Literature DB >> 29020005

Antigen receptor repertoire profiling from RNA-seq data.

Dmitriy A Bolotin1,2,3, Stanislav Poslavsky1,3, Alexey N Davydov4, Felix E Frenkel5, Lorenzo Fanchi6, Olga I Zolotareva5, Saskia Hemmers7, Ekaterina V Putintseva2,8, Anna S Obraztsova2,9, Mikhail Shugay1,2,3,10,11, Ravshan I Ataullakhanov5,12,13, Alexander Y Rudensky7,14, Ton N Schumacher6, Dmitriy M Chudakov2,3,4,10,11.   

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Year:  2017        PMID： 29020005      PMCID： PMC6169298          DOI： 10.1038/nbt.3979

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


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  37 in total

1.  Thymic selection of CD4+CD25+ regulatory T cells induced by an agonist self-peptide.

Authors:  M S Jordan; A Boesteanu; A J Reed; A L Petrone; A E Holenbeck; M A Lerman; A Naji; A J Caton
Journal:  Nat Immunol       Date:  2001-04       Impact factor: 25.606

2.  A computationally efficient evolutionary algorithm for real-parameter optimization.

Authors:  Kalyanmoy Deb; Ashish Anand; Dhiraj Joshi
Journal:  Evol Comput       Date:  2002       Impact factor: 3.277

Review 3.  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

4.  MiXCR: software for comprehensive adaptive immunity profiling.

Authors:  Dmitriy A Bolotin; Stanislav Poslavsky; Igor Mitrophanov; Mikhail Shugay; Ilgar Z Mamedov; Ekaterina V Putintseva; Dmitriy M Chudakov
Journal:  Nat Methods       Date:  2015-05       Impact factor: 28.547

5.  Dynamics of Individual T Cell Repertoires: From Cord Blood to Centenarians.

Authors:  Olga V Britanova; Mikhail Shugay; Ekaterina M Merzlyak; Dmitriy B Staroverov; Ekaterina V Putintseva; Maria A Turchaninova; Ilgar Z Mamedov; Mikhail V Pogorelyy; Dmitriy A Bolotin; Mark Izraelson; Alexey N Davydov; Evgeny S Egorov; Sofya A Kasatskaya; Denis V Rebrikov; Sergey Lukyanov; Dmitriy M Chudakov
Journal:  J Immunol       Date:  2016-05-13       Impact factor: 5.422

6.  Regulatory T cell-derived interleukin-10 limits inflammation at environmental interfaces.

Authors:  Yuri P Rubtsov; Jeffrey P Rasmussen; Emil Y Chi; Jason Fontenot; Luca Castelli; Xin Ye; Piper Treuting; Lisa Siewe; Axel Roers; William R Henderson; Werner Muller; Alexander Y Rudensky
Journal:  Immunity       Date:  2008-04       Impact factor: 31.745

7.  Immunosuppressive plasma cells impede T-cell-dependent immunogenic chemotherapy.

Authors:  Shabnam Shalapour; Joan Font-Burgada; Giuseppe Di Caro; Zhenyu Zhong; Elsa Sanchez-Lopez; Debanjan Dhar; Gerald Willimsky; Massimo Ammirante; Amy Strasner; Donna E Hansel; Christina Jamieson; Christopher J Kane; Tobias Klatte; Peter Birner; Lukas Kenner; Michael Karin
Journal:  Nature       Date:  2015-04-29       Impact factor: 49.962

Review 8.  αβ T cell receptors as predictors of health and disease.

Authors:  Meriem Attaf; Eric Huseby; Andrew K Sewell
Journal:  Cell Mol Immunol       Date:  2015-01-26       Impact factor: 11.530

9.  FastUniq: a fast de novo duplicates removal tool for paired short reads.

Authors:  Haibin Xu; Xiang Luo; Jun Qian; Xiaohui Pang; Jingyuan Song; Guangrui Qian; Jinhui Chen; Shilin Chen
Journal:  PLoS One       Date:  2012-12-20       Impact factor: 3.240

10.  Long non-coding RNA profiling of human lymphoid progenitor cells reveals transcriptional divergence of B cell and T cell lineages.

Authors:  David Casero; Salemiz Sandoval; Christopher S Seet; Jessica Scholes; Yuhua Zhu; Vi Luan Ha; Annie Luong; Chintan Parekh; Gay M Crooks
Journal:  Nat Immunol       Date:  2015-10-26       Impact factor: 25.606
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  95 in total

1.  SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery.

Authors:  Siwen Hu-Lieskovan; Srabani Bhaumik; Kavita Dhodapkar; Jean-Charles J B Grivel; Sumati Gupta; Brent A Hanks; Sylvia Janetzki; Thomas O Kleen; Yoshinobu Koguchi; Amanda W Lund; Cristina Maccalli; Yolanda D Mahnke; Ruslan D Novosiadly; Senthamil R Selvan; Tasha Sims; Yingdong Zhao; Holden T Maecker
Journal:  J Immunother Cancer       Date:  2020-12       Impact factor: 13.751

Review 2.  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

3.  T-ALL can evolve to oncogene independence.

Authors:  Hesham Abdulla; Anh Vo; Benjamin J Shields; Tenae J Davies; Jacob T Jackson; Raed Alserihi; Elizabeth M Viney; Tin Wong; Feng Yan; Nicholas C Wong; Lisa Demoen; David J Curtis; Warren S Alexander; Pieter Van Vlierberghe; Ross A Dickins; Matthew P McCormack
Journal:  Leukemia       Date:  2021-01-22       Impact factor: 11.528

Review 4.  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

5.  Prognostic implications of the expression levels of different immunoglobulin heavy chain-encoding RNAs in early breast cancer.

Authors:  Christer Larsson; Anna Ehinger; Sofia Winslow; Karin Leandersson; Marie Klintman; Ludvig Dahl; Johan Vallon-Christersson; Jari Häkkinen; Cecilia Hegardt; Jonas Manjer; Lao Saal; Lisa Rydén; Martin Malmberg; Åke Borg; Niklas Loman
Journal:  NPJ Breast Cancer       Date:  2020-07-06

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

Authors:  Dmitriy A Bolotin; Stanislav Poslavsky; Alexey N Davydov; Dmitriy M Chudakov
Journal:  Nat Biotechnol       Date:  2018-11-09       Impact factor: 54.908

7.  Evaluation of immune repertoire inference methods from RNA-seq data.

Authors:  Xihao Hu; Jian Zhang; Jun S Liu; Bo Li; Xiaole Shirley Liu
Journal:  Nat Biotechnol       Date:  2018-11-09       Impact factor: 54.908

8.  Dengue-specific CD8+ T cell subsets display specialized transcriptomic and TCR profiles.

Authors:  Yuan Tian; Mariana Babor; Jerome Lane; Grégory Seumois; Shu Liang; N D Suraj Goonawardhana; Aruna D De Silva; Elizabeth J Phillips; Simon A Mallal; Ricardo da Silva Antunes; Alba Grifoni; Pandurangan Vijayanand; Daniela Weiskopf; Bjoern Peters; Alessandro Sette
Journal:  J Clin Invest       Date:  2019-03-18       Impact factor: 14.808

Review 9.  Ushering in Integrated T Cell Repertoire Profiling in Cancer.

Authors:  Ning Jiang; Alexandra A Schonnesen; Ke-Yue Ma
Journal:  Trends Cancer       Date:  2018-12-26

10.  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
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