A citation-based method for searching scientific literature

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, Daniel G Deschler, Mark A Varvares, Ravi Mylvaganam, Orit Rozenblatt-Rosen, James W Rocco, William C Faquin, Derrick T Lin, Aviv Regev, Bradley E Bernstein. Cell 2017
Times Cited: 628







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



Times Cited
  Times     Co-cited
Similarity


Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.
Itay Tirosh, Benjamin Izar, Sanjay M Prakadan, Marc H Wadsworth, Daniel Treacy, John J Trombetta, Asaf Rotem, Christopher Rodman, Christine Lian, George Murphy,[...]. Science 2016
30

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma.
Anoop P Patel, Itay Tirosh, John J Trombetta, Alex K Shalek, Shawn M Gillespie, Hiroaki Wakimoto, Daniel P Cahill, Brian V Nahed, William T Curry, Robert L Martuza,[...]. Science 2014
24

Phenotype molding of stromal cells in the lung tumor microenvironment.
Diether Lambrechts, Els Wauters, Bram Boeckx, Sara Aibar, David Nittner, Oliver Burton, Ayse Bassez, Herbert Decaluwé, Andreas Pircher, Kathleen Van den Eynde,[...]. Nat Med 2018
413
18

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment.
Elham Azizi, Ambrose J Carr, George Plitas, Andrew E Cornish, Catherine Konopacki, Sandhya Prabhakaran, Juozas Nainys, Kenmin Wu, Vaidotas Kiseliovas, Manu Setty,[...]. Cell 2018
512
17

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.
Cole Trapnell, Davide Cacchiarelli, Jonna Grimsby, Prapti Pokharel, Shuqiang Li, Michael Morse, Niall J Lennon, Kenneth J Livak, Tarjei S Mikkelsen, John L Rinn. Nat Biotechnol 2014
16

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
16

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
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
15

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.
Evan Z Macosko, Anindita Basu, Rahul Satija, James Nemesh, Karthik Shekhar, Melissa Goldman, Itay Tirosh, Allison R Bialas, Nolan Kamitaki, Emily M Martersteck,[...]. Cell 2015
14

Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing.
Chunhong Zheng, Liangtao Zheng, Jae-Kwang Yoo, Huahu Guo, Yuanyuan Zhang, Xinyi Guo, Boxi Kang, Ruozhen Hu, Julie Y Huang, Qiming Zhang,[...]. Cell 2017
657
13


Comprehensive Integration of Single-Cell Data.
Tim Stuart, Andrew Butler, Paul Hoffman, Christoph Hafemeister, Efthymia Papalexi, William M Mauck, Yuhan Hao, Marlon Stoeckius, Peter Smibert, Rahul Satija. Cell 2019
13

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing.
Xinyi Guo, Yuanyuan Zhang, Liangtao Zheng, Chunhong Zheng, Jintao Song, Qiming Zhang, Boxi Kang, Zhouzerui Liu, Liang Jin, Rui Xing,[...]. Nat Med 2018
337
13

Identification of the tumour transition states occurring during EMT.
Ievgenia Pastushenko, Audrey Brisebarre, Alejandro Sifrim, Marco Fioramonti, Tatiana Revenco, Soufiane Boumahdi, Alexandra Van Keymeulen, Daniel Brown, Virginie Moers, Sophie Lemaire,[...]. Nature 2018
484
11

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.
Patrik L Ståhl, Fredrik Salmén, Sanja Vickovic, Anna Lundmark, José Fernández Navarro, Jens Magnusson, Stefania Giacomello, Michaela Asp, Jakub O Westholm, Mikael Huss,[...]. Science 2016
576
11

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
11

Hallmarks of cancer: the next generation.
Douglas Hanahan, Robert A Weinberg. Cell 2011
11

Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer.
Woosung Chung, Hye Hyeon Eum, Hae-Ock Lee, Kyung-Min Lee, Han-Byoel Lee, Kyu-Tae Kim, Han Suk Ryu, Sangmin Kim, Jeong Eon Lee, Yeon Hee Park,[...]. Nat Commun 2017
337
11

Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species.
Rapolas Zilionis, Camilla Engblom, Christina Pfirschke, Virginia Savova, David Zemmour, Hatice D Saatcioglu, Indira Krishnan, Giorgia Maroni, Claire V Meyerovitz, Clara M Kerwin,[...]. Immunity 2019
278
11

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma.
Itay Tirosh, Andrew S Venteicher, Christine Hebert, Leah E Escalante, Anoop P Patel, Keren Yizhak, Jonathan M Fisher, Christopher Rodman, Christopher Mount, Mariella G Filbin,[...]. Nature 2016
401
10

Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis.
Peter Savas, Balaji Virassamy, Chengzhong Ye, Agus Salim, Christopher P Mintoff, Franco Caramia, Roberto Salgado, David J Byrne, Zhi L Teo, Sathana Dushyanthen,[...]. Nat Med 2018
321
10

EMT: 2016.
M Angela Nieto, Ruby Yun-Ju Huang, Rebecca A Jackson, Jean Paul Thiery. Cell 2016
10

Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma.
Qiming Zhang, Yao He, Nan Luo, Shashank J Patel, Yanjie Han, Ranran Gao, Madhura Modak, Sebastian Carotta, Christian Haslinger, David Kind,[...]. Cell 2019
203
10

Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts.
Ela Elyada, Mohan Bolisetty, Pasquale Laise, William F Flynn, Elise T Courtois, Richard A Burkhart, Jonathan A Teinor, Pascal Belleau, Giulia Biffi, Matthew S Lucito,[...]. Cancer Discov 2019
303
9

Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma.
Junya Peng, Bao-Fa Sun, Chuan-Yuan Chen, Jia-Yi Zhou, Yu-Sheng Chen, Hao Chen, Lulu Liu, Dan Huang, Jialin Jiang, Guan-Shen Cui,[...]. Cell Res 2019
155
9

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors.
Huipeng Li, Elise T Courtois, Debarka Sengupta, Yuliana Tan, Kok Hao Chen, Jolene Jie Lin Goh, Say Li Kong, Clarinda Chua, Lim Kiat Hon, Wah Siew Tan,[...]. Nat Genet 2017
375
9

Simultaneous epitope and transcriptome measurement in single cells.
Marlon Stoeckius, Christoph Hafemeister, William Stephenson, Brian Houck-Loomis, Pratip K Chattopadhyay, Harold Swerdlow, Rahul Satija, Peter Smibert. Nat Methods 2017
673
9

The molecular landscape of head and neck cancer.
C René Leemans, Peter J F Snijders, Ruud H Brakenhoff. Nat Rev Cancer 2018
392
9

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer.
Lei Zhang, Xin Yu, Liangtao Zheng, Yuanyuan Zhang, Yansen Li, Qiao Fang, Ranran Gao, Boxi Kang, Qiming Zhang, Julie Y Huang,[...]. Nature 2018
226
9

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma.
Moshe Sade-Feldman, Keren Yizhak, Stacey L Bjorgaard, John P Ray, Carl G de Boer, Russell W Jenkins, David J Lieb, Jonathan H Chen, Dennie T Frederick, Michal Barzily-Rokni,[...]. Cell 2018
448
9

Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer.
Lei Zhang, Ziyi Li, Katarzyna M Skrzypczynska, Qiao Fang, Wei Zhang, Sarah A O'Brien, Yao He, Lynn Wang, Qiming Zhang, Aeryon Kim,[...]. Cell 2020
118
9

A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer.
Johanna Wagner, Maria Anna Rapsomaniki, Stéphane Chevrier, Tobias Anzeneder, Claus Langwieder, August Dykgers, Martin Rees, Annette Ramaswamy, Simone Muenst, Savas Deniz Soysal,[...]. Cell 2019
201
9

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
500
9

Exponential scaling of single-cell RNA-seq in the past decade.
Valentine Svensson, Roser Vento-Tormo, Sarah A Teichmann. Nat Protoc 2018
244
9

Full-length RNA-seq from single cells using Smart-seq2.
Simone Picelli, Omid R Faridani, Asa K Björklund, Gösta Winberg, Sven Sagasser, Rickard Sandberg. Nat Protoc 2014
9

Distinct populations of inflammatory fibroblasts and myofibroblasts in pancreatic cancer.
Daniel Öhlund, Abram Handly-Santana, Giulia Biffi, Ela Elyada, Ana S Almeida, Mariano Ponz-Sarvise, Vincenzo Corbo, Tobiloba E Oni, Stephen A Hearn, Eun Jung Lee,[...]. J Exp Med 2017
682
8

A framework for advancing our understanding of cancer-associated fibroblasts.
Erik Sahai, Igor Astsaturov, Edna Cukierman, David G DeNardo, Mikala Egeblad, Ronald M Evans, Douglas Fearon, Florian R Greten, Sunil R Hingorani, Tony Hunter,[...]. Nat Rev Cancer 2020
477
8

Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq.
Andrew S Venteicher, Itay Tirosh, Christine Hebert, Keren Yizhak, Cyril Neftel, Mariella G Filbin, Volker Hovestadt, Leah E Escalante, McKenzie L Shaw, Christopher Rodman,[...]. Science 2017
327
8

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
8


Tumour evolution inferred by single-cell sequencing.
Nicholas Navin, Jude Kendall, Jennifer Troge, Peter Andrews, Linda Rodgers, Jeanne McIndoo, Kerry Cook, Asya Stepansky, Dan Levy, Diane Esposito,[...]. Nature 2011
8

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution.
Samuel G Rodriques, Robert R Stickels, Aleksandrina Goeva, Carly A Martin, Evan Murray, Charles R Vanderburg, Joshua Welch, Linlin M Chen, Fei Chen, Evan Z Macosko. Science 2019
402
8

GSVA: gene set variation analysis for microarray and RNA-seq data.
Sonja Hänzelmann, Robert Castelo, Justin Guinney. BMC Bioinformatics 2013
8

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
8

Fibroblast Heterogeneity and Immunosuppressive Environment in Human Breast Cancer.
Ana Costa, Yann Kieffer, Alix Scholer-Dahirel, Floriane Pelon, Brigitte Bourachot, Melissa Cardon, Philemon Sirven, Ilaria Magagna, Laetitia Fuhrmann, Charles Bernard,[...]. Cancer Cell 2018
415
7


Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity.
Peter van Galen, Volker Hovestadt, Marc H Wadsworth Ii, Travis K Hughes, Gabriel K Griffin, Sofia Battaglia, Julia A Verga, Jason Stephansky, Timothy J Pastika, Jennifer Lombardi Story,[...]. Cell 2019
205
7

Emerging Biological Principles of Metastasis.
Arthur W Lambert, Diwakar R Pattabiraman, Robert A Weinberg. Cell 2017
7

Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas.
Reuben Moncada, Dalia Barkley, Florian Wagner, Marta Chiodin, Joseph C Devlin, Maayan Baron, Cristina H Hajdu, Diane M Simeone, Itai Yanai. Nat Biotechnol 2020
100
7

mRNA-Seq whole-transcriptome analysis of a single cell.
Fuchou Tang, Catalin Barbacioru, Yangzhou Wang, Ellen Nordman, Clarence Lee, Nanlan Xu, Xiaohui Wang, John Bodeau, Brian B Tuch, Asim Siddiqui,[...]. Nat Methods 2009
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.