Literature DB >> 28358132

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

Bo Li1,2, Taiwen Li3, Binbin Wang4, Ruoxu Dou5, Jian Zhang1, Jun S Liu2, X Shirley Liu1,2,4.   

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Year:  2017        PMID： 28358132     DOI： 10.1038/ng.3820

Source DB:  PubMed          Journal:  Nat Genet        ISSN： 1061-4036            Impact factor:   38.330


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  9 in total

1.  Profiling model T-cell metagenomes with short reads.

Authors:  René L Warren; Brad H Nelson; Robert A Holt
Journal:  Bioinformatics       Date:  2009-01-09       Impact factor: 6.937

2.  IMGT, the International ImMunoGeneTics Information System.

Authors:  Marie-Paule Lefranc
Journal:  Cold Spring Harb Protoc       Date:  2011-06-01

3.  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

4.  Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine.

Authors:  Niclas Thomas; James Heather; Wilfred Ndifon; John Shawe-Taylor; Benjamin Chain
Journal:  Bioinformatics       Date:  2013-01-09       Impact factor: 6.937

5.  Genetic basis for clinical response to CTLA-4 blockade in melanoma.

Authors:  Alexandra Snyder; Vladimir Makarov; Taha Merghoub; Jianda Yuan; Jedd D Wolchok; Timothy A Chan; Jesse M Zaretsky; Alexis Desrichard; Logan A Walsh; Michael A Postow; Phillip Wong; Teresa S Ho; Travis J Hollmann; Cameron Bruggeman; Kasthuri Kannan; Yanyun Li; Ceyhan Elipenahli; Cailian Liu; Christopher T Harbison; Lisu Wang; Antoni Ribas
Journal:  N Engl J Med       Date:  2014-11-19       Impact factor: 91.245

Review 6.  The immune contexture in human tumours: impact on clinical outcome.

Authors:  Wolf Herman Fridman; Franck Pagès; Catherine Sautès-Fridman; Jérôme Galon
Journal:  Nat Rev Cancer       Date:  2012-03-15       Impact factor: 60.716

Review 7.  Innate and adaptive immune cells in the tumor microenvironment.

Authors:  Thomas F Gajewski; Hans Schreiber; Yang-Xin Fu
Journal:  Nat Immunol       Date:  2013-10       Impact factor: 25.606

8.  Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting.

Authors:  Hirokazu Matsushita; Matthew D Vesely; Daniel C Koboldt; Charles G Rickert; Ravindra Uppaluri; Vincent J Magrini; Cora D Arthur; J Michael White; Yee-Shiuan Chen; Lauren K Shea; Jasreet Hundal; Michael C Wendl; Ryan Demeter; Todd Wylie; James P Allison; Mark J Smyth; Lloyd J Old; Elaine R Mardis; Robert D Schreiber
Journal:  Nature       Date:  2012-02-08       Impact factor: 49.962

9.  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
  9 in total
  28 in total

1.  Recovery of Immunoglobulin VJ Recombinations from Pancreatic Cancer Exome Files Strongly Correlates with Reduced Survival.

Authors:  Jacob C Kinskey; Yaping N Tu; Wei Lue Tong; John M Yavorski; George Blanck
Journal:  Cancer Microenviron       Date:  2018-02-05

2.  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

3.  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

Review 4.  Computational approaches for characterizing the tumor immune microenvironment.

Authors:  Candace C Liu; Chloé B Steen; Aaron M Newman
Journal:  Immunology       Date:  2019-10       Impact factor: 7.397

Review 5.  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

6.  Proceedings of the fourth international molecular pathological epidemiology (MPE) meeting.

Authors:  Peter T Campbell; Christine B Ambrosone; Timothy R Rebbeck; Shuji Ogino; Reiko Nishihara; Hugo J W L Aerts; Melissa Bondy; Nilanjan Chatterjee; Montserrat Garcia-Closas; Marios Giannakis; Jeffrey A Golden; Yujing J Heng; N Sertac Kip; Jill Koshiol; X Shirley Liu; Camila M Lopes-Ramos; Lorelei A Mucci; Jonathan A Nowak; Amanda I Phipps; John Quackenbush; Robert E Schoen; Lynette M Sholl; Rulla M Tamimi; Molin Wang; Matty P Weijenberg; Catherine J Wu; Kana Wu; Song Yao; Kun-Hsing Yu; Xuehong Zhang
Journal:  Cancer Causes Control       Date:  2019-05-08       Impact factor: 2.506

7.  De novo prediction of cancer-associated T cell receptors for noninvasive cancer detection.

Authors:  Daria Beshnova; Jianfeng Ye; Oreoluwa Onabolu; Benjamin Moon; Wenxin Zheng; Yang-Xin Fu; James Brugarolas; Jayanthi Lea; Bo Li
Journal:  Sci Transl Med       Date:  2020-08-19       Impact factor: 17.956

8.  A scoring system for the electrostatic complementarities of T-cell receptors and cancer-mutant amino acids: multi-cancer analyses of associated survival rates.

Authors:  Boris I Chobrutskiy; Michelle Yeagley; Andrea Diviney; Saif Zaman; Etienne C Gozlan; Price Tipping; Darush M Koohestani; Andrea M Roca; George Blanck
Journal:  Immunology       Date:  2020-01-21       Impact factor: 7.397

9.  Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy.

Authors:  Chirag Krishna; Renzo G DiNatale; Fengshen Kuo; Raghvendra M Srivastava; Lynda Vuong; Diego Chowell; Sounak Gupta; Chad Vanderbilt; Tanaya A Purohit; Ming Liu; Emily Kansler; Briana G Nixon; Ying-Bei Chen; Vladimir Makarov; Kyle A Blum; Kyrollis Attalla; Stanley Weng; Michael L Salmans; Mahdi Golkaram; Li Liu; Shile Zhang; Raakhee Vijayaraghavan; Traci Pawlowski; Victor Reuter; Maria I Carlo; Martin H Voss; Jonathan Coleman; Paul Russo; Robert J Motzer; Ming O Li; Christina S Leslie; Timothy A Chan; A Ari Hakimi
Journal:  Cancer Cell       Date:  2021-04-15       Impact factor: 31.743

10.  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
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