A citation-based method for searching scientific literature

Peng Jiang, Shengqing Gu, Deng Pan, Jingxin Fu, Avinash Sahu, Xihao Hu, Ziyi Li, Nicole Traugh, Xia Bu, Bo Li, Jun Liu, Gordon J Freeman, Myles A Brown, Kai W Wucherpfennig, X Shirley Liu. Nat Med 2018
Times Cited: 1284







List of co-cited articles
476 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


GSVA: gene set variation analysis for microarray and RNA-seq data.
Sonja Hänzelmann, Robert Castelo, Justin Guinney. BMC Bioinformatics 2013
34

Inferring tumour purity and stromal and immune cell admixture from expression data.
Kosuke Yoshihara, Maria Shahmoradgoli, Emmanuel Martínez, Rahulsimham Vegesna, Hoon Kim, Wandaliz Torres-Garcia, Victor Treviño, Hui Shen, Peter W Laird, Douglas A Levine,[...]. Nat Commun 2013
31

Robust enumeration of cell subsets from tissue expression profiles.
Aaron M Newman, Chih Long Liu, Michael R Green, Andrew J Gentles, Weiguo Feng, Yue Xu, Chuong D Hoang, Maximilian Diehn, Ash A Alizadeh. Nat Methods 2015
30

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
23

Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries.
Freddie Bray, Jacques Ferlay, Isabelle Soerjomataram, Rebecca L Siegel, Lindsey A Torre, Ahmedin Jemal. CA Cancer J Clin 2018
17

TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells.
Sanjeev Mariathasan, Shannon J Turley, Dorothee Nickles, Alessandra Castiglioni, Kobe Yuen, Yulei Wang, Edward E Kadel, Hartmut Koeppen, Jillian L Astarita, Rafael Cubas,[...]. Nature 2018
17

limma powers differential expression analyses for RNA-sequencing and microarray studies.
Matthew E Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, Gordon K Smyth. Nucleic Acids Res 2015
17

Maftools: efficient and comprehensive analysis of somatic variants in cancer.
Anand Mayakonda, De-Chen Lin, Yassen Assenov, Christoph Plass, H Phillip Koeffler. Genome Res 2018
16

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
16


IFN-γ-related mRNA profile predicts clinical response to PD-1 blockade.
Mark Ayers, Jared Lunceford, Michael Nebozhyn, Erin Murphy, Andrey Loboda, David R Kaufman, Andrew Albright, Jonathan D Cheng, S Peter Kang, Veena Shankaran,[...]. J Clin Invest 2017
15

The Immune Landscape of Cancer.
Vésteinn Thorsson, David L Gibbs, Scott D Brown, Denise Wolf, Dante S Bortone, Tai-Hsien Ou Yang, Eduard Porta-Pardo, Galen F Gao, Christopher L Plaisier, James A Eddy,[...]. Immunity 2018
15

Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade.
Pornpimol Charoentong, Francesca Finotello, Mihaela Angelova, Clemens Mayer, Mirjana Efremova, Dietmar Rieder, Hubert Hackl, Zlatko Trajanoski. Cell Rep 2017
14

Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries.
Hyuna Sung, Jacques Ferlay, Rebecca L Siegel, Mathieu Laversanne, Isabelle Soerjomataram, Ahmedin Jemal, Freddie Bray. CA Cancer J Clin 2021
14


Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer.
Gabriela Bindea, Bernhard Mlecnik, Marie Tosolini, Amos Kirilovsky, Maximilian Waldner, Anna C Obenauf, Helen Angell, Tessa Fredriksen, Lucie Lafontaine, Anne Berger,[...]. Immunity 2013
11

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.
Tathiane M Malta, Artem Sokolov, Andrew J Gentles, Tomasz Burzykowski, Laila Poisson, John N Weinstein, Bożena Kamińska, Joerg Huelsken, Larsson Omberg, Olivier Gevaert,[...]. Cell 2018
703
11

Molecular and genetic properties of tumors associated with local immune cytolytic activity.
Michael S Rooney, Sachet A Shukla, Catherine J Wu, Gad Getz, Nir Hacohen. Cell 2015
10

Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression.
Etienne Becht, Nicolas A Giraldo, Laetitia Lacroix, Bénédicte Buttard, Nabila Elarouci, Florent Petitprez, Janick Selves, Pierre Laurent-Puig, Catherine Sautès-Fridman, Wolf H Fridman,[...]. Genome Biol 2016
10

Subclass mapping: identifying common subtypes in independent disease data sets.
Yujin Hoshida, Jean-Philippe Brunet, Pablo Tamayo, Todd R Golub, Jill P Mesirov. PLoS One 2007
252
9

xCell: digitally portraying the tissue cellular heterogeneity landscape.
Dvir Aran, Zicheng Hu, Atul J Butte. Genome Biol 2017
9

Cancer Statistics, 2021.
Rebecca L Siegel, Kimberly D Miller, Hannah E Fuchs, Ahmedin Jemal. CA Cancer J Clin 2021
9

TIMER2.0 for analysis of tumor-infiltrating immune cells.
Taiwen Li, Jingxin Fu, Zexian Zeng, David Cohen, Jing Li, Qianming Chen, Bo Li, X Shirley Liu. Nucleic Acids Res 2020
9

Development of tumor mutation burden as an immunotherapy biomarker: utility for the oncology clinic.
T A Chan, M Yarchoan, E Jaffee, C Swanton, S A Quezada, A Stenzinger, S Peters. Ann Oncol 2019
8

TIMER: A Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells.
Taiwen Li, Jingyu Fan, Binbin Wang, Nicole Traugh, Qianming Chen, Jun S Liu, Bo Li, X Shirley Liu. Cancer Res 2017
8

Cancer immunotherapy using checkpoint blockade.
Antoni Ribas, Jedd D Wolchok. Science 2018
8

CD8+ T cells regulate tumour ferroptosis during cancer immunotherapy.
Weimin Wang, Michael Green, Jae Eun Choi, Miguel Gijón, Paul D Kennedy, Jeffrey K Johnson, Peng Liao, Xueting Lang, Ilona Kryczek, Amanda Sell,[...]. Nature 2019
820
8

Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells.
Wanjuan Yang, Jorge Soares, Patricia Greninger, Elena J Edelman, Howard Lightfoot, Simon Forbes, Nidhi Bindal, Dave Beare, James A Smith, I Richard Thompson,[...]. Nucleic Acids Res 2013
8

ImmuCellAI: A Unique Method for Comprehensive T-Cell Subsets Abundance Prediction and its Application in Cancer Immunotherapy.
Ya-Ru Miao, Qiong Zhang, Qian Lei, Mei Luo, Gui-Yan Xie, Hongxiang Wang, An-Yuan Guo. Adv Sci (Weinh) 2020
323
7


Pan-tumor genomic biomarkers for PD-1 checkpoint blockade-based immunotherapy.
Razvan Cristescu, Robin Mogg, Mark Ayers, Andrew Albright, Erin Murphy, Jennifer Yearley, Xinwei Sher, Xiao Qiao Liu, Hongchao Lu, Michael Nebozhyn,[...]. Science 2018
7

Cancer statistics, 2020.
Rebecca L Siegel, Kimberly D Miller, Ahmedin Jemal. CA Cancer J Clin 2020
7

The Molecular Signatures Database (MSigDB) hallmark gene set collection.
Arthur Liberzon, Chet Birger, Helga Thorvaldsdóttir, Mahmoud Ghandi, Jill P Mesirov, Pablo Tamayo. Cell Syst 2015
7

WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
7

TIP: A Web Server for Resolving Tumor Immunophenotype Profiling.
Liwen Xu, Chunyu Deng, Bo Pang, Xinxin Zhang, Wei Liu, Gaoming Liao, Huating Yuan, Peng Cheng, Feng Li, Zhilin Long,[...]. Cancer Res 2018
158
6

Understanding the tumor immune microenvironment (TIME) for effective therapy.
Mikhail Binnewies, Edward W Roberts, Kelly Kersten, Vincent Chan, Douglas F Fearon, Miriam Merad, Lisa M Coussens, Dmitry I Gabrilovich, Suzanne Ostrand-Rosenberg, Catherine C Hedrick,[...]. Nat Med 2018
6

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
6

Comprehensive molecular characterization of clinical responses to PD-1 inhibition in metastatic gastric cancer.
Seung Tae Kim, Razvan Cristescu, Adam J Bass, Kyoung-Mee Kim, Justin I Odegaard, Kyung Kim, Xiao Qiao Liu, Xinwei Sher, Hun Jung, Mijin Lee,[...]. Nat Med 2018
674
6

Tumor mutational load predicts survival after immunotherapy across multiple cancer types.
Robert M Samstein, Chung-Han Lee, Alexander N Shoushtari, Matthew D Hellmann, Ronglai Shen, Yelena Y Janjigian, David A Barron, Ahmet Zehir, Emmet J Jordan, Antonio Omuro,[...]. Nat Genet 2019
6

Large-scale public data reuse to model immunotherapy response and resistance.
Jingxin Fu, Karen Li, Wubing Zhang, Changxin Wan, Jing Zhang, Peng Jiang, X Shirley Liu. Genome Med 2020
204
6

Hallmarks of cancer: the next generation.
Douglas Hanahan, Robert A Weinberg. Cell 2011
6

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.
Christina Curtis, Sohrab P Shah, Suet-Feung Chin, Gulisa Turashvili, Oscar M Rueda, Mark J Dunning, Doug Speed, Andy G Lynch, Shamith Samarajiwa, Yinyin Yuan,[...]. Nature 2012
6

Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma.
Willy Hugo, Jesse M Zaretsky, Lu Sun, Chunying Song, Blanca Homet Moreno, Siwen Hu-Lieskovan, Beata Berent-Maoz, Jia Pang, Bartosz Chmielowski, Grace Cherry,[...]. Cell 2016
6

Oncology meets immunology: the cancer-immunity cycle.
Daniel S Chen, Ira Mellman. Immunity 2013
6

Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden.
Zachary R Chalmers, Caitlin F Connelly, David Fabrizio, Laurie Gay, Siraj M Ali, Riley Ennis, Alexa Schrock, Brittany Campbell, Adam Shlien, Juliann Chmielecki,[...]. Genome Med 2017
6

Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology.
Gregor Sturm, Francesca Finotello, Florent Petitprez, Jitao David Zhang, Jan Baumbach, Wolf H Fridman, Markus List, Tatsiana Aneichyk. Bioinformatics 2019
268
6

Gasdermin E suppresses tumour growth by activating anti-tumour immunity.
Zhibin Zhang, Ying Zhang, Shiyu Xia, Qing Kong, Shunying Li, Xing Liu, Caroline Junqueira, Karla F Meza-Sosa, Temy Mo Yin Mok, James Ansara,[...]. Nature 2020
433
6

Ferroptosis: A Regulated Cell Death Nexus Linking Metabolism, Redox Biology, and Disease.
Brent R Stockwell, José Pedro Friedmann Angeli, Hülya Bayir, Ashley I Bush, Marcus Conrad, Scott J Dixon, Simone Fulda, Sergio Gascón, Stavroula K Hatzios, Valerian E Kagan,[...]. Cell 2017
6

Primary, Adaptive, and Acquired Resistance to Cancer Immunotherapy.
Padmanee Sharma, Siwen Hu-Lieskovan, Jennifer A Wargo, Antoni Ribas. Cell 2017
5

Genomic correlates of response to CTLA-4 blockade in metastatic melanoma.
Eliezer M Van Allen, Diana Miao, Bastian Schilling, Sachet A Shukla, Christian Blank, Lisa Zimmer, Antje Sucker, Uwe Hillen, Marnix H Geukes Foppen, Simone M Goldinger,[...]. Science 2015
5


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.