Integrative Systems Biology Program

Program Director: Dr. Rasha Hammamieh

Introduction

The Integrative Systems Biology program at USACEHR is focused on comprehending the etiology of and finding solutions for military-relevant health issues. Integrative research and analyses are designed to understand, compare, and combine animal studies and human studies, computational simulations, and biologics (i.e., products derived from living organisms) acquired from human samples. The group consists of six PhD-level and ten MS/BS-level scientists.

Capabilities/Tools

Bench Work

We have multi-Omics platform facilitating the genomic, transcriptomic, proteomic and metabolomic investigations. A vast and constantly growing collection of tools and equipment are available in-house for conducting whole genome transcriptional analyses, deep panel proteomics and pyrosequencing. Our resources include automated biomolecule extraction tool - liquid handler and a spectrum of assay validation platforms. The lab automation is conducted by recruiting several cutting edge robotics modules and liquid handlers.

Animal Work

We also have access to a newly developed in-house vivarium to perform animal research with the capability to assess animal phenotypes using video photography. We also have a state-of-art necropsy room capable to support complex animal surgery. We maintain the highest standards of ethics and regulation in handling animals and biologics.

Bioinformatics and Statistics

A number of cutting edge statistical analysis suites and mining platforms are available for the back stream refinement and validation of the acquired data. A central data warehouse is leveraged to integrate intramural and extramural data across the enterprise and to perform analyses in order to convert knowledge to discovery. A mission critical task is to efficiently archive the knowledge for long term use.

Path Forward

We are also actively seeking opportunities to extend our expertise towards other emerging branches of Omics, such as microbiomics and lipidomics. At present, the program is focused to conduct multidisciplinary applied research using the Integrative Systems Biology approaches and tools to probe Post Traumatic Stress Disorder (PTSD), coagulopathy, and other diseases and injuries of military interest.

Software and Web Applications

We develop in-house software and web applications to facilitate analysis and visualization of complex systems biology projects.

Panoromics: This tool is a free web application designed to explore time-series network models online with full support of interactive animation functionalities. The users can not only display a network, but also track the changes, deposit network models, and compare with existing models. (https://bioinfo-abcc.ncifcrf.gov/panoromics)

COMBINER: This tool is a Matlab/R tool developed for identifying distinct conserved and unique expression patterns across various assay and longitudinal conditions. (BMC bioinformatics, 13(1), 2012; BMC systems biology, 7(1), 2013)

Functional heatcube: This tool is a free web application to analyze time-series data for heatmap-based visualization, pathway analysis, and comparison to different cohorts. (https://bioinfo-abcc.ncifcrf.gov/heatcube)

Current Projects

  • Systems Biology approach to find solutions for Post Traumatic Stress Disorder (PTSD). Read more in our list of publications.
  • Pan-omics approach to identify markers of Acute Coagulopathy of Trauma-Shock (ACoTS)
  • High Throughput Pan-omic approaches to study the effect of microgravity on responses of skin endothelial cells to endotoxic insult. Read more about our collaboration with NASA and Indiana University (IU) School of Medicine.
  • Systems biology approach to identify host therapeutic targets in non-human primates (NHP) exposed to Y. pestis
  • Pan-omics approach to find stress markers associated with the Rangers in a US military program
  • Complementary diets and medicines: a pan-omics approach
  • SysBioCube: a minable platform to archive and integrate the knowledge associated with Military health issues
  • Multi-omics approach to understanding pain signaling in the brain and identifying biomarkers for pain
  • Multi-omics approach to identifying determinants of successful burn wound grafting and healing

Collaborations

Our group maintains productive relationships with a number of internationally acclaimed hospitals and clinical sites to procure the biologics of interest.

We have active collaborations with a number of academic, commercial and clinical teams across the continents. Primary collaborators include Washington Hospital Center, Washington, DC; Mount Sinai School of Medicine, NY; the National Cancer Institute, MD; Naval Medical Center, CA; the Institute for Systems Biology, WA; the University of California - San Diego, CA; the University of California - Santa Barbara, CA; the Max Plank Institute of Psychiatry, Germany; Indiana University school of Medicine - Indianapolis, IN; The Geneva Foundation, WA; Science Applications International Corporation (SAIC), VA; United States Army Institute of Surgical Research (USAISR); and The Defense and Veterans Center for Integrative Pain Management (DVCIPM)

We actively seek partnership opportunities to share our expertise and expand our scientific reach for the betterment of military and civilian health. Below are some of the seminal projects presently underway.