Special Issue "Computational Studies of Immune System Function"

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A special issue of Computation (ISSN 2079-3197). This special issue belongs to the section "Computational Biology".

Deadline for manuscript submissions: closed (15 January 2015)

Special Issue Editors

Guest Editor
Dr. Filippo Castiglione

Institute for Applied Mathematics, National Research Council of Italy, Via dei Taurini 19, 00185 Rome, Italy
Website | E-Mail
Fax: +39 06 7716461
Interests: computational immunology; bioinformatics; mathematical modelling; agent-based modelling; high performance computing; machine learning; pattern recognition
Guest Editor
Dr. Paolo Tieri

Institute for Applied Mathematics, National Research Council of Italy, Via dei Taurini 19, 00185 Rome, Italy
Website | E-Mail
Phone: +39 06 49 27 09 49
Interests: network biology; systems immunology; computational immunology; bioinformatics; systems biology; data integration

Special Issue Information

Dear Colleagues,

This special issue will focus on the computational methods and models employed to study immune system functioning under health and disease conditions.

Papers discussing computational models, at any level of description (e.g., microscopic/intracellular, mesoscopic/intercellular, macroscopic/tissue or organs), along with their application in understanding the pathogenesis of specific diseases (e.g., infectious diseases, cancers, hypersensitivities, autoimmune disorders), are all welcome.

Topics of interest include, but are not limited to:

  • modeling techniques (agent vs. equation based, continuous vs. discrete, bioinformatics, network studies);
  • spatially-extended models (e.g., models of lymph channels and/or lymph nodes);
  • models of cell homing in (and trafficking among) lymph nodes;
  • computational applications to diseases, in silico testing and optimization of therapeutic/vaccination regimes;
  • models encompassing two or more spatial or temporal scales (e.g., from cell functions to organs);
  • computational methods of network analysis.

The computation aspect of these models should be posed in evidence, as it often constitutes a limiting factor (e.g., in the development of micro-simulation models). Moreover, methods addressing the issue of parameter estimation and the fast exploration of large parameter spaces, as well as the analysis of experimental data, are considered important in the field.

Research papers, reviews, and short communications on all topics related to the above issues are invited.

Dr. Filippo Castiglione
Dr. Paolo Tieri
Guest Editors

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Computation is an international peer-reviewed Open Access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. For the first couple of issues the Article Processing Charge (APC) will be waived for well-prepared manuscripts. English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.


Keywords

  • computational immunology
  • immuno-informatics
  • methods in systems immunology
  • multi-scale immune models
  • immune-related disease models
  • high performance simulations
  • micro-simulation
  • models of immune cell traffic
  • methods in network analysis

Published Papers (5 papers)

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Research

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Open AccessCommunication Computational Approach to 3D Modeling of the Lymph Node Geometry
Computation 2015, 3(2), 222-234; doi:10.3390/computation3020222
Received: 16 January 2015 / Revised: 3 May 2015 / Accepted: 8 May 2015 / Published: 22 May 2015
Cited by 4 | PDF Full-text (3209 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
In this study we present a computational approach to the generation of the major geometric structures of an idealized murine lymph node (LN). In this generation, we consider the major compartments such as the subcapsular sinus, B cell follicles, trabecular and medullar sinuses,
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In this study we present a computational approach to the generation of the major geometric structures of an idealized murine lymph node (LN). In this generation, we consider the major compartments such as the subcapsular sinus, B cell follicles, trabecular and medullar sinuses, blood vessels and the T cell zone with a primary focus on the fibroblastic reticular cell (FRC) network. Confocal microscopy data of LN macroscopic structures and structural properties of the FRC network have been generated and utilized in the present model. The methodology sets a library of modules that can be used to assemble a solid geometric LN model and subsequently generate an adaptive mesh model capable of implementing transport phenomena. Overall, based on the use of high-resolution confocal microscopy and morphological analysis of cell 3D reconstructions, we have developed a computational model of the LN geometry, suitable for further investigation in studies of fluid transport and cell migration in this immunologically essential organ. Full article
(This article belongs to the Special Issue Computational Studies of Immune System Function)
Figures

Open AccessArticle Coupling of Petri Net Models of the Mycobacterial Infection Process and Innate Immune Response
Computation 2015, 3(2), 150-176; doi:10.3390/computation3020150
Received: 23 January 2015 / Revised: 19 March 2015 / Accepted: 26 March 2015 / Published: 8 April 2015
Cited by 1 | PDF Full-text (1596 KB) | HTML Full-text | XML Full-text
Abstract
Computational and mathematical modeling is important in support of a better understanding of complex behavior in biology. For the investigation of biological systems, researchers have used computers to construct, verify, and validate models that describe the mechanisms behind biological processes in multi-scale representations.
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Computational and mathematical modeling is important in support of a better understanding of complex behavior in biology. For the investigation of biological systems, researchers have used computers to construct, verify, and validate models that describe the mechanisms behind biological processes in multi-scale representations. In this paper we combine Petri net models that represent the mycobacterial infection process and innate immune response at various levels of organization, from molecular interaction to granuloma dissemination. In addition to the conventional graphical representation of the Petri net, the outcome of the model is projected onto a 3D model representing the zebrafish embryo. In this manner we provide a visualization of the process in a simulation framework that portrays the infection in the living system. Full article
(This article belongs to the Special Issue Computational Studies of Immune System Function)
Open AccessArticle Multiscale Modeling of the Early CD8 T-Cell Immune Response in Lymph Nodes: An Integrative Study
Computation 2014, 2(4), 159-181; doi:10.3390/computation2040159
Received: 28 May 2014 / Revised: 18 July 2014 / Accepted: 4 September 2014 / Published: 29 September 2014
Cited by 4 | PDF Full-text (1775 KB) | HTML Full-text | XML Full-text
Abstract
CD8 T-cells are critical  in controlling infection by intracellular  pathogens. Upon encountering antigen presenting cells, T-cell receptor activation promotes the differentiation of naïve CD8 T-cells into strongly proliferating  activated and effector stages. We propose a 2D-multiscale computational model to study the maturation of
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CD8 T-cells are critical  in controlling infection by intracellular  pathogens. Upon encountering antigen presenting cells, T-cell receptor activation promotes the differentiation of naïve CD8 T-cells into strongly proliferating  activated and effector stages. We propose a 2D-multiscale computational model to study the maturation of CD8 T-cells in a lymph node controlled by their molecular profile. A novel molecular pathway is presented and converted into an ordinary differential  equation model, coupled with a cellular Potts model to describe cell-cell interactions. Key molecular  players such as activated IL2 receptor and Tbet levels  control the differentiation  from naïve into activated and effector stages, respectively,  while caspases and Fas-Fas ligand interactions control cell apoptosis.  Coupling  this molecular model to the cellular scale successfully  reproduces  qualitatively the evolution of total CD8 T-cell counts observed in mice lymph node, between Day 3 and 5.5 post-infection. Furthermore, this model allows us to make testable predictions  of the evolution of the different CD8 T-cell stages. Full article
(This article belongs to the Special Issue Computational Studies of Immune System Function)

Review

Jump to: Research

Open AccessReview Computational Studies of the Intestinal Host-Microbiota Interactome
Computation 2015, 3(1), 2-28; doi:10.3390/computation3010002
Received: 24 September 2014 / Accepted: 18 December 2014 / Published: 14 January 2015
Cited by 1 | PDF Full-text (3674 KB) | HTML Full-text | XML Full-text
Abstract
A large and growing body of research implicates aberrant immune response and compositional shifts of the intestinal microbiota in the pathogenesis of many intestinal disorders. The molecular and physical interaction between the host and the microbiota, known as the host-microbiota interactome, is one
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A large and growing body of research implicates aberrant immune response and compositional shifts of the intestinal microbiota in the pathogenesis of many intestinal disorders. The molecular and physical interaction between the host and the microbiota, known as the host-microbiota interactome, is one of the key drivers in the pathophysiology of many of these disorders. This host-microbiota interactome is a set of dynamic and complex processes, and needs to be treated as a distinct entity and subject for study. Disentangling this complex web of interactions will require novel approaches, using a combination of data-driven bioinformatics with knowledge-driven computational modeling. This review describes the computational approaches for investigating the host-microbiota interactome, with emphasis on the human intestinal tract and innate immunity, and highlights open challenges and existing gaps in the computation methodology for advancing our knowledge about this important facet of human health. Full article
(This article belongs to the Special Issue Computational Studies of Immune System Function)
Open AccessReview Computational Models of the NF-KB Signalling Pathway
Computation 2014, 2(4), 131-158; doi:10.3390/computation2040131
Received: 12 May 2014 / Revised: 30 July 2014 / Accepted: 19 August 2014 / Published: 29 September 2014
Cited by 11 | PDF Full-text (1143 KB) | HTML Full-text | XML Full-text
Abstract
In this review article, we discuss the current state of computational modelling of the nuclear factor-kappa B (NF-ΚB) signalling pathway. NF-ΚB is a transcription factor, which is ubiquitous within cells and controls a number of immune responses, including inflammation
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In this review article, we discuss the current state of computational modelling of the nuclear factor-kappa B (NF-ΚB) signalling pathway. NF-ΚB is a transcription factor, which is ubiquitous within cells and controls a number of immune responses, including inflammation and apoptosis. The NF-ΚB signalling pathway is tightly regulated, commencing with activation at the cell membrane, signal transduction through various components within the cytoplasm, translocation of NF-ΚB into the nucleus and, finally, the transcription of various genes relating to the innate and adaptive immune responses. There have been a number of computational (mathematical) models developed of the signalling pathway over the past decade. This review describes how these approaches have helped advance our understanding of NF-ΚB control. Full article
(This article belongs to the Special Issue Computational Studies of Immune System Function)

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