Third Immunoinformatics and Computational Immunology Workshop (ICIW 2012)


To be held in conjunction with the ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB) (, Orlando, FL, U.S.A. October 7-10, 2012

Naturally emerging or reemerging diseases pose some of the most serious threats to human health. Computational methods are urgently needed for developing new vaccines, therapies, and models to improve our understanding of the immune system, and reliable tools for focusing experimental investigations.

The main theme of this meeting is “Bridging Immunology and Computer Science”. Nowadays computational methods are integral to virtually every research and development project in every discipline. Immunology is not an exception and the need for sophisticated computational methods for research and development in immunology is increasing. At the same time, because of the extreme domain complexity of immunology, the lag between availability of sophisticated computational methods and their implementation in this field is increasing. The ICIW 2012 will include presentations that describe theoretical advances and practical applications that will help bridge this gap and, as a consequence, accelerate the development of immunology. Topics of interest include, but are not limited to:

  • Structural Immunoinformatics
  • Epitope analysis and prediction
  • MHC-peptide binding site analysis and prediction
  • Immunoinformatics Databases, Knowledge Bases, Ontologies
  • Computational modeling of immune system
  • Analysis and prediction of minor histocompatibility antigens
  • Predictive models for organ transplantation
  • Immunogenomics
  • Immunomics
  • Vaccine design
  • Artificial immune systems and other biologically-inspired paradigms
  • Multi-agent based modeling of immune response
  • Allergenicity prediction
  • Gene expression changes in adaptive immune response
  • Comparative approaches to immunology

Important Dates

Paper Submission deadline: June 22, 2012
Poster Submission deadline: August 3, 2012
Notification of acceptance: July 22, 2012
Camera-ready of accepted papers: August 16, 2012

Poster Submission

We invite authors to submit one-page extended abstracts. Submissions should be sent to before August 3, 2012. Notification of acceptance will be given by August 10, 2012. Accepted abstracts will be selected for oral or poster presentation and will be included in the workshop Web page.



Research in immunology is characterized by the production of increasingly vast amounts of data, fuelled by genomics and proteomics projects and large-scale screening of pathogen- and antigen-host interactions. The need to store, manage and analyze this rapidly growing resource of experimental, clinical and epidemiologic data has given rise to the field known as immunoinformatics. Immunoinformatics represents computational methods and resources that are used in the study of immune function. It lies at the intersection of experimental and computational sciences and encompasses domain-specific databases, computational models and strategies drawn from artificial intelligence.

In this tutorial, representatives from several immunoinformatics research groups will present some state-of-the-art resources and tools for immunoinformatics.  The major goals are two-fold: i) demonstrate the utility of selected computational tools and resources to target users (i.e., immunologists); ii) understanding strengths and limitations of existing computational methods and highlighting current challenges.

Intended audience

Participants in this tutorial should have a basic understanding of immunology. No advanced coursework in biology or computer science is required.


  • Introduction (15 minutes)
    • Speaker: Vladimir Brusic, Harvard University
  • Part I: Immunoinformatics Resources
    • Immune Epitope Database (30 minutes)
      • Speaker: Bjoern Peters, La Jolla Institute of Allergy and Immunology
    • Eukaryotic Pathogen Database Resources (30 minutes)
      • Speaker: Jessica Kissinger, University of Georgia
  • Part II: Immunoinformatics Tools
    • Predicting long MHC-I binders (30 minutes)
      • Speaker: Claus Lundegaard, Technical University of Denmark
    • iVAX: Interactive Vaccine Design Toolkit (45 minutes)
      • Speaker: Anne De Groot, URI Institute for Immunology and Informatics
    • Interactive Screening and Protein Re-engineering Interface (ISPRI) (45 minutes)
      • Speaker: Anne De Groot, URI Institute for Immunology and Informatics
  • Discussion and Conclusions (15 minutes)
    • Speaker: Vasant Honavar, Iowa State University

Organizing committee
Vasant Honavar (Iowa State University, USA)
Vladimir Brusic (Harvard University, USA)
Yasser EL-Manzalawy (Iowa State University, USA)

Program Committee (Tentative)
Becca Asquith (Imperial College London, UK)
Raffaele Calogero (University of Torino, Italy)
Anne De Groot (URI Institute for Immunology and Informatics, USA)
Salvador Eugenio Caoili (University of the Philippines Manila, Philippines)
Tomer Hertz (Fred Hutchinson Cancer Research Center, USA)
Can Kesmir (Utrecht University, Netherlands)
Andrzej Kloczkowski (Ohio State University, USA)
Oliver Kohlbacher (University of Tübingen, Germany)
Christophe Magnan (University of California, Irvine, USA)
German Nudelman (Mount Sinai School of Medicine, USA)
Francesco Pappalardo (University of Catania, Italy)
Bjoern Peters (La Jolla Institute of Allergy and Immunology, USA)
Nikolai Petrovsky (Flinders University, Australia)
Julia Ponomarenko (University of California, San Diego, USA)
Johannes Sollner (Emergentec Biodevelopment GmbH, Austria)
Anna Tramontano (Sapienza University of Rome, Italy)
Guanglan Zhang (Dana-Farber Cancer Institute, USA)