Above, the Bioinformatics and Analytics core used 10X Genomics Visium technology to measure expression in specific tissue sections, connecting biological process with biological architecture.
The size and complexity of research data continue to grow as more investigators solve problems and answer questions using multidisciplinary approaches like one health, precision health, precision agriculture and others.
According to Lyndon Coghill, director of the University of Missouri Bioinformatics and Analytics advanced technology core facility, many of these data sets have now reached scales and complexities that require tools and skills that researchers may not have, such as new statistical methods, high-performance computing and storage and software engineering to tie it all together.
“Our mission is to allow researchers to focus on the questions important to their research while we tackle the data science, code and data architecture needed,” Coghill said of the core’s five full-time staff members and two students. “This allows them to conduct translational work without needing to hire their own data science teams or spend years learning a different field of research.”
Bioinformatics and Analytics is located in suite 106 of the Bond Life Sciences Center. Coghill, who has led the core since 2021, shares more details about this important campus resource.
Which research disciplines benefit the most from your services?
Any discipline that is connected broadly to the life sciences can benefit from our help. We support researchers across a variety of fields, including medicine, animal sciences, veterinary medicine, agriculture and natural resources. If you have a data-intensive study or question, we can likely help.
How has the core evolved since it was founded 13 years ago?
The core previously offered limited support and training in bioinformatics and high-performance computing. Since I came to MU, we have been growing our staff and adding infrastructure and capabilities. Much of that growth and development has been in contemporary research areas like single cell, spatial transcriptomics, high-throughput genomics and machine learning. Those are methods the core wasn’t staffed or equipped to handle previously, so many of them are new services. We continue to offer support in areas such as bulk RNASeq and metagenomics.
What are the core’s main services?
Broadly speaking, if it involves computationally working with data, we can help. Here are a few of our common services, but if you have a custom project in mind, we can probably help you accomplish your goals. We also have access to other significant computational resources that we can leverage for researchers, which can relieve you from the burden of trying to understand and find those resources yourself.
- RNASeq and transcriptomics
- 10X single cell and single nucleus transcriptomics
- 10X Visium spatial gene expression
- Genomics
- Metagenomics
- Custom reproducible and scalable pipeline development
- Data management
- Statistical analyses
- Machine learning model development
- Training and support
What new service is generating the most excitement?
In collaboration with the Genomics Technology and Advanced Light Microscopy cores, we now have the ability to process 10X Visium spatial samples. This enables researchers to study gene expression inside diverse cell populations and connect their raw data with biological architecture. We are in a unique situation at MU because we have three advanced technology cores with expertise in all the areas needed to help researchers with every step in this complex process.
How are Mizzou faculty using the core for their research?
We support researchers all over campus in a variety of different areas. Most of our data scientists have doctorates in life sciences fields. This background really helps our team understand the nuance of the questions researchers are studying and allows us to provide much more customized support. Recent examples:
- Aaron Ericsson, assistant professor of veterinary pathobiology, uses targeted amplicon and metagenomic sequencing, single cell transcriptomics and epigenomic arrays to identify features of the maternal microbiome influencing offspring neurodevelopment. The core helps him with analyses for 10X single cell and metagenomics projects.
- Olga Baker, professor of otolaryngology and biochemistry, uses spatial transcriptomics to study how specialized pro-resolving lipid mediators reduce inflammatory molecules in the autoimmune disease Sjogren’s syndrome. The core provides advanced data analyses and connects transcription profiles with biological structure.
- Chris Lorson, Curators Distinguished Professor and chief scientific officer of Shift Pharmaceuticals, studies neurodegenerative disorders Spinal Muscular Atrophy and Charcot-Marie-Tooth disease. The core helped identify potential off-target binding sites for various antisense oligonucleotides for his research program.
- Melissa Terpstra, professor of radiology and biomedical sciences and director of the NextGen Imaging Facility, uses ultra-high field MRI to measure chemistry in the living human brain to study aging and Alzheimer’s disease. She and core staff are collaborating on combining MRI results with other data to understand the etiology of cognitive decline.
- Wes Warren, professor of animal sciences, uses companion animal multiomic data to study similarities and differences to humans. The core provided sequence variant calls for canine hepatocellular carcinoma, a lethal liver cancer, to accelerate the biological interpretation of their potential role in tumor metastasis.
What is something people might not know about the core?
Many life sciences researchers on campus (perhaps most) have used our services even if they don’t know it. For example, we help build and maintain the genomics research infrastructure on campus by processing and distributing sequencing data for the Genomics Technology Core. This allows researchers to get their data easier and faster.
How do researchers request services?
We encourage you to contact us early in your research even if just for a discussion about experimental design. Many downstream aspects of bioinformatics and data science are affected by decisions made early in study design. We love to talk about science, computing and technology, so don’t hesitate to reach out often at 573-882-8831 or bioinformatics@missouri.edu.