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Whole Genome Annotation: In Silico Analysis [chapter]

Vasco Azevedo, Vinicius Abreu, Sintia Almeida, Anderson Santos, Siomar Soares, Amjad Ali, Anne Pinto, Aryane Magalhaes, Eudes Barbosa, Rommel Ramos, Louise Cerdeira, Adriana Carneiro (+3 others)
2011 Bioinformatics - Trends and Methodologies  
Automated functional annotation Automated functional annotation of genomes can be quite efficient because it is a computational process based on the alignment of ORF sequences of the organism with sequences  ...  The International ImMunoGeneTics information system (IMGT), the world reference databank for immunogenetics and immunoinformatics, was created by Marie-Paule Lefranc in 1989 (Lefranc et al., 2009 ).  ...  Because of the rapid development of new technologies in molecular biology, new bioinformatic techniques emerge accordingly to keep the pace of in silico development of life science.  ... 
doi:10.5772/23724 fatcat:of53q6bc4fbdxply64hl63sjqe

IMGT unique numbering for MHC groove G-DOMAIN and MHC superfamily (MhcSF) G-LIKE-DOMAIN

Marie-Paule Lefranc, Elodie Duprat, Quentin Kaas, Madeleine Tranne, Aude Thiriot, Gérard Lefranc
2005 Developmental and Comparative Immunology  
IMGT, the international ImMunoGeneTics information system w (http://imgt.cines.fr) provides a common access to expertly annotated data on the genome, proteome, genetics and structure of immunoglobulins  ...  More particularly, the IMGT unique numbering [18-21], based on the NUMEROTATION concept of IMGT-ONTOL-OGY, has been set up to provide a standardized description of mutations, allelic polymorphisms, twodimensional  ...  K.Q. was the recipient of a doctoral grant from the MENESR and is currently supported by a grant from the Association pour la  ... 
doi:10.1016/j.dci.2005.03.003 pmid:15936075 fatcat:3fcp36ol7jhfxpema5hv73yp44

IG and TR single chain fragment variable (scFv) sequence analysis: a new advanced functionality of IMGT/V-QUEST and IMGT/HighV-QUEST

Véronique Giudicelli, Patrice Duroux, Sofia Kossida, Marie-Paule Lefranc
2017 BMC Immunology  
IMGT/HighV-QUEST, the high throughput version of IMGT/V-QUEST (portal begun in 2010, 500,000 sequences per batch).  ...  The analysis can also be performed on concatenated paired chains of expressed antigen receptor IG or TR repertoires.  ...  Acknowledgements We thank Gisèle Clofent-Sanchez and Audrey Hemadou for scFv sequences samples and their implication in the development of the project.  ... 
doi:10.1186/s12865-017-0218-8 pmid:28651553 pmcid:PMC5485737 fatcat:vlkvfytryzh4ricc22dsukuxqe

IMGT/HighV-QUEST Statistical Significance of IMGT Clonotype (AA) Diversity per Gene for Standardized Comparisons of Next Generation Sequencing Immunoprofiles of Immunoglobulins and T Cell Receptors

Safa Aouinti, Dhafer Malouche, Véronique Giudicelli, Sofia Kossida, Marie-Paule Lefranc, Rachel Louise Allen
2015 PLoS ONE  
IMGT built on IMGT-ONTOLOGY concepts of identification (keywords), description (labels), classification (gene and allele nomenclature) and numerotation (IMGT unique numbering), is at the origin of immunoinformatics  ...  IMGT/HighV-QUEST, the first web portal, and so far the only one, for the next generation sequencing (NGS) analysis of IG and TR, is the paradigm for immune repertoire standardized outputs and immunoprofiles  ...  IMGT is Academic Institutional Member of the International Medical Informatics Association (IMIA) and of the Global Alliance for the Genomics and Health (GA4GH).  ... 
doi:10.1371/journal.pone.0142353 pmid:26540440 pmcid:PMC4634997 fatcat:5jco3veq6jfnhpdgw2hya4ik34

IMGT standardization for statistical analyses of T cell receptor junctions: the TRAV-TRAJ example

Kevin Bleakley, Véronique Giudicelli, Yan Wu, Marie-Paule Lefranc, Gérard Biau
2006 In Silico Biology  
We have chosen the human TRAV-TRAJ junctions as an example in order to characterize the required criteria for a standardized analysis of the IG and TR V-J and V-D-J junctions, based on the IMGT-ONTOLOGY  ...  The diversity of immunoglobulin (IG) and T cell receptor (TR) chains depends on several mechanisms: combinatorial diversity, which is a consequence of the number of V, D and J genes and the N-REGION diversity  ...  We are grateful to Xavier Brochet for his contribution to the improvement of the IMGT/V-QUEST software. We thank Gérard Lefranc for fruitful discussion and the IMGT team for its constant  ... 
pmid:17518765 fatcat:p4hdldbd3bbvdoehszed57rfve

IMGT/PhyloGene: an on-line tool for comparative analysis of immunoglobulin and T cell receptor genes

Olivier Elemento, Marie-Paule Lefranc
2003 Developmental and Comparative Immunology  
IMGT/PhyloGene is an on-line software package for comparative analysis of immunoglobulin (IG) and T cell receptor (TR) variable genes of all vertebrate species, newly implemented in IMGT, the international  ...  Starting from a standardized alignment of selected sequences, IMGT/PhyloGene computes a matrix of evolutionary distances, builds a tree using the Neighbor-Joining (NJ) algorithm, and outputs various graphical  ...  IMGT is funded by the European Union's fifth PCRDT (QLG2-2000-01287) program, the Centre National de la Recherche Scientifique (CNRS), the Ministère de l'Education Nationale and the Ministère de la Recherche  ... 
doi:10.1016/s0145-305x(03)00078-8 pmid:12818634 fatcat:dpdfjiclibemnnljajlqvdqgty

The Past, Present, and Future of Immune Repertoire Biology – The Rise of Next-Generation Repertoire Analysis

Adrien Six, Maria Encarnita Mariotti-Ferrandiz, Wahiba Chaara, Susana Magadan, Hang-Phuong Pham, Marie-Paule Lefranc, Thierry Mora, Véronique Thomas-Vaslin, Aleksandra M. Walczak, Pierre Boudinot
2013 Frontiers in Immunology  
sequencing of IG/TR transcripts in a short amount of time.  ...  In this line, we discuss the recent efforts made for nomenclature standardization and ontology development.  ...  The accuracy and the consistency of the IMGT® data are based on IMGT-ONTOLOGY, the first, and so far, unique ontology for immunogenetics and immunoinformatics (147) .  ... 
doi:10.3389/fimmu.2013.00413 pmid:24348479 pmcid:PMC3841818 fatcat:vzxd6e6xuvbz5a67i7ynigtvji

The design and implementation of the immune epitope database and analysis resource

Bjoern Peters, John Sidney, Phil Bourne, Huynh-Hoa Bui, Soeren Buus, Grace Doh, Ward Fleri, Mitch Kronenberg, Ralph Kubo, Ole Lund, David Nemazee, Julia V. Ponomarenko (+7 others)
2005 Immunogenetics  
by X-ray crystallography to clinical studies analyzing correlates of protection for epitope based vaccines.  ...  Epitopes are defined as parts of antigens interacting with receptors of the immune system.  ...  Acknowledgements This work was supported by the National Institutes of Health Contract HHSN26620040006C.  ... 
doi:10.1007/s00251-005-0803-5 pmid:15895191 pmcid:PMC4780685 fatcat:ejparbxbfzgwtni32os2syqcsq

Histoimmunogenetics Markup Language 1.0: Reporting Next Generation Sequencing-based HLA and KIR Genotyping [article]

Robert P Milius, Michael Heuer, Daniel Valiga, Kathryn J Doroschak, Caleb J. Kennedy, Yung-Tsi Bolon, Joel Schneider, Jane Pollack, Hwa Ran Kim, Nezih Cereb, Jill A Hollenbach, Steven J Mack (+1 others)
2015 bioRxiv   pre-print
HML also continues to enable the transmission of legacy methods (e.g. site-specific oligonucleotide, sequence-specific priming, and sequence based typing (SBT)), adding features such as allowing multiple  ...  A full genotype, consensus sequence, and the surrounding metadata are included directly, while the raw sequence reads and platform documentation are externally referenced.  ...  One of the goals of these meetings has been to identify the Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) [9] based on the principles of the reporting guidelines for the Minimum  ... 
doi:10.1101/014951 fatcat:636yonxbqjb7vjfs6xb37fon4y

Receptor editing constrains development of phosphatidyl choline-specific B cells in VH12-transgenic mice

Alexandra N. Worth, Victoria L. Palmer, N. Max Schabla, Greg A. Perry, Anna N. Fraser-Philbin, Patrick C. Swanson
2022 Cell Reports  
positive selection based on PtC binding, often requiring LC receptor editing to salvage PtC- B cells and acquire PtC reactivity.  ...  Sequencing also reveals occasional in-frame hybrid LC genes, reminiscent of type 2 gene replacement, that, testing suggests, arise via a recombination-activating gene (RAG)-independent mechanism.  ...  Haddix President's Faculty Research Fund and by revenue from Nebraska's excise tax on cigarettes awarded to Creighton University through the Nebraska Department of Health & Human Services (DHHS).  ... 
doi:10.1016/j.celrep.2022.110899 pmid:35705027 fatcat:kznvivmhgbh6jfxzsibx73i324

Avian Immunome DB: an example of a user-friendly interface for extracting genetic information

Ralf C. Mueller, Nicolai Mallig, Jacqueline Smith, Lél Eöery, Richard I. Kuo, Robert H. S. Kraus
2020 BMC Bioinformatics  
With the ever-growing number of sequenced genomes and a variety of different annotation strategies, comes the potential for ambiguous gene symbols, making it cumbersome to capture the "correct" set of  ...  The foundation stone or the "seed" for the initial set of avian immune genes is based on the well-studied model organism chicken (Gallus gallus).  ...  Acknowledgements The authors are grateful for the early access to 363 sequenced bird genomes and annotations through the B10K consortium, which sparked the idea for this project.  ... 
doi:10.1186/s12859-020-03764-3 pmid:33176685 pmcid:PMC7661159 fatcat:5ir2ivfpsrcghnuy3xbvjnhmrq

Unifying immunology with informatics and multiscale biology

Brian A Kidd, Lauren A Peters, Eric E Schadt, Joel T Dudley
2014 Nature Immunology  
High-throughput technologies can be used to measure thousands of parameters of the immune system at a genome-wide scale.  ...  Here we review some of the computational analysis tools for high-dimensional data and how they can be applied to immunology.  ...  Tato for critical reading and feedback on the manuscript.  ... 
doi:10.1038/ni.2787 pmid:24448569 pmcid:PMC4345400 fatcat:ewhxb4ebq5gjnoijzjscnuvnwi

Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data

Florian Rubelt, Christian E Busse, Syed Ahmad Chan Bukhari, Jean-Philippe Bürckert, Encarnita Mariotti-Ferrandiz, Lindsay G Cowell, Corey T Watson, Nishanth Marthandan, William J Faison, Uri Hershberg, Uri Laserson, Brian D Corrie (+7 others)
2017 Nature Immunology  
The Adaptive Immune Receptor Repertoire (AIRR) Community was formed in 2015 to address issues in AIRR sequencing studies, including the development of reporting standards for the sharing of data sets.  ...  Luxembourg 5 Sorbonne Universités, UPMC Univ Paris 06, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Abstract High-throughput sequencing of B and T cell receptors is routinely being  ...  We invite all interested parties to join the AIRR Community, to attend the annual meetings, and to participate in one or more of the AIRR Community working groups.  ... 
doi:10.1038/ni.3873 pmid:29144493 pmcid:PMC5790180 fatcat:vfzzmxmi45c2fig636nzzmrnt4

Histoimmunogenetics Markup Language 1.0: Reporting next generation sequencing-based HLA and KIR genotyping

Robert P. Milius, Michael Heuer, Daniel Valiga, Kathryn J. Doroschak, Caleb J. Kennedy, Yung-Tsi Bolon, Joel Schneider, Jane Pollack, Hwa Ran Kim, Nezih Cereb, Jill A. Hollenbach, Steven J. Mack (+1 others)
2015 Human Immunology  
HML also continues to enable the transmission of legacy methods (e.g. site-specific oligonucleotide, sequence-specific priming, and Sequence Based Typing (SBT)), adding features such as allowing multiple  ...  A full genotype, consensus sequence, and the surrounding metadata are included directly, while the raw sequence reads and platform documentation are externally referenced.  ...  HML is an electronic messaging format based on XML and developed as a community standard allowing explicit representation of genotyping results for polymorphic immunogenetic gene systems such as HLA and  ... 
doi:10.1016/j.humimm.2015.08.001 pmid:26319908 pmcid:PMC4674307 fatcat:csy73ai3n5hchkhkwpoe7szrhm

Ontology-supported research on vaccine efficacy, safety and integrative biological networks

Yongqun He
2014 Expert Review of Vaccines  
of Life, and ontology-based approaches to study and apply the OneNet theory.  ...  The author further proposes minimal vaccine information standards and their ontology representations, ontology-based linked open vaccine data and meta-analysis, an integrative One Network ("OneNet") Theory  ...  Acknowledgments The author appreciates three anonymous reviewers for their insightful comments. This work was supported by NIH-NIAID grant R01AI081062.  ... 
doi:10.1586/14760584.2014.923762 pmid:24909153 pmcid:PMC4815432 fatcat:t3xq23efsrgyrn5zp3xo2v2dji
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