Omics Working group

SMDA’s Omics working group focuses on enhancing training and fostering collaboration within genomics, proteomics, and metabolomics. Recent advances in sequencing, chromatography, and mass spectrometry have enabled comprehensive measurement of gene expression, protein expression, and metabolite concentrations, significantly disrupting traditional laboratory practices. These new “-Omic” datasets are highly analogous to traditional laboratory methods and data (e.g., RT-PCR, western blot, flow cytometry, TLC, LC-MS). This similarity makes it increasingly important for computational and experimental investigators to work closely together due to their complementary expertise.

For instance, as illustrated in the figure to the right, experimental biologists are very comfortable with the mechanisms underlying the “Central Dogma,” while computational biologists are more familiar with the “normal range” of protein and mRNA expression within a cell. Overall, experimental science provides us with concepts and pathways, while computational science allows us to analyze these pathways and their components at scale. The goal of SMDA is to bring together computational and experimental expertise on these “-Omics” datasets here at UGA.

 

University of Georgia Focus-Areas

A major focus of the SMDA is to better coordinate Omic research across different animal models of disease (see figure below). Traditionally, biomedical research is often siloed based on the animal models used, due to practical variabilities in studying diseases in rodents, dogs, cats, and human patients. At UGA, we possess significant scientific and clinical expertise in all these areas, which we aim to leverage to improve patient outcomes in both veterinary and human medicine. Currently, a key focus of the Omics Working Group is on new single-cell and spatial transcriptomic technologies, which specifically require the combined expertise of both communities.

 

Computational and Experimental Protocols:

In addition to the data itself, understanding the process of generating that data is critical for addressing different scientific questions. These procedures, conducted by experimental investigators, can be highly significant to computational investigators because they may introduce biases and gaps in the dataset due to technical variations in data generation, rather than the underlying biology.

For example, the cellular organization of molecules is often studied through a combination of microscopy and serial centrifugation, which separates different cellular compartments based on their physical properties. Variations in these procedures can directly impact the measurement of nuclei-specific proteins and RNA. On the other hand, Genomic data generation (DNA/RNA) is based on separation by chemical properties through serial extraction techniques, enabling the separation of this material based on their chemical properties. These procedures separate proteins, lipids, DNA, and different types of RNA for downstream analysis.

Proteomic data generation typically relies on the physical separation of proteins by size. Size exclusion chromatography can enrich proteins of a specific size by over 20 times, while affinity purification can concentrate specific proteins by approximately 1000 times. Subsequent mass spectrometry has revealed that the majority of the cellular proteome is actually devoted to housekeeping functions like translation, protein folding, cellular metabolism, and the cytoskeleton. Finally, metabolomics involves chemical separation techniques similar to those used for DNA/RNA and proteins, such as serial extraction and chromatography. This enables the separation of lipids, sugars, amino acids, and nucleic acids, which constitute the majority of small molecules within a cell.

 

 


Tactical Priorities

  • Recruit Workforce:  with interests in bioinformatics and medicine
  • Train Workforce:  to use emerging tools of
    • bioinformatics
    • data-science
    • artificial intelligence
  • Build Collaborations:  between relevant disciplines
    • clinicians
    • scientists
    • data scientists
  • Automate:   laborious and iterative processes to:
    • increase efficiency of research
    • increase access to advanced computational methods
  • Map Community Datasets:
    • cancer genomics
    • infectious disease genomics
    • immunology

Strategic Priorities

  • Single-Cell Transcriptomic Technologies:
    • spatial transcriptomics
    • single-cell RNAseq
  • Cross-species analyses infrastructure:
    • rodent models
    • canine models
    • human data
  • Clinical Collaborations:
    • veterinary medicine
  • Industrial Partnerships:
    • post-graduate training
    • doctoral student internships
    • collaborations


Current Members

  • Eugene Douglass
  • Jonathan Mochel
  • Karin Allenspach
  • Blake Billmyre
  • LeighAnne Clark
  • Lok Joshi
  • Tatum Mortimer
  • Natarajan Kannan
  • Shaying Zhao
  • Kaixiong Ye
  • Lohitash Karumbaia
  • Aditya Mishram
  • Fabio Santori
  • Anthony Ruberto
  • Jarrod Call

Software Tools


Cleaned Datasets


Key Performance Indicators: summary statistics

 

KPI Category KPI Current Value
Research and Publications Number of Published Papers
Impact Factor of Journals
Citations
Conference Presentations
Collaboration and Engagement Interdisciplinary Projects
External Collaborations
Collaborative Publications %
Workshops and Seminars
Funding and Grants Research Grants Received $
Grant Applications Submitted
Grant Success Rate %
Data and Tools Datasets Published
Software Tools Developed
Tool Adoption downloads
Training and Development Students Supervised
Training Programs
Skill Development certificates
Impact and Outreach Societal Impact
Media Mentions
Public Engagement events
Operational Efficiency Project Completion Rate
Data Management Practices % compliance
Resource Utilization % efficiency
Innovation and Excellence Awards and Recognitions
Innovative Solutions breakthroughs
Feedback and Improvement Stakeholder Feedback satisfaction
Continuous Improvement # iterations

 

 

 


Key Performance Indicators: specific items list

 


Protected Content

  • Research and Publications
    • Number of Published Papers
    • Impact Factor of Journals
    • Citations
    • Conference Presentations
  • Collaboration and Engagement
    • Interdisciplinary Projects
    • External Collaborations
    • Collaborative Publications
    • Workshops and Seminars
  • Funding and Grants
    • Research Grants Received
    • Grant Applications Submitted
    • Grant Success Rate
  • Data and Tools
    • Datasets Published
    • Software Tools Developed
    • Tool Adoption
  • Training and Development
    • Students Supervised
    • Training Programs
    • Skill Development
  • Impact and Outreach
    • Societal Impact
    • Media Mentions
    • Public Engagement
  • Operational Efficiency
    • Project Completion Rate
    • Data Management Practices
    • Resource Utilization
  • Innovation and Excellence
    • Awards and Recognitions
    • Innovative Solutions
  • Feedback and Improvement
    • Stakeholder Feedback
    • Continuous Improvement