A citation-based method for searching scientific literature

Arjun Raj, Patrick van den Bogaard, Scott A Rifkin, Alexander van Oudenaarden, Sanjay Tyagi. Nat Methods 2008
Times Cited: 1098







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



Times Cited
  Times     Co-cited
Similarity


Visualization of single RNA transcripts in situ.
A M Femino, F S Fay, K Fogarty, R H Singer. Science 1998
771
33

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
679
27

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
329
25

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
22

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
16

Single-cell in situ RNA profiling by sequential hybridization.
Eric Lubeck, Ahmet F Coskun, Timur Zhiyentayev, Mubhij Ahmad, Long Cai. Nat Methods 2014
322
15

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
15

In situ sequencing for RNA analysis in preserved tissue and cells.
Rongqin Ke, Marco Mignardi, Alexandra Pacureanu, Jessica Svedlund, Johan Botling, Carolina Wählby, Mats Nilsson. Nat Methods 2013
289
14

Spatial organization of the somatosensory cortex revealed by osmFISH.
Simone Codeluppi, Lars E Borm, Amit Zeisel, Gioele La Manno, Josina A van Lunteren, Camilla I Svensson, Sten Linnarsson. Nat Methods 2018
106
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
303
13

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression.
Chenglong Xia, Jean Fan, George Emanuel, Junjie Hao, Xiaowei Zhuang. Proc Natl Acad Sci U S A 2019
118
12

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization.
Jeffrey R Moffitt, Junjie Hao, Guiping Wang, Kok Hao Chen, Hazen P Babcock, Xiaowei Zhuang. Proc Natl Acad Sci U S A 2016
160
12

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
11

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues.
Je Hyuk Lee, Evan R Daugharthy, Jonathan Scheiman, Reza Kalhor, Thomas C Ferrante, Richard Terry, Brian M Turczyk, Joyce L Yang, Ho Suk Lee, John Aach,[...]. Nat Protoc 2015
211
11


High-definition spatial transcriptomics for in situ tissue profiling.
Sanja Vickovic, Gökcen Eraslan, Fredrik Salmén, Johanna Klughammer, Linnea Stenbeck, Denis Schapiro, Tarmo Äijö, Richard Bonneau, Ludvig Bergenstråhle, José Fernandéz Navarro,[...]. Nat Methods 2019
177
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

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
10

Single-cell gene expression profiling.
Jeffrey M Levsky, Shailesh M Shenoy, Rossanna C Pezo, Robert H Singer. Science 2002
342
10

Highly multiplexed subcellular RNA sequencing in situ.
Je Hyuk Lee, Evan R Daugharthy, Jonathan Scheiman, Reza Kalhor, Joyce L Yang, Thomas C Ferrante, Richard Terry, Sauveur S F Jeanty, Chao Li, Ryoji Amamoto,[...]. Science 2014
459
10

RNAscope: a novel in situ RNA analysis platform for formalin-fixed, paraffin-embedded tissues.
Fay Wang, John Flanagan, Nan Su, Li-Chong Wang, Son Bui, Allissa Nielson, Xingyong Wu, Hong-Thuy Vo, Xiao-Jun Ma, Yuling Luo. J Mol Diagn 2012
10

Localization of ASH1 mRNA particles in living yeast.
E Bertrand, P Chartrand, M Schaefer, S M Shenoy, R H Singer, R M Long. Mol Cell 1998
10

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
528
10

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
370
9

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
777
9

Fluorescence in situ hybridization: past, present and future.
Jeffrey M Levsky, Robert H Singer. J Cell Sci 2003
281
8

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
676
8

Synthetic recording and in situ readout of lineage information in single cells.
Kirsten L Frieda, James M Linton, Sahand Hormoz, Joonhyuk Choi, Ke-Huan K Chow, Zakary S Singer, Mark W Budde, Michael B Elowitz, Long Cai. Nature 2017
186
8

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region.
Jeffrey R Moffitt, Dhananjay Bambah-Mukku, Stephen W Eichhorn, Eric Vaughn, Karthik Shekhar, Julio D Perez, Nimrod D Rubinstein, Junjie Hao, Aviv Regev, Catherine Dulac,[...]. Science 2018
265
8

Efficient in situ barcode sequencing using padlock probe-based BaristaSeq.
Xiaoyin Chen, Yu-Chi Sun, George M Church, Je Hyuk Lee, Anthony M Zador. Nucleic Acids Res 2018
33
24

Stochastic mRNA synthesis in mammalian cells.
Arjun Raj, Charles S Peskin, Daniel Tranchina, Diana Y Vargas, Sanjay Tyagi. PLoS Biol 2006
8

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
996
8

In the right place at the right time: visualizing and understanding mRNA localization.
Adina R Buxbaum, Gal Haimovich, Robert H Singer. Nat Rev Mol Cell Biol 2015
295
8

Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing.
Sheel Shah, Eric Lubeck, Maayan Schwarzkopf, Ting-Fang He, Alon Greenbaum, Chang Ho Sohn, Antti Lignell, Harry M T Choi, Viviana Gradinaru, Niles A Pierce,[...]. Development 2016
103
7

Probabilistic cell typing enables fine mapping of closely related cell types in situ.
Xiaoyan Qian, Kenneth D Harris, Thomas Hauling, Dimitris Nicoloutsopoulos, Ana B Muñoz-Manchado, Nathan Skene, Jens Hjerling-Leffler, Mats Nilsson. Nat Methods 2020
37
18

High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing.
Jeffrey R Moffitt, Junjie Hao, Dhananjay Bambah-Mukku, Tian Lu, Catherine Dulac, Xiaowei Zhuang. Proc Natl Acad Sci U S A 2016
116
7

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
7

Nanoscale imaging of RNA with expansion microscopy.
Fei Chen, Asmamaw T Wassie, Allison J Cote, Anubhav Sinha, Shahar Alon, Shoh Asano, Evan R Daugharthy, Jae-Byum Chang, Adam Marblestone, George M Church,[...]. Nat Methods 2016
149
7


A Growing Toolbox to Image Gene Expression in Single Cells: Sensitive Approaches for Demanding Challenges.
Xavier Pichon, Mounia Lagha, Florian Mueller, Edouard Bertrand. Mol Cell 2018
63
11


Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust.
Harry M T Choi, Maayan Schwarzkopf, Mark E Fornace, Aneesh Acharya, Georgios Artavanis, Johannes Stegmaier, Alexandre Cunha, Niles A Pierce. Development 2018
177
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
673
7

Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq.
Amit Zeisel, Ana B Muñoz-Manchado, Simone Codeluppi, Peter Lönnerberg, Gioele La Manno, Anna Juréus, Sueli Marques, Hermany Munguba, Liqun He, Christer Betsholtz,[...]. Science 2015
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

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
6

Single-cell multimodal omics: the power of many.
Chenxu Zhu, Sebastian Preissl, Bing Ren. Nat Methods 2020
68
8

Programmable RNA Tracking in Live Cells with CRISPR/Cas9.
David A Nelles, Mark Y Fang, Mitchell R O'Connell, Jia L Xu, Sebastian J Markmiller, Jennifer A Doudna, Gene W Yeo. Cell 2016
282
6

Single-molecule analysis of gene expression using two-color RNA labeling in live yeast.
Sami Hocine, Pascal Raymond, Daniel Zenklusen, Jeffrey A Chao, Robert H Singer. Nat Methods 2013
178
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.