A citation-based method for searching scientific literature

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, Robert S Balderas, Sylvia K Plevritis, Karen Sachs, Dana Pe'er, Scott D Tanner, Garry P Nolan. Science 2011
Times Cited: 1499







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



Times Cited
  Times     Co-cited
Similarity


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
738
23

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
694
21

Mass Cytometry: Single Cells, Many Features.
Matthew H Spitzer, Garry P Nolan. Cell 2016
622
20

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
18

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
917
18

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
841
17

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
634
16

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
308
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
548
15

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
15

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
446
14

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
13

A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging.
Leeat Keren, Marc Bosse, Diana Marquez, Roshan Angoshtari, Samir Jain, Sushama Varma, Soo-Ryum Yang, Allison Kurian, David Van Valen, Robert West,[...]. Cell 2018
381
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
402
11

Normalization of mass cytometry data with bead standards.
Rachel Finck, Erin F Simonds, Astraea Jager, Smita Krishnaswamy, Karen Sachs, Wendy Fantl, Dana Pe'er, Garry P Nolan, Sean C Bendall. Cytometry A 2013
424
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
355
11


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
899
10

A deep profiler's guide to cytometry.
Sean C Bendall, Garry P Nolan, Mario Roederer, Pratip K Chattopadhyay. Trends Immunol 2012
431
10

A platinum-based covalent viability reagent for single-cell mass cytometry.
Harris G Fienberg, Erin F Simonds, Wendy J Fantl, Garry P Nolan, Bernd Bodenmiller. Cytometry A 2012
147
10

Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry.
Stéphane Chevrier, Helena L Crowell, Vito R T Zanotelli, Stefanie Engler, Mark D Robinson, Bernd Bodenmiller. Cell Syst 2018
146
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
273
9

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
9


Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development.
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
537
8

flowCore: a Bioconductor package for high throughput flow cytometry.
Florian Hahne, Nolwenn LeMeur, Ryan R Brinkman, Byron Ellis, Perry Haaland, Deepayan Sarkar, Josef Spidlen, Errol Strain, Robert Gentleman. BMC Bioinformatics 2009
287
8

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
8

Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue.
Michael J Gerdes, Christopher J Sevinsky, Anup Sood, Sudeshna Adak, Musodiq O Bello, Alexander Bordwell, Ali Can, Alex Corwin, Sean Dinn, Robert J Filkins,[...]. Proc Natl Acad Sci U S A 2013
369
8

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
8

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
642
7

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
7

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
7

Single-cell mass cytometry for analysis of immune system functional states.
Zach B Bjornson, Garry P Nolan, Wendy J Fantl. Curr Opin Immunol 2013
132
7

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
7

The single-cell pathology landscape of breast cancer.
Hartland W Jackson, Jana R Fischer, Vito R T Zanotelli, H Raza Ali, Robert Mechera, Savas D Soysal, Holger Moch, Simone Muenst, Zsuzsanna Varga, Walter P Weber,[...]. Nature 2020
287
7

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
389
7

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
7

MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure.
Leeat Keren, Marc Bosse, Steve Thompson, Tyler Risom, Kausalia Vijayaragavan, Erin McCaffrey, Diana Marquez, Roshan Angoshtari, Noah F Greenwald, Harris Fienberg,[...]. Sci Adv 2019
106
7

Single-cell analysis tools for drug discovery and development.
James R Heath, Antoni Ribas, Paul S Mischel. Nat Rev Drug Discov 2016
260
7

Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes.
Jia-Ren Lin, Benjamin Izar, Shu Wang, Clarence Yapp, Shaolin Mei, Parin M Shah, Sandro Santagata, Peter K Sorger. Elife 2018
224
7

CytoNorm: A Normalization Algorithm for Cytometry Data.
Sofie Van Gassen, Brice Gaudilliere, Martin S Angst, Yvan Saeys, Nima Aghaeepour. Cytometry A 2020
45
13

Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy.
Felix J Hartmann, Joel Babdor, Pier Federico Gherardini, El-Ad D Amir, Kyle Jones, Bita Sahaf, Diana M Marquez, Peter Krutzik, Erika O'Donnell, Natalia Sigal,[...]. Cell Rep 2019
50
12

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
895
6

A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer.
Johanna Wagner, Maria Anna Rapsomaniki, Stéphane Chevrier, Tobias Anzeneder, Claus Langwieder, August Dykgers, Martin Rees, Annette Ramaswamy, Simone Muenst, Savas Deniz Soysal,[...]. Cell 2019
326
6

Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method.
Jia-Ren Lin, Mohammad Fallahi-Sichani, Peter K Sorger. Nat Commun 2015
259
6

Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues.
Sinem K Saka, Yu Wang, Jocelyn Y Kishi, Allen Zhu, Yitian Zeng, Wenxin Xie, Koray Kirli, Clarence Yapp, Marcelo Cicconet, Brian J Beliveau,[...]. Nat Biotechnol 2019
153
6

Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front.
Christian M Schürch, Salil S Bhate, Graham L Barlow, Darci J Phillips, Luca Noti, Inti Zlobec, Pauline Chu, Sarah Black, Janos Demeter, David R McIlwain,[...]. Cell 2020
156
6

Single-cell immune landscape of human atherosclerotic plaques.
Dawn M Fernandez, Adeeb H Rahman, Nicolas F Fernandez, Aleksey Chudnovskiy, El-Ad David Amir, Letizia Amadori, Nayaab S Khan, Christine K Wong, Roza Shamailova, Christopher A Hill,[...]. Nat Med 2019
284
5

Visual analysis of mass cytometry data by hierarchical stochastic neighbour embedding reveals rare cell types.
Vincent van Unen, Thomas Höllt, Nicola Pezzotti, Na Li, Marcel J T Reinders, Elmar Eisemann, Frits Koning, Anna Vilanova, Boudewijn P F Lelieveldt. Nat Commun 2017
110
5

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
5


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.