Save the Date!

May 15th – 19th, 2017 

iCubed, 80 Washington Street
Providence RI, United States


The Institute for Immunology and Informatics (iCubed) will once again be hosting our training workshop in vaccine design for Neglected Tropical Diseases and Emerging Infectious Diseases (NTD/EID)

This May, the Institute for Immunology and Informatics (iCubed) will once again be hosting a training workshop in vaccine design for neglected tropical diseases and emerging infectious diseases (NTD/EID). This workshop will give interested researchers an opportunity to bring a research topic of their choice to Providence, RI and to work one-on-one on the topic with the developers and expert users of the iVAX Toolkit.

The iVAX Toolkit has been developed and refined by EpiVax, Inc., and it is available for collaborative research projects under agreement with iCubed. Previous NTD/EID fellows have worked on leishmania, cysticercosis, Chagas disease, hepatitis C (genotype IV), and PRRSV.

A few of the publications that resulted from previous workshops are shown here:

  1. An immunoinformatic approach for identification of Trypanosoma cruzi HLA-A2-restricted CD8(+) T cell epitopes.
  2. Preclinical development of HIvax: Human survivin highly immunogenic vaccines.
  3. Identification and retrospective validation of T-cell epitopes in the hepatitis C virus genotype 4 proteome: an accelerated approach toward epitope-driven vaccine development.
  4. Time for T? Immunoinformatics addresses vaccine design for neglected tropical and emerging infectious diseases.
  5. Development and validation of an epitope prediction tool for swine (PigMatrix) based on the pocket profile method

Over the course of the week-long workshop, NTD/EID research fellows will learn to apply these state-of-the-art informatics tools to their project of choice, and learn a better understanding of how to use the iVAX toolkit to design vaccines. Fellows will train at iCubed and then return to their home institutions to proceed with their projects. They will have continued support from the iVAX team at URI to sustain their projects as needed, until the project has been completed. Access to the tools and expertise is provided at no extra cost. 

Space is limited! Only six NTD/EID fellows will be selected from the list of applicants, based on the applicant’s current involvement in research on neglected tropical diseases, prior doctoral or equivalent training in immunology (or a related area in the vaccine development field) and documented commitment from the applicant’s home institution to their research career. The fellows will be expected to generate data and publications after the training, and to submit grants for research using the toolkit.
How to Apply

Currently we do not have scholarships for this workshop. The all-inclusive cost for food, course materials and lodging for the week is $2,225*. To apply, please provide the following information:

  • A description of the fellow’s work, including proposed application of the iVAX toolkit to their research program (maximum two paragraphs).
  • Curriculum Vitae.
  • 2 letters of support from the fellow’s research mentor at their home institution.

All application materials should be sent electronically to Matt Parrillo at by March 1, 2017.
We look forward to hearing from you!
Annie De Groot MD
Professor and Director,
Institute for Immunology and Informatics.

*Organizational costs, course materials, food and accommodation for five days/four nights (in local hotels) for the fellows. The price of the workshop can be adjusted if lower-cost housing (e.g. AirBnB) is identified.

Past Events

1st Immunogenicity – Determinates and Correlates
May 9, 10 and 11
Providence, RI

Annie De Groot, University of Rhode Island
Advisory Board
Eric Furfine
Terry Goletz, Amgen
Chris Bailey-Kellogg, Dartmouth
Leslie Cousens, EpiVax Inc.
Daniela Verthelyi, FDA
Eric Wakshull, Genentech
Sara Brett, GlaxoSmithKline
Bonita Rup, Pfizer
Michael Brehm, UMass
David Scott, Uniformed Services University of Health Sciences
Anish Suri, Bristol Myers Squibb
Nick Marsh, Adnexus
Andy Glasebrook, Eli Lilly
Dale Greiner, UMass
Amy Rosenberg, FDA
Naren Chirmule, Amgen
Michel Awwad, Pfizer
Denice Spero, University of Rhode Island
Alan Rothman, University of Massachusetts

Preliminary Agenda

Session I:   Determinants – Predicting Immunogenicity
Session Chair and Panel Leaders: Bonnie Rup, Pfizer and Terry Goletz, Amgen

Session II: Correlates – Biomarkers and Model Systems
Session Chair and Panel Leaders: Michel Brehm, UMass and David Scott, USUHS

Session III: Risk Mitigation – Preclinical Studies and Clinical Studies
Session Chair and Panel Leaders: Eric Furfine and Naren Chirmule, Amgen

Session IV: Case Studies

To be held in conjunction with the TRIAD Toolkit and Tregitope Meeting May 11th.


TRIAD Toolkit Training and Pilot Project Grant Announcement

On May 11, 2011 the Institute for Immunology and Informatics (iCubed) at the University of Rhode Island’s Providence campus will hold a training session on vaccine design. This training will include hands-on training to use state of the art immunoinformatics tools to predict vaccine candidates. The purpose of the Pilot Projects is to train new researchers to use advanced immunoinformatics tools in order to accelerate vaccine design in the area of human immunology and Category A, B and C priority pathogens, their toxins and other emerging infectious diseases. The program is designed to facilitate investigators to obtain “preliminary data” and to be successful at securing future research grants. Ph.D.s who attend this training will be eligible to apply for a Pilot Project grant through the Translational Immunology Research and Accelerated Vaccine Development (TRIAD) program. $150,000 is available and it is anticipated 2-3 grants will be awarded.

Second Immunoinformatics and Computational Immunology Workshop (ICIW 2011)
Chicago, IL, U.S.A. August 1-3, 2011

To be held in conjunction with the ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB)

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 workshop aims to attract researchers from computer science, information science, biomedicine, bioinformatics, systems biology, and immunology to share research challenges, research results, methods, and advances in immunoinformatics and computational 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
– 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

Organizing committee

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

Program Committee (Tentative)
Becca Asquith (Imperial College London, UK)
Anne De Groot (URI Institute for Immunology and Informatics, USA)
Salvador Eugenio Caoili (University of the Philippines Mani)
Can Kesmir (Utrecht University, Netherlands)
Andrzej Kloczkowski (Ohio State University, USA)
Santo Motta (University of Catania, Italy)
German Nudelman (Mount Sinai School of Medicine, USA)
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)

Dr. Yasser EL-Manzalawy
Assistant Professor
Systems and Computer Engineering
Al-Azhar University
Cairo, Egypt

Visiting Research Associate
Artificial Intelligence Research Laboratory
Center for Computational Intelligence, Learning,&  Discovery
Department of Computer Science
215 Atanasoff Hall
Iowa State University
Ames, Iowa 50011-1040

Neglected Tropical Diseases Workshop Set for January [January 4-21]

The Institute for Immunology and Informatics (I’Cubed) will hold a training session targeting neglected tropical diseases over three weeks in January 2011 at the URI Providence Biotechnology Center.

I’Cubed selected 13 fellows for the training. Selections were based on the applicant’s current involvement in research on neglected tropical diseases, prior doctoral or equivalent training in immunology or a related area in the vaccine development field and substantial commitment from the applicant’s home institution to their future research career.

Keynote speakers include:

Professor Maria Botazzi, George Washington University

Professor Michael Cappello, Yale School of Medicine

Professor Diane McMahon-Pratt, Yale School of Public Health

Professor Steve Williams, Smith College

Professor Alan Rothman, University of Massachusetts Medical School

Professor Matt Waldor, Harvard University

Professor Loren Fast, Division of Hematology/Oncology at Brown University

Mini-Symposium on HIV/AIDS [November 8]

An interdisciplinary program to bring forth the different issues in global health through the lens of HIV/AIDS around the world.

 University of Rhode Island (Kingston Campus) Galanti Lounge

4th Annual Vaccine Renaissance Conference [October 21-23]

The 4th Vaccine Renaissance is dedicated to creating a dynamic interchange, by bridging disciplines (immunoinformatics, vaccine delivery, clinical vaccine trials and basic research) while offering multiple opportunities for contact between academic researchers and members of the vaccine R&D biotech industry.

Speakers will describe new approaches to developing vaccines for today’s most significant infectious disease threats such as influenza, neglected tropical diseases, multidrug resistant tuberculosis, and HIV.

University of Rhode Island (Feinstein Providence Campus), 80 Washington Street, Providence, RI 02903 & The Hotel Providence

Smart Vaccines for Entrepreneurs Class

We are excited to announce that the Institute for Immunology and Informatics (I’Cubed) will conduct a workshop for scientists and business students to be trained in the principals of biotechnology startup. The area of focus is vaccine design and businesses that support vaccine research and development. Participants will develop knowledge related to the development of ‘smart vaccines’ and infectious disease diagnostics and will be trained by experienced and successful vaccine and business experts. The goal of this program is to bring together scientists and business-savvy entrepreneurs who have the drive and desire to start health care-related businesses in Rhode Island.

The program will feature presentations such as:
• Practical uses of immunology and related market categories: vaccines, diagnostics, and delivery systems.
• Operating a Biotechnology company and options for funding a new company (presented by RI-based CEOs and COOs).
• Businesses that support vaccines which are not available in RI such as protein production and diagnostics.
• How to write a business plan including marketing and sales management, market analysis, supply chain management and financials.
Participants will be eligible to compete for a $2500 cash prize given to the student (or team) who has the best idea and business plan for a vaccine related start- up company. This award can be used for seed funding to establish a web site or apply toward incorporation fees.

WHO SHOULD APPLY: Participants should have business training OR a background in biology, technology or immunology. Participants must have the drive and ambition to start a company in RI and to expand RI’s knowledge economy.
ORGANIZERS: Denice Spero, Ph.D. and Annie De Groot, M.D. Research Professors, I’Cubed
University of Rhode Island (Feinstein Providence Campus), 80 Washington Street, Providence, RI 02903


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    10th Annual Vaccine Renaissance Save the Date Postcard

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