A citation-based method for searching scientific literature

Vanessa M Peterson, Kelvin Xi Zhang, Namit Kumar, Jerelyn Wong, Lixia Li, Douglas C Wilson, Renee Moore, Terrill K McClanahan, Svetlana Sadekova, Joel A Klappenbach. Nat Biotechnol 2017
Times Cited: 278







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



Times Cited
  Times     Co-cited
Similarity


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
628
87

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
34

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
28

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
25

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
535
24

Joint profiling of chromatin accessibility and gene expression in thousands of single cells.
Junyue Cao, Darren A Cusanovich, Vijay Ramani, Delasa Aghamirzaie, Hannah A Pliner, Andrew J Hill, Riza M Daza, Jose L McFaline-Figueroa, Jonathan S Packer, Lena Christiansen,[...]. Science 2018
222
23

Integrative single-cell analysis.
Tim Stuart, Rahul Satija. Nat Rev Genet 2019
285
23

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
22

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

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
376
21

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes.
Iain C Macaulay, Wilfried Haerty, Parveen Kumar, Yang I Li, Tim Xiaoming Hu, Mabel J Teng, Mubeen Goolam, Nathalie Saurat, Paul Coupland, Lesley M Shirley,[...]. Nat Methods 2015
327
20

Single-cell chromatin accessibility reveals principles of regulatory variation.
Jason D Buenrostro, Beijing Wu, Ulrike M Litzenburger, Dave Ruff, Michael L Gonzales, Michael P Snyder, Howard Y Chang, William J Greenleaf. Nature 2015
745
18

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
18

The Human Cell Atlas.
Aviv Regev, Sarah A Teichmann, Eric S Lander, Ido Amit, Christophe Benoist, Ewan Birney, Bernd Bodenmiller, Peter Campbell, Piero Carninci, Menna Clatworthy,[...]. Elife 2017
632
17

RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells.
Kok Hao Chen, Alistair N Boettiger, Jeffrey R Moffitt, Siyuan Wang, Xiaowei Zhuang. Science 2015
655
17

Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells.
Eleni P Mimitou, Anthony Cheng, Antonino Montalbano, Stephanie Hao, Marlon Stoeckius, Mateusz Legut, Timothy Roush, Alberto Herrera, Efthymia Papalexi, Zhengqing Ouyang,[...]. Nat Methods 2019
99
17


Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types.
Diego Adhemar Jaitin, Ephraim Kenigsberg, Hadas Keren-Shaul, Naama Elefant, Franziska Paul, Irina Zaretsky, Alexander Mildner, Nadav Cohen, Steffen Jung, Amos Tanay,[...]. Science 2014
852
16

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells.
Stephen J Clark, Ricard Argelaguet, Chantriolnt-Andreas Kapourani, Thomas M Stubbs, Heather J Lee, Celia Alda-Catalinas, Felix Krueger, Guido Sanguinetti, Gavin Kelsey, John C Marioni,[...]. Nat Commun 2018
196
16

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
16

Multiplexed ion beam imaging of human breast tumors.
Michael Angelo, Sean C Bendall, Rachel Finck, Matthew B Hale, Chuck Hitzman, Alexander D Borowsky, Richard M Levenson, John B Lowe, Scot D Liu, Shuchun Zhao,[...]. Nat Med 2014
424
15

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
588
15

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH.
Chee-Huat Linus Eng, Michael Lawson, Qian Zhu, Ruben Dries, Noushin Koulena, Yodai Takei, Jina Yun, Christopher Cronin, Christoph Karp, Guo-Cheng Yuan,[...]. Nature 2019
303
15

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
613
14

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state.
Assaf Rotem, Oren Ram, Noam Shoresh, Ralph A Sperling, Alon Goren, David A Weitz, Bradley E Bernstein. Nat Biotechnol 2015
405
14

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry.
Charlotte Giesen, Hao A O Wang, Denis Schapiro, Nevena Zivanovic, Andrea Jacobs, Bodo Hattendorf, Peter J Schüffler, Daniel Grolimund, Joachim M Buhmann, Simone Brandt,[...]. Nat Methods 2014
643
14

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity.
Christof Angermueller, Stephen J Clark, Heather J Lee, Iain C Macaulay, Mabel J Teng, Tim Xiaoming Hu, Felix Krueger, Sebastien Smallwood, Chris P Ponting, Thierry Voet,[...]. Nat Methods 2016
303
14

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
14

Current best practices in single-cell RNA-seq analysis: a tutorial.
Malte D Luecken, Fabian J Theis. Mol Syst Biol 2019
269
14

Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas.
Yu Hou, Huahu Guo, Chen Cao, Xianlong Li, Boqiang Hu, Ping Zhu, Xinglong Wu, Lu Wen, Fuchou Tang, Yanyi Huang,[...]. Cell Res 2016
247
14

Mass cytometry: technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry.
Dmitry R Bandura, Vladimir I Baranov, Olga I Ornatsky, Alexei Antonov, Robert Kinach, Xudong Lou, Serguei Pavlov, Sergey Vorobiev, John E Dick, Scott D Tanner. Anal Chem 2009
636
13

Smart-seq2 for sensitive full-length transcriptome profiling in single cells.
Simone Picelli, Åsa K Björklund, Omid R Faridani, Sven Sagasser, Gösta Winberg, Rickard Sandberg. Nat Methods 2013
961
13

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells.
Daniel Ramsköld, Shujun Luo, Yu-Chieh Wang, Robin Li, Qiaolin Deng, Omid R Faridani, Gregory A Daniels, Irina Khrebtukova, Jeanne F Loring, Louise C Laurent,[...]. Nat Biotechnol 2012
788
13

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding.
Alexander B Rosenberg, Charles M Roco, Richard A Muscat, Anna Kuchina, Paul Sample, Zizhen Yao, Lucas T Graybuck, David J Peeler, Sumit Mukherjee, Wei Chen,[...]. Science 2018
350
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
339
13

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
13

Three-dimensional intact-tissue sequencing of single-cell transcriptional states.
Xiao Wang, William E Allen, Matthew A Wright, Emily L Sylwestrak, Nikolay Samusik, Sam Vesuna, Kathryn Evans, Cindy Liu, Charu Ramakrishnan, Jia Liu,[...]. Science 2018
280
13

Massively parallel single-nucleus RNA-seq with DroNc-seq.
Naomi Habib, Inbal Avraham-Davidi, Anindita Basu, Tyler Burks, Karthik Shekhar, Matan Hofree, Sourav R Choudhury, François Aguet, Ellen Gelfand, Kristin Ardlie,[...]. Nat Methods 2017
321
12

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput.
Todd M Gierahn, Marc H Wadsworth, Travis K Hughes, Bryan D Bryson, Andrew Butler, Rahul Satija, Sarah Fortune, J Christopher Love, Alex K Shalek. Nat Methods 2017
313
12

Integrated genome and transcriptome sequencing of the same cell.
Siddharth S Dey, Lennart Kester, Bastiaan Spanjaard, Magda Bienko, Alexander van Oudenaarden. Nat Biotechnol 2015
242
12

CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq.
Tamar Hashimshony, Naftalie Senderovich, Gal Avital, Agnes Klochendler, Yaron de Leeuw, Leon Anavy, Dave Gennert, Shuqiang Li, Kenneth J Livak, Orit Rozenblatt-Rosen,[...]. Genome Biol 2016
402
12

Comparative Analysis of Single-Cell RNA Sequencing Methods.
Christoph Ziegenhain, Beate Vieth, Swati Parekh, Björn Reinius, Amy Guillaumet-Adkins, Martha Smets, Heinrich Leonhardt, Holger Heyn, Ines Hellmann, Wolfgang Enard. Mol Cell 2017
502
12

Exponential scaling of single-cell RNA-seq in the past decade.
Valentine Svensson, Roser Vento-Tormo, Sarah A Teichmann. Nat Protoc 2018
228
12

Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging.
Yury Goltsev, Nikolay Samusik, Julia Kennedy-Darling, Salil Bhate, Matthew Hale, Gustavo Vazquez, Sarah Black, Garry P Nolan. Cell 2018
248
12

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
577
12

Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding.
Payam Shahi, Samuel C Kim, John R Haliburton, Zev J Gartner, Adam R Abate. Sci Rep 2017
109
11

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
466
11

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
558
11

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.
Laleh Haghverdi, Aaron T L Lun, Michael D Morgan, John C Marioni. Nat Biotechnol 2018
428
11

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
11


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.