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  1. Research

    Factors important in evolutionary shaping of immunoglobulin gene loci

    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 regi...

    Michal Barak, Guy Eilat, Ron Unger and Ramit Mehr

    Immunome Research 2010 6:13

    Published on: 6 December 2010

  2. Research

    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

    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 found...

    Hua Cong, Ernest J Mui, William H Witola, John Sidney, Jeff Alexander, Alessandro Sette, Ajesh Maewal and Rima McLeod

    Immunome Research 2010 6:12

    Published on: 3 December 2010

  3. Research

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

    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...

    Duccio Cavalieri, Damariz Rivero, Luca Beltrame, Sonja I Buschow, Enrica Calura, Lisa Rizzetto, Sandra Gessani, Maria C Gauzzi, Walter Reith, Andreas Baur, Roberto Bonaiuti, Marco Brandizi, Carlotta De Filippo, Ugo D'Oro, Sorin Draghici, Isabelle Dunand-Sauthier…

    Immunome Research 2010 6:10

    Published on: 19 November 2010

  4. Research

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

    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...

    Robert J Milewski, Yutaro Kumagai, Katsumasa Fujita, Daron M Standley and Nicholas I Smith

    Immunome Research 2010 6:11

    Published on: 19 November 2010

  5. Research

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

    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 spa...

    Morten Nielsen, Sune Justesen, Ole Lund, Claus Lundegaard and Søren Buus

    Immunome Research 2010 6:9

    Published on: 13 November 2010

  6. Research

    Concept and application of a computational vaccinology workflow

    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 technologica...

    Johannes Söllner, Andreas Heinzel, Georg Summer, Raul Fechete, Laszlo Stipkovits, Susan Szathmary and Bernd Mayer

    Immunome Research 2010 6(Suppl 2):S7

    Published on: 3 November 2010

    This article is part of a Supplement: Volume 6 Supplement 2

  7. Review

    Computer aided selection of candidate vaccine antigens

    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 ...

    Darren R Flower, Isabel K Macdonald, Kamna Ramakrishnan, Matthew N Davies and Irini A Doytchinova

    Immunome Research 2010 6(Suppl 2):S1

    Published on: 3 November 2010

    This article is part of a Supplement: Volume 6 Supplement 2

  8. Review

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

    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 synt...

    Galina F Denisova, Dimitri A Denisov and Jonathan L Bramson

    Immunome Research 2010 6(Suppl 2):S6

    Published on: 3 November 2010

    This article is part of a Supplement: Volume 6 Supplement 2

  9. Review

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

    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 theoreticall...

    Darren R Flower, Kanchan Phadwal, Isabel K Macdonald, Peter V Coveney, Matthew N Davies and Shunzhou Wan

    Immunome Research 2010 6(Suppl 2):S4

    Published on: 3 November 2010

    This article is part of a Supplement: Volume 6 Supplement 2

  10. Review

    Recent advances in B-cell epitope prediction methods

    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 te...

    Yasser EL-Manzalawy and Vasant Honavar

    Immunome Research 2010 6(Suppl 2):S2

    Published on: 3 November 2010

    This article is part of a Supplement: Volume 6 Supplement 2

  11. Methodology

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

    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 t...

    Robert D Bremel and E Jane Homan

    Immunome Research 2010 6:7

    Published on: 2 November 2010

  12. Proceedings

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

    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...

    Di Wu, Jing Sun, Tianlei Xu, Shuning Wang, Guoqing Li, Yixue Li and Zhiwei Cao

    Immunome Research 2010 6(Suppl 1):S1

    Published on: 27 September 2010

    This article is part of a Supplement: Volume 6 Supplement 1

  13. Proceedings

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

    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 comp...

    Javed Mohammed Khan and Shoba Ranganathan

    Immunome Research 2010 6(Suppl 1):S2

    Published on: 27 September 2010

    This article is part of a Supplement: Volume 6 Supplement 1

  14. Proceedings

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

    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 m...

    Tze Hau Lam, Hiroshi Mamitsuka, Ee Chee Ren and Joo Chuan Tong

    Immunome Research 2010 6(Suppl 1):S6

    Published on: 27 September 2010

    This article is part of a Supplement: Volume 6 Supplement 1

  15. Proceedings

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

    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 b...

    Zhiliang Chen, Andrew M Collins, Yan Wang and Bruno A Gaëta

    Immunome Research 2010 6(Suppl 1):S4

    Published on: 27 September 2010

    This article is part of a Supplement: Volume 6 Supplement 1

  16. Research

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

    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 Are...

    Maya F Kotturi, Jason Botten, Matt Maybeno, John Sidney, Jean Glenn, Huynh-Hoa Bui, Carla Oseroff, Shane Crotty, Bjoern Peters, Howard Grey, Daniel M Altmann, Michael J Buchmeier and Alessandro Sette

    Immunome Research 2010 6:4

    Published on: 17 May 2010

  17. Research

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

    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 ...

    German Nudelman, Yongchao Ge, Jianzhong Hu, Madhu Kumar, Jeremy Seto, Jamie L Duke, Steven H Kleinstein, Fernand Hayot, Stuart C Sealfon and James G Wetmur

    Immunome Research 2010 6:2

    Published on: 18 March 2010

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