A citation-based method for searching scientific literature

Sean C Bendall, Kara L Davis, El-Ad David Amir, Michelle D Tadmor, Erin F Simonds, Tiffany J Chen, Daniel K Shenfeld, Garry P Nolan, Dana Pe'er. Cell 2014
Times Cited: 482







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



Times Cited
  Times     Co-cited
Similarity


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
46

A comparison of single-cell trajectory inference methods.
Wouter Saelens, Robrecht Cannoodt, Helena Todorov, Yvan Saeys. Nat Biotechnol 2019
292
24

Wishbone identifies bifurcating developmental trajectories from single-cell data.
Manu Setty, Michelle D Tadmor, Shlomit Reich-Zeliger, Omer Angel, Tomer Meir Salame, Pooja Kathail, Kristy Choi, Sean Bendall, Nir Friedman, Dana Pe'er. Nat Biotechnol 2016
280
24

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
23

Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum.
Sean C Bendall, Erin F Simonds, Peng Qiu, El-ad D Amir, Peter O Krutzik, Rachel Finck, Robert V Bruggner, Rachel Melamed, Angelica Trejo, Olga I Ornatsky,[...]. Science 2011
23

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis.
Jacob H Levine, Erin F Simonds, Sean C Bendall, Kara L Davis, El-ad D Amir, Michelle D Tadmor, Oren Litvin, Harris G Fienberg, Astraea Jager, Eli R Zunder,[...]. Cell 2015
678
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

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
744
20

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia.
El-ad David Amir, Kara L Davis, Michelle D Tadmor, Erin F Simonds, Jacob H Levine, Sean C Bendall, Daniel K Shenfeld, Smita Krishnaswamy, Garry P Nolan, Dana Pe'er. Nat Biotechnol 2013
922
20

Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE.
Peng Qiu, Erin F Simonds, Sean C Bendall, Kenneth D Gibbs, Robert V Bruggner, Michael D Linderman, Karen Sachs, Garry P Nolan, Sylvia K Plevritis. Nat Biotechnol 2011
581
20

Dimensionality reduction for visualizing single-cell data using UMAP.
Etienne Becht, Leland McInnes, John Healy, Charles-Antoine Dutertre, Immanuel W H Kwok, Lai Guan Ng, Florent Ginhoux, Evan W Newell. Nat Biotechnol 2018
821
19

Diffusion pseudotime robustly reconstructs lineage branching.
Laleh Haghverdi, Maren Büttner, F Alexander Wolf, Florian Buettner, Fabian J Theis. Nat Methods 2016
355
18

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
17

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.
Kelly Street, Davide Risso, Russell B Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom, Sandrine Dudoit. BMC Genomics 2018
337
16

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
15

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
15

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
14

FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data.
Sofie Van Gassen, Britt Callebaut, Mary J Van Helden, Bart N Lambrecht, Piet Demeester, Tom Dhaene, Yvan Saeys. Cytometry A 2015
446
14

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
869
13

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
13

PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells.
F Alexander Wolf, Fiona K Hamey, Mireya Plass, Jordi Solana, Joakim S Dahlin, Berthold Göttgens, Nikolaus Rajewsky, Lukas Simon, Fabian J Theis. Genome Biol 2019
199
13

Diffusion maps for high-dimensional single-cell analysis of differentiation data.
Laleh Haghverdi, Florian Buettner, Fabian J Theis. Bioinformatics 2015
247
12

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion.
David van Dijk, Roshan Sharma, Juozas Nainys, Kristina Yim, Pooja Kathail, Ambrose J Carr, Cassandra Burdziak, Kevin R Moon, Christine L Chaffer, Diwakar Pattabiraman,[...]. Cell 2018
352
12

A deep profiler's guide to cytometry.
Sean C Bendall, Garry P Nolan, Mario Roederer, Pratip K Chattopadhyay. Trends Immunol 2012
403
12

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
645
12

Multiplexed quantification of proteins and transcripts in single cells.
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
293
11

Mass Cytometry: Single Cells, Many Features.
Matthew H Spitzer, Garry P Nolan. Cell 2016
500
11

Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm.
Eli R Zunder, Rachel Finck, Gregory K Behbehani, El-Ad D Amir, Smita Krishnaswamy, Veronica D Gonzalez, Cynthia G Lorang, Zach Bjornson, Matthew H Spitzer, Bernd Bodenmiller,[...]. Nat Protoc 2015
245
11

Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators.
Bernd Bodenmiller, Eli R Zunder, Rachel Finck, Tiffany J Chen, Erica S Savig, Robert V Bruggner, Erin F Simonds, Sean C Bendall, Karen Sachs, Peter O Krutzik,[...]. Nat Biotechnol 2012
327
11

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
11

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
668
11

Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape.
Eugenio Marco, Robert L Karp, Guoji Guo, Paul Robson, Adam H Hart, Lorenzo Trippa, Guo-Cheng Yuan. Proc Natl Acad Sci U S A 2014
148
11

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
10

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
10

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo.
Daniel E Wagner, Caleb Weinreb, Zach M Collins, James A Briggs, Sean G Megason, Allon M Klein. Science 2018
270
10


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
400
10

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
809
9

Single-cell mRNA quantification and differential analysis with Census.
Xiaojie Qiu, Andrew Hill, Jonathan Packer, Dejun Lin, Yi-An Ma, Cole Trapnell. Nat Methods 2017
398
9

Automated identification of stratifying signatures in cellular subpopulations.
Robert V Bruggner, Bernd Bodenmiller, David L Dill, Robert J Tibshirani, Garry P Nolan. Proc Natl Acad Sci U S A 2014
237
9

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis.
Jeffrey A Farrell, Yiqun Wang, Samantha J Riesenfeld, Karthik Shekhar, Aviv Regev, Alexander F Schier. Science 2018
238
9

Single-cell mass cytometry adapted to measurements of the cell cycle.
Gregory K Behbehani, Sean C Bendall, Matthew R Clutter, Wendy J Fantl, Garry P Nolan. Cytometry A 2012
134
9

Computational flow cytometry: helping to make sense of high-dimensional immunology data.
Yvan Saeys, Sofie Van Gassen, Bart N Lambrecht. Nat Rev Immunol 2016
206
9

The single-cell transcriptional landscape of mammalian organogenesis.
Junyue Cao, Malte Spielmann, Xiaojie Qiu, Xingfan Huang, Daniel M Ibrahim, Andrew J Hill, Fan Zhang, Stefan Mundlos, Lena Christiansen, Frank J Steemers,[...]. Nature 2019
444
9

A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution.
Jonathan S Packer, Qin Zhu, Chau Huynh, Priya Sivaramakrishnan, Elicia Preston, Hannah Dueck, Derek Stefanik, Kai Tan, Cole Trapnell, Junhyong Kim,[...]. Science 2019
97
9

Fundamental limits on dynamic inference from single-cell snapshots.
Caleb Weinreb, Samuel Wolock, Betsabeh K Tusi, Merav Socolovsky, Allon M Klein. Proc Natl Acad Sci U S A 2018
88
10

Computational methods for trajectory inference from single-cell transcriptomics.
Robrecht Cannoodt, Wouter Saelens, Yvan Saeys. Eur J Immunol 2016
69
13

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
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

Visualizing structure and transitions in high-dimensional biological data.
Kevin R Moon, David van Dijk, Zheng Wang, Scott Gigante, Daniel B Burkhardt, William S Chen, Kristina Yim, Antonia van den Elzen, Matthew J Hirn, Ronald R Coifman,[...]. Nat Biotechnol 2019
96
9


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.