Literature DB >> 30412202

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

Xihao Hu1, Jian Zhang2, Jun S Liu3, Bo Li4, Xiaole Shirley Liu1,3.   

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Year:  2018        PMID： 30412202     DOI： 10.1038/nbt.4294

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


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  8 in total

1.  Identifying specificity groups in the T cell receptor repertoire.

Authors:  Jacob Glanville; Huang Huang; Allison Nau; Olivia Hatton; Lisa E Wagar; Florian Rubelt; Xuhuai Ji; Arnold Han; Sheri M Krams; Christina Pettus; Nikhil Haas; Cecilia S Lindestam Arlehamn; Alessandro Sette; Scott D Boyd; Thomas J Scriba; Olivia M Martinez; Mark M Davis
Journal:  Nature       Date:  2017-06-21       Impact factor: 49.962

2.  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

Review 3.  The blockade of immune checkpoints in cancer immunotherapy.

Authors:  Drew M Pardoll
Journal:  Nat Rev Cancer       Date:  2012-03-22       Impact factor: 60.716

4.  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

5.  MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.

Authors:  Kai Wang; Darshan Singh; Zheng Zeng; Stephen J Coleman; Yan Huang; Gleb L Savich; Xiaping He; Piotr Mieczkowski; Sara A Grimm; Charles M Perou; James N MacLeod; Derek Y Chiang; Jan F Prins; Jinze Liu
Journal:  Nucleic Acids Res       Date:  2010-08-27       Impact factor: 16.971

6.  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

7.  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

8.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.

Authors:  Daehwan Kim; Geo Pertea; Cole Trapnell; Harold Pimentel; Ryan Kelley; Steven L Salzberg
Journal:  Genome Biol       Date:  2013-04-25       Impact factor: 13.583
  8 in total
  5 in total

1.  Characterization of the Intra-tumoral B Cell Immunoglobulin Repertoire Is of Prognostic Value for Esophageal Squamous Cell Carcinoma.

Authors:  Zhizhong Wang; Zhenguo Cheng; Shuangshuang Lu; Louisa S Chard Dunmall; Jun Wang; Yongjun Guo; Yaohe Wang
Journal:  Front Immunol       Date:  2022-06-22       Impact factor: 8.786

2.  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

3.  Immune receptor repertoires in pediatric and adult acute myeloid leukemia.

Authors:  Jian Zhang; Xihao Hu; Jin Wang; Avinash Das Sahu; David Cohen; Li Song; Zhangyi Ouyang; Jingyu Fan; Binbin Wang; Jingxin Fu; Shengqing Gu; Moshe Sade-Feldman; Nir Hacohen; Wuju Li; Xiaomin Ying; Bo Li; X Shirley Liu
Journal:  Genome Med       Date:  2019-11-26       Impact factor: 11.117

4.  Loss of H3K36 Methyltransferase SETD2 Impairs V(D)J Recombination during Lymphoid Development.

Authors:  S Haihua Chu; Jonathan R Chabon; Chloe N Matovina; Janna C Minehart; Bo-Ruei Chen; Jian Zhang; Vipul Kumar; Yijun Xiong; Elsa Callen; Putzer J Hung; Zhaohui Feng; Richard P Koche; X Shirley Liu; Jayanta Chaudhuri; Andre Nussenzweig; Barry P Sleckman; Scott A Armstrong
Journal:  iScience       Date:  2020-02-27

5.  Long non-coding RNAs as novel therapeutic targets in juvenile myelomonocytic leukemia.

Authors:  Mattias Hofmans; Tim Lammens; Barbara Depreter; Ying Wu; Miriam Erlacher; Aurélie Caye; Hélène Cavé; Christian Flotho; Valerie de Haas; Charlotte M Niemeyer; Jan Stary; Filip Van Nieuwerburgh; Dieter Deforce; Wouter Van Loocke; Pieter Van Vlierberghe; Jan Philippé; Barbara De Moerloose
Journal:  Sci Rep       Date:  2021-02-02       Impact factor: 4.379
  5 in total

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