Computational Genomics Challenges in Immuno-oncology


Pacific Symposium on Biocomputing
January 3-7, 2019
Fairmont Orchid Resort
The Big Island of Hawaii, USA


// Motivation


The discovery and development of drugs that can trigger or reinvigorate an effective and durable immune response to tumoral growth, or even wholesale elimination of the tumor, has led to the current immunotherapy revolution in cancer treatment. In spite of many striking successes, not all patients respond to such therapies, and a host of key personalized-medicine questions remain. Many of these questions are amenable to computational approaches, and the growth of genomics datasets being compiled worldwide, at both the single cell and bulk level, provides many opportunities for computational biologists and data scientists to meaningfully impact the course of cancer immunotherapy development.

// Topics

This session is devoted to computational issues and open questions related to extracting useful molecular predictors of tumor specific immune response and testing them on emerging checkpoint response data.  A primary focus will be on the algorithmic and computational challenges of analyzing high-dimensional bulk and single-cell omics data which sample the tumor and its microenvironment. There will also be time devoted to sharing progress and discussing strategies to solve the Immuno-oncology DREAM Challenge, currently under preparation. This Challenge will provide clinical, imaging, and molecular data to predict survival and stratify patient response using data from a recent checkpoint inhibitor clinical trial that will be shared through the DREAM Challenge.

Some broad areas of interest include but are not limited to:

  • Algorithmic challenges and improvements in neo-epitope identification (for both class I and class II presentation) workflows

  • Deconvolution of bulk or single-cell data from the tumor microenvironment (TME) to characterize tumor-infiltrating immune response or immunosuppressive stromal state

  • Characterization and joint modeling of tumor subclonality (intra tumoral heterogeneity) and immune response heterogeneity

  • Identification of biomarkers of primary or acquired resistance to checkpoint inhibition

  • Identification of circulating biomarkers of response to immunotherapy

  • Machine learning models of immunotherapy response and survival using new and legacy datasets (e.g. TCGA)

  • Microbiotal correlates and models of immunotherapy response

  • Strategies to solve the Immuno-oncology DREAM Challenge, to stratify patient response and predict survival based on clinical, and omics data


// Key Dates


Paper submissions // 
11:59PM EST


Notification of paper acceptance


Final paper deadline // 11:59PM EST


Abstract Deadline //
11:59PM EST



// Submission Info

The PSB proceedings are unique in that they are an archival, peer-reviewed publication which is indexed in Pubmed.  In that sense, submissions are equivalent to short journal articles. Correspondingly, all submitted papers are reviewed by at least three reviewers and all accepted papers have met a rigorous standard which makes their future citation meaningful.  

Submitted papers are limited to twelve (12) pages in our pre-specificed publication format. If figures cannot be easily resized and placed precisely in the text, then it should be clear that with appropriate modifications the total manuscript length would be within the page limit. 

// Paper Format

Please see the official PSB website for more details on manuscript submission: 

Each paper must be accompanied by a cover letter. The cover letter must state the following:

  • The email address of the corresponding author.
  • The specific PSB session that should review the paper or abstract.
  • The submitted paper contains original, unpublished results, and is not currently under consideration elsewhere.
  • A very brief synopsis of the work and its relevance and impact for the session. 
  • All co-authors concur with the contents of the paper.