Literature DB >> 29144493

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

Florian Rubelt1, Christian E Busse2, Syed Ahmad Chan Bukhari3, Jean-Philippe Bürckert4, Encarnita Mariotti-Ferrandiz5, Lindsay G Cowell6, Corey T Watson7, Nishanth Marthandan8, William J Faison9, Uri Hershberg10, Uri Laserson11, Brian D Corrie12,13, Mark M Davis1,14, Bjoern Peters15, Marie-Paule Lefranc16, Jamie K Scott8,12,17, Felix Breden12,13, Eline T Luning Prak18, Steven H Kleinstein3,19.   

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Year:  2017        PMID： 29144493      PMCID： PMC5790180          DOI： 10.1038/ni.3873

Source DB:  PubMed          Journal:  Nat Immunol        ISSN： 1529-2908            Impact factor:   25.606


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  23 in total

1.  Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Authors:  A Brazma; P Hingamp; J Quackenbush; G Sherlock; P Spellman; C Stoeckert; J Aach; W Ansorge; C A Ball; H C Causton; T Gaasterland; P Glenisson; F C Holstege; I F Kim; V Markowitz; J C Matese; H Parkinson; A Robinson; U Sarkans; S Schulze-Kremer; J Stewart; R Taylor; J Vilo; M Vingron
Journal:  Nat Genet       Date:  2001-12       Impact factor: 38.330

Review 2.  Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires.

Authors:  Victor Greiff; Enkelejda Miho; Ulrike Menzel; Sai T Reddy
Journal:  Trends Immunol       Date:  2015-10-25       Impact factor: 16.687

Review 3.  Reconstructing immune phylogeny: new perspectives.

Authors:  Gary W Litman; John P Cannon; Larry J Dishaw
Journal:  Nat Rev Immunol       Date:  2005-11       Impact factor: 53.106

4.  Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data.

Authors:  Namita T Gupta; Jason A Vander Heiden; Mohamed Uduman; Daniel Gadala-Maria; Gur Yaari; Steven H Kleinstein
Journal:  Bioinformatics       Date:  2015-06-10       Impact factor: 6.937

Review 5.  NIH's genomic data sharing policy: timing and tradeoffs.

Authors:  Jorge L Contreras
Journal:  Trends Genet       Date:  2015-01-22       Impact factor: 11.639

6.  Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles.

Authors:  Daniel Gadala-Maria; Gur Yaari; Mohamed Uduman; Steven H Kleinstein
Journal:  Proc Natl Acad Sci U S A       Date:  2015-02-09       Impact factor: 11.205

Review 7.  Novel Approaches to Analyze Immunoglobulin Repertoires.

Authors:  Hedda Wardemann; Christian E Busse
Journal:  Trends Immunol       Date:  2017-05-26       Impact factor: 16.687

8.  Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges.

Authors:  Alvis Brazma
Journal:  ScientificWorldJournal       Date:  2009-05-29

9.  The International Nucleotide Sequence Database Collaboration.

Authors:  Yasukazu Nakamura; Guy Cochrane; Ilene Karsch-Mizrachi
Journal:  Nucleic Acids Res       Date:  2012-11-24       Impact factor: 16.971

10.  The FAIR Guiding Principles for scientific data management and stewardship.

Authors:  Mark D Wilkinson; Michel Dumontier; I Jsbrand Jan Aalbersberg; Gabrielle Appleton; Myles Axton; Arie Baak; Niklas Blomberg; Jan-Willem Boiten; Luiz Bonino da Silva Santos; Philip E Bourne; Jildau Bouwman; Anthony J Brookes; Tim Clark; Mercè Crosas; Ingrid Dillo; Olivier Dumon; Scott Edmunds; Chris T Evelo; Richard Finkers; Alejandra Gonzalez-Beltran; Alasdair J G Gray; Paul Groth; Carole Goble; Jeffrey S Grethe; Jaap Heringa; Peter A C 't Hoen; Rob Hooft; Tobias Kuhn; Ruben Kok; Joost Kok; Scott J Lusher; Maryann E Martone; Albert Mons; Abel L Packer; Bengt Persson; Philippe Rocca-Serra; Marco Roos; Rene van Schaik; Susanna-Assunta Sansone; Erik Schultes; Thierry Sengstag; Ted Slater; George Strawn; Morris A Swertz; Mark Thompson; Johan van der Lei; Erik van Mulligen; Jan Velterop; Andra Waagmeester; Peter Wittenburg; Katherine Wolstencroft; Jun Zhao; Barend Mons
Journal:  Sci Data       Date:  2016-03-15       Impact factor: 6.444
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  56 in total

1.  Alignment free identification of clones in B cell receptor repertoires.

Authors:  Ofir Lindenbaum; Nima Nouri; Yuval Kluger; Steven H Kleinstein
Journal:  Nucleic Acids Res       Date:  2021-02-26       Impact factor: 16.971

2.  AIRR Community Guide to Planning and Performing AIRR-Seq Experiments.

Authors:  Anne Eugster; Magnolia L Bostick; Nidhi Gupta; Encarnita Mariotti-Ferrandiz; Gloria Kraus; Wenzhao Meng; Cinque Soto; Johannes Trück; Ulrik Stervbo; Eline T Luning Prak
Journal:  Methods Mol Biol       Date:  2022

3.  Data Sharing and Reuse: A Method by the AIRR Community.

Authors:  Brian D Corrie; Scott Christley; Christian E Busse; Lindsay G Cowell; Kira C M Neller; Florian Rubelt; Nicholas Schwab
Journal:  Methods Mol Biol       Date:  2022

4.  Adaptive Immune Receptor Repertoire (AIRR) Community Guide to TR and IG Gene Annotation.

Authors:  Lmar Babrak; Susanna Marquez; Christian E Busse; William D Lees; Enkelejda Miho; Mats Ohlin; Aaron M Rosenfeld; Ulrik Stervbo; Corey T Watson; Chaim A Schramm
Journal:  Methods Mol Biol       Date:  2022

Review 5.  An overview of immunoinformatics approaches and databases linking T cell receptor repertoires to their antigen specificity.

Authors:  Ivan V Zvyagin; Vasily O Tsvetkov; Dmitry M Chudakov; Mikhail Shugay
Journal:  Immunogenetics       Date:  2019-11-18       Impact factor: 2.846

6.  Computational Evaluation of B-Cell Clone Sizes in Bulk Populations.

Authors:  Aaron M Rosenfeld; Wenzhao Meng; Dora Y Chen; Bochao Zhang; Tomer Granot; Donna L Farber; Uri Hershberg; Eline T Luning Prak
Journal:  Front Immunol       Date:  2018-06-29       Impact factor: 7.561

7.  ImmuneDB, a Novel Tool for the Analysis, Storage, and Dissemination of Immune Repertoire Sequencing Data.

Authors:  Aaron M Rosenfeld; Wenzhao Meng; Eline T Luning Prak; Uri Hershberg
Journal:  Front Immunol       Date:  2018-09-21       Impact factor: 7.561

8.  TCR+/BCR+ dual-expressing cells and their associated public BCR clonotype are not enriched in type 1 diabetes.

Authors:  Alberto Sada Japp; Wenzhao Meng; Aaron M Rosenfeld; Daniel J Perry; Puchong Thirawatananond; Rhonda L Bacher; Chengyang Liu; Jay S Gardner; Mark A Atkinson; Klaus H Kaestner; Todd M Brusko; Ali Naji; Eline T Luning Prak; Michael R Betts
Journal:  Cell       Date:  2021-02-04       Impact factor: 41.582

Review 9.  A review of COVID-19 biomarkers and drug targets: resources and tools.

Authors:  Francesca P Caruso; Giovanni Scala; Luigi Cerulo; Michele Ceccarelli
Journal:  Brief Bioinform       Date:  2021-03-22       Impact factor: 11.622

10.  Sex-Biased Aging Effects on Ig Somatic Hypermutation Targeting.

Authors:  Ang Cui; Daniel G Chawla; Steven H Kleinstein
Journal:  J Immunol       Date:  2020-12-07       Impact factor: 5.422
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