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IL-17 mediated the anti-microbial actions of PPAR gamma blockade during EAEC infection
Philipson, C., R. Hontecillas, and J. Bassaganya-Riera (2013) IL-17 mediated the anti-microbial actions of PPAR gamma blockade during [...]

Modulation of mucosal immune responses to Clostridium difficile by probiotic bacteria
Viladomiu M., R. Hontecillas, M. Pedragosa, C. Philipson and J. Bassaganya-Riera (2013) Modulation of mucosal immune responses to [...]

Vitamin D receptor regulates mucosal immune responses to Clostridium difficile infection
Viladomiu, M., R. Hontecillas, M. Pedragosa, P. Michalak, K. Michalak, P. Lu and J. Bassaganya-Riera (2013) Vitamin D receptor [...]

IL-21 is required for maintaining mucosal Th1 and Th17 responses during Helicobacter pylori infection
Carbo, A., R. Hontecillas, M.K. Washignton, R. Chatuverdi, D. Olivares-Villagomez, K.T. Wilson, J. Bassaganya-Riera and H.S. Algood [...]

Pharmacokinetic and preclinical evaluation of amixicile, a novel inhibitor of Clostridium difficile
Hoffman, P.S., A. Marshall, I. Olekhnovich, C.A. Warren, R.L. Guerrant, T.L. Macdonald, R. Hontecillas, M. Viladomiu, and J. [...]

Pilot study of the effect of conjugated linoleic acid on the modulation of immune responses in patients with mild to moderately active Crohn’s disease
Isaacs, K.L., R. Hontecillas, W.T. Horne, M. Sandridge, H. Herfarth and J. Bassaganya-Riera (2011) Pilot study of the effect of [...]

VSL#3 and conjugated linoleic acid ameliorate colitis and inflammation-driven colorectal cancer
Viladomiu, M., M. Pedragosa, C. De Simone, R. Hontecillas and J. Bassaganya-Riera (2011) VSL#3 and conjugated linoleic acid ameliorate [...]

Modulation of mucosal effector and regulatory T cell responses by Helicobacter pylori
Carbo, A., M. Climent, K. Muite, M. Viladomiu, M. Pedragosa, I. Fonseca, M. Humedas, M. Humedas, P. Lu, W. T. Horne, R. Hontecillas, [...]

Host immunological conditions that determine status of Helicobacter pylori as a pathogenic or commensal bacterium
Wendelsdorf, K., A. Carbo, S. Hoops, R. Hontecillas, and J. Bassaganya-Riera, (2011) Host immunological conditions that determine [...]

Enteric Immunity Simulator: A tool for in silico study of gut immunopathologies
Wendelsdorf, K., J. Bassaganya-Riera, K. Bisset, S. Eubank, R. Hontecillas and M. Marathe (2011) Enteric Immunity Simulator: A tool for [...]

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Peroxisome Proliferator-Activated Receptors: Molecular Targets for Therapies Against IBD
Bassaganya-Riera, J. (2006) Invited speaker in the System’s Biology Seminar; Peroxisome Proliferator-Activated Receptors: Molecular Targets for Therapies Against IBD; Universitat de Vic, Barcelona, Spain.

The Role of Peroxisome Proliferator-Activated Receptor gamma in the Immunopathogenesis of IBD
Bassaganya-Riera, J. (2006) Invited speaker in the Genetics, Bioinformatics and Computational Biology Seminar; The Role of Peroxisome Proliferator-Activated Receptor gamma in the Immunopathogenesis of IBD; Blacksburg, VA.

Immunosuppressive effects of arachidonic and docosahexaenoic-enriched infant formulas
Bassaganya-Riera, J., (2006) Invited speaker at Mead Johnson Nutritionals/Bristol Myers Squibb Headquarters; Immunosuppressive effects of arachidonic and docosahexaenoic-enriched infant formulas; Evansville, IN.

Nutritional Regulation of IBD by Natural Agonists of Peroxisome Proliferator-Activated Receptor gamma
Bassaganya-Riera, J. (2006) Invited speaker in the Gastroenterology Research Conference at Wake Forrest University Baptist Medical Center; Nutritional Regulation of IBD byNatural Agonists of Peroxisome Proliferator-Activated Receptor gamma; [...]

Immunomodulatory Effects and Mechanisms of Conjugated Linoleic Acid
Bassaganya-Riera, J. (2005) Invited speaker in the 2^nd U.S. CLA Network Symposium and Chair of the Immunology panel; Immunomodulatory Effects and Mechanisms of Conjugated Linoleic Acid; Chicago, IL.

The Health Benefits of Conjugated Linoleic Acid
Bassaganya-Riera, J. (2004) The Health Benefits of Conjugated Linoleic Acid; Nutrition Seminars; Department of Animal and Poultry Sciences, Blacksburg, VA

Nutritional Immunoregulation of Colonic Inflammation by CLA
Bassaganya-Riera, J. (2003) Invited speaker in the 94^th American Oil Chemists Society Annual Meeting; Nutritional Immunoregulation of Colonic Inflammation by CLA; Kansas City, MO.

Differential Regulation of PPAR α, γ, δ expression by Fatty Acids
Bassaganya-Riera, J. (2002) Invited speaker to the 12^th Annual Growth Factor and Signal Transduction Symposium on molecular targets for dietary intervention in disease; Differential Regulation of PPAR a, g, d expression by Fatty Acids; Ames, IA. [...]

Mechanisms of Action of CLA in Health and Disease
Bassaganya-Riera, J. (2002) Invited panel discussant in a workshop on the Health Benefits of CLA by the National Institutes of Health (Office of Dietary Supplements/National Institutes of Health); Mechanisms of Action of CLA in Health and [...]

Nutraceuticals/Edible Vaccines; Conjugated Linoleic Acid: A Nutraceutical with Immunomodulatory Properties
Bassaganya-Riera, J. (2001) Invited Speaker by the Society for In Vitro Biology. 2001 Congress Symposium on Nutraceuticals/Edible Vaccines; Conjugated Linoleic Acid: A Nutraceutical with Immunomodulatory Properties; St. Louis, MO

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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 [...]