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Immunoregulatory actions of Treg PPAR gamma in the gut mucosa
Bassaganya-Riera, J and R. Hontecillas (2007) Immunoregulatory actions of Treg PPAR gamma in the gut mucosa. AAI Annual Meeting, [...]

Dietary abscisic acid modulates T cell proliferation and cytokine production
Hontecillas, R., A.J. Guri, U. Wankhade, G. Lopez-Velasco, E.T. McCall, and J. Bassaganya-Riera (2007) Dietary abscisic acid modulates [...]

Docosahexaenoic and arachidonic acid-enriched infant formulas modulate antigen-specific T cell responses in the neonatal piglet
Bassaganya-Riera, J., A.J. Guri, A.M. Noble, K.A. Reynolds, J. King, C. Wood, M. Ashby, D. Rai, and R. Hontecillas (2007) [...]

The loss of PPAR γ in immune cells abrogates the ability of abscisic acid to improve insulin sensitivity through a mechanism involving suppression of MCP-1 expression and macrophage infiltration into white adipose tissue
Guri, A.J., R. Hontecillas, G. Ferrer, O. Casagran, U. Wankhade, A.M. Noble and J. Bassaganya-Riera (2007) The loss of PPAR g in immune [...]

Immunoregulatory actions of PPAR γ in CD4+ T cells and dendritic cells
Bassaganya-Riera, J. and R. Hontecillas (2006) Immunoregulatory actions of PPAR g in CD4+ T cells and dendritic cells. AAI Annual [...]

Activation of PPAR γ and δ by CLA mediates protection against colitis
J. Bassaganya-Riera, K. Reynolds, S. Martino-Catt, Y. Cui, L. Hennighausen, F.J. Gonzalez, and R. Hontecillas (2004) Activation of PPAR [...]

CD4+ T cell-depleted splenocytes in MDX Mice Post Weaning
Nakamura, A., J. Bassaganya-Riera, R. Grange, and M.E. Houston (2004) CD4⁺T cell-depleted splenocytes in MDX Mice Post Weaning. The [...]

Modulation of the Immune Response by CLA: Clinical Development
O’Shea, M., J. Bassaganya-Riera, R. Hontecillas, and I. Mohede. (2003) Modulation of the Immune Response by CLA: Clinical [...]

Dietary Interventions Against PCV2-induced Immunosuppression using conjugated linoleic acid
Bassaganya-Riera, J., R. Hontecillas, P.G. Halbur, K.J. Yoon, and R.M. Progranichniy (2003) Dietary Interventions Against PCV2-induced [...]

Dietary conjugated linoleic acid ameliorates CD4+-induced colitis in the RAG-2-/- adoptive transfer model
Hontecillas, R., and J. Bassaganya-Riera (2003) Dietary conjugated linoleic acid ameliorates CD4⁺-induced colitis in the RAG-2^-/- [...]

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Using Big Data to Inform Mental Health Policies
Andalib, M., G. Hughes, N. Hosseinichimeh, A.B. Lakeh, V. Abedi, R. Zand, N. Ghaffarzadegan. INFORMS 2015. Philadelphia, PA. November 1-4, 2015

ENISI Multiscale modeling of mucosal immune responses driven by high performance computing
Vida Abedi, Raquel Hontecillas, Stefan Hoops, Nathan Liles, Adria Carbo, Pinyi Lu, Cassandra Philipson and Josep Bassaganya-Riera. IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2015). Washington, DC, USA. 2015

Modeling Immunity to Enteric Pathogens
Bassaganya-Riera, J. (2015) Invited Speaker; Modeling Immunity to Enteric Pathogens, Modeling Immunity for Biodefense Summer School/Symposia, Rochester, NY

Modeling Immune responses to Helicobacter pylori
Bassaganya-Riera, J. (2015) Invited Speaker; Modeling Immune responses to Helicobacter pylori, Modeling Immunity for Biodefense, Rockville, MD

Computational modeling of mechanisms underlying immune responses to Helicobacter pylori
Bassaganya-Riera, J. (2015) Invited Speaker; Computational modeling of mechanisms underlying immune responses to Helicobacter pylori, AMS Esteren Sectional, Georgetown University, Washington, DC

Computational immunology in autoimmune diseases
Bassaganya-Riera, J. (2014) Invited Speaker; Computational immunology in autoimmune diseases, Feinstein Institute for Medical Research, Manhasset, NY

ENISI MSM: A novel multiscale modeling platform
Bassaganya-Riera, J. (2014) Invited Speaker; ENISI MSM: A novel multiscale modeling platform, IEEE International Conference: BIBM, Belfast, UK

Multiscale Modeling and Computational Immunology in Infectious Diseases
Bassaganya-Riera, J. (2014) Invited Speaker; Multiscale Modeling and Computational Immunology in Infectious Diseases, DoD, Dahlgren, VA

Mechanisms underlying immune responses to enteric pathogens
Bassaganya-Riera, J. (2013) Invited speaker; Mechanisms underlying immune responses to enteric pathogens, Division of Gastroenterology, VT Carilion School of Medicine, Roanoke, VA.

From the past to the future
Bassaganya-Riera, J. (2013) Session Chair; International Conference on Computational Biology: From the past to the future, Virginia Tech, Blacksburg, VA.

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Phase III Placebo-Controlled, Randomized Clinical Trial with Synthetic Crohn's disease Patients to Evaluate Treatment Response
Abedi, V., P. Lu, R. Hontecillas, M. Verma, G. Vess, C. Philipson, A. Carbo, A. Leber, N.T. Juni, S. Hoops, J. Bassaganya-Riera. Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology – Systems & Applications. In Press: Elsevier/MK 2015.

Modeling exercises
Abedi, V., S. Hoops, R. Hontecillas, A. Carbo, C. Philipson, M. Viladomiu, A. Leber, P. Lu, J. Bassaganya-Riera. Computational Immunology: Models and Tools. Elsevier 2015.

Multiscale Modeling: Concepts, Technologies, and Use Cases in Immunology
Abedi, V., R. Hontecillas, A. Carbo, C. Philipson, S. Hoops, J. Bassaganya-Riera. Computational Immunology: Models and Tools. Elsevier 2015.

From Big Data Analytics and Network Inference to Systems Modeling
Michalak, P., B.W. Sobral, V. Abedi, Y.B. Kim, X. Deng, C. Philipson, M. Viladomiu, P. Lu, K. Wendelsdorf, R. Hontecillas, J. Bassaganya-Riera. Computational Immunology: Models and Tools. Elsevier 2015.

Agent-Based Modeling and High Performance Computing
Alam, M., V. Abedi, J. Bassaganya-Riera, K. Wendelsdorf, K. Bisset, X. Deng, S. Eubank, R. Hontecillas, S. Hoops, M. Marathe. Computational Immunology: Models and Tools. Elsevier 2015.

Ordinary Differential Equations (ODE) based Modeling
Hoops, S., R. Hontecillas, V. Abedi, A. Leber, C. Philipson, A. Carbo, J. Bassaganya-Riera. Computational Immunology: Models and Tools. Elsevier 2015.

Immunoinformatics cybernfrastructure for modeling and analytics
Hoops, S., B.W. Sobral, P. Michalak, V. Abedi, B. Kronsteiner, R. Hontecillas, M. Viladomiu, J. Bassaganya-Riera. Computational Immunology: Models and Tools. Elsevier 2015.

Use of Computational Modeling in Immunological Research
Hontecillas, R., J. Bassaganya-Riera, C. Philipson, A. Leber, M. Viladomiu, A. Carbo, K. Wendelsdorf, S. Hoops. Computational Immunology: Models and Tools. Elsevier 2015.

Computational Modeling
Bassaganya-Riera, J., R. Hontecillas, V. Abedi, A. Carbo, C. Philipson, S. Hoops. Computational Immunology: Models and Tools. Elsevier 2015.

Introduction to Computational Immunology
Bassaganya-Riera, J., R. Hontecillas. Computational Immunology: Models and Tools. Elsevier 2015.

Modulation of CD8+ T cell Responses by Conjugated Linoleic Acid
Bassaganya-Riera, J, R. Hontecillas. Advances in CLA Research. Champaign, IL: American Oil Chemists Society Press 2006.

Computational Immunology: Models, tools and approaches for systems immunology
Bassaganya-Riera, J.. Elsevier 2015.

Literature mining and ontology mapping applied to big data
Abedi V, M. Yeasin, R. Zand. Mining Big Data to Improve National Security. Elsevier 2015.

Supervised Learning with Artificial Neural Network in Modeling of Cell Differentiation Process
Lu, P, V. Abedi, Y. Mei, R. Hontecillas, C. Philipson, S. Hoops, A. Carbo, J. Bassaganya-Riera,. Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology (1st ed.). Burlington, Massachusetts: Morgan Kaufmann (an imprint of Elsevier) 2015. 1-18

The M2 Pipeline: A Novel Tool for Rapidly Analyzing Host Metabolic Profiles from RNA-seq Data
Abstract— A novel bioinformatics and data analytics pipeline that utilizes global gene expression datasets in combination with [...]