A citation-based method for searching scientific literature

Bo Li, Eric Severson, Jean-Christophe Pignon, Haoquan Zhao, Taiwen Li, Jesse Novak, Peng Jiang, Hui Shen, Jon C Aster, Scott Rodig, Sabina Signoretti, Jun S Liu, X Shirley Liu. Genome Biol 2016
Times Cited: 891







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



Times Cited
  Times     Co-cited
Similarity


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
48

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
29

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
25

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
25

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
22

xCell: digitally portraying the tissue cellular heterogeneity landscape.
Dvir Aran, Zicheng Hu, Atul J Butte. Genome Biol 2017
19

GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses.
Zefang Tang, Chenwei Li, Boxi Kang, Ge Gao, Cheng Li, Zemin Zhang. Nucleic Acids Res 2017
18

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
18

UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and Survival Analyses.
Darshan S Chandrashekar, Bhuwan Bashel, Sai Akshaya Hodigere Balasubramanya, Chad J Creighton, Israel Ponce-Rodriguez, Balabhadrapatruni V S K Chakravarthi, Sooryanarayana Varambally. Neoplasia 2017
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

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
17

GSVA: gene set variation analysis for microarray and RNA-seq data.
Sonja Hänzelmann, Robert Castelo, Justin Guinney. BMC Bioinformatics 2013
16

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
15

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
15

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
15

Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.
Jianjiong Gao, Bülent Arman Aksoy, Ugur Dogrusoz, Gideon Dresdner, Benjamin Gross, S Onur Sumer, Yichao Sun, Anders Jacobsen, Rileen Sinha, Erik Larsson,[...]. Sci Signal 2013
14

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
207
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

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
10

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
10

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics.
Jianfang Liu, Tara Lichtenberg, Katherine A Hoadley, Laila M Poisson, Alexander J Lazar, Andrew D Cherniack, Albert J Kovatich, Christopher C Benz, Douglas A Levine, Adrian V Lee,[...]. Cell 2018
10

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Damian Szklarczyk, Annika L Gable, David Lyon, Alexander Junge, Stefan Wyder, Jaime Huerta-Cepas, Milan Simonovic, Nadezhda T Doncheva, John H Morris, Peer Bork,[...]. Nucleic Acids Res 2019
10

TISIDB: an integrated repository portal for tumor-immune system interactions.
Beibei Ru, Ching Ngar Wong, Yin Tong, Jia Yi Zhong, Sophia Shek Wa Zhong, Wai Chung Wu, Ka Chi Chu, Choi Yiu Wong, Chit Ying Lau, Ian Chen,[...]. Bioinformatics 2019
426
10

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

KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
9

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
9

GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis.
Zefang Tang, Boxi Kang, Chenwei Li, Tianxiang Chen, Zemin Zhang. Nucleic Acids Res 2019
937
9

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
8

Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles.
Daniel R Rhodes, Shanker Kalyana-Sundaram, Vasudeva Mahavisno, Radhika Varambally, Jianjun Yu, Benjamin B Briggs, Terrence R Barrette, Matthew J Anstet, Colleen Kincead-Beal, Prakash Kulkarni,[...]. Neoplasia 2007
8

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
8

Proteomics. Tissue-based map of the human proteome.
Mathias Uhlén, Linn Fagerberg, Björn M Hallström, Cecilia Lindskog, Per Oksvold, Adil Mardinoglu, Åsa Sivertsson, Caroline Kampf, Evelina Sjöstedt, Anna Asplund,[...]. Science 2015
7


Cancer Statistics, 2021.
Rebecca L Siegel, Kimberly D Miller, Hannah E Fuchs, Ahmedin Jemal. CA Cancer J Clin 2021
7

Visualizing and interpreting cancer genomics data via the Xena platform.
Mary J Goldman, Brian Craft, Mim Hastie, Kristupas Repečka, Fran McDade, Akhil Kamath, Ayan Banerjee, Yunhai Luo, Dave Rogers, Angela N Brooks,[...]. Nat Biotechnol 2020
673
7

The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.
Damian Szklarczyk, Annika L Gable, Katerina C Nastou, David Lyon, Rebecca Kirsch, Sampo Pyysalo, Nadezhda T Doncheva, Marc Legeay, Tao Fang, Peer Bork,[...]. Nucleic Acids Res 2021
518
7

Pancancer survival analysis of cancer hallmark genes.
Ádám Nagy, Gyöngyi Munkácsy, Balázs Győrffy. Sci Rep 2021
241
6

PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes.
Vamsi K Mootha, Cecilia M Lindgren, Karl-Fredrik Eriksson, Aravind Subramanian, Smita Sihag, Joseph Lehar, Pere Puigserver, Emma Carlsson, Martin Ridderstråle, Esa Laurila,[...]. Nat Genet 2003
6

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
6

ONCOMINE: a cancer microarray database and integrated data-mining platform.
Daniel R Rhodes, Jianjun Yu, K Shanker, Nandan Deshpande, Radhika Varambally, Debashis Ghosh, Terrence Barrette, Akhilesh Pandey, Arul M Chinnaiyan. Neoplasia 2004
6

Cancer statistics, 2020.
Rebecca L Siegel, Kimberly D Miller, Ahmedin Jemal. CA Cancer J Clin 2020
6

The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.
Ethan Cerami, Jianjiong Gao, Ugur Dogrusoz, Benjamin E Gross, Selcuk Onur Sumer, Bülent Arman Aksoy, Anders Jacobsen, Caitlin J Byrne, Michael L Heuer, Erik Larsson,[...]. Cancer Discov 2012
6

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
6

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

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
5

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
M Ashburner, C A Ball, J A Blake, D Botstein, H Butler, J M Cherry, A P Davis, K Dolinski, S S Dwight, J T Eppig,[...]. Nat Genet 2000
5

The 2016 World Health Organization Classification of Tumors of the Central Nervous System: a summary.
David N Louis, Arie Perry, Guido Reifenberger, Andreas von Deimling, Dominique Figarella-Branger, Webster K Cavenee, Hiroko Ohgaki, Otmar D Wiestler, Paul Kleihues, David W Ellison. Acta Neuropathol 2016
5

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
5

MethSurv: a web tool to perform multivariable survival analysis using DNA methylation data.
Vijayachitra Modhukur, Tatjana Iljasenko, Tauno Metsalu, Kaie Lokk, Triin Laisk-Podar, Jaak Vilo. Epigenomics 2018
149
4

Gene expression markers of Tumor Infiltrating Leukocytes.
Patrick Danaher, Sarah Warren, Lucas Dennis, Leonard D'Amico, Andrew White, Mary L Disis, Melissa A Geller, Kunle Odunsi, Joseph Beechem, Steven P Fling. J Immunother Cancer 2017
310
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.