Literature DB >> 34653367

Deciphering the cancer microenvironment from bulk data with EcoTyper.

Andrea Rolong1, Bob Chen2, Ken S Lau3.   

Abstract

In this issue of Cell, Luca, Steen et al. develop the EcoTyper software to deconvolve tumor-microenvironment interactions from high volume bulk transcriptomics data. They demonstrate its effectiveness in improving predictions for tumor progression and patient prognosis for a variety of tumor types from multiple data sources.
Copyright © 2021 Elsevier Inc. All rights reserved.

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Year:  2021        PMID： 34653367      PMCID： PMC8655686          DOI： 10.1016/j.cell.2021.09.028

Source DB:  PubMed          Journal:  Cell        ISSN： 0092-8674            Impact factor:   66.850


  12 in total

1.  Anti-CD47 antibody synergizes with rituximab to promote phagocytosis and eradicate non-Hodgkin lymphoma.

Authors:  Mark P Chao; Ash A Alizadeh; Chad Tang; June H Myklebust; Bindu Varghese; Saar Gill; Max Jan; Adriel C Cha; Charles K Chan; Brent T Tan; Christopher Y Park; Feifei Zhao; Holbrook E Kohrt; Raquel Malumbres; Javier Briones; Randy D Gascoyne; Izidore S Lossos; Ronald Levy; Irving L Weissman; Ravindra Majeti
Journal:  Cell       Date:  2010-09-03       Impact factor: 41.582

2.  Genomic and transcriptomic profiling expands precision cancer medicine: the WINTHER trial.

Authors:  Jordi Rodon; Jean-Charles Soria; Raanan Berger; Wilson H Miller; Eitan Rubin; Aleksandra Kugel; Apostolia Tsimberidou; Pierre Saintigny; Aliza Ackerstein; Irene Braña; Yohann Loriot; Mohammad Afshar; Vincent Miller; Fanny Wunder; Catherine Bresson; Jean-François Martini; Jacques Raynaud; John Mendelsohn; Gerald Batist; Amir Onn; Josep Tabernero; Richard L Schilsky; Vladimir Lazar; J Jack Lee; Razelle Kurzrock
Journal:  Nat Med       Date:  2019-04-22       Impact factor: 53.440

3.  The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma.

Authors:  Chloé B Steen; Bogdan A Luca; Mohammad S Esfahani; Armon Azizi; Brian J Sworder; Barzin Y Nabet; David M Kurtz; Chih Long Liu; Farnaz Khameneh; Ranjana H Advani; Yasodha Natkunam; June H Myklebust; Maximilian Diehn; Andrew J Gentles; Aaron M Newman; Ash A Alizadeh
Journal:  Cancer Cell       Date:  2021-09-30       Impact factor: 38.585

4.  Atlas of clinically distinct cell states and ecosystems across human solid tumors.

Authors:  Bogdan A Luca; Chloé B Steen; Magdalena Matusiak; Armon Azizi; Sushama Varma; Chunfang Zhu; Joanna Przybyl; Almudena Espín-Pérez; Maximilian Diehn; Ash A Alizadeh; Matt van de Rijn; Andrew J Gentles; Aaron M Newman
Journal:  Cell       Date:  2021-09-30       Impact factor: 66.850

5.  CD47 Blockade by Hu5F9-G4 and Rituximab in Non-Hodgkin's Lymphoma.

Authors:  Ranjana Advani; Ian Flinn; Leslie Popplewell; Andres Forero; Nancy L Bartlett; Nilanjan Ghosh; Justin Kline; Mark Roschewski; Ann LaCasce; Graham P Collins; Thu Tran; Judith Lynn; James Y Chen; Jens-Peter Volkmer; Balaji Agoram; Jie Huang; Ravindra Majeti; Irving L Weissman; Chris H Takimoto; Mark P Chao; Sonali M Smith
Journal:  N Engl J Med       Date:  2018-11-01       Impact factor: 91.245

Review 6.  Role of tumor microenvironment in tumorigenesis.

Authors:  Maonan Wang; Jingzhou Zhao; Lishen Zhang; Fang Wei; Yu Lian; Yingfeng Wu; Zhaojian Gong; Shanshan Zhang; Jianda Zhou; Ke Cao; Xiayu Li; Wei Xiong; Guiyuan Li; Zhaoyang Zeng; Can Guo
Journal:  J Cancer       Date:  2017-02-25       Impact factor: 4.207

7.  TIMER2.0 for analysis of tumor-infiltrating immune cells.

Authors:  Taiwen Li; Jingxin Fu; Zexian Zeng; David Cohen; Jing Li; Qianming Chen; Bo Li; X Shirley Liu
Journal:  Nucleic Acids Res       Date:  2020-07-02       Impact factor: 16.971

8.  The immune microenvironment in non-small cell lung cancer is predictive of prognosis after surgery.

Authors:  Åsa Kristina Öjlert; Ann Rita Halvorsen; Daniel Nebdal; Marius Lund-Iversen; Steinar Solberg; Odd Terje Brustugun; Ole Christian Lingjaerde; Åslaug Helland
Journal:  Mol Oncol       Date:  2019-04-10       Impact factor: 6.603

9.  Determining cell type abundance and expression from bulk tissues with digital cytometry.

Authors:  Aaron M Newman; Chloé B Steen; Chih Long Liu; Andrew J Gentles; Aadel A Chaudhuri; Florian Scherer; Michael S Khodadoust; Mohammad S Esfahani; Bogdan A Luca; David Steiner; Maximilian Diehn; Ash A Alizadeh
Journal:  Nat Biotechnol       Date:  2019-05-06       Impact factor: 54.908

Review 10.  The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution.

Authors:  Orit Rozenblatt-Rosen; Aviv Regev; Philipp Oberdoerffer; Tal Nawy; Anna Hupalowska; Jennifer E Rood; Orr Ashenberg; Ethan Cerami; Robert J Coffey; Emek Demir; Li Ding; Edward D Esplin; James M Ford; Jeremy Goecks; Sharmistha Ghosh; Joe W Gray; Justin Guinney; Sean E Hanlon; Shannon K Hughes; E Shelley Hwang; Christine A Iacobuzio-Donahue; Judit Jané-Valbuena; Bruce E Johnson; Ken S Lau; Tracy Lively; Sarah A Mazzilli; Dana Pe'er; Sandro Santagata; Alex K Shalek; Denis Schapiro; Michael P Snyder; Peter K Sorger; Avrum E Spira; Sudhir Srivastava; Kai Tan; Robert B West; Elizabeth H Williams
Journal:  Cell       Date:  2020-04-16       Impact factor: 66.850
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