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: 1000







List of co-cited articles
814 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
24

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
18

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

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
694
15

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
15

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
710
14

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
14

GSVA: gene set variation analysis for microarray and RNA-seq data.
Sonja Hänzelmann, Robert Castelo, Justin Guinney. BMC Bioinformatics 2013
14

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
805
13

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
12


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
607
11

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
674
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
483
11

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade.
Livnat Jerby-Arnon, Parin Shah, Michael S Cuoco, Christopher Rodman, Mei-Ju Su, Johannes C Melms, Rachel Leeson, Abhay Kanodia, Shaolin Mei, Jia-Ren Lin,[...]. Cell 2018
539
11

EMT Subtype Influences Epithelial Plasticity and Mode of Cell Migration.
Nicole M Aiello, Ravikanth Maddipati, Robert J Norgard, David Balli, Jinyang Li, Salina Yuan, Taiji Yamazoe, Taylor Black, Amine Sahmoud, Emma E Furth,[...]. Dev Cell 2018
328
10

Guidelines and definitions for research on epithelial-mesenchymal transition.
Jing Yang, Parker Antin, Geert Berx, Cédric Blanpain, Thomas Brabletz, Marianne Bronner, Kyra Campbell, Amparo Cano, Jordi Casanova, Gerhard Christofori,[...]. Nat Rev Mol Cell Biol 2020
647
10

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
10

CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes.
Mirjana Efremova, Miquel Vento-Tormo, Sarah A Teichmann, Roser Vento-Tormo. Nat Protoc 2020
778
10

EMT Transition States during Tumor Progression and Metastasis.
Ievgenia Pastushenko, Cédric Blanpain. Trends Cell Biol 2019
10


EMT: 2016.
M Angela Nieto, Ruby Yun-Ju Huang, Rebecca A Jackson, Jean Paul Thiery. Cell 2016
9

Circulating breast tumor cells exhibit dynamic changes in epithelial and mesenchymal composition.
Min Yu, Aditya Bardia, Ben S Wittner, Shannon L Stott, Malgorzata E Smas, David T Ting, Steven J Isakoff, Jordan C Ciciliano, Marissa N Wells, Ajay M Shah,[...]. Science 2013
9

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
9

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage.
Dvir Aran, Agnieszka P Looney, Leqian Liu, Esther Wu, Valerie Fong, Austin Hsu, Suzanna Chak, Ram P Naikawadi, Paul J Wolters, Adam R Abate,[...]. Nat Immunol 2019
965
9

Emerging Biological Principles of Metastasis.
Arthur W Lambert, Diwakar R Pattabiraman, Robert A Weinberg. Cell 2017
9

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
981
9

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
620
9

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
9

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
9

Acquisition of a hybrid E/M state is essential for tumorigenicity of basal breast cancer cells.
Cornelia Kröger, Alexander Afeyan, Jasmin Mraz, Elinor Ng Eaton, Ferenc Reinhardt, Yevgenia L Khodor, Prathapan Thiru, Brian Bierie, Xin Ye, Christopher B Burge,[...]. Proc Natl Acad Sci U S A 2019
218
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
465
8

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
483
8

SCENIC: single-cell regulatory network inference and clustering.
Sara Aibar, Carmen Bravo González-Blas, Thomas Moerman, Vân Anh Huynh-Thu, Hana Imrichova, Gert Hulselmans, Florian Rambow, Jean-Christophe Marine, Pierre Geurts, Jan Aerts,[...]. Nat Methods 2017
8

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
8

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
950
8

Hallmarks of cancer: the next generation.
Douglas Hanahan, Robert A Weinberg. Cell 2011
8

Spatiotemporal regulation of epithelial-mesenchymal transition is essential for squamous cell carcinoma metastasis.
Jeff H Tsai, Joana Liu Donaher, Danielle A Murphy, Sandra Chau, Jing Yang. Cancer Cell 2012
763
7

Single-Cell RNA Sequencing Reveals Stromal Evolution into LRRC15+ Myofibroblasts as a Determinant of Patient Response to Cancer Immunotherapy.
Claudia X Dominguez, Sören Müller, Shilpa Keerthivasan, Hartmut Koeppen, Jeffrey Hung, Sarah Gierke, Beatrice Breart, Oded Foreman, Travis W Bainbridge, Alessandra Castiglioni,[...]. Cancer Discov 2020
263
7

IL1-Induced JAK/STAT Signaling Is Antagonized by TGFβ to Shape CAF Heterogeneity in Pancreatic Ductal Adenocarcinoma.
Giulia Biffi, Tobiloba E Oni, Benjamin Spielman, Yuan Hao, Ela Elyada, Youngkyu Park, Jonathan Preall, David A Tuveson. Cancer Discov 2019
492
7

Context specificity of the EMT transcriptional response.
David P Cook, Barbara C Vanderhyden. Nat Commun 2020
77
9

A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition.
José L McFaline-Figueroa, Andrew J Hill, Xiaojie Qiu, Dana Jackson, Jay Shendure, Cole Trapnell. Nat Genet 2019
76
9

Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.
Marco Gerlinger, Andrew J Rowan, Stuart Horswell, M Math, James Larkin, David Endesfelder, Eva Gronroos, Pierre Martinez, Nicholas Matthews, Aengus Stewart,[...]. N Engl J Med 2012
7

Immune Landscape of Viral- and Carcinogen-Driven Head and Neck Cancer.
Anthony R Cillo, Cornelius H L Kürten, Tracy Tabib, Zengbiao Qi, Sayali Onkar, Ting Wang, Angen Liu, Umamaheswar Duvvuri, Seungwon Kim, Ryan J Soose,[...]. Immunity 2020
209
7

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
526
7

Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors.
Matthew D Young, Thomas J Mitchell, Felipe A Vieira Braga, Maxine G B Tran, Benjamin J Stewart, John R Ferdinand, Grace Collord, Rachel A Botting, Dorin-Mirel Popescu, Kevin W Loudon,[...]. Science 2018
315
7

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
406
7

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
535
7

RNA-Seq of single prostate CTCs implicates noncanonical Wnt signaling in antiandrogen resistance.
David T Miyamoto, Yu Zheng, Ben S Wittner, Richard J Lee, Huili Zhu, Katherine T Broderick, Rushil Desai, Douglas B Fox, Brian W Brannigan, Julie Trautwein,[...]. Science 2015
488
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.