October 4, 2016  |  Announcements, CITRUS, Release Notes  |  By  |  0 Comments

Fresh Squeezed News: Introducing CITRUS

Automatically Identify Predictive Biomarkers with Our Newest Algorithm


Why do some cancer patients respond well to immunotherapy but others do not?

Why do some people have a slow and painful recovery from surgery but others have a speedy recovery?

What are the biomarkers that can help predict these outcomes ahead of time?  

The Challenge:
High-dimensional single-cell analysis approaches are excellent for investigating such questions because many mechanisms of disease may only be visible at the single-cell level, eluding bulk analysis techniques. Emerging technologies such as high parameter fluorescence and mass cytometry, and powerful data analysis platforms like Cytobank, are providing unprecedented resolution for measuring single-cell biology. With these new technologies, a variety of specific cellular populations can be simultaneously identified, and anomalies can define different clinically relevant cohorts and serve as predictive diagnostics and prognostics.

The challenge of going from high-dimensional data to these useful findings lies in the analysis, which is often cumbersome, manual, subjective, and irreproducible. Our new version of the CITRUS algorithm aims to change that.

Introducing: CITRUS
CITRUS (cluster identification, characterization, and regression) is now available in Cytobank Enterprise and Cytobank Premium. The CITRUS algorithm enables automated discovery of statistically relevant stratifying biomarkers within single-cell datasets containing numerous samples across multiple known endpoints (e.g., responders versus non-responders). In collaboration with Stanford’s Nolan Lab, we’ve integrated the algorithm to work seamlessly with Cytobank.

CITRUS can be used in any analysis requiring the comparison of groups of samples. Examples could include clinical comparisons, biomarker discovery, and any application relevant to building predictive or correlative models for the classification of samples in other independent data sets.

How it Works:
CITRUS in Cytobank uses an unsupervised and supervised Machine Learning pipeline to automatically find biomarkers that are correlated with an outcome group, or find a set of biomarkers that best predicts that outcome group. The results of a CITRUS run are clusters and associated features that differentiate the observed endpoint of the samples.

A visual explanation of CITRUS method – in this example a cluster is discovered with differential pS6 signaling between the responder and non-responder groups

CITRUS is only available in Cytobank Premium and Enterprise Editions.
cyobankarrow40x40Start Your Free 30-day Trial of Premium Cytobank

The Cytobank CITRUS Advantage:

  • Get Started in Minutes
    No need to know R, and no need for additional Computational Biology resources. The CITRUS tool is integrated seamlessly with Cytobank, and is easy to use.

“CITRUS is very easy to use and integrated into the Cytobank platform, which makes handling and organization of raw data possible. All of the algorithms (SPADE, viSNE, and CITRUS) are implemented in a way that allows easy execution of workflows.”

–Thomas Liechti
Institute of Medical Virology
University of Zurich

  • Improve Efficiency and Accuracy of Your Data Analysis.
    Instead of a raw data dump that is then subject to interpretation, CITRUS delivers automated identification of statistically-significant biomarkers.
  • Gain the Cloud Advantage in Productivity and Data Integrity
    Leverage the speed and efficiency of our high-powered servers in the Cytobank Cloud to gain results in a fraction of the time. Unlike slower, local plugins that require dedicated memory and limit your ability to multi-task, Cytobank’s CITRUS analysis can run imperceptibly in the background while while you use other parts of Cytobank, or exit the platform entirely. By storing in the cloud, your advanced analysis results remain integrated, well-managed for quick recall, and secure collaboration and preservation throughout time.

“With our CyTOF studies and analysis we often have the impression of assembling a railroad track right in front of the train, and incorporating CITRUS has helped us build the track out faster and further ahead than before. We can now do in two weeks what would otherwise take months of slicing populations into smaller groups to conduct the analysis”

— Patrick Reeves Ph.D.
Team Leader, Vaccine & Immunotherapy Center
Massachusetts General Hospital

Learn More About CITRUS:
cyobankarrow40x40Visit Our Support Site for Full Documentation

cyobankarrow40x40See It in Action (Video)

CITRUS is only available in Cytobank Premium and Enterprise Editions.
cyobankarrow40x40Start Your Free 30-day Trial of Premium Cytobank

View a Recording of our CITRUS Webinar:
cyobankarrow40x40Watch it Now