Literature DB >> 34002093

Diversity in immunogenomics: the value and the challenge.

Houda Alachkar1, Cathrine Scheepers2,3, Corey T Watson4, Gunilla B Karlsson Hedestam5, Serghei Mangul6, Kerui Peng1, Yana Safonova7,4, Mikhail Shugay8,9, Alice B Popejoy10, Oscar L Rodriguez4, Felix Breden11, Petter Brodin12,13, Amanda M Burkhardt1, Carlos Bustamante10, Van-Mai Cao-Lormeau14, Martin M Corcoran5, Darragh Duffy15, Macarena Fuentes-Guajardo16, Ricardo Fujita17, Victor Greiff18, Vanessa D Jönsson19, Xiao Liu20, Lluis Quintana-Murci21,22, Maura Rossetti23, Jianming Xie24, Gur Yaari25, Wei Zhang26, Malak S Abedalthagafi27, Khalid O Adekoya28, Rahaman A Ahmed28, Wei-Chiao Chang29,30, Clive Gray31,32, Yusuke Nakamura33, William D Lees34, Purvesh Khatri35,36.   

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Year:  2021        PMID： 34002093      PMCID： PMC8842483          DOI： 10.1038/s41592-021-01169-5

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   47.990


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  35 in total

Review 1.  B cells, plasma cells and antibody repertoires in the tumour microenvironment.

Authors:  George V Sharonov; Ekaterina O Serebrovskaya; Diana V Yuzhakova; Olga V Britanova; Dmitriy M Chudakov
Journal:  Nat Rev Immunol       Date:  2020-01-27       Impact factor: 53.106

2.  Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing.

Authors:  J Douglas Freeman; René L Warren; John R Webb; Brad H Nelson; Robert A Holt
Journal:  Genome Res       Date:  2009-06-18       Impact factor: 9.043

Review 3.  Advancing an HIV vaccine; advancing vaccinology.

Authors:  Dennis R Burton
Journal:  Nat Rev Immunol       Date:  2019-02       Impact factor: 53.106

4.  The Missing Diversity in Human Genetic Studies.

Authors:  Giorgio Sirugo; Scott M Williams; Sarah A Tishkoff
Journal:  Cell       Date:  2019-05-02       Impact factor: 41.582

5.  Recalibrating the Use of Race in Medical Research.

Authors:  John P A Ioannidis; Neil R Powe; Clyde Yancy
Journal:  JAMA       Date:  2021-02-16       Impact factor: 56.272

Review 6.  The Individual and Population Genetics of Antibody Immunity.

Authors:  Corey T Watson; Jacob Glanville; Wayne A Marasco
Journal:  Trends Immunol       Date:  2017-05-20       Impact factor: 16.687

Review 7.  Inferred Allelic Variants of Immunoglobulin Receptor Genes: A System for Their Evaluation, Documentation, and Naming.

Authors:  Mats Ohlin; Cathrine Scheepers; Martin Corcoran; William D Lees; Christian E Busse; Davide Bagnara; Linnea Thörnqvist; Jean-Philippe Bürckert; Katherine J L Jackson; Duncan Ralph; Chaim A Schramm; Nishanth Marthandan; Felix Breden; Jamie Scott; Frederick A Matsen Iv; Victor Greiff; Gur Yaari; Steven H Kleinstein; Scott Christley; Jacob S Sherkow; Sofia Kossida; Marie-Paule Lefranc; Menno C van Zelm; Corey T Watson; Andrew M Collins
Journal:  Front Immunol       Date:  2019-03-18       Impact factor: 7.561

8.  Improved genome inference in the MHC using a population reference graph.

Authors:  Alexander Dilthey; Charles Cox; Zamin Iqbal; Matthew R Nelson; Gil McVean
Journal:  Nat Genet       Date:  2015-04-27       Impact factor: 38.330

9.  A Novel Framework for Characterizing Genomic Haplotype Diversity in the Human Immunoglobulin Heavy Chain Locus.

Authors:  Oscar L Rodriguez; William S Gibson; Tom Parks; Matthew Emery; James Powell; Maya Strahl; Gintaras Deikus; Kathryn Auckland; Evan E Eichler; Wayne A Marasco; Robert Sebra; Andrew J Sharp; Melissa L Smith; Ali Bashir; Corey T Watson
Journal:  Front Immunol       Date:  2020-09-23       Impact factor: 7.561

10.  The ADC API: A Web API for the Programmatic Query of the AIRR Data Commons.

Authors:  Scott Christley; Ademar Aguiar; George Blanck; Felix Breden; Syed Ahmad Chan Bukhari; Christian E Busse; Jerome Jaglale; Srilakshmy L Harikrishnan; Uri Laserson; Bjoern Peters; Artur Rocha; Chaim A Schramm; Sarah Taylor; Jason Anthony Vander Heiden; Bojan Zimonja; Corey T Watson; Brian Corrie; Lindsay G Cowell
Journal:  Front Big Data       Date:  2020-06-17
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  10 in total

1.  Stitchr: stitching coding TCR nucleotide sequences from V/J/CDR3 information.

Authors:  James M Heather; Matthew J Spindler; Marta Herrero Alonso; Yifang Ivana Shui; David G Millar; David S Johnson; Mark Cobbold; Aaron N Hata
Journal:  Nucleic Acids Res       Date:  2022-07-08       Impact factor: 19.160

2.  T cell receptor beta germline variability is revealed by inference from repertoire data.

Authors:  Aviv Omer; Ayelet Peres; Oscar L Rodriguez; Corey T Watson; William Lees; Pazit Polak; Andrew M Collins; Gur Yaari
Journal:  Genome Med       Date:  2022-01-07       Impact factor: 11.117

3.  Commentary on Population matched (pm) germline allelic variants of immunoglobulin (IG) loci: relevance in infectious diseases and vaccination studies in human populations.

Authors:  Andrew M Collins; Ayelet Peres; Martin M Corcoran; Corey T Watson; Gur Yaari; William D Lees; Mats Ohlin
Journal:  Genes Immun       Date:  2021-10-19       Impact factor: 2.676

4.  COVID-19 Pandemic: Escape of Pathogenic Variants and MHC Evolution.

Authors:  Pierre Pontarotti; Julien Paganini
Journal:  Int J Mol Sci       Date:  2022-02-28       Impact factor: 5.923

5.  Addressing IGHV Gene Structural Diversity Enhances Immunoglobulin Repertoire Analysis: Lessons From Rhesus Macaque.

Authors:  Mateusz Kaduk; Martin Corcoran; Gunilla B Karlsson Hedestam
Journal:  Front Immunol       Date:  2022-03-28       Impact factor: 7.561

6.  Current strategies for detecting functional convergence across B-cell receptor repertoires.

Authors:  Matthew I J Raybould; Anthony R Rees; Charlotte M Deane
Journal:  MAbs       Date:  2021 Jan-Dec       Impact factor: 5.857

7.  Profiling genes encoding the adaptive immune receptor repertoire with gAIRR Suite.

Authors:  Mao-Jan Lin; Yu-Chun Lin; Nae-Chyun Chen; Allen Chilun Luo; Sheng-Kai Lai; Chia-Lang Hsu; Jacob Shujui Hsu; Chien-Yu Chen; Wei-Shiung Yang; Pei-Lung Chen
Journal:  Front Immunol       Date:  2022-09-08       Impact factor: 8.786

8.  Enhanced neutralization potency of an identical HIV neutralizing antibody expressed as different isotypes is achieved through genetically distinct mechanisms.

Authors:  Thandeka Moyo-Gwete; Cathrine Scheepers; Zanele Makhado; Prudence Kgagudi; Nonkululeko B Mzindle; Rutendo Ziki; Sharon Madzorera; Nelia P Manamela; Frances Ayres; Bronwen E Lambson; Simone I Richardson; Lynn Morris; Penny L Moore
Journal:  Sci Rep       Date:  2022-10-01       Impact factor: 4.996

9.  A Pan-Cancer Analysis of Tumor-Infiltrating B Cell Repertoires.

Authors:  Katharine Yu; Akshay Ravoor; Núria Malats; Silvia Pineda; Marina Sirota
Journal:  Front Immunol       Date:  2022-01-05       Impact factor: 7.561

Review 10.  Immunoglobulin germline gene variation and its impact on human disease.

Authors:  Ivana Mikocziova; Victor Greiff; Ludvig M Sollid
Journal:  Genes Immun       Date:  2021-06-26       Impact factor: 2.676
  10 in total

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