A citation-based method for searching scientific literature

Jordi Barretina, Giordano Caponigro, Nicolas Stransky, Kavitha Venkatesan, Adam A Margolin, Sungjoon Kim, Christopher J Wilson, Joseph Lehár, Gregory V Kryukov, Dmitriy Sonkin, Anupama Reddy, Manway Liu, Lauren Murray, Michael F Berger, John E Monahan, Paula Morais, Jodi Meltzer, Adam Korejwa, Judit Jané-Valbuena, Felipa A Mapa, Joseph Thibault, Eva Bric-Furlong, Pichai Raman, Aaron Shipway, Ingo H Engels, Jill Cheng, Guoying K Yu, Jianjun Yu, Peter Aspesi, Melanie de Silva, Kalpana Jagtap, Michael D Jones, Li Wang, Charles Hatton, Emanuele Palescandolo, Supriya Gupta, Scott Mahan, Carrie Sougnez, Robert C Onofrio, Ted Liefeld, Laura MacConaill, Wendy Winckler, Michael Reich, Nanxin Li, Jill P Mesirov, Stacey B Gabriel, Gad Getz, Kristin Ardlie, Vivien Chan, Vic E Myer, Barbara L Weber, Jeff Porter, Markus Warmuth, Peter Finan, Jennifer L Harris, Matthew Meyerson, Todd R Golub, Michael P Morrissey, William R Sellers, Robert Schlegel, Levi A Garraway. Nature 2012
Times Cited: 3820







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



Times Cited
  Times     Co-cited
Similarity


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
535
17

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
648
12

Systematic identification of genomic markers of drug sensitivity in cancer cells.
Mathew J Garnett, Elena J Edelman, Sonja J Heidorn, Chris D Greenman, Anahita Dastur, King Wai Lau, Patricia Greninger, I Richard Thompson, Xi Luo, Jorge Soares,[...]. Nature 2012
12

Defining a Cancer Dependency Map.
Aviad Tsherniak, Francisca Vazquez, Phil G Montgomery, Barbara A Weir, Gregory Kryukov, Glenn S Cowley, Stanley Gill, William F Harrington, Sasha Pantel, John M Krill-Burger,[...]. Cell 2017
570
11

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
791
11

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
10

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
9

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
8

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
8

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
8

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
8

Harnessing Connectivity in a Large-Scale Small-Molecule Sensitivity Dataset.
Brinton Seashore-Ludlow, Matthew G Rees, Jaime H Cheah, Murat Cokol, Edmund V Price, Matthew E Coletti, Victor Jones, Nicole E Bodycombe, Christian K Soule, Joshua Gould,[...]. Cancer Discov 2015
280
7


Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens.
Fiona M Behan, Francesco Iorio, Gabriele Picco, Emanuel Gonçalves, Charlotte M Beaver, Giorgia Migliardi, Rita Santos, Yanhua Rao, Francesco Sassi, Marika Pinnelli,[...]. Nature 2019
280
7

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

A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.
Aravind Subramanian, Rajiv Narayan, Steven M Corsello, David D Peck, Ted E Natoli, Xiaodong Lu, Joshua Gould, John F Davis, Andrew A Tubelli, Jacob K Asiedu,[...]. Cell 2017
720
6



COSMIC: the Catalogue Of Somatic Mutations In Cancer.
John G Tate, Sally Bamford, Harry C Jubb, Zbyslaw Sondka, David M Beare, Nidhi Bindal, Harry Boutselakis, Charlotte G Cole, Celestino Creatore, Elisabeth Dawson,[...]. Nucleic Acids Res 2019
934
6

Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells.
Robin M Meyers, Jordan G Bryan, James M McFarland, Barbara A Weir, Ann E Sizemore, Han Xu, Neekesh V Dharia, Phillip G Montgomery, Glenn S Cowley, Sasha Pantel,[...]. Nat Genet 2017
475
6

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
6

Resistance to PARP inhibitors by SLFN11 inactivation can be overcome by ATR inhibition.
Junko Murai, Ying Feng, Guoying K Yu, Yuanbin Ru, Sai-Wen Tang, Yuqiao Shen, Yves Pommier. Oncotarget 2016
120
5

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

High-throughput screening using patient-derived tumor xenografts to predict clinical trial drug response.
Hui Gao, Joshua M Korn, Stéphane Ferretti, John E Monahan, Youzhen Wang, Mallika Singh, Chao Zhang, Christian Schnell, Guizhi Yang, Yun Zhang,[...]. Nat Med 2015
573
5

Discovering the anti-cancer potential of non-oncology drugs by systematic viability profiling.
Steven M Corsello, Rohith T Nagari, Ryan D Spangler, Jordan Rossen, Mustafa Kocak, Jordan G Bryan, Ranad Humeidi, David Peck, Xiaoyun Wu, Andrew A Tang,[...]. Nat Cancer 2020
71
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
5


Hallmarks of cancer: the next generation.
Douglas Hanahan, Robert A Weinberg. Cell 2011
5

Inconsistency in large pharmacogenomic studies.
Benjamin Haibe-Kains, Nehme El-Hachem, Nicolai Juul Birkbak, Andrew C Jin, Andrew H Beck, Hugo J W L Aerts, John Quackenbush. Nature 2013
291
5


Drug repurposing: progress, challenges and recommendations.
Sudeep Pushpakom, Francesco Iorio, Patrick A Eyers, K Jane Escott, Shirley Hopper, Andrew Wells, Andrew Doig, Tim Guilliams, Joanna Latimer, Christine McNamee,[...]. Nat Rev Drug Discov 2019
776
4

Correlating chemical sensitivity and basal gene expression reveals mechanism of action.
Matthew G Rees, Brinton Seashore-Ludlow, Jaime H Cheah, Drew J Adams, Edmund V Price, Shubhroz Gill, Sarah Javaid, Matthew E Coletti, Victor L Jones, Nicole E Bodycombe,[...]. Nat Chem Biol 2016
254
4

KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
4


Specific killing of BRCA2-deficient tumours with inhibitors of poly(ADP-ribose) polymerase.
Helen E Bryant, Niklas Schultz, Huw D Thomas, Kayan M Parker, Dan Flower, Elena Lopez, Suzanne Kyle, Mark Meuth, Nicola J Curtin, Thomas Helleday. Nature 2005
4

Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy.
Hannah Farmer, Nuala McCabe, Christopher J Lord, Andrew N J Tutt, Damian A Johnson, Tobias B Richardson, Manuela Santarosa, Krystyna J Dillon, Ian Hickson, Charlotte Knights,[...]. Nature 2005
4

Putative DNA/RNA helicase Schlafen-11 (SLFN11) sensitizes cancer cells to DNA-damaging agents.
Gabriele Zoppoli, Marie Regairaz, Elisabetta Leo, William C Reinhold, Sudhir Varma, Alberto Ballestrero, James H Doroshow, Yves Pommier. Proc Natl Acad Sci U S A 2012
142
4

Dynamic variations in epithelial-to-mesenchymal transition (EMT), ATM, and SLFN11 govern response to PARP inhibitors and cisplatin in small cell lung cancer.
C Allison Stewart, Pan Tong, Robert J Cardnell, Triparna Sen, Lerong Li, Carl M Gay, Fatemah Masrorpour, You Fan, Rasha O Bara, Ying Feng,[...]. Oncotarget 2017
87
4

Trapping of PARP1 and PARP2 by Clinical PARP Inhibitors.
Junko Murai, Shar-yin N Huang, Benu Brata Das, Amelie Renaud, Yiping Zhang, James H Doroshow, Jiuping Ji, Shunichi Takeda, Yves Pommier. Cancer Res 2012
945
4

SLFN11 Blocks Stressed Replication Forks Independently of ATR.
Junko Murai, Sai-Wen Tang, Elisabetta Leo, Simone A Baechler, Christophe E Redon, Hongliang Zhang, Muthana Al Abo, Vinodh N Rajapakse, Eijiro Nakamura, Lisa M Miller Jenkins,[...]. Mol Cell 2018
92
4

An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules.
Amrita Basu, Nicole E Bodycombe, Jaime H Cheah, Edmund V Price, Ke Liu, Giannina I Schaefer, Richard Y Ebright, Michelle L Stewart, Daisuke Ito, Stephanie Wang,[...]. Cell 2013
298
4

Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer.
A Gordon Robertson, Jaegil Kim, Hikmat Al-Ahmadie, Joaquim Bellmunt, Guangwu Guo, Andrew D Cherniack, Toshinori Hinoue, Peter W Laird, Katherine A Hoadley, Rehan Akbani,[...]. Cell 2017
768
4

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool.
Edward Y Chen, Christopher M Tan, Yan Kou, Qiaonan Duan, Zichen Wang, Gabriela Vaz Meirelles, Neil R Clark, Avi Ma'ayan. BMC Bioinformatics 2013
4

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
77
5


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
426
4

A community effort to assess and improve drug sensitivity prediction algorithms.
James C Costello, Laura M Heiser, Elisabeth Georgii, Mehmet Gönen, Michael P Menden, Nicholas J Wang, Mukesh Bansal, Muhammad Ammad-ud-din, Petteri Hintsanen, Suleiman A Khan,[...]. Nat Biotechnol 2014
334
4

The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
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.