Innovator Awardees and Projects


Focus Areas:

  • Leverage ISB data assets and resources created by current and previous projects (understanding that the proposal must define a new research direction), including but not limited to:
    • relationship with Providence for clinical studies and e-consent platform
    • mobile phlebotomy, in-house blood processing, biobanking
    • deep immunophenotyping
    • compendium of drug-treated mycobacterium transcriptomes
    • spectral libraries for model organisms (E. coli, Mycobacterium sp., Halobacterium sp.)
    • single cell analytics technologies
    • knowledge graphs
    • longitudinal phenotype and exposure data from EHR
    • longitudinal multi-omic data from Arivale
  • Move current basic research and education insights toward a translational application.
  • Specifically connect the proposed research or education plan to a future external funding opportunity and articulate clearly how the proposed project will produce evidence or preliminary results for a competitive external application.
  • Leverage what we’ve learned from remote teaching and learning to improve student and teacher experiences (e.g. ISB education programs, workshops, or sponsored town hall events).


Lead Investigator: Yue Lu, Postdoctoral Fellow (Heath Lab)
ISB research team and collaborators: Christopher Lausted (Hood-Price Lab), Kai Wang (Hood-Price Lab)
Project Title: Multiparameter profiling of exosomes from body fluids to detect and determine site of infection.

Lead Investigator: Yin Tang, Postdoctoral Fellow (Wei Lab)
ISB research team and collaborators: Guangrong Qin (Shmulevich Lab), David L. Gibbs (Shmulevich Lab)
External collaborators: Raymond S. Yeung, University of Washington
Project Title: Joint spatial molecular and metabolic function profiling in single tissue section at single cell sensitivity

Lead Investigator: Bahar Tercan, Postdoctoral Fellow (Shmulevich lab)
ISB research team and collaborators: Cory Funk (Hood-Price Lab), Boris Aguilar (Shmulevich Lab), Max Robinson (Hood-Price Lab)
Project Title: Discerning the combinatorial regulatory circuitry of microglial differentiation in Alzheimer’s disease using probabilistic Boolean networks


Focus Areas:

Proposals with novel approaches to address the questions identified below were encouraged.

Scientific Research Proposals:

  • How does the gut microbiome modulate host responses to drugs/diet/lifestyle?
  • How do you quantify relationships between Alzheimer’s Disease (AD) and the immune system?
  • How do you extract disease-specific information from data clouds?
  • How do you link electronic health records (EHR) to causal mechanistic underpinnings of disease?
  • What are the differences between men and women’s response to multi-modal AD therapy or rates of Sepsis?
  • How do you identify novel risk factors (such as exposures, phenotypes, EHR) to predict risk to inform better care decisions?
  • How do you develop systems biology tools to characterize cell state transitions in health and disease?
  • How do you integrate multi-modal imaging and molecular data with machine learning approaches for predictive clinical decision making?
  • How would you develop a program to mine drug databases (DrugBank, SIDER, Pharao, GINA, etc) for side effects that could be used for drug repurposing (example: Viagra)?
  • How is cancer progression correlated with co-morbidities?
  • Proposals that leverage ISB’s resources (biobanks Arivale software platforms, EHR records, etc.) are encouraged. A list of resources can be found here.

Education proposals:

  • How can we scale ISB Education’s programs?
  • How can we develop physical toys that convey in an intuitive manner emergent properties to high-school students?


Lead Investigator: Cheng Dai
ISB Collaborators: Brett Smith, Ryan Roper, Jewel Lee, Alison Paquette
Project Title: Incorporating health-related social needs and social determinants into electronic health records to promote population health
View the proposal and review (internal use only)

Lead Investigator: Jen Eklund
ISB Collaborators: Becky Howsmon, Dave Gibbs, Noa Rappaport, Rachel Calder
Project Title: Exploring Stability and Change in Education Data
View the proposal and review (internal use only)

Lead Investigator: Jie Luo
ISB Collaborators: Marlee Ng, Jacob Bassett
Project Title: Development of 3’dCDP-DAG prodrug for antiviral treatment
View the proposal and review (internal use only)


Focus Areas:

  • Multiscale interactions
  • Quantitative definition of uniqueness and states
  • Concept to classroom


Lead Investigator: Jacob Valenzuela (Baliga Group)
ISB Collaborators: Becky Howsmon, Wei-ju Wu, Nyasha Chambwe, and Jen Eklund
Project Title: Central Dogma–The development of an interactive gaming pipeline that teaches critical STEM concepts directly to the classroom
View the proposal and review (internal use only)

Lead investigator: Shiqun Shao  (Wei Group)
ISB Collaborators: Dan Yuan and Chunmei Liu
Project Title: Development of A Massively Parallel Single-cell ChIP-Seq Technology
View the proposal and review (internal use only)

Lead Investigator: Shizhen Qin (Hood-Price Group)
ISB Collaborators: Christian Diener, Sushmita Patwardhan, Yong Zhou, Li Tang, Gustavo Glusman, and John Earls
Project Title: Integrating genetics, blood proteomics and the gut microbiome to understand transitions from high to lower weights
View the proposal and review (internal use only)


Focus Areas:

  • Novel experimental systems
  • Therapeutics/interventions
  • Diagnostics
  • Tracking spatiotemporal heterogeneity of biological phenomena


Lead investigator: Matt Idso (Heath Group)
Collaborators: Mario Arrieta-Ortiz (Baliga Group), Ajay Akhade (Subramanian Group)
Project title: Peptide-based immunotherapeutics to combat drug-resistant bacteria
View the proposal and review (internal use only)

Lead investigator: John Earls (Hood-Price Group)
Collaborators: Theo Knijnenburg (Shmulevich Group), Michael Strasser (Huang Group)
Project Title: High-throughput Artificial Neural Net Architecture for Health using pD3 clouds
View the proposal and review (internal use only)

Lead investigator: Yapeng Su (Heath Group)
Collaborators: Joseph Zhou (Huang Group), Theo Knijnenburg (Shmulevich Group), John Earls (Hood-Price Group), Alphonsus Ng (Heath Group), Priyanka Baloni (Hood-Price Group)
Project Title: Model driven discovery of central ligand-receptor pairs that maintain the drug resistance of a tumor cell ecosystem community
View the proposal and review (internal use only)

Lead investigator: Adrian Lopez Garcia De Lomana (Baliga Group)
Collaborators: Martin Shelton (Hood-Price Group), Chris Lausted (Hood-Price Group), Jessica Day (Baliga Group)
Project Title: One day of HIV infection one cell at a time
View the proposal and review (internal use only)


Focus Areas:

  • Single cell analytics
  • Interactomics
  • Genome editing
  • Big data analytics & modeling


Lead investigator: Chris Lausted (Hood-Price Group)
Collaborators: Neda Jabbari (Hood-Price Group), Changting Meng (Hood-Price Group), Vesteinn Thorsson (Shmulevich Group)
Project title: Sequence of the COLO320 double minute chromosome and its effect on gene expression

Lead investigator: Eliza Peterson (Baliga Group)
Collaborators: Eliza Peterson (Baliga Group), Mark Gillespie (Ranish Group), Fred Mast (Aitchison Group)
Project title:  High-Throughput Analysis of Regulatory Interactions in Mycobacterium Tuberculosis

Lead investigator: Joseph Zhou (Huang Group)
Collaborators: Irit Ruben (Huang Group), Chris Lausted (Hood-Price Group), Theo Knijnenberg (Shmulevich Group)
Project title: A Novel Technique to Monitor Single-Cell Transcriptome over Time Using Barcoding