67 results match your criteria Immunome Research [Journal]


Interleukin-6 cytokine: a multifunctional glycoprotein for cancer.

Immunome Res 2013 Aug;9(62):16535

Pulmonary Department-Oncology Unit, "G. Papanikolaou" General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece ; Department of Interventional Pneumology, Ruhrlandklinik, West German Lung Center, University Hospital, University Duisburg-Essen, Essen, Germany.

Interleukin 6 is a multifunctional cytokine. Its increased levels have been associated with elevated cancer risk, and also these levels have been found to be a prognostic factor for several cancer types. In addition, increased levels have been found in coronary heart disease, insulin resistant patients, advance stage cancer patients, atopy/asthma and in patients with blood circulating micrometastasis. Read More

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http://dx.doi.org/10.1186/2090-5009-9-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784310PMC
August 2013
8 Reads

Navigating diabetes-related immune epitope data: resources and tools provided by the Immune Epitope Database (IEDB).

Immunome Res 2013 ;9(1)

Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA.

Background: The Immune Epitope Database (IEDB), originally focused on infectious diseases, was recently expanded to allergy, transplantation and autoimmunity diseases. Here we focus on diabetes, chosen as a prototype autoimmune disease. We utilize a combined tutorial and meta-analysis format, which demonstrates how common questions, related to diabetes epitopes can be answered. Read More

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https://www.omicsonline.com/open-access/navigating-diabetesr
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http://dx.doi.org/10.4172/1745-7580.1000063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4134942PMC
January 2013
16 Reads

A computational pipeline to generate MHC binding motifs.

Immunome Res 2011 May;7(2)

La Jolla Institute for Allergy & Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA.

Background: Major histocompatibility complex (MHC) class I molecules play key roles in host immunity against pathogens by presenting peptide antigens to CD8+ T-cells. Many variants of MHC molecules exist, and each has a unique preference for certain peptide ligands. Both experimental approaches and computational algorithms have been utilized to analyze these peptide MHC binding characteristics. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5524134PMC
May 2011
3 Reads

Immunogenic Consensus Sequence T helper Epitopes for a Pan- Biodefense Vaccine.

Immunome Res 2011 May;7(2)

EpiVax 146 Clifford St, Providence, RI 02903, USA.

Background: Biodefense vaccines against Category B bioterror agents (BPM) and (BM) are needed, as they are both easily accessible to terrorists and have strong weaponization potential. (BC), a related pathogen, causes chronic lung infections in cystic fibrosis patients. Since BPM, BM and BC are all intracellular bacteria, they are excellent targets for T cell-based vaccines. Read More

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http://dx.doi.org/10.4172/1745-7580.1000043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4206550PMC
May 2011
4 Reads

A comparison of two methods for T cell epitope mapping: "cell free" in vitro versus immunoinformatics.

Immunome Res 2011 May;7(2)

EpiVax, Inc., Providence, RI, USA ; Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, USA ; The Warren Alpert Medical School of Brown University, Providence, RI, USA.

Background: Methods for identifying physiologically relevant T-cell epitopes are critically important for development of vaccines and the design of therapeutic proteins. As the number of proteins that are being evaluated for putative immunogenicity expands, rapid and accurate tools are in great demand. Several methods to identify T-cell epitopes have been developed, the most recent of which is a cell free system consisting of a minimal set of proteases incubated with HLA DRB1*0101, HLA-DM and whole antigen. Read More

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http://dx.doi.org/10.4172/1745-7580.1000045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4206547PMC
May 2011
41 Reads

FLAVIdB: A data mining system for knowledge discovery in flaviviruses with direct applications in immunology and vaccinology.

Immunome Res 2011 ;7(3)

Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA ; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.

Background: The genus is unusually large, comprising more than 70 species, of which more than half are known human pathogens. It includes a set of clinically relevant infectious agents such as dengue, West Nile, yellow fever, and Japanese encephalitis viruses. Although these pathogens have been studied extensively, safe and efficient vaccines lack for the majority of the flaviviruses. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4276368PMC
January 2011
9 Reads

Immunoglobulin Structure Exhibits Control over CDR Motion.

Immunome Res 2011 ;7(5)

L. H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA ; Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA ; Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA.

Motions of the IgG structure are evaluated using normal mode analysis of an elastic network model to detect hinges, the dominance of low frequency modes, and the most important internal motions. One question we seek to answer is whether or not IgG hinge motions facilitate antigen binding. We also evaluate the protein crystal and packing effects on the experimental temperature factors and disorder predictions. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4151861PMC
January 2011
36 Reads

An Integrated Genomic and Immunoinformatic Approach to Vaccine Design.

Immunome Res 2011 ;7(2)

EpiVax, Inc., Providence, Rhode Island 02903, USA ; Institute for Immunology and Informatics, University of Rhode Island, Providence, Rhode Island 02903, USA.

Background: One useful application of pattern matching algorithms is identification of major histocompatability complex (MHC) ligands and T-cell epitopes. Peptides that bind to MHC molecules and interact with T cell receptors to stimulate the immune system are critical antigens for protection against infectious pathogens. We describe a genomes-to-vaccine approach to vaccine design that takes advantage of immunoinformatics algorithms to rapidly identify T-cell epitope sequences from large genomic datasets. Read More

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http://dx.doi.org/10.4172/1745-7580.1000049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4138956PMC
January 2011
9 Reads

HLA mismatches and hematopoietic cell transplantation: structural simulations assess the impact of changes in peptide binding specificity on transplant outcome.

Immunome Res 2011 ;7(2)

Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

The success of hematopoietic cell transplantation from an unrelated donor depends in part on the degree of Human Histocompatibility Leukocyte Antigen (HLA) matching between donor and patient. We present a structure-based analysis of HLA mismatching, focusing on individual amino acid mismatches and their effect on peptide binding specificity. Using molecular modeling simulations of HLA-peptide interactions, we find evidence that amino acid mismatches predicted to perturb peptide binding specificity are associated with higher risk of mortality in a large and diverse dataset of patient-donor pairs assembled by the International Histocompatibility Working Group in Hematopoietic Cell Transplantation consortium. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3904355PMC
January 2011
13 Reads

Factors important in evolutionary shaping of immunoglobulin gene loci.

Immunome Res 2010 Dec 6;6:13. Epub 2010 Dec 6.

The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.

Background: The extraordinary diversity characterizing the antibody repertoire is generated by both evolution and lymphocyte development. Much of this diversity is due to the existence of immunoglobulin (Ig) variable region gene segment libraries, which were diversified during evolution and, in higher vertebrates, are used in generating the combinatorial diversity of antibody genes. The aim of the present study was to address the following questions: What evolutionary parameters affect the size and structure of gene libraries? Are the number of genes in libraries of contemporary species, and the corresponding gene locus structure, a random result of evolutionary history, or have these properties been optimized with respect to individual or population fitness? If a larger number of genes or different genome structures do not increase the fitness, then the current structure is probably optimized. Read More

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http://dx.doi.org/10.1186/1745-7580-6-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3006366PMC
December 2010
6 Reads

Human immunome, bioinformatic analyses using HLA supermotifs and the parasite genome, binding assays, studies of human T cell responses, and immunization of HLA-A*1101 transgenic mice including novel adjuvants provide a foundation for HLA-A03 restricted CD8+T cell epitope based, adjuvanted vaccine protective against Toxoplasma gondii.

Immunome Res 2010 Dec 3;6:12. Epub 2010 Dec 3.

Departments of Surgery (Ophthalmology and Visual Sciences) and Pediatrics (Infectious Disease), Committees on Immunology, Molecular Medicine, and Genetics, Institute of Genomics and Systems Biology, and The College, The University of Chicago, Chicago, Illinois 60637, USA.

Background: Toxoplasmosis causes loss of life, cognitive and motor function, and sight. A vaccine is greatly needed to prevent this disease. The purpose of this study was to use an immmunosense approach to develop a foundation for development of vaccines to protect humans with the HLA-A03 supertype. Read More

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http://www.immunome-research.com/content/6/1/12
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http://dx.doi.org/10.1186/1745-7580-6-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009956PMC
December 2010
8 Reads

Automated processing of label-free Raman microscope images of macrophage cells with standardized regression for high-throughput analysis.

Immunome Res 2010 Nov 19;6:11. Epub 2010 Nov 19.

Laboratory of Systems Immunology, WPI Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.

Background: Macrophages represent the front lines of our immune system; they recognize and engulf pathogens or foreign particles thus initiating the immune response. Imaging macrophages presents unique challenges, as most optical techniques require labeling or staining of the cellular compartments in order to resolve organelles, and such stains or labels have the potential to perturb the cell, particularly in cases where incomplete information exists regarding the precise cellular reaction under observation. Label-free imaging techniques such as Raman microscopy are thus valuable tools for studying the transformations that occur in immune cells upon activation, both on the molecular and organelle levels. Read More

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http://dx.doi.org/10.1186/1745-7580-6-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995782PMC
November 2010
5 Reads

DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells.

Immunome Res 2010 Nov 19;6:10. Epub 2010 Nov 19.

Department of Pharmacology, University of Firenze, Firenze, Italy.

Background: The advent of Systems Biology has been accompanied by the blooming of pathway databases. Currently pathways are defined generically with respect to the organ or cell type where a reaction takes place. The cell type specificity of the reactions is the foundation of immunological research, and capturing this specificity is of paramount importance when using pathway-based analyses to decipher complex immunological datasets. Read More

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http://dx.doi.org/10.1186/1745-7580-6-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000836PMC
November 2010
36 Reads

NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure.

Immunome Res 2010 Nov 13;6. Epub 2010 Nov 13.

Center A for Biological Sequence Analysis, BioCentrum-DTU, Building 208, Technical University of Denmark, DK-2800 Lyngby, Denmark.

Background: Binding of peptides to Major Histocompatibility class II (MHC-II) molecules play a central role in governing responses of the adaptive immune system. MHC-II molecules sample peptides from the extracellular space allowing the immune system to detect the presence of foreign microbes from this compartment. Predicting which peptides bind to an MHC-II molecule is therefore of pivotal importance for understanding the immune response and its effect on host-pathogen interactions. Read More

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http://dx.doi.org/10.1186/1745-7580-6-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2994798PMC
November 2010
10 Reads

Concept and application of a computational vaccinology workflow.

Immunome Res 2010 Nov 3;6 Suppl 2:S7. Epub 2010 Nov 3.

emergentec biodevelopment GmbH, Rathausstrasse 5/3, 1010 Vienna, Austria.

Background: The last years have seen a renaissance of the vaccine area, driven by clinical needs in infectious diseases but also chronic diseases such as cancer and autoimmune disorders. Equally important are technological improvements involving nano-scale delivery platforms as well as third generation adjuvants. In parallel immunoinformatics routines have reached essential maturity for supporting central aspects in vaccinology going beyond prediction of antigenic determinants. Read More

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http://dx.doi.org/10.1186/1745-7580-6-S2-S7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981879PMC
November 2010
12 Reads

Applying bioinformatics for antibody epitope prediction using affinity-selected mimotopes - relevance for vaccine design.

Immunome Res 2010 Nov 3;6 Suppl 2:S6. Epub 2010 Nov 3.

Department of Pathology and Molecular Medicine, Centre for Gene Therapeutics, McMaster University, 1200 Main Street West, Hamilton, Ontario, Canada, L8N 3Z5.

To properly characterize protective polyclonal antibody responses, it is necessary to examine epitope specificity. Most antibody epitopes are conformational in nature and, thus, cannot be identified using synthetic linear peptides. Cyclic peptides can function as mimetics of conformational epitopes (termed mimotopes), thereby providing targets, which can be selected by immunoaffinity purification. Read More

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http://dx.doi.org/10.1186/1745-7580-6-S2-S6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981875PMC
November 2010
6 Reads

Models of RNA virus evolution and their roles in vaccine design.

Immunome Res 2010 Nov 3;6 Suppl 2:S5. Epub 2010 Nov 3.

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.

Viruses are fast evolving pathogens that continuously adapt to the highly variable environments they live and reproduce in. Strategies devoted to inhibit virus replication and to control their spread among hosts need to cope with these extremely heterogeneous populations and with their potential to avoid medical interventions. Computational techniques such as phylogenetic methods have broadened our picture of viral evolution both in time and space, and mathematical modeling has contributed substantially to our progress in unraveling the dynamics of virus replication, fitness, and virulence. Read More

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http://dx.doi.org/10.1186/1745-7580-6-S2-S5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981881PMC
November 2010
6 Reads

T-cell epitope prediction and immune complex simulation using molecular dynamics: state of the art and persisting challenges.

Immunome Res 2010 Nov 3;6 Suppl 2:S4. Epub 2010 Nov 3.

Centre for Computational Science, Chemistry Department, University College of London, 20 Gordon Street, WC1H 0AJ, London, UK.

Atomistic Molecular Dynamics provides powerful and flexible tools for the prediction and analysis of molecular and macromolecular systems. Specifically, it provides a means by which we can measure theoretically that which cannot be measured experimentally: the dynamic time-evolution of complex systems comprising atoms and molecules. It is particularly suitable for the simulation and analysis of the otherwise inaccessible details of MHC-peptide interaction and, on a larger scale, the simulation of the immune synapse. Read More

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http://dx.doi.org/10.1186/1745-7580-6-S2-S4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981876PMC
November 2010
4 Reads

State of the art and challenges in sequence based T-cell epitope prediction.

Immunome Res 2010 Nov 3;6 Suppl 2:S3. Epub 2010 Nov 3.

The Technical University of Denmark - DTU, Dept, of Systems Biology, Center for Biological Sequence Analysis - CBS, Kemitorvet 208, DK-2800 Kgs, Lyngby, Denmark.

Sequence based T-cell epitope predictions have improved immensely in the last decade. From predictions of peptide binding to major histocompatibility complex molecules with moderate accuracy, limited allele coverage, and no good estimates of the other events in the antigen-processing pathway, the field has evolved significantly. Methods have now been developed that produce highly accurate binding predictions for many alleles and integrate both proteasomal cleavage and transport events. Read More

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http://dx.doi.org/10.1186/1745-7580-6-S2-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981877PMC
November 2010
6 Reads

Recent advances in B-cell epitope prediction methods.

Immunome Res 2010 Nov 3;6 Suppl 2:S2. Epub 2010 Nov 3.

Department of Systems and Computer Engineering, Al-Azhar University, Egypt.

Identification of epitopes that invoke strong responses from B-cells is one of the key steps in designing effective vaccines against pathogens. Because experimental determination of epitopes is expensive in terms of cost, time, and effort involved, there is an urgent need for computational methods for reliable identification of B-cell epitopes. Although several computational tools for predicting B-cell epitopes have become available in recent years, the predictive performance of existing tools remains far from ideal. Read More

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http://dx.doi.org/10.1186/1745-7580-6-S2-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981878PMC
November 2010
6 Reads
37 Citations

Computer aided selection of candidate vaccine antigens.

Immunome Res 2010 Nov 3;6 Suppl 2:S1. Epub 2010 Nov 3.

School of Life and Health Sciences, University of Aston, Aston Triangle, Birmingham, B4 7ET, UK.

Immunoinformatics is an emergent branch of informatics science that long ago pullulated from the tree of knowledge that is bioinformatics. It is a discipline which applies informatic techniques to problems of the immune system. To a great extent, immunoinformatics is typified by epitope prediction methods. Read More

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http://dx.doi.org/10.1186/1745-7580-6-S2-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981880PMC
November 2010
4 Reads

An integrated approach to epitope analysis II: A system for proteomic-scale prediction of immunological characteristics.

Immunome Res 2010 Nov 2;6. Epub 2010 Nov 2.

1ioGenetics LLC, 3591 Anderson Street, Madison, WI 53704, USA.

Background: Improving our understanding of the immune response is fundamental to developing strategies to combat a wide range of diseases. We describe an integrated epitope analysis system which is based on principal component analysis of sequences of amino acids, using a multilayer perceptron neural net to conduct QSAR regression predictions for peptide binding affinities to 35 MHC-I and 14 MHC-II alleles.

Results: The approach described allows rapid processing of single proteins, entire proteomes or subsets thereof, as well as multiple strains of the same organism. Read More

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http://dx.doi.org/10.1186/1745-7580-6-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2991286PMC
November 2010
4 Reads

An integrated approach to epitope analysis I: Dimensional reduction, visualization and prediction of MHC binding using amino acid principal components and regression approaches.

Immunome Res 2010 Nov 2;6. Epub 2010 Nov 2.

ioGenetics LLC, 3591 Anderson Street, Madison, WI 53704, USA.

Background: Operation of the immune system is multivariate. Reduction of the dimensionality is essential to facilitate understanding of this complex biological system. One multi-dimensional facet of the immune system is the binding of epitopes to the MHC-I and MHC-II molecules by diverse populations of individuals. Read More

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http://dx.doi.org/10.1186/1745-7580-6-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990731PMC
November 2010
6 Reads

Identification of conformational B-cell Epitopes in an antigen from its primary sequence.

Immunome Res 2010 Oct 20;6. Epub 2010 Oct 20.

Bioinformatics Center, Institute of Microbial Technology, Sector 39-A, Chandigarh, India.

Background: One of the major challenges in the field of vaccine design is to predict conformational B-cell epitopes in an antigen. In the past, several methods have been developed for predicting conformational B-cell epitopes in an antigen from its tertiary structure. This is the first attempt in this area to predict conformational B-cell epitope in an antigen from its amino acid sequence. Read More

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http://dx.doi.org/10.1186/1745-7580-6-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2974664PMC
October 2010
20 Reads

TAP Hunter: a SVM-based system for predicting TAP ligands using local description of amino acid sequence.

Immunome Res 2010 Sep 27;6 Suppl 1:S6. Epub 2010 Sep 27.

Laboratory of Immunogenetics and Viral Host-Pathogen Genomics, Singapore Immunology Network, 8A Biomedical Grove, #03-06, Immunos, Singapore 138648.

Background: Selective peptide transport by the transporter associated with antigen processing (TAP) represents one of the main candidate mechanisms that may regulate the presentation of antigenic peptides to HLA class I molecules. Because TAP-binding preferences may significant impact T-cell epitope selection, there is great interest in applying computational techniques to systematically discover these elements.

Results: We describe TAP Hunter, a web-based computational system for predicting TAP-binding peptides. Read More

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http://dx.doi.org/10.1186/1745-7580-6-S1-S6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2946784PMC
September 2010
6 Reads

Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN.

Immunome Res 2010 Sep 27;6 Suppl 1:S5. Epub 2010 Sep 27.

Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, and Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.

Background: Brucella spp. are Gram-negative, facultative intracellular bacteria that cause brucellosis, one of the commonest zoonotic diseases found worldwide in humans and a variety of animal species. While several animal vaccines are available, there is no effective and safe vaccine for prevention of brucellosis in humans. Read More

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http://dx.doi.org/10.1186/1745-7580-6-S1-S5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2946783PMC
September 2010
6 Reads

Clustering-based identification of clonally-related immunoglobulin gene sequence sets.

Immunome Res 2010 Sep 27;6 Suppl 1:S4. Epub 2010 Sep 27.

School of Computer Science and Engineering, University of New South Wales, NSW 2052, Australia.

Background: Clonal expansion of B lymphocytes coupled with somatic mutation and antigen selection allow the mammalian humoral immune system to generate highly specific immunoglobulins (IG) or antibodies against invading bacteria, viruses and toxins. The availability of high-throughput DNA sequencing methods is providing new avenues for studying this clonal expansion and identifying the factors guiding the generation of antibodies. The identification of groups of rearranged immunoglobulin gene sequences descended from the same rearrangement (clonally-related sets) in very large sets of sequences is facilitated by the availability of immunoglobulin gene sequence alignment and partitioning software that can accurately predict component germline gene, but has required painstaking visual inspection and analysis of sequences. Read More

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http://dx.doi.org/10.1186/1745-7580-6-S1-S4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2946782PMC
September 2010
5 Reads

Model refinement through high-performance computing: an agent-based HIV example.

Immunome Res 2010 Sep 27;6 Suppl 1:S3. Epub 2010 Sep 27.

Centre for Scientific Computing & Complex Systems Modelling, Dublin City University, Glasnevin, Dublin 9, Ireland.

Background: Recent advances in Immunology highlighted the importance of local properties on the overall progression of HIV infection. In particular, the gastrointestinal tract is seen as a key area during early infection, and the massive cell depletion associated with it may influence subsequent disease progression. This motivated the development of a large-scale agent-based model. Read More

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http://dx.doi.org/10.1186/1745-7580-6-S1-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2946781PMC
September 2010
5 Reads

pDOCK: a new technique for rapid and accurate docking of peptide ligands to Major Histocompatibility Complexes.

Immunome Res 2010 Sep 27;6 Suppl 1:S2. Epub 2010 Sep 27.

Department of Chemistry and Biomolecular Sciences and ARC Center of Excellence in Bioinformatics, Macquarie University, NSW 2109, Australia.

Background: Identification of antigenic peptide epitopes is an essential prerequisite in T cell-based molecular vaccine design. Computational (sequence-based and structure-based) methods are inexpensive and efficient compared to experimental approaches in screening numerous peptides against their cognate MHC alleles. In structure-based protocols, suited to alleles with limited epitope data, the first step is to identify high-binding peptides using docking techniques, which need improvement in speed and efficiency to be useful in large-scale screening studies. Read More

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http://dx.doi.org/10.1186/1745-7580-6-S1-S2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2946780PMC
September 2010
53 Reads

Stacking and energetic contribution of aromatic islands at the binding interface of antibody proteins.

Immunome Res 2010 Sep 27;6 Suppl 1:S1. Epub 2010 Sep 27.

Department of Biomedical Engineering, College Life Science and Technology, Tongji University, Shanghai, 200092, China.

Background: The enrichment and importance of some aromatic residues, such as Tyr and Trp, have been widely noticed at the binding interfaces of antibodies from many experimental and statistical results, some of which were even identified as "hot spots" contributing significantly greater to the binding affinity than other amino acids. However, how these aromatic residues influence the immune binding still deserves further investigation. A large-scale examination was done regarding the local spatial environment around the interfacial Tyr or Trp residues. Read More

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http://dx.doi.org/10.1186/1745-7580-6-S1-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2946779PMC
September 2010
5 Reads

Motif prediction to distinguish LPS-stimulated pro-inflammatory vs. antibacterial macrophage genes.

Immunome Res 2010 Sep 21;6. Epub 2010 Sep 21.

School of Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, USA.

Background: Innate immunity is the first line of defence offered by host cells to infections. Macrophage cells involved in innate immunity are stimulated by lipopolysaccharide (LPS), found on bacterial cell surface, to express a complex array of gene products. Persistent LPS stimulation makes a macrophage tolerant to LPS with down regulation of inflammatory genes ("pro-inflammatory") while continually expressing genes to fight the bacterial infection ("antibacterial"). Read More

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http://dx.doi.org/10.1186/1745-7580-6-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2949756PMC
September 2010
4 Reads

Polyfunctional CD4+ T cell responses to a set of pathogenic arenaviruses provide broad population coverage.

Immunome Res 2010 May 17;6. Epub 2010 May 17.

Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, California, 92037 USA.

Background: Several arenaviruses cause severe hemorrhagic fever and aseptic meningitis in humans for which no licensed vaccines are available. A major obstacle for vaccine development is pathogen heterogeneity within the Arenaviridae family. Evidence in animal models and humans indicate that T cell and antibody-mediated immunity play important roles in controlling arenavirus infection and replication. Read More

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http://dx.doi.org/10.1186/1745-7580-6-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880318PMC
May 2010
12 Reads

Evolution of a cluster of innate immune genes (beta-defensins) along the ancestral lines of chicken and zebra finch.

Immunome Res 2010 Apr 1;6. Epub 2010 Apr 1.

Edward Grey Institute, Department of Zoology, South Parks Road, Oxford, OX1 3PS, UK.

Background: Avian beta-defensins (AvBDs) represent a group of innate immune genes with broad antimicrobial activity. Within the chicken genome, previous work identified 14 AvBDs in a cluster on chromosome three. The release of a second bird genome, the zebra finch, allows us to study the comparative evolutionary history of these gene clusters between from two species that shared a common ancestor about 100 million years ago. Read More

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http://www.immunome-research.com/content/6/1/3
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http://dx.doi.org/10.1186/1745-7580-6-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3161384PMC
April 2010
6 Reads

Coregulation mapping based on individual phenotypic variation in response to virus infection.

Immunome Res 2010 Mar 18;6. Epub 2010 Mar 18.

Department of Microbiology, Mount Sinai School of Medicine, New York, NY 10029, USA.

Background: Gene coregulation across a population is an important aspect of the considerable variability of the human immune response to virus infection. Methodology to investigate it must rely on a number of ingredients ranging from gene clustering to transcription factor enrichment analysis.

Results: We have developed a methodology to investigate the gene to gene correlations for the expression of 34 genes linked to the immune response of Newcastle Disease Virus (NDV) infected conventional dendritic cells (DCs) from 145 human donors. Read More

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http://dx.doi.org/10.1186/1745-7580-6-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3161383PMC
March 2010
9 Reads

A novel paradigm for cell and molecule interaction ontology: from the CMM model to IMGT-ONTOLOGY.

Immunome Res 2010 Feb 18;6(1). Epub 2010 Feb 18.

Institute for Computing Applications 'M. Picone', National Research Council (CNR), Rome, Italy.

Background: Biology is moving fast toward the virtuous circle of other disciplines: from data to quantitative modeling and back to data. Models are usually developed by mathematicians, physicists, and computer scientists to translate qualitative or semi-quantitative biological knowledge into a quantitative approach. To eliminate semantic confusion between biology and other disciplines, it is necessary to have a list of the most important and frequently used concepts coherently defined. Read More

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http://dx.doi.org/10.1186/1745-7580-6-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2834662PMC
February 2010
4 Reads

Ribosomal protein mRNAs are translationally-regulated during human dendritic cells activation by LPS.

Immunome Res 2009 Nov 27;5. Epub 2009 Nov 27.

Centre d'Immunologie de Marseille-Luminy, Université de la Méditerranée, Case 906, 13288 Marseille cedex 9, France.

Background: Dendritic cells (DCs) are the sentinels of the mammalian immune system, characterized by a complex maturation process driven by pathogen detection. Although multiple studies have described the analysis of activated DCs by transcriptional profiling, recent findings indicate that mRNAs are also regulated at the translational level. A systematic analysis of the mRNAs being translationally regulated at various stages of DC activation was performed using translational profiling, which combines sucrose gradient fractionation of polysomal-bound mRNAs with DNA microarray analysis. Read More

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http://dx.doi.org/10.1186/1745-7580-5-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788525PMC
November 2009
18 Reads

Critical role of glycosylation in determining the length and structure of T cell epitopes.

Immunome Res 2009 Sep 24;5. Epub 2009 Sep 24.

Department of Genetics, Cell- and Immunobiology, Semmelweis University, Nagyvárad tér 4, Budapest, Hungary.

Background: Using a combined in silico approach, we investigated the glycosylation of T cell epitopes and autoantigens. The present systems biology analysis was made possible by currently available databases (representing full proteomes, known human T cell epitopes and autoantigens) as well as glycosylation prediction tools.

Results: We analyzed the probable glycosylation of human T cell epitope sequences extracted from the ImmuneEpitope Database. Read More

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http://dx.doi.org/10.1186/1745-7580-5-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760507PMC
September 2009
4 Reads
6 Citations

Of mice and humans: how good are HLA transgenic mice as a model of human immune responses?

Immunome Res 2009 Jun 17;5. Epub 2009 Jun 17.

Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA.

Background: Previous studies have defined vaccinia virus (VACV)-derived T cell epitopes in VACV-infected human leukocyte antigen-A*0201 (HLA-A2.1) transgenic (Tg) mice and A2.1-positive human Dryvax vaccinees. Read More

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http://dx.doi.org/10.1186/1745-7580-5-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2702351PMC
June 2009
44 Reads

Functional recombinant MHC class II molecules and high-throughput peptide-binding assays.

Immunome Res 2009 May 5;5. Epub 2009 May 5.

Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.

Background: Molecules of the class II major histocompability complex (MHC-II) specifically bind and present exogenously derived peptide epitopes to CD4+ T helper cells. The extreme polymorphism of the MHC-II hampers the complete analysis of peptide binding. It is also a significant hurdle in the generation of MHC-II molecules as reagents to study and manipulate specific T helper cell responses. Read More

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http://dx.doi.org/10.1186/1745-7580-5-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690590PMC
May 2009
7 Reads

Genetic correlates of autoreactivity and autoreactive potential in human Ig heavy chains.

Immunome Res 2009 Feb 27;5. Epub 2009 Feb 27.

Center for Computational Immunology, Duke University, Durham, NC, USA.

Background: Immature bone marrow B cells are known to have longer CDR3 than mature peripheral B cells, and this genetic characteristic has been shown to correlate with autoreactivity in these early cells. B-cell Central tolerance eliminates these cells, but it is known that autoreactive B cells nevertheless appear commonly in healthy human blood. We examined over 7,300 Ig genes from Genbank, including those annotated by their discoverers as associated with autoreactivity, to determine the genetic correlates of autoreactivity in mature B cells. Read More

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http://dx.doi.org/10.1186/1745-7580-5-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2669064PMC
February 2009
4 Reads

Data mining of cancer vaccine trials: a bird's-eye view.

Immunome Res 2008 Dec 12;4. Epub 2008 Dec 12.

Babson College, Wellesley, MA, USA.

Background: A wealth of information on clinical trials has been provided by publicly accessible online registries. Information technology and data exchange standards enable rapid extraction, summarization, and visualization of information and derived knowledge from these data sets. Clinical trials data was extracted in the XML format from the National Library of Medicine ClinicalTrials. Read More

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http://dx.doi.org/10.1186/1745-7580-4-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639543PMC
December 2008
8 Reads

Peptide length significantly influences in vitro affinity for MHC class II molecules.

Immunome Res 2008 Nov 26;4. Epub 2008 Nov 26.

Department of Immunology and Institute of Molecular Medicine, St James's Hospital and Trinity College Dublin, Ireland.

Background: Class II Major Histocompatibility Complex (MHC) molecules have an open-ended binding groove which can accommodate peptides of varying lengths. Several studies have demonstrated that peptide flanking residues (PFRs) which lie outside the core binding groove can influence peptide binding and T cell recognition. By using data from the AntiJen database we were able to characterise systematically the influence of PFRs on peptide affinity for MHC class II molecules. Read More

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http://dx.doi.org/10.1186/1745-7580-4-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2640366PMC
November 2008
6 Reads

Expression analysis of G Protein-Coupled Receptors in mouse macrophages.

Immunome Res 2008 Apr 29;4. Epub 2008 Apr 29.

Cooperative Research Centre for Chronic Inflammatory Diseases and Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, 4072, Australia.

Background: Monocytes and macrophages express an extensive repertoire of G Protein-Coupled Receptors (GPCRs) that regulate inflammation and immunity. In this study we performed a systematic micro-array analysis of GPCR expression in primary mouse macrophages to identify family members that are either enriched in macrophages compared to a panel of other cell types, or are regulated by an inflammatory stimulus, the bacterial product lipopolysaccharide (LPS).

Results: Several members of the P2RY family had striking expression patterns in macrophages; P2ry6 mRNA was essentially expressed in a macrophage-specific fashion, whilst P2ry1 and P2ry5 mRNA levels were strongly down-regulated by LPS. Read More

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http://www.immunome-research.com/content/4/1/5
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http://dx.doi.org/10.1186/1745-7580-4-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2394514PMC
April 2008
7 Reads

Efficiency of the immunome protein interaction network increases during evolution.

Immunome Res 2008 Apr 22;4. Epub 2008 Apr 22.

Institute of Medical Technology, FI-33014 University of Tampere, Finland.

Background: Details of the mechanisms and selection pressures that shape the emergence and development of complex biological systems, such as the human immune system, are poorly understood. A recent definition of a reference set of proteins essential for the human immunome, combined with information about protein interaction networks for these proteins, facilitates evolutionary study of this biological machinery.

Results: Here, we present a detailed study of the development of the immunome protein interaction network during eight evolutionary steps from Bilateria ancestors to human. Read More

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http://dx.doi.org/10.1186/1745-7580-4-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2373292PMC
April 2008
3 Reads

Large-scale analysis of human heavy chain V(D)J recombination patterns.

Immunome Res 2008 Feb 27;4. Epub 2008 Feb 27.

Center for Computational Immunology, Duke University, Durham, NC, USA.

Background: The processes involved in the somatic assembly of antigen receptor genes are unique to the immune system and are driven largely by random events. Subtle biases, however, may exist and provide clues to the molecular mechanisms involved in their assembly and selection. Large-scale efforts to provide baseline data about the genetic characteristics of immunoglobulin (Ig) genes and the mechanisms involved in their assembly have recently become possible due to the rapid growth of genetic databases. Read More

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http://dx.doi.org/10.1186/1745-7580-4-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275228PMC
February 2008
5 Reads

Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries.

Immunome Res 2008 Jan 25;4. Epub 2008 Jan 25.

La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA.

Background: It has been previously shown that combinatorial peptide libraries are a useful tool to characterize the binding specificity of class I MHC molecules. Compared to other methodologies, such as pool sequencing or measuring the affinities of individual peptides, utilizing positional scanning combinatorial libraries provides a baseline characterization of MHC molecular specificity that is cost effective, quantitative and unbiased.

Results: Here, we present a large-scale application of this technology to 19 different human and mouse class I alleles. Read More

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http://www.immunome-research.com/content/4/1/2
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http://dx.doi.org/10.1186/1745-7580-4-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2248166PMC
January 2008
8 Reads

Analysis and prediction of protective continuous B-cell epitopes on pathogen proteins.

Immunome Res 2008 Jan 7;4. Epub 2008 Jan 7.

Emergentec Biodevelopment GmbH, Rathausstrasse 5/3, A-1010 Vienna, Austria.

Background: The application of peptide based diagnostics and therapeutics mimicking part of protein antigen is experiencing renewed interest. So far selection and design rationale for such peptides is usually driven by T-cell epitope prediction, available experimental and modelled 3D structure, B-cell epitope predictions such as hydrophilicity plots or experience. If no structure is available the rational selection of peptides for the production of functionally altering or neutralizing antibodies is practically impossible. Read More

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http://dx.doi.org/10.1186/1745-7580-4-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2244602PMC
January 2008
6 Reads

An analysis of the epitope knowledge related to Mycobacteria.

Immunome Res 2007 Dec 14;3:10. Epub 2007 Dec 14.

Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, California, 92037, USA.

Background: Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, remains a leading cause of infectious disease morbidity and mortality, and is responsible for more than 2 million deaths a year. Reports about extremely drug resistant (XDR) strains have further heightened the sense of urgency for the development of novel strategies to prevent and treat TB. Detailed knowledge of the epitopes recognized by immune responses can aid in vaccine and diagnostics development, and provides important tools for basic research. Read More

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http://dx.doi.org/10.1186/1745-7580-3-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2228276PMC
December 2007
10 Reads

Amino acid biophysical properties in the statistical prediction of peptide-MHC class I binding.

Immunome Res 2007 Oct 29;3. Epub 2007 Oct 29.

Department of Mathematics and Statistics, Boston University, Boston, MA, USA.

Background: A key step in the development of an adaptive immune response to pathogens or vaccines is the binding of short peptides to molecules of the Major Histocompatibility Complex (MHC) for presentation to T lymphocytes, which are thereby activated and differentiate into effector and memory cells. The rational design of vaccines consists in part in the identification of appropriate peptides to effect this process. There are several algorithms currently in use for making such predictions, but these are limited to a small number of MHC molecules and have good but imperfect prediction power. Read More

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http://dx.doi.org/10.1186/1745-7580-3-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2186325PMC
October 2007
4 Reads

Using the natural evolution of a rotavirus-specific human monoclonal antibody to predict the complex topography of a viral antigenic site.

Immunome Res 2007 Sep 18;3. Epub 2007 Sep 18.

Department of Genetics, University of Alabama School of Medicine, 720 20th Street South, Birmingham, 35294, USA.

Background: Understanding the interaction between viral proteins and neutralizing antibodies at atomic resolution is hindered by a lack of experimentally solved complexes. Progress in computational docking has led to the prediction of increasingly high-quality model antibody-antigen complexes. The accuracy of atomic-level docking predictions is improved when integrated with experimental information and expert knowledge. Read More

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http://www.immunome-research.com/content/3/1/8
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http://dx.doi.org/10.1186/1745-7580-3-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2042970PMC
September 2007
6 Reads