A citation-based method for searching scientific literature

Binbin Chen, Michael S Khodadoust, Chih Long Liu, Aaron M Newman, Ash A Alizadeh. Methods Mol Biol 2018
Times Cited: 662







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



Times Cited
  Times     Co-cited
Similarity


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
32

GSVA: gene set variation analysis for microarray and RNA-seq data.
Sonja Hänzelmann, Robert Castelo, Justin Guinney. BMC Bioinformatics 2013
22

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
21

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
21

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
19

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
16

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
15

Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker. Genome Res 2003
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
13

xCell: digitally portraying the tissue cellular heterogeneity landscape.
Dvir Aran, Zicheng Hu, Atul J Butte. Genome Biol 2017
13

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
894
12

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
781
11

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
11


WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
10

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
10

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
9

NCBI GEO: archive for functional genomics data sets--update.
Tanya Barrett, Stephen E Wilhite, Pierre Ledoux, Carlos Evangelista, Irene F Kim, Maxim Tomashevsky, Kimberly A Marshall, Katherine H Phillippy, Patti M Sherman, Michelle Holko,[...]. Nucleic Acids Res 2013
8

The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge.
Katarzyna Tomczak, Patrycja Czerwińska, Maciej Wiznerowicz. Contemp Oncol (Pozn) 2015
8

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
777
8

Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data.
Julien Racle, Kaat de Jonge, Petra Baumgaertner, Daniel E Speiser, David Gfeller. Elife 2017
297
8

Deconvoluting tumor-infiltrating immune cells from RNA-seq data using quanTIseq.
Christina Plattner, Francesca Finotello, Dietmar Rieder. Methods Enzymol 2020
37
18

The prognostic landscape of genes and infiltrating immune cells across human cancers.
Andrew J Gentles, Aaron M Newman, Chih Long Liu, Scott V Bratman, Weiguo Feng, Dongkyoon Kim, Viswam S Nair, Yue Xu, Amanda Khuong, Chuong D Hoang,[...]. Nat Med 2015
7

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
7

KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
7

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets.
Yingyao Zhou, Bin Zhou, Lars Pache, Max Chang, Alireza Hadj Khodabakhshi, Olga Tanaseichuk, Christopher Benner, Sumit K Chanda. Nat Commun 2019
7


Cancer Statistics, 2021.
Rebecca L Siegel, Kimberly D Miller, Hannah E Fuchs, Ahmedin Jemal. CA Cancer J Clin 2021
6

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
Damian Szklarczyk, John H Morris, Helen Cook, Michael Kuhn, Stefan Wyder, Milan Simonovic, Alberto Santos, Nadezhda T Doncheva, Alexander Roth, Peer Bork,[...]. Nucleic Acids Res 2017
6

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nat Protoc 2009
6

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
6

Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response.
Peng Jiang, Shengqing Gu, Deng Pan, Jingxin Fu, Avinash Sahu, Xihao Hu, Ziyi Li, Nicole Traugh, Xia Bu, Bo Li,[...]. Nat Med 2018
824
6

cytoHubba: identifying hub objects and sub-networks from complex interactome.
Chia-Hao Chin, Shu-Hwa Chen, Hsin-Hung Wu, Chin-Wen Ho, Ming-Tat Ko, Chung-Yen Lin. BMC Syst Biol 2014
6

Relative contribution of clinicopathological variables, genomic markers, transcriptomic subtyping and microenvironment features for outcome prediction in stage II/III colorectal cancer.
R Dienstmann, G Villacampa, A Sveen, M J Mason, D Niedzwiecki, A Nesbakken, V Moreno, R S Warren, R A Lothe, J Guinney. Ann Oncol 2019
61
9

The sva package for removing batch effects and other unwanted variation in high-throughput experiments.
Jeffrey T Leek, W Evan Johnson, Hilary S Parker, Andrew E Jaffe, John D Storey. Bioinformatics 2012
5

Chemokines in the cancer microenvironment and their relevance in cancer immunotherapy.
Nisha Nagarsheth, Max S Wicha, Weiping Zou. Nat Rev Immunol 2017
826
5

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
5


Determining cell type abundance and expression from bulk tissues with digital cytometry.
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,[...]. Nat Biotechnol 2019
729
5

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
5

pROC: an open-source package for R and S+ to analyze and compare ROC curves.
Xavier Robin, Natacha Turck, Alexandre Hainard, Natalia Tiberti, Frédérique Lisacek, Jean-Charles Sanchez, Markus Müller. BMC Bioinformatics 2011
5

STRING: a database of predicted functional associations between proteins.
Christian von Mering, Martijn Huynen, Daniel Jaeggi, Steffen Schmidt, Peer Bork, Berend Snel. Nucleic Acids Res 2003
5

Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data.
Francesca Finotello, Clemens Mayer, Christina Plattner, Gerhard Laschober, Dietmar Rieder, Hubert Hackl, Anne Krogsdam, Zuzana Loncova, Wilfried Posch, Doris Wilflingseder,[...]. Genome Med 2019
241
5


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
5

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data.
Jun-Hao Li, Shun Liu, Hui Zhou, Liang-Hu Qu, Jian-Hua Yang. Nucleic Acids Res 2014
4

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
4

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
4

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
4

Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses.
Yonit Lavin, Soma Kobayashi, Andrew Leader, El-Ad David Amir, Naama Elefant, Camille Bigenwald, Romain Remark, Robert Sweeney, Christian D Becker, Jacob H Levine,[...]. Cell 2017
617
4


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.