MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Immunome Research' source. Fri, 04 Feb 2011 15:00:01 +0100 http://www.immunome-research.com/content/6/1/13 Conclusions: We conclude that contemporary species' Ig libraries have been optimized by evolution in terms of Ig sequence lengths, the number and diversity of Ig genes, and antibody-antigen affinities. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=4230590 Mon, 06 Dec 2010 00:00:00 +0100 4230590 http://www.immunome-research.com/content/6/1/10 Conclusions: The initiative significantly improves our understanding of DC biology and regulatory networks. Developing a systems biology approach for immune system holds the promise of translating knowledge on the immune system into more successful immunotherapy strategies. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=4183755 Fri, 19 Nov 2010 00:00:00 +0100 4183755 http://www.immunome-research.com/content/6/1/11 Conclusions: The computational efficiency of Z-LSR enables automated resolution of sub-cellular features in large Raman microscopy data sets without compromise in image quality or information loss in associated spectra. These results motivate further use of label free microscopy techniques in real-time imaging of live immune cells. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=4183754 Fri, 19 Nov 2010 00:00:00 +0100 4183754 http://www.immunome-research.com/content/6/1/9 Conclusions: The method thus shows great potential for efficient boosting the accuracy of MHC-II binding prediction, as accurate predictions can be obtained for novel alleles at highly reduced experimental costs. Pan-specific binding predictions can be obtained for all alleles with know protein sequence and the method can benefit by including data in the training from alleles even where only few binders are known. The method and benchmark data are available at www.cbs.dtu.dk/services/NetMHCIIpan-2.0 (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=4163183 Sat, 13 Nov 2010 00:00:00 +0100 4163183 http://www.immunome-research.com/content/6/1/7 Conclusions: As opposed to the highly constrained user-interaction paradigms of web-server approaches, local computational approaches enable interactive analysis and visualization of complex multidimensional data using robust mathematical tools. Our work shows that prediction tools such as these can be constructed on the widely available JMP platform, can operate in a spreadsheet environment on a desktop computer, and are capable of handling proteome-scale analysis with high throughput. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=4126346 Tue, 02 Nov 2010 00:00:00 +0100 4126346 http://www.immunome-research.com/content/6/1/8 Conclusions: A desktop application with interactive graphic capability is shown to be a useful platform for development of prediction and visualization tools for epitope mapping at scales ranging from individual proteins to proteomes from multiple strains of an organism. The possible functional implications of the patterns of peptide epitopes observed are discussed, including their implications for B-cell and T-cell cooperation and cross presentation. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=4126345 Tue, 02 Nov 2010 00:00:00 +0100 4126345 http://www.immunome-research.com/content/6/1/6 Conclusion: This study demonstrates that prediction of conformational B-cell epitope in an antigen is possible from is primary sequence. This study will be very useful in predicting conformational B-cell epitopes in antigens whose tertiary structures are not available. A web server CBTOPE has been developed for predicting B-cell epitope (http://www.imtech.res.in/raghava/cbtope/). (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=4088986 Tue, 19 Oct 2010 23:00:00 +0100 4088986 http://www.immunome-research.com/content/6/1/5 Conclusions: Our analysis distinguished pro-inflammatory vs. antibacterial transcriptomic signatures that classified their respective gene expression patterns and the corresponding TF-TFBS interactions in LPS-stimulated macrophages. By doing so, this study has attempted to characterize the temporal differences in gene expression associated with LPS tolerance, a major immune phenomenon implicated in various pathological disorders. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=3988784 Mon, 20 Sep 2010 23:00:00 +0100 3988784 http://www.immunome-research.com/content/6/1/4 Conclusions: The identification of CD4+ T cell epitopes, with promiscuous binding properties, derived from 7 different arenavirus species will aid in the development of a T cell-based vaccine strategy with the potential to target a broad range of ethnicities within the general population and to protect against both Old and New World arenavirus infection. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=3570567 Sun, 16 May 2010 23:00:00 +0100 3570567 http://www.immunome-research.com/content/6/1/3 Conclusion: The genomic comparisons of the beta-defensins gene clusters of the chicken and zebra finch illuminate the evolutionary history of this gene complex. Along their ancestral lines, several gene duplication events have occurred in the passerine line after the galliformes-passeriformes split giving rise to 12 novel genes compared to a single duplication event in the galliformes line. After the duplication events, the duplicated genes have been subject to a relaxed selection pressure compared to the non-duplicated genes, thus supporting models of evolution by gene duplication. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=3425969 Wed, 31 Mar 2010 23:00:00 +0100 3425969 http://www.immunome-research.com/content/6/1/2 Conclusions: MDS mapping based on correlation in conjunction with TF enrichment analysis represents a useful computational method to generate predictions underlying gene coregulation across a population. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=3379862 Thu, 18 Mar 2010 00:00:00 +0100 3379862 http://www.immunome-research.com/content/6/1/1 Conclusions: This effort represents the first attempt at linking molecule ontology with cell ontology, in IMGT-ONTOLOGY, the well established ontology in immunogenetics and immunoinformatics, and a paradigm for life science biology. With the increasing use of models in biology and medicine, the need to link different levels, from molecules to cells to tissues and organs, is increasingly important. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=3284908 Thu, 18 Feb 2010 00:00:00 +0100 3284908 http://www.immunome-research.com/content/5/1/5 Conclusion: Our observations highlight the importance of translation regulation during the immune response, and may favor the identification of novel protein networks relevant for immunity. Our study also provides information on the potential absence of correlation between gene expression and protein production for specific mRNA molecules present in DCs. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=3034771 Fri, 27 Nov 2009 00:00:00 +0100 3034771 http://www.immunome-research.com/content/5/1/4 Conclusions The findings of this bioinformatical approach shed light on fundamental factors that might have shaped adaptive immunity during evolution. Our data suggest that amino acid sequence-based hypo/non-glycosylation of certain segments of proteins might be substantial for determining T cell immunity/autoimmunity. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=2825572 Wed, 23 Sep 2009 23:00:00 +0100 2825572 http://www.immunome-research.com/content/5/1/3 Conclusions: These data suggest that differences in immunodominance patterns might explain the incomplete response overlap, and that with limitations, HLA Tg mice represent a relevant and suitable model system to study immune responses against complex pathogens. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=2485573 Tue, 16 Jun 2009 23:00:00 +0100 2485573 http://www.immunome-research.com/content/5/1/2 Conclusions: We have successfully developed versatile MHC-II resources, which may assist in the generation of MHC class II -wide reagents, data, and tools. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=2390590 Tue, 05 May 2009 04:00:00 +0100 2390590 http://www.immunome-research.com/content/5/1/1 Conclusions: We hypothesize that peripheral autoreactivity results primarily from somatic mutation, and that the genetic correlates of autoreactivity in mature B-cells are not the same as those for autoreactivity in immature B cells. What is seen in mature autoreactive B cells are the correlates of {\it autoreactive potential}, not of autoreactivity per se. The autoreactive potential is higher for V(D)J rearrangements encoded to a large extent by N-nucleotides rather than by the gene segments that, we posit, have been selected in germline evolution for their suppression of autoreactive potential. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=2220029 Fri, 27 Feb 2009 05:00:00 +0100 2220029 http://www.immunome-research.com/content/4/1/7 Conclusion: We have developed a data mining approach that enables rapid extraction of complex data from the major clinical trial repository. Summarization and visualization of these data represents a cost-effective means of making informed decisions about the future cancer vaccine clinical trials. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=2031080 Fri, 12 Dec 2008 05:00:00 +0100 2031080 http://www.immunome-research.com/content/4/1/6 Conclusions: The observed relationship between peptide length and MHC class II affinity is likely to have clear implications for vaccine design and the study of immunological disease. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=1987819 Wed, 26 Nov 2008 05:00:00 +0100 1987819 http://www.immunome-research.com/content/4/1/5 Conclusion: The constitutive or regulated expression in macrophages of several GPCRs identified in this study has not previously been described. Future studies on such GPCRs and their agonists are likely to provide important insights into macrophage biology, as well as novel inflammatory pathways that could be future targets for drug discovery. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=1404680 Tue, 29 Apr 2008 04:00:00 +0100 1404680 http://www.immunome-research.com/content/4/1/4 Conclusions: Our results shed light on selective forces acting on the emergence of biological networks. It is likely that the high efficiency and low vulnerability are intrinsic properties of many biological networks, which arise from the effects of evolutionary processes yet to be uncovered. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=1389934 Tue, 22 Apr 2008 04:00:00 +0100 1389934 http://www.immunome-research.com/content/4/1/3 Conclusions: We present here the most precise estimates of gene segment usage frequencies currently available along with analyses regarding n-nucleotide distributions and D-J segment pair preferences. Additionally, we provide the first statistical evidence that sequential D-J recombinations occur at the human heavy chain locus during B-cell ontogeny with an approximate frequency of 20%. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=1260604 Wed, 27 Feb 2008 05:00:00 +0100 1260604 http://www.immunome-research.com/content/4/1/2 Conclusions: These data confirm, on a large scale, including 15 human and 4 mouse class I alleles, the efficacy of the positional scanning combinatorial library approach for describing MHC class I binding specificity and identifying high affinity binding peptides. These libraries were shown to be useful for identifying specific primary and secondary anchor positions, and thereby simpler motifs, analogous to those described by other approaches. The present study also provides matrices useful for predicting high affinity binders for several alleles for which detailed quantitative descriptions of binding specificity were previously unavailable, including A*3001, A*3201, B*0801, B*1501 and B*1503. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=1176690 Fri, 25 Jan 2008 05:00:00 +0100 1176690 http://www.immunome-research.com/content/4/1/1 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. Specifically if many alternative antigen are available the reduction of required synthesized peptides until one successful candidate is found is of central technical interest. We have investigated the integration of B-cell epitope prediction with the variability of antig... Immunome Research journals http://www.medworm.com/rss/comments.php?id=1133171 Mon, 07 Jan 2008 05:00:00 +0100 1133171 http://www.immunome-research.com/content/3/1/10 Conclusions: All current TB-related epitope data was cataloged for the first time from the published literature. The resulting inventory of more than a thousand different epitopes should prove a useful tool for the broad scientific community. Knowledge gaps specific to TB epitope data were also identified. In summary, few non-peptidic or post-translationally modified epitopes have been defined. Most importantly epitopes have apparently been defined from only 7% of all ORFs, and the top 30 most frequently studied protein antigens contain 65% of the epitopes, leaving the majority of M. tuberculosis genome unexplored. A lack of information related to the specific strains from which epitopes are derived is also evident. Finally, the generation of reference lists of mycobacterial epitopes shoul... Immunome Research journals http://www.medworm.com/rss/comments.php?id=1094906 Fri, 14 Dec 2007 05:00:00 +0100 1094906 http://www.immunome-research.com/content/3/1/9 Conclusion: Representation of amino acids using a few important bio-physio-chemical property provide a natural basis for representing peptides and greatly improves peptide-MHC class I binding prediction. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=986448 Mon, 29 Oct 2007 04:00:00 +0100 986448 http://www.immunome-research.com/content/3/1/8 Conclusions: The use of mutagenesis constraints in docking calculations allows for the identification of a small number of alternative arrangements of the antigen-antibody interface. The mutagenesis information from the natural evolution of a neutralizing antibody can be used to discriminate between residue-scale models and create distance constraints for atomic-resolution docking. The integration of binding affinity data or other information with computation may be an advantageous approach to assist peptide engineering or therapeutic antibody design. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=880955 Tue, 18 Sep 2007 04:00:00 +0100 880955 http://www.immunome-research.com/content/3/1/7 Conclusions: The analysis of predicted Cw*0401-binding peptides showed that anchor residues may not be restrictive and the Cw*0401 binding pockets may possibly accommodate a wide variety of peptides with common physico-chemical properties. The potential Cw*0401-specific T-cell epitope repertoires for HIV-1 p24gag and gp160gag glycoproteins are well distributed throughout both glycoproteins, with thirteen and nine immunological hot spots for HIV-1 p24gag and gp160gag glycoproteins respectively. These findings provide new insights into HLA-C peptide selectivity, indicating that pre-selection of candidate HLA-C peptides may occur at the TAP level, prior to peptide loading in the endoplasmic reticulum. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=809185 Mon, 20 Aug 2007 04:00:00 +0100 809185 http://www.immunome-research.com/content/3/1/6 Conclusions: The IDR is the first knowledge base specifically designed to capture in a systematic and validated way both clinical and molecular information for primary immunodeficiency. The service is freely available at http://bioinf.uta.fi/idr and is regularly updated. The IDR facilitates primary immunodeficiency informatics and helps to parameterise in silico modelling of these diseases. The IDR is useful also as an advanced education tool for medical students, and physicians. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=519347 Thu, 29 Mar 2007 04:00:00 +0100 519347 http://www.immunome-research.com/content/3/1/5 Conclusions: A heuristic-based method of combining the results of the individual tools better facilitates the scanning of large proteomes for potential epitopes, yielding more actual high-affinity binders while reporting very few false positives. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=507159 Sat, 24 Mar 2007 04:00:00 +0100 507159 http://www.immunome-research.com/content/3/1/4 Conclusions: ImmTree provides a unique data set of genes and proteins from the human immune system, their phylogenetics, and information for comparisons of human-mouse ortholog pairs, synonymous and non-synonymous mutation rates, as well as other statistical information. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=490088 Wed, 21 Mar 2007 04:00:00 +0100 490088 http://www.immunome-research.com/content/3/1/3 Conclusion: The EpitopeViewer is designed and been tested for use by immunologists with little or no training in molecular graphics. The EpitopeViewer can be launched from most popular Web browsers without user intervention. A Java Runtime Environment (RJE) 1.4.2 or higher is required. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=431867 Wed, 21 Feb 2007 07:00:00 +0100 431867 http://www.immunome-research.com/content/3/1/2 Conclusions: The identification of an antigen containing multiple CTL epitopes and its apparent immunodominance during a protective anti-parasite response makes Tp2 an attractive candidate for evaluation of its vaccine potential. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=407896 Fri, 09 Feb 2007 07:00:00 +0100 407896 http://www.immunome-research.com/content/3/1/1 Conclusions: The database is available at http://epitope.liai.org:8080/projects/arena and can be used to aid in studies that require proteomic information from pathogenic arenaviruses. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=407897 Thu, 08 Feb 2007 07:00:00 +0100 407897 http://www.immunome-research.com/content/2/1/4 Conclusions: The power of this approach was demonstrated by the identification of orthologous cytokines between marsupials and eutherians that share only 30% identity at the amino acid level. Furthermore, the presence of key immunological genes suggests that marsupials do indeed possess a sophisticated immune system, whose function may parallel that of eutherian mammals. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=277545 Fri, 10 Nov 2006 07:00:00 +0100 277545 http://www.immunome-research.com/content/2/1/3 Conclusion: PREDTAP can be integrated with prediction systems for MHC class I binding peptides for improved performance of in silico prediction of T-cell epitopes. PREDTAP is available at http://antigen.i2r.a-star.edu.sg/predTAP. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=32660 Tue, 23 May 2006 06:00:00 +0100 32660 http://www.immunome-research.com/content/2/1/2 Conclusions: The best single method for predicting linear B-cell epitopes is the hidden Markov model. Combining the hidden Markov model with one of the best propensity scale methods, we obtained the BepiPred method. When tested on the validation data set this method performs significantly better than any of the other methods tested. The server and data sets are publicly available at www.cbs.dtu.dk/services/BepiPred. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=189 Mon, 24 Apr 2006 06:00:00 +0100 189 http://www.immunome-research.com/content/2/1/1 Conclusion: Our docking simulations are entirely consistent with functional data obtained from in vitro competitive binding assays and T cell proliferation studies in DR4 and DR6 PV patients. Our findings ascertain that DRB1*0402 plays a crucial role in the selection of specific self-peptides in DR4 PV. DRB1*0402 and DQB1*0503 do not necessarily share the same core residues, indicating that both alleles may have different binding specificities. In addition, our results lend credence to the hypothesis that the alleles DQB1*0201 and *0202 play a protective role by binding Dsg3 peptides with greater affinity than the susceptible alleles, allowing for efficient deletion of autoreactive T cells. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=190 Sat, 21 Jan 2006 07:00:00 +0100 190 http://www.immunome-research.com/content/1/1/6 Conclusion: The iterative learning procedure appears to be effective in prediction of MHC class II binders. It offers an alternative approach to this important predictionproblem. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=191 Tue, 13 Dec 2005 07:00:00 +0100 191 http://www.immunome-research.com/content/1/1/5 We present a systematic approach to search for an effective vaccination schedule using mathematical computerized models. Our study is based on our previous model that simulates the cancer vs immune system competition activated by tumor vaccine. This model accurately reproduces in-vivo experiments results on HER-2/neu mice treated with the immuno-prevention cancer vaccine (Triplex) for mammary carcinoma. In vivo experiments have shown the effectiveness of Triplex vaccine in protection of mice from mammary carcinoma. The full protection was conferred using chronic (prophylactic) vaccination protocol while therapeutic vaccination was less effcient.In the present paper we use the computer simulations to systematically search for a vaccination schedule which prevents solid tumor formation. The ... Immunome Research journals http://www.medworm.com/rss/comments.php?id=192 Fri, 07 Oct 2005 06:00:00 +0100 192 http://www.immunome-research.com/content/1/1/4 AntiJen is a database system focused on the integration of kinetic, thermodynamic, functional, and cellular data within the context of immunology and vaccinology. Compared to its progenitor JenPep, the interface has been completely rewritten and redesigned and now offers a wider variety of search methods, including a nucleotide and a peptide BLAST search. In terms of data archived, AntiJen has a richer and more complete breadth, depth, and scope, and this has seen the database increase to over 31,000 entries. AntiJen provides the most complete and up-to-date dataset of its kind. While AntiJen v2.0 retains a focus on both T cell and B cell epitopes, its greatest novelty is the archiving of continuous quantitative data on a variety of immunological molecular interactions. This includes therm... Immunome Research journals http://www.medworm.com/rss/comments.php?id=193 Thu, 06 Oct 2005 06:00:00 +0100 193 http://www.immunome-research.com/content/1/1/1 Immunology research has been transformed in the post-genomics era, with high throughput molecular biology and information technologies taking an increasingly central role. This has led to the development of a new area of science termed "Immunomics", that encompasses genomic, high throughput and bioinformatic approaches to immunology. In recognition of the increasing importance of this field, Immunome Research is a new Open Access, online journal, that will publish cutting edge research across the field of Immunomics. Immunome Research will publish a wide range of article types including specialty immunology databases, immunology database tools, immunome epitope research, epitope analysis tools, high-throughput technologies (gene sequencing, microarrays, proteomics), white papers, mathemati... Immunome Research journals http://www.medworm.com/rss/comments.php?id=196 Tue, 20 Sep 2005 06:00:00 +0100 196 http://www.immunome-research.com/content/1/1/2 Conclusion: The IEDB's ontology is the first ontology specifically designed to capture both intrinsic chemical and biochemical information relating to immune epitopes with information relating to the interaction of these structures with molecules derived from the host immune system. We anticipate that the development of this type of ontology and associated databases will facilitate rigorous description of data related to immune epitopes, and might ultimately lead to completely new methods for describing and modeling immune responses. (Source: Immunome Research) Immunome Research journals http://www.medworm.com/rss/comments.php?id=195 Tue, 20 Sep 2005 06:00:00 +0100 195 http://www.immunome-research.com/content/1/1/3 IMGT, the international ImMunoGeneTics information system®http://imgt.cines.fr, was created in 1989 by the Laboratoire d'ImmunoGénétique Moléculaire (LIGM) (Université Montpellier II and CNRS) at Montpellier, France. IMGT is a high quality integrated knowledge resource specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins of the immune system (RPI) of any species which belong to the immunoglobulin superfamily (IgSF) and to the MHC superfamily (MhcSF). IMGT consists of five databases, ten on-line tools and more than 8,000 HTML pages of Web resources. IMGT provides a common access to standardized data from genome, genetics, proteome and three-dimensional structures. The accuracy and the con... Immunome Research journals http://www.medworm.com/rss/comments.php?id=194 Tue, 20 Sep 2005 06:00:00 +0100 194