A citation-based method for searching scientific literature

Chen Huang, Lijun Chen, Sara R Savage, Rodrigo Vargas Eguez, Yongchao Dou, Yize Li, Felipe da Veiga Leprevost, Eric J Jaehnig, Jonathan T Lei, Bo Wen, Michael Schnaubelt, Karsten Krug, Xiaoyu Song, Marcin Cieślik, Hui-Yin Chang, Matthew A Wyczalkowski, Kai Li, Antonio Colaprico, Qing Kay Li, David J Clark, Yingwei Hu, Liwei Cao, Jianbo Pan, Yuefan Wang, Kyung-Cho Cho, Zhiao Shi, Yuxing Liao, Wen Jiang, Meenakshi Anurag, Jiayi Ji, Seungyeul Yoo, Daniel Cui Zhou, Wen-Wei Liang, Michael Wendl, Pankaj Vats, Steven A Carr, D R Mani, Zhen Zhang, Jiang Qian, Xi S Chen, Alexander R Pico, Pei Wang, Arul M Chinnaiyan, Karen A Ketchum, Christopher R Kinsinger, Ana I Robles, Eunkyung An, Tara Hiltke, Mehdi Mesri, Mathangi Thiagarajan, Alissa M Weaver, Andrew G Sikora, Jan Lubiński, Małgorzata Wierzbicka, Maciej Wiznerowicz, Shankha Satpathy, Michael A Gillette, George Miles, Matthew J Ellis, Gilbert S Omenn, Henry Rodriguez, Emily S Boja, Saravana M Dhanasekaran, Li Ding, Alexey I Nesvizhskii, Adel K El-Naggar, Daniel W Chan, Hui Zhang, Bing Zhang. Cancer Cell 2021
Times Cited: 90







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



Times Cited
  Times     Co-cited
Similarity


Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma.
Michael A Gillette, Shankha Satpathy, Song Cao, Saravana M Dhanasekaran, Suhas V Vasaikar, Karsten Krug, Francesca Petralia, Yize Li, Wen-Wei Liang, Boris Reva,[...]. Cell 2020
190
27

Proteogenomics connects somatic mutations to signalling in breast cancer.
Philipp Mertins, D R Mani, Kelly V Ruggles, Michael A Gillette, Karl R Clauser, Pei Wang, Xianlong Wang, Jana W Qiao, Song Cao, Francesca Petralia,[...]. Nature 2016
941
26

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma.
David J Clark, Saravana M Dhanasekaran, Francesca Petralia, Jianbo Pan, Xiaoyu Song, Yingwei Hu, Felipe da Veiga Leprevost, Boris Reva, Tung-Shing M Lih, Hui-Yin Chang,[...]. Cell 2019
211
25

Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy.
Karsten Krug, Eric J Jaehnig, Shankha Satpathy, Lili Blumenberg, Alla Karpova, Meenakshi Anurag, George Miles, Philipp Mertins, Yifat Geffen, Lauren C Tang,[...]. Cell 2020
108
24

Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities.
Suhas Vasaikar, Chen Huang, Xiaojing Wang, Vladislav A Petyuk, Sara R Savage, Bo Wen, Yongchao Dou, Yun Zhang, Zhiao Shi, Osama A Arshad,[...]. Cell 2019
293
24

Proteogenomic Characterization of Endometrial Carcinoma.
Yongchao Dou, Emily A Kawaler, Daniel Cui Zhou, Marina A Gritsenko, Chen Huang, Lili Blumenberg, Alla Karpova, Vladislav A Petyuk, Sara R Savage, Shankha Satpathy,[...]. Cell 2020
150
20

Proteogenomic characterization of human colon and rectal cancer.
Bing Zhang, Jing Wang, Xiaojing Wang, Jing Zhu, Qi Liu, Zhiao Shi, Matthew C Chambers, Lisa J Zimmerman, Kent F Shaddox, Sangtae Kim,[...]. Nature 2014
905
18

Proteogenomic and metabolomic characterization of human glioblastoma.
Liang-Bo Wang, Alla Karpova, Marina A Gritsenko, Jennifer E Kyle, Song Cao, Yize Li, Dmitry Rykunov, Antonio Colaprico, Joseph H Rothstein, Runyu Hong,[...]. Cancer Cell 2021
123
18

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer.
Hui Zhang, Tao Liu, Zhen Zhang, Samuel H Payne, Bai Zhang, Jason E McDermott, Jian-Ying Zhou, Vladislav A Petyuk, Li Chen, Debjit Ray,[...]. Cell 2016
536
17


Head and neck squamous cell carcinoma.
Daniel E Johnson, Barbara Burtness, C René Leemans, Vivian Wai Yan Lui, Julie E Bauman, Jennifer R Grandis. Nat Rev Dis Primers 2020
656
17

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
17

Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer.
Sidharth V Puram, Itay Tirosh, Anuraag S Parikh, Anoop P Patel, Keren Yizhak, Shawn Gillespie, Christopher Rodman, Christina L Luo, Edmund A Mroz, Kevin S Emerick,[...]. Cell 2017
983
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
14

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
14

Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer.
Francesca Petralia, Nicole Tignor, Boris Reva, Mateusz Koptyra, Shrabanti Chowdhury, Dmitry Rykunov, Azra Krek, Weiping Ma, Yuankun Zhu, Jiayi Ji,[...]. Cell 2020
78
15

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

Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma.
Qiang Gao, Hongwen Zhu, Liangqing Dong, Weiwei Shi, Ran Chen, Zhijian Song, Chen Huang, Junqiang Li, Xiaowei Dong, Yanting Zhou,[...]. Cell 2019
302
12

xCell: digitally portraying the tissue cellular heterogeneity landscape.
Dvir Aran, Zicheng Hu, Atul J Butte. Genome Biol 2017
12

GSVA: gene set variation analysis for microarray and RNA-seq data.
Sonja Hänzelmann, Robert Castelo, Justin Guinney. BMC Bioinformatics 2013
12

The changing therapeutic landscape of head and neck cancer.
John D Cramer, Barbara Burtness, Quynh Thu Le, Robert L Ferris. Nat Rev Clin Oncol 2019
257
11

Next-generation characterization of the Cancer Cell Line Encyclopedia.
Mahmoud Ghandi, Franklin W Huang, Judit Jané-Valbuena, Gregory V Kryukov, Christopher C Lo, E Robert McDonald, Jordi Barretina, Ellen T Gelfand, Craig M Bielski, Haoxin Li,[...]. Nature 2019
11

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
11

A proteogenomic portrait of lung squamous cell carcinoma.
Shankha Satpathy, Karsten Krug, Pierre M Jean Beltran, Sara R Savage, Francesca Petralia, Chandan Kumar-Sinha, Yongchao Dou, Boris Reva, M Harry Kane, Shayan C Avanessian,[...]. Cell 2021
41
24

Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry.
Philipp Mertins, Lauren C Tang, Karsten Krug, David J Clark, Marina A Gritsenko, Lijun Chen, Karl R Clauser, Therese R Clauss, Punit Shah, Michael A Gillette,[...]. Nat Protoc 2018
182
10

The molecular landscape of head and neck cancer.
C René Leemans, Peter J F Snijders, Ruud H Brakenhoff. Nat Rev Cancer 2018
601
10

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
10


Quantitative Proteomics of the Cancer Cell Line Encyclopedia.
David P Nusinow, John Szpyt, Mahmoud Ghandi, Christopher M Rose, E Robert McDonald, Marian Kalocsay, Judit Jané-Valbuena, Ellen Gelfand, Devin K Schweppe, Mark Jedrychowski,[...]. Cell 2020
282
10

Proteogenomic characterization of pancreatic ductal adenocarcinoma.
Liwei Cao, Chen Huang, Daniel Cui Zhou, Yingwei Hu, T Mamie Lih, Sara R Savage, Karsten Krug, David J Clark, Michael Schnaubelt, Lijun Chen,[...]. Cell 2021
67
13

Microscaled proteogenomic methods for precision oncology.
Shankha Satpathy, Eric J Jaehnig, Karsten Krug, Beom-Jun Kim, Alexander B Saltzman, Doug W Chan, Kimberly R Holloway, Meenakshi Anurag, Chen Huang, Purba Singh,[...]. Nat Commun 2020
42
19

Proteogenomic Characterization of Human Early-Onset Gastric Cancer.
Dong-Gi Mun, Jinhyuk Bhin, Sangok Kim, Hyunwoo Kim, Jae Hun Jung, Yeonjoo Jung, Ye Eun Jang, Jong Moon Park, Hokeun Kim, Yeonhwa Jung,[...]. Cancer Cell 2019
111
8

Integrated Proteomic and Glycoproteomic Characterization of Human High-Grade Serous Ovarian Carcinoma.
Yingwei Hu, Jianbo Pan, Punit Shah, Minghui Ao, Stefani N Thomas, Yang Liu, Lijun Chen, Michael Schnaubelt, David J Clark, Henry Rodriguez,[...]. Cell Rep 2020
37
21

A Landscape of Pharmacogenomic Interactions in Cancer.
Francesco Iorio, Theo A Knijnenburg, Daniel J Vis, Graham R Bignell, Michael P Menden, Michael Schubert, Nanne Aben, Emanuel Gonçalves, Syd Barthorpe, Howard Lightfoot,[...]. Cell 2016
891
8

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers.
Craig H Mermel, Steven E Schumacher, Barbara Hill, Matthew L Meyerson, Rameen Beroukhim, Gad Getz. Genome Biol 2011
8

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1.
David A Barbie, Pablo Tamayo, Jesse S Boehm, So Young Kim, Susan E Moody, Ian F Dunn, Anna C Schinzel, Peter Sandy, Etienne Meylan, Claudia Scholl,[...]. Nature 2009
8

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics.
Andy T Kong, Felipe V Leprevost, Dmitry M Avtonomov, Dattatreya Mellacheruvu, Alexey I Nesvizhskii. Nat Methods 2017
411
8


The next horizon in precision oncology: Proteogenomics to inform cancer diagnosis and treatment.
Henry Rodriguez, Jean Claude Zenklusen, Louis M Staudt, James H Doroshow, Douglas R Lowy. Cell 2021
33
24

Pembrolizumab alone or with chemotherapy versus cetuximab with chemotherapy for recurrent or metastatic squamous cell carcinoma of the head and neck (KEYNOTE-048): a randomised, open-label, phase 3 study.
Barbara Burtness, Kevin J Harrington, Richard Greil, Denis Soulières, Makoto Tahara, Gilberto de Castro, Amanda Psyrri, Neus Basté, Prakash Neupane, Åse Bratland,[...]. Lancet 2019
8

Human papillomavirus and survival of patients with oropharyngeal cancer.
K Kian Ang, Jonathan Harris, Richard Wheeler, Randal Weber, David I Rosenthal, Phuc Felix Nguyen-Tân, William H Westra, Christine H Chung, Richard C Jordan, Charles Lu,[...]. N Engl J Med 2010
8

Genomic and transcriptomic profiling expands precision cancer medicine: the WINTHER trial.
Jordi Rodon, Jean-Charles Soria, Raanan Berger, Wilson H Miller, Eitan Rubin, Aleksandra Kugel, Apostolia Tsimberidou, Pierre Saintigny, Aliza Ackerstein, Irene Braña,[...]. Nat Med 2019
221
7

The molecular biology of head and neck cancer.
C René Leemans, Boudewijn J M Braakhuis, Ruud H Brakenhoff. Nat Rev Cancer 2011
7

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
7

The Proteogenomic Landscape of Curable Prostate Cancer.
Ankit Sinha, Vincent Huang, Julie Livingstone, Jenny Wang, Natalie S Fox, Natalie Kurganovs, Vladimir Ignatchenko, Katharina Fritsch, Nilgun Donmez, Lawrence E Heisler,[...]. Cancer Cell 2019
96
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


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
7

The Cancer Genome Atlas Pan-Cancer analysis project.
John N Weinstein, Eric A Collisson, Gordon B Mills, Kenna R Mills Shaw, Brad A Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, Joshua M Stuart. Nat Genet 2013
7

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
7


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.