Literature DB >> 30412204

Reply to "Evaluation of immune repertoire inference methods from RNA-seq data".

Dmitriy A Bolotin1,2,3, Stanislav Poslavsky1,3, Alexey N Davydov4, Dmitriy M Chudakov2,3,4,5,6.   

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Year:  2018        PMID： 30412204     DOI： 10.1038/nbt.4296

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


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  9 in total

1.  Quantifiable predictive features define epitope-specific T cell receptor repertoires.

Authors:  Pradyot Dash; Andrew J Fiore-Gartland; Tomer Hertz; George C Wang; Shalini Sharma; Aisha Souquette; Jeremy Chase Crawford; E Bridie Clemens; Thi H O Nguyen; Katherine Kedzierska; Nicole L La Gruta; Philip Bradley; Paul G Thomas
Journal:  Nature       Date:  2017-06-21       Impact factor: 49.962

2.  Diversity and clonal selection in the human T-cell repertoire.

Authors:  Qian Qi; Yi Liu; Yong Cheng; Jacob Glanville; David Zhang; Ji-Yeun Lee; Richard A Olshen; Cornelia M Weyand; Scott D Boyd; Jörg J Goronzy
Journal:  Proc Natl Acad Sci U S A       Date:  2014-08-25       Impact factor: 11.205

Review 3.  Comparative analysis of murine T-cell receptor repertoires.

Authors:  Mark Izraelson; Tatiana O Nakonechnaya; Bruno Moltedo; Evgeniy S Egorov; Sofya A Kasatskaya; Ekaterina V Putintseva; Ilgar Z Mamedov; Dmitriy B Staroverov; Irina I Shemiakina; Maria Y Zakharova; Alexey N Davydov; Dmitriy A Bolotin; Mikhail Shugay; Dmitriy M Chudakov; Alexander Y Rudensky; Olga V Britanova
Journal:  Immunology       Date:  2017-11-27       Impact factor: 7.397

4.  Statistical inference of the generation probability of T-cell receptors from sequence repertoires.

Authors:  Anand Murugan; Thierry Mora; Aleksandra M Walczak; Curtis G Callan
Journal:  Proc Natl Acad Sci U S A       Date:  2012-09-17       Impact factor: 11.205

5.  Ultrasensitive detection of TCR hypervariable-region sequences in solid-tissue RNA-seq data.

Authors:  Bo Li; Taiwen Li; Binbin Wang; Ruoxu Dou; Jian Zhang; Jun S Liu; X Shirley Liu
Journal:  Nat Genet       Date:  2017-03-30       Impact factor: 38.330

6.  A mechanism for TCR sharing between T cell subsets and individuals revealed by pyrosequencing.

Authors:  Vanessa Venturi; Máire F Quigley; Hui Yee Greenaway; Pauline C Ng; Zachary S Ende; Tina McIntosh; Tedi E Asher; Jorge R Almeida; Samuel Levy; David A Price; Miles P Davenport; Daniel C Douek
Journal:  J Immunol       Date:  2011-03-07       Impact factor: 5.422

7.  Landscape of tumor-infiltrating T cell repertoire of human cancers.

Authors:  Bo Li; Taiwen Li; Jean-Christophe Pignon; Binbin Wang; Jinzeng Wang; Sachet A Shukla; Ruoxu Dou; Qianming Chen; F Stephen Hodi; Toni K Choueiri; Catherine Wu; Nir Hacohen; Sabina Signoretti; Jun S Liu; X Shirley Liu
Journal:  Nat Genet       Date:  2016-05-30       Impact factor: 38.330

8.  Method for identification of condition-associated public antigen receptor sequences.

Authors:  Yuri B Lebedev; Thierry Mora; Aleksandra M Walczak; Mikhail V Pogorelyy; Anastasia A Minervina; Dmitriy M Chudakov; Ilgar Z Mamedov
Journal:  Elife       Date:  2018-03-13       Impact factor: 8.140

9.  Antigen receptor repertoire profiling from RNA-seq data.

Authors:  Dmitriy A Bolotin; Stanislav Poslavsky; Alexey N Davydov; Felix E Frenkel; Lorenzo Fanchi; Olga I Zolotareva; Saskia Hemmers; Ekaterina V Putintseva; Anna S Obraztsova; Mikhail Shugay; Ravshan I Ataullakhanov; Alexander Y Rudensky; Ton N Schumacher; Dmitriy M Chudakov
Journal:  Nat Biotechnol       Date:  2017-10-11       Impact factor: 54.908
  9 in total
  4 in total

Review 1.  Next-generation computational tools for interrogating cancer immunity.

Authors:  Francesca Finotello; Dietmar Rieder; Hubert Hackl; Zlatko Trajanoski
Journal:  Nat Rev Genet       Date:  2019-09-12       Impact factor: 59.581

2.  Measuring Intratumoral Heterogeneity of Immune Repertoires.

Authors:  Diana Vladimirovna Yuzhakova; Lilia N Volchkova; Mikhail Valerievich Pogorelyy; Ekaterina O Serebrovskaya; Irina A Shagina; Ekaterina A Bryushkova; Tatiana O Nakonechnaya; Anna V Izosimova; Daria S Zavyalova; Maria M Karabut; Mark Izraelson; Igor V Samoylenko; Vladimir E Zagainov; Dmitriy M Chudakov; Elena V Zagaynova; George Vladimirovich Sharonov
Journal:  Front Oncol       Date:  2020-05-08       Impact factor: 6.244

3.  Functionally specialized human CD4+ T-cell subsets express physicochemically distinct TCRs.

Authors:  Sofya A Kasatskaya; Kristin Ladell; David A Price; Dmitriy M Chudakov; Evgeniy S Egorov; Kelly L Miners; Alexey N Davydov; Maria Metsger; Dmitry B Staroverov; Elena K Matveyshina; Irina A Shagina; Ilgar Z Mamedov; Mark Izraelson; Pavel V Shelyakin; Olga V Britanova
Journal:  Elife       Date:  2020-12-08       Impact factor: 8.140

4.  RNA-Seq-Based TCR Profiling Reveals Persistently Increased Intratumoral Clonality in Responders to Anti-PD-1 Therapy.

Authors:  Ekaterina A Zhigalova; Anna I Izosimova; Diana V Yuzhakova; Lilia N Volchkova; Irina A Shagina; Maria A Turchaninova; Ekaterina O Serebrovskaya; Elena V Zagaynova; Dmitriy M Chudakov; George V Sharonov
Journal:  Front Oncol       Date:  2020-04-28       Impact factor: 6.244
  4 in total

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