A citation-based method for searching scientific literature

Marlon Stoeckius, Christoph Hafemeister, William Stephenson, Brian Houck-Loomis, Pratip K Chattopadhyay, Harold Swerdlow, Rahul Satija, Peter Smibert. Nat Methods 2017
Times Cited: 580







List of co-cited articles
838 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
28

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
258
28

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
27

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
27

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
23

Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics.
Marlon Stoeckius, Shiwei Zheng, Brian Houck-Loomis, Stephanie Hao, Bertrand Z Yeung, William M Mauck, Peter Smibert, Rahul Satija. Genome Biol 2018
145
19

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
334
18

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
203
18

A comparison of single-cell trajectory inference methods.
Wouter Saelens, Robrecht Cannoodt, Helena Todorov, Yvan Saeys. Nat Biotechnol 2019
244
17

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

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
478
15

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
316
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
528
15

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
285
15

Comprehensive single-cell transcriptional profiling of a multicellular organism.
Junyue Cao, Jonathan S Packer, Vijay Ramani, Darren A Cusanovich, Chau Huynh, Riza Daza, Xiaojie Qiu, Choli Lee, Scott N Furlan, Frank J Steemers,[...]. Science 2017
387
14

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
326
14

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
13

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
13

Current best practices in single-cell RNA-seq analysis: a tutorial.
Malte D Luecken, Fabian J Theis. Mol Syst Biol 2019
235
13

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
298
12

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
182
12


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
12

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
343
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

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
216
11

Integrative single-cell analysis.
Tim Stuart, Rahul Satija. Nat Rev Genet 2019
252
11

Lineage tracing on transcriptional landscapes links state to fate during differentiation.
Caleb Weinreb, Alejo Rodriguez-Fraticelli, Fernando D Camargo, Allon M Klein. Science 2020
91
12

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
88
12

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
772
11

Eleven grand challenges in single-cell data science.
David Lähnemann, Johannes Köster, Ewa Szczurek, Davis J McCarthy, Stephanie C Hicks, Mark D Robinson, Catalina A Vallejos, Kieran R Campbell, Niko Beerenwinkel, Ahmed Mahfouz,[...]. Genome Biol 2020
94
11

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
398
10

Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity.
Peter van Galen, Volker Hovestadt, Marc H Wadsworth Ii, Travis K Hughes, Gabriel K Griffin, Sofia Battaglia, Julia A Verga, Jason Stephansky, Timothy J Pastika, Jennifer Lombardi Story,[...]. Cell 2019
173
10

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
10

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
524
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
162
10

Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species.
Rapolas Zilionis, Camilla Engblom, Christina Pfirschke, Virginia Savova, David Zemmour, Hatice D Saatcioglu, Indira Krishnan, Giorgia Maroni, Claire V Meyerovitz, Clara M Kerwin,[...]. Immunity 2019
225
10

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
379
10

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
588
10

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
700
10

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation.
Hyun Min Kang, Meena Subramaniam, Sasha Targ, Michelle Nguyen, Lenka Maliskova, Elizabeth McCarthy, Eunice Wan, Simon Wong, Lauren Byrnes, Cristina M Lanata,[...]. Nat Biotechnol 2018
185
10

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
833
9

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
602
9

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
9

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia.
Jeffrey M Granja, Sandy Klemm, Lisa M McGinnis, Arwa S Kathiria, Anja Mezger, M Ryan Corces, Benjamin Parks, Eric Gars, Michaela Liedtke, Grace X Y Zheng,[...]. Nat Biotechnol 2019
59
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
269
9

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
293
9

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
493
9

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
428
9

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
651
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.