A citation-based method for searching scientific literature

Yasin Şenbabaoğlu, Ron S Gejman, Andrew G Winer, Ming Liu, Eliezer M Van Allen, Guillermo de Velasco, Diana Miao, Irina Ostrovnaya, Esther Drill, Augustin Luna, Nils Weinhold, William Lee, Brandon J Manley, Danny N Khalil, Samuel D Kaffenberger, Yingbei Chen, Ludmila Danilova, Martin H Voss, Jonathan A Coleman, Paul Russo, Victor E Reuter, Timothy A Chan, Emily H Cheng, David A Scheinberg, Ming O Li, Toni K Choueiri, James J Hsieh, Chris Sander, A Ari Hakimi. Genome Biol 2016
Times Cited: 311







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



Times Cited
  Times     Co-cited
Similarity


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

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
24

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
24

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
24

GSVA: gene set variation analysis for microarray and RNA-seq data.
Sonja Hänzelmann, Robert Castelo, Justin Guinney. BMC Bioinformatics 2013
20

Nivolumab plus Ipilimumab versus Sunitinib in Advanced Renal-Cell Carcinoma.
Robert J Motzer, Nizar M Tannir, David F McDermott, Osvaldo Arén Frontera, Bohuslav Melichar, Toni K Choueiri, Elizabeth R Plimack, Philippe Barthélémy, Camillo Porta, Saby George,[...]. N Engl J Med 2018
20

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
19

Clinical activity and molecular correlates of response to atezolizumab alone or in combination with bevacizumab versus sunitinib in renal cell carcinoma.
David F McDermott, Mahrukh A Huseni, Michael B Atkins, Robert J Motzer, Brian I Rini, Bernard Escudier, Lawrence Fong, Richard W Joseph, Sumanta K Pal, James A Reeves,[...]. Nat Med 2018
435
19

Pembrolizumab plus Axitinib versus Sunitinib for Advanced Renal-Cell Carcinoma.
Brian I Rini, Elizabeth R Plimack, Viktor Stus, Rustem Gafanov, Robert Hawkins, Dmitry Nosov, Frédéric Pouliot, Boris Alekseev, Denis Soulières, Bohuslav Melichar,[...]. N Engl J Med 2019
993
18

An Immune Atlas of Clear Cell Renal Cell Carcinoma.
Stéphane Chevrier, Jacob Harrison Levine, Vito Riccardo Tomaso Zanotelli, Karina Silina, Daniel Schulz, Marina Bacac, Carola Hermine Ries, Laurie Ailles, Michael Alexander Spencer Jewett, Holger Moch,[...]. Cell 2017
411
17

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
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

Avelumab plus Axitinib versus Sunitinib for Advanced Renal-Cell Carcinoma.
Robert J Motzer, Konstantin Penkov, John Haanen, Brian Rini, Laurence Albiges, Matthew T Campbell, Balaji Venugopal, Christian Kollmannsberger, Sylvie Negrier, Motohide Uemura,[...]. N Engl J Med 2019
805
16


Nivolumab versus Everolimus in Advanced Renal-Cell Carcinoma.
Robert J Motzer, Bernard Escudier, David F McDermott, Saby George, Hans J Hammers, Sandhya Srinivas, Scott S Tykodi, Jeffrey A Sosman, Giuseppe Procopio, Elizabeth R Plimack,[...]. N Engl J Med 2015
15

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
14

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
14

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
740
14


Cancer statistics, 2020.
Rebecca L Siegel, Kimberly D Miller, Ahmedin Jemal. CA Cancer J Clin 2020
13

Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma.
Diana Miao, Claire A Margolis, Wenhua Gao, Martin H Voss, Wei Li, Dylan J Martini, Craig Norton, Dominick Bossé, Stephanie M Wankowicz, Dana Cullen,[...]. Science 2018
448
13

Tumor-Infiltrating and Peripheral Blood T-cell Immunophenotypes Predict Early Relapse in Localized Clear Cell Renal Cell Carcinoma.
Nicolas A Giraldo, Etienne Becht, Yann Vano, Florent Petitprez, Laetitia Lacroix, Pierre Validire, Rafael Sanchez-Salas, Alexandre Ingels, Stephane Oudard, Audrey Moatti,[...]. Clin Cancer Res 2017
143
13

Atezolizumab plus bevacizumab versus sunitinib in patients with previously untreated metastatic renal cell carcinoma (IMmotion151): a multicentre, open-label, phase 3, randomised controlled trial.
Brian I Rini, Thomas Powles, Michael B Atkins, Bernard Escudier, David F McDermott, Cristina Suarez, Sergio Bracarda, Walter M Stadler, Frede Donskov, Jae Lyun Lee,[...]. Lancet 2019
358
13

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
12

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
12

Orchestration and Prognostic Significance of Immune Checkpoints in the Microenvironment of Primary and Metastatic Renal Cell Cancer.
Nicolas A Giraldo, Etienne Becht, Franck Pagès, Georgios Skliris, Virginie Verkarre, Yann Vano, Arnaud Mejean, Nicolas Saint-Aubert, Laetitia Lacroix, Ivo Natario,[...]. Clin Cancer Res 2015
205
12

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
12

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
11

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
752
10

Tumor Mutational Burden and Response Rate to PD-1 Inhibition.
Mark Yarchoan, Alexander Hopkins, Elizabeth M Jaffee. N Engl J Med 2017
10

Insertion-and-deletion-derived tumour-specific neoantigens and the immunogenic phenotype: a pan-cancer analysis.
Samra Turajlic, Kevin Litchfield, Hang Xu, Rachel Rosenthal, Nicholas McGranahan, James L Reading, Yien Ning S Wong, Andrew Rowan, Nnennaya Kanu, Maise Al Bakir,[...]. Lancet Oncol 2017
391
10

Transcriptomic Profiling of the Tumor Microenvironment Reveals Distinct Subgroups of Clear Cell Renal Cell Cancer: Data from a Randomized Phase III Trial.
A Ari Hakimi, Martin H Voss, Fengshen Kuo, Alejandro Sanchez, Ming Liu, Briana G Nixon, Lynda Vuong, Irina Ostrovnaya, Ying-Bei Chen, Victor Reuter,[...]. Cancer Discov 2019
70
12

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
507
9

Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma.
David A Braun, Yue Hou, Ziad Bakouny, Miriam Ficial, Miriam Sant' Angelo, Juliet Forman, Petra Ross-Macdonald, Ashton C Berger, Opeyemi A Jegede, Liudmilla Elagina,[...]. Nat Med 2020
74
12

Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer.
Naiyer A Rizvi, Matthew D Hellmann, Alexandra Snyder, Pia Kvistborg, Vladimir Makarov, Jonathan J Havel, William Lee, Jianda Yuan, Phillip Wong, Teresa S Ho,[...]. Science 2015
9

Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade.
Nicholas McGranahan, Andrew J S Furness, Rachel Rosenthal, Sofie Ramskov, Rikke Lyngaa, Sunil Kumar Saini, Mariam Jamal-Hanjani, Gareth A Wilson, Nicolai J Birkbak, Crispin T Hiley,[...]. Science 2016
8

Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab.
Nadeem Riaz, Jonathan J Havel, Vladimir Makarov, Alexis Desrichard, Walter J Urba, Jennifer S Sims, F Stephen Hodi, Salvador Martín-Algarra, Rajarsi Mandal, William H Sharfman,[...]. Cell 2017
634
8

xCell: digitally portraying the tissue cellular heterogeneity landscape.
Dvir Aran, Zicheng Hu, Atul J Butte. Genome Biol 2017
643
8

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
522
8

Mining TCGA database for genes of prognostic value in glioblastoma microenvironment.
Di Jia, Shenglan Li, Dali Li, Haipeng Xue, Dan Yang, Ying Liu. Aging (Albany NY) 2018
155
8

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
8

Renal cell carcinoma.
James J Hsieh, Mark P Purdue, Sabina Signoretti, Charles Swanton, Laurence Albiges, Manuela Schmidinger, Daniel Y Heng, James Larkin, Vincenzo Ficarra. Nat Rev Dis Primers 2017
714
8

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
8


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

Type, density, and location of immune cells within human colorectal tumors predict clinical outcome.
Jérôme Galon, Anne Costes, Fatima Sanchez-Cabo, Amos Kirilovsky, Bernhard Mlecnik, Christine Lagorce-Pagès, Marie Tosolini, Matthieu Camus, Anne Berger, Philippe Wind,[...]. Science 2006
7

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


Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal.
Samra Turajlic, Hang Xu, Kevin Litchfield, Andrew Rowan, Stuart Horswell, Tim Chambers, Tim O'Brien, Jose I Lopez, Thomas B K Watkins, David Nicol,[...]. Cell 2018
224
7

An Empirical Approach Leveraging Tumorgrafts to Dissect the Tumor Microenvironment in Renal Cell Carcinoma Identifies Missing Link to Prognostic Inflammatory Factors.
Tao Wang, Rong Lu, Payal Kapur, Bijay S Jaiswal, Raquibul Hannan, Ze Zhang, Ivan Pedrosa, Jason J Luke, He Zhang, Leonard D Goldstein,[...]. Cancer Discov 2018
53
13


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.