab’ background and do not have many opportunities to learn from other computational researchers. As a fellow, I am interested in providing more opportunities for researchers from different fields to cross paths and learn how computational methods can be used in their work.” Ruiz. alongside other Institute GSFs,  will organize events sponsored by the Institute such as the ‘Did you know..?’ series, and is excited to serve as a bridge for researchers at the Medical Center and Charles River campuses.