Relevant bibliographies by topics / Immune repertoire visualization

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  1. Journal articles
  2. Dissertations / Theses

Academic literature on the topic 'Immune repertoire visualization'

Author: Grafiati
Published: 25 May 2024
Last updated: 31 July 2025

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Journal articles on the topic "Immune repertoire visualization"

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Kitanovski, Simo, Kai Wollek, and Daniel Hoffmann. "Quantitative Visualisierung von HTseq-Daten." BIOspektrum 31, no. 1 (2025): 49–51. https://doi.org/10.1007/s12268-025-2369-0.

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Abstract High-throughput sequencing (HTseq) characterizes complex entities at the level of nucleic acid sequences, e. g. the transcriptome in a biopsy at cellular resolution, or an immune-receptor-repertoire. The complexity of HTseq data makes analysis challenging. Suitable methods are often missing. We therefore develop computational tools for quantitative visualization (quantitative modelling of data, then visualization of meaningful summaries) as illustrated with two examples, scBubble-tree and ClustIRR.
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Toby, Inimary, Scott Christley, Walter Scarborough, et al. "VDJServer – a web-accessible analysis portal for immune repertoire sequencing analysis." Journal of Immunology 198, no. 1_Supplement (2017): 55.49. http://dx.doi.org/10.4049/jimmunol.198.supp.55.49.

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Abstract VDJServer is a comprehensive, web-accessible system for analysis of immune repertoire sequencing data. VDJServer provides a complete analysis workflow from pre-processing of sequence reads, to V(D)J assignment, to repertoire characterization and comparison. Recent enhancements in VDJServer include: --Automatic parallelization of analysis tools to handle very large data sets running on a high-performance supercomputer--Import and export subject and sample metadata. User-defined sample groups allows for sophisticated group analysis and comparison.--Extensive analysis functionality such
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Chen, Si-Yi, Tao Yue, Qian Lei, and An-Yuan Guo. "TCRdb: a comprehensive database for T-cell receptor sequences with powerful search function." Nucleic Acids Research 49, no. D1 (2020): D468—D474. http://dx.doi.org/10.1093/nar/gkaa796.

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Abstract T cells and the T-cell receptor (TCR) repertoire play pivotal roles in immune response and immunotherapy. TCR sequencing (TCR-Seq) technology has enabled accurate profiling TCR repertoire and currently a large number of TCR-Seq data are available in public. Based on the urgent need to effectively re-use these data, we developed TCRdb, a comprehensive human TCR sequences database, by a uniform pipeline to characterize TCR sequences on TCR-Seq data. TCRdb contains more than 277 million highly reliable TCR sequences from over 8265 TCR-Seq samples across hundreds of tissues/clinical condi
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Sarda, Shrutii, Geoffrey Lowman, Michelle Toro, Loni Pickle, Timothy Looney, and Fiona Hyland. "Fully Automated Workflows Quantify and Report Key T-Cell and B-Cell Receptor Biomarkers Relevant to Immuno-Oncology and Heme-Oncology Research." Blood 138, Supplement 1 (2021): 4002. http://dx.doi.org/10.1182/blood-2021-151154.

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Abstract Background T-cell and B-cell repertoire analysis is used in oncology research, to understand the etiology of complex disease phenotypes, for the identification of biomarkers predictive of disease burden, outcome, and response to treatment, and for research in diagnosis and recurrence monitoring. Key predictors include secondary and tertiary repertoire features not reported by existing sequencing software solutions. For example, due to ongoing somatic hypermutation in mature B-cell receptors, the underlying sequence of a given clone can accumulate base differences and appear as several
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Omer, Aviv, Or Shemesh, Ayelet Peres, et al. "VDJbase: an adaptive immune receptor genotype and haplotype database." Nucleic Acids Research 48, no. D1 (2019): D1051—D1056. http://dx.doi.org/10.1093/nar/gkz872.

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Abstract VDJbase is a publicly available database that offers easy searching of data describing the complete sets of gene sequences (genotypes and haplotypes) inferred from adaptive immune receptor repertoire sequencing datasets. VDJbase is designed to act as a resource that will allow the scientific community to explore the genetic variability of the immunoglobulin (Ig) and T cell receptor (TR) gene loci. It can also assist in the investigation of Ig- and TR-related genetic predispositions to diseases. Our database includes web-based query and online tools to assist in visualization and analy
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Sauteraud, Renan, Lev Dashevskiy, Greg Finak, and Raphael Gottardo. "ImmuneSpace: Enabling integrative modeling of human immunological data." Journal of Immunology 196, no. 1_Supplement (2016): 124.65. http://dx.doi.org/10.4049/jimmunol.196.supp.124.65.

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Abstract Recent technical advances have transformed the field of immunology. We are now capable of measuring features of immune responses, including B- and T-cell specificity and repertoire, serum and intracellular cytokines, and more, on a scale never imagined before. As a consequence, the generation of big data sets has become routine and there is an urgent need for an analysis platform to facilitate data exploration and integration across assays and studies. Here we present ImmuneSpace, the data repository and analysis platform of the Human Immunology Project Consortium (HIPC). The HIPC pro
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Stalika, Evangelia, Anastasia Hadzidimitriou, Athanasios Gkoufas, et al. "High-Throughput Profiling of the T-Cell Receptor Gene Repertoire Supports Antigen Drive in the Pathogenesis of Chronic Idiopathic Neutropenia." Blood 124, no. 21 (2014): 2731. http://dx.doi.org/10.1182/blood.v124.21.2731.2731.

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Abstract Chronic idiopathic neutropenia (CIN) is an acquired disorder of granulopoiesis characterized by prolonged neutropenia, mainly affecting middle-age females of the HLA-DRB1*1302 type. The defective hematopoiesis in CIN can be mainly attributed to accelerated Fas-mediated death of the CD34+/CD33+ granulocytic progenitors, secondary to an inflammatory bone marrow (BM) microenvironment. Crucial to CIN pathogenesis are the increased numbers of activated T cells identified in both peripheral blood (PB) and BM of CIN patients, supporting an immune pathogenesis. Using Sanger sequencing, we pre
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Gemenetzi, Katerina, Evangelia Stalika, Andreas Agathangelidis, et al. "Evidence for Epitope-Specific T Cell Responses in HIV-Associated Non Neoplastic Lymphadenopathy: High-Throughput Immunogenetic Evidence." Blood 132, Supplement 1 (2018): 1117. http://dx.doi.org/10.1182/blood-2018-99-118975.

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Abstract Non-neoplastic lymphadenopathy (NNL) associated with the human immunodeficiency virus (HIV) infection may develop concurrently with the onset of HIV viremia (acute retroviral syndrome) that can persist beyond the acute phase. Histopathological findings at this early phase mainly pertain to hyperplastic changes with large lymphoid follicles; with time, the number of lymphoid follicles diminishes, while plasma cells increase; at the extreme is a pattern characterized by sclerosis of the germinal centers in the residual follicles. HIV-specific CD8+ T cell responses have been reported and
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Huang, Alex Yee-Chen, Jay T. Myers, Youmna Othman, Deborah Sim Barkauskas, and Agne Petrosiute. "Real-time dynamic and sequential tracking of tumor propagation and associated immune responses in the CNS microenvironment." Journal of Clinical Oncology 30, no. 15_suppl (2012): 9520. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.9520.

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9520 Background: Ex vivo experimental systems are often unable to fully capture complex intercellular communication between tumor cells and surrounding tissues - a critical feature in understanding cancer development and immune evasion. Imaging modality such as bioluminescence lacks the resolution necessary to discern subtle structural differences and heterogeneity in the tumor niche. Microscopic examination of fixed specimens is devoid of the 3-dimensional context or evolution of tumor progression within the same host. Methods: New insights have come from studies involving the use of intravit
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Vetter, Julia, Constantin Aschauer, Andreas Heinzel, et al. "Identification of immunologic factors associated with allograft rejection using NGS T cell receptor repertoire data." Journal of Immunology 204, no. 1_Supplement (2020): 161.3. http://dx.doi.org/10.4049/jimmunol.204.supp.161.3.

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Abstract T and B cells are known to play an important role in transplant rejection. Nevertheless, the factors that lead to rejection are not yet fully understood. We have developed a general bioinformatics pipeline for processing T cell receptor (TCR) and immunoglobulin (IG) repertoire next-generation sequencing (NGS) data for comparing immune repertoire properties between multiple groups of samples. Using such a pipeline can help to identify properties of the immune repertoire increasing the risk of allograft rejection after transplantation. Our pipeline is implemented in Python 3.7. Various
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Dissertations / Theses on the topic "Immune repertoire visualization"

1

Abdollahi, Nika. "B cell receptor repertoire analysis in clinical context : new approaches for clonal grouping, intra-clonal diversity studies, and repertoire visualization." Electronic Thesis or Diss., Sorbonne université, 2021. http://www.theses.fr/2021SORUS063.

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Le séquençage de nouvelle génération a permis aux chercheurs de réaliser des analyses approfondies du paysage du répertoire immunologique. Cependant, une préoccupation importante dans ces études est le coût informatique de l'analyse de millions de séquences avec une complexité, une variabilité et une capacité de mutation inhérentes, imposant des défis informatiques et nécessitant le développement de méthodes efficaces. Ce défi est encore plus évident dans le contexte clinique qui n'a pas nécessairement accès à des professionnels ayant des compétences informatiques ou des ressources informatiqu
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