A citation-based method for searching scientific literature

Itay Tirosh, Benjamin Izar, Sanjay M Prakadan, Marc H Wadsworth, Daniel Treacy, John J Trombetta, Asaf Rotem, Christopher Rodman, Christine Lian, George Murphy, Mohammad Fallahi-Sichani, Ken Dutton-Regester, Jia-Ren Lin, Ofir Cohen, Parin Shah, Diana Lu, Alex S Genshaft, Travis K Hughes, Carly G K Ziegler, Samuel W Kazer, Aleth Gaillard, Kellie E Kolb, Alexandra-Chloé Villani, Cory M Johannessen, Aleksandr Y Andreev, Eliezer M Van Allen, Monica Bertagnolli, Peter K Sorger, Ryan J Sullivan, Keith T Flaherty, Dennie T Frederick, Judit Jané-Valbuena, Charles H Yoon, Orit Rozenblatt-Rosen, Alex K Shalek, Aviv Regev, Levi A Garraway. Science 2016
Times Cited: 1936







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



Times Cited
  Times     Co-cited
Similarity


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
26

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
21

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
960
18

Integrated analysis of multimodal single-cell data.
Yuhan Hao, Stephanie Hao, Erica Andersen-Nissen, William M Mauck, Shiwei Zheng, Andrew Butler, Maddie J Lee, Aaron J Wilk, Charlotte Darby, Michael Zager,[...]. Cell 2021
15

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

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
13

Fast, sensitive and accurate integration of single-cell data with Harmony.
Ilya Korsunsky, Nghia Millard, Jean Fan, Kamil Slowikowski, Fan Zhang, Kevin Wei, Yuriy Baglaenko, Michael Brenner, Po-Ru Loh, Soumya Raychaudhuri. Nat Methods 2019
955
13

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
12

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
506
11

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
11

Massively parallel digital transcriptional profiling of single cells.
Grace X Y Zheng, Jessica M Terry, Phillip Belgrader, Paul Ryvkin, Zachary W Bent, Ryan Wilson, Solongo B Ziraldo, Tobias D Wheeler, Geoff P McDermott, Junjie Zhu,[...]. Nat Commun 2017
11

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
881
11

Toward Minimal Residual Disease-Directed Therapy in Melanoma.
Florian Rambow, Aljosja Rogiers, Oskar Marin-Bejar, Sara Aibar, Julia Femel, Michael Dewaele, Panagiotis Karras, Daniel Brown, Young Hwan Chang, Maria Debiec-Rychter,[...]. Cell 2018
276
10

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
448
10

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
775
10

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
942
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
711
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
9

Hallmarks of cancer: the next generation.
Douglas Hanahan, Robert A Weinberg. Cell 2011
9

Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing.
Ashley Maynard, Caroline E McCoach, Julia K Rotow, Lincoln Harris, Franziska Haderk, D Lucas Kerr, Elizabeth A Yu, Erin L Schenk, Weilun Tan, Alexander Zee,[...]. Cell 2020
151
9

RNA velocity of single cells.
Gioele La Manno, Ruslan Soldatov, Amit Zeisel, Emelie Braun, Hannah Hochgerner, Viktor Petukhov, Katja Lidschreiber, Maria E Kastriti, Peter Lönnerberg, Alessandro Furlan,[...]. Nature 2018
9

Inference and analysis of cell-cell communication using CellChat.
Suoqin Jin, Christian F Guerrero-Juarez, Lihua Zhang, Ivan Chang, Raul Ramos, Chen-Hsiang Kuan, Peggy Myung, Maksim V Plikus, Qing Nie. Nat Commun 2021
401
9

Reversed graph embedding resolves complex single-cell trajectories.
Xiaojie Qiu, Qi Mao, Ying Tang, Li Wang, Raghav Chawla, Hannah A Pliner, Cole Trapnell. Nat Methods 2017
9

Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma.
Hanjie Li, Anne M van der Leun, Ido Yofe, Yaniv Lubling, Dikla Gelbard-Solodkin, Alexander C J van Akkooi, Marlous van den Braber, Elisa A Rozeman, John B A G Haanen, Christian U Blank,[...]. Cell 2019
410
8

Clonal replacement of tumor-specific T cells following PD-1 blockade.
Kathryn E Yost, Ansuman T Satpathy, Daniel K Wells, Yanyan Qi, Chunlin Wang, Robin Kageyama, Katherine L McNamara, Jeffrey M Granja, Kavita Y Sarin, Ryanne A Brown,[...]. Nat Med 2019
538
8

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
8

Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.
Allon M Klein, Linas Mazutis, Ilke Akartuna, Naren Tallapragada, Adrian Veres, Victor Li, Leonid Peshkin, David A Weitz, Marc W Kirschner. Cell 2015
8

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
8

Generalizing RNA velocity to transient cell states through dynamical modeling.
Volker Bergen, Marius Lange, Stefan Peidli, F Alexander Wolf, Fabian J Theis. Nat Biotechnol 2020
479
8

SC3: consensus clustering of single-cell RNA-seq data.
Vladimir Yu Kiselev, Kristina Kirschner, Michael T Schaub, Tallulah Andrews, Andrew Yiu, Tamir Chandra, Kedar N Natarajan, Wolf Reik, Mauricio Barahona, Anthony R Green,[...]. Nat Methods 2017
616
8

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
465
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
522
7

TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion.
Omar Khan, Josephine R Giles, Sierra McDonald, Sasikanth Manne, Shin Foong Ngiow, Kunal P Patel, Michael T Werner, Alexander C Huang, Katherine A Alexander, Jennifer E Wu,[...]. Nature 2019
522
7

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
583
7

Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade.
Brian C Miller, Debattama R Sen, Rose Al Abosy, Kevin Bi, Yamini V Virkud, Martin W LaFleur, Kathleen B Yates, Ana Lako, Kristen Felt, Girish S Naik,[...]. Nat Immunol 2019
619
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
386
7

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Damian Szklarczyk, Annika L Gable, David Lyon, Alexander Junge, Stefan Wyder, Jaime Huerta-Cepas, Milan Simonovic, Nadezhda T Doncheva, John H Morris, Peer Bork,[...]. Nucleic Acids Res 2019
7

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
446
7

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
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

Multi-stage Differentiation Defines Melanoma Subtypes with Differential Vulnerability to Drug-Induced Iron-Dependent Oxidative Stress.
Jennifer Tsoi, Lidia Robert, Kim Paraiso, Carlos Galvan, Katherine M Sheu, Johnson Lay, Deborah J L Wong, Mohammad Atefi, Roksana Shirazi, Xiaoyan Wang,[...]. Cancer Cell 2018
320
6

TOX is a critical regulator of tumour-specific T cell differentiation.
Andrew C Scott, Friederike Dündar, Paul Zumbo, Smita S Chandran, Christopher A Klebanoff, Mojdeh Shakiba, Prerak Trivedi, Laura Menocal, Heather Appleby, Steven Camara,[...]. Nature 2019
409
6

Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy.
Se Jin Im, Masao Hashimoto, Michael Y Gerner, Junghwa Lee, Haydn T Kissick, Matheus C Burger, Qiang Shan, J Scott Hale, Judong Lee, Tahseen H Nasti,[...]. Nature 2016
900
6

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
6

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
683
6

An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma.
Cyril Neftel, Julie Laffy, Mariella G Filbin, Toshiro Hara, Marni E Shore, Gilbert J Rahme, Alyssa R Richman, Dana Silverbush, McKenzie L Shaw, Christine M Hebert,[...]. Cell 2019
682
6

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
6

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
6


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.