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Modeling the mechanisms of action underlying the plasticity of the CD4+ T cell differentiation process
Carbo, A., R. Hontecillas, M. Climent, S. Hoops, P. Lu, K. Wendelsdorf, S. Eubank, M. Marathe, and J. Bassaganya-Riera (2011) Modeling [...]

Punicic acid prevents diet induced obesity and insulin resistance in mice
Voshol, P., I. Vroegnijk, J. van Diepen, S. van den Berg, I. Westbroek, K. Hiskias, L. Gambelli, R. Hontecillas, J. Bassaganya-Riera, [...]

Role of Regulatory Mechanisms in Pathogen Persistence Systems Biology Representation of Gut Mucosal Immunity
Wendelsdorf, K., J. Bassaganya-Riera, R. Hontecillas, S. Eubank, and M. Marathe (2010) Role of Regulatory Mechanisms in Pathogen [...]

Role of Regulatory Mechanisms in Pathogen Persistence
Wendelsdorf, K., J. Bassaganya-Riera, R. Hontecillas, S. Eubank, and M. Marathe (2010) Role of Regulatory Mechanisms in Pathogen [...]

Punicic acid modulates mucosal immune responses and prevents gut inflammation through PPAR γ and δ-dependent mechanisms
Bassaganya-Riera, J., M. Diguardo, M. Climent, C. Vives, A. de Horna, S. Sanchez, M. Orpi, E. Duran, A. W.C. Einerhand, M. O’Shea, [...]

Soluble fibers and resistant starch ameliorate disease activity in an experimental model of IBD
Bassaganya-Riera, J., M. Diguardo, A. de Horna, S. Sanchez, A.W.C. Einerhand, L. Sanders, and R. Hontecillas (2010) Soluble fibers and [...]

Discovery of potential therapeutics for treatment of type II diabetes via virtual screening
Lewis, N, J. Bassaganya-Riera and D. Bevan (2009) Discovery of potential therapeutics for treatment of type II diabetes via virtual [...]

Differential PPAR gamma and delta expression in F4/80hi and F4/80lo adipose tissue macrophages
Bassaganya-Riera, J., A.J. Guri, and R. Hontecillas (2009) Differential PPAR gamma and delta expression in F4/80^hi and F4/80^lo adipose [...]

Modulation of the lipoxygenase pathway in bone marrow-derived dendritic cells by PPAR gamma
Hontecillas, R., S. Misyak, and J. Bassaganya-Riera (2009) Modulation of the lipoxygenase pathway in bone marrow-derived dendritic [...]

Quantification of muscle pathology and inflammation during early disease time course of mdx mice
Evans, N.P., A.J. Guri, J. Bassaganya-Riera, and R.W. Grange (2008) Quantification of muscle pathology and inflammation during early [...]

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The CLA mini-Symposium; The immunomodulatory properties of CLA
Bassaganya-Riera, J. (2000) Invited Speaker to The CLA mini-Symposium; The immunomodulatory properties of CLA; Ames, IA.

Dr. Bassaganya-Riera gave an invited talk at Mount Sinai School of Medicine
On Oct 25, 2012, Dr. Josep Bassaganya-Riera was invited to give a talk at the Mount Sinai school of medicine. The NIMML Director presented the Center for Modeling Immunity to Enteric Pathogens research program, especially focusing on the [...]

VBI Immunology Research Thrust
VBI Spring Retreat was held May 15, from 8:30 am until 3:00pm at the Inn at Virginia Tech, Latham Ballroom B and C. Dr. Josep Bassaganya‐Riera gave a presentation on VBI Immunology Research Thrust. The following are the summary points of [...]

Dr. Josep Bassaganya-Riera Gave a Talk at Annual Meeting of the Modeling Immunity
MIEP team attended the Annual Meeting of the Modeling Immunity for Biodefense Program, Bethesda, MD Nov 1-2. MIEP PI, Dr. Josep Bassaganya-Riera gave a talk on MIEP progresses made in the first program year during the meeting and the slides are [...]

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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 [...]