A citation-based method for searching scientific literature

Junyue Cao, Malte Spielmann, Xiaojie Qiu, Xingfan Huang, Daniel M Ibrahim, Andrew J Hill, Fan Zhang, Stefan Mundlos, Lena Christiansen, Frank J Steemers, Cole Trapnell, Jay Shendure. Nature 2019
Times Cited: 872







List of co-cited articles
590 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
48

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
32

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
29

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
24

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
17

Generalizing RNA velocity to transient cell states through dynamical modeling.
Volker Bergen, Marius Lange, Stefan Peidli, F Alexander Wolf, Fabian J Theis. Nat Biotechnol 2020
479
17

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
17

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
16

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
15

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
15

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
14

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
14

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

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
12

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
12


SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
10

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
612
10

Mapping the Mouse Cell Atlas by Microwell-Seq.
Xiaoping Han, Renying Wang, Yincong Zhou, Lijiang Fei, Huiyu Sun, Shujing Lai, Assieh Saadatpour, Ziming Zhou, Haide Chen, Fang Ye,[...]. Cell 2018
590
10

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
586
9

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.
Greg Finak, Andrew McDavid, Masanao Yajima, Jingyuan Deng, Vivian Gersuk, Alex K Shalek, Chloe K Slichter, Hannah W Miller, M Juliana McElrath, Martin Prlic,[...]. Genome Biol 2015
941
9

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
9

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors.
Christopher S McGinnis, Lyndsay M Murrow, Zev J Gartner. Cell Syst 2019
471
8

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage.
Dvir Aran, Agnieszka P Looney, Leqian Liu, Esther Wu, Valerie Fong, Austin Hsu, Suzanna Chak, Ram P Naikawadi, Paul J Wolters, Adam R Abate,[...]. Nat Immunol 2019
881
8

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
686
8

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
8

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
8

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin.
Sai Ma, Bing Zhang, Lindsay M LaFave, Andrew S Earl, Zachary Chiang, Yan Hu, Jiarui Ding, Alison Brack, Vinay K Kartha, Tristan Tay,[...]. Cell 2020
188
8

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
711
8

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
917
8

A single-cell molecular map of mouse gastrulation and early organogenesis.
Blanca Pijuan-Sala, Jonathan A Griffiths, Carolina Guibentif, Tom W Hiscock, Wajid Jawaid, Fernando J Calero-Nieto, Carla Mulas, Ximena Ibarra-Soria, Richard C V Tyser, Debbie Lee Lian Ho,[...]. Nature 2019
310
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


A scalable SCENIC workflow for single-cell gene regulatory network analysis.
Bram Van de Sande, Christopher Flerin, Kristofer Davie, Maxime De Waegeneer, Gert Hulselmans, Sara Aibar, Ruth Seurinck, Wouter Saelens, Robrecht Cannoodt, Quentin Rouchon,[...]. Nat Protoc 2020
142
7

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
7

From Louvain to Leiden: guaranteeing well-connected communities.
V A Traag, L Waltman, N J van Eck. Sci Rep 2019
582
7

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
7

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
997
7

Cells of the adult human heart.
Monika Litviňuková, Carlos Talavera-López, Henrike Maatz, Daniel Reichart, Catherine L Worth, Eric L Lindberg, Masatoshi Kanda, Krzysztof Polanski, Matthias Heinig, Michael Lee,[...]. Nature 2020
358
6

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
6

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
6

A human cell atlas of fetal gene expression.
Junyue Cao, Diana R O'Day, Hannah A Pliner, Paul D Kingsley, Mei Deng, Riza M Daza, Michael A Zager, Kimberly A Aldinger, Ronnie Blecher-Gonen, Fan Zhang,[...]. Science 2020
168
6

Construction of a human cell landscape at single-cell level.
Xiaoping Han, Ziming Zhou, Lijiang Fei, Huiyu Sun, Renying Wang, Yao Chen, Haide Chen, Jingjing Wang, Huanna Tang, Wenhao Ge,[...]. Nature 2020
327
6

PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.
Oscar Franzén, Li-Ming Gan, Johan L M Björkegren. Database (Oxford) 2019
275
6

Current best practices in single-cell RNA-seq analysis: a tutorial.
Malte D Luecken, Fabian J Theis. Mol Syst Biol 2019
532
6

Single-cell reconstruction of the early maternal-fetal interface in humans.
Roser Vento-Tormo, Mirjana Efremova, Rachel A Botting, Margherita Y Turco, Miquel Vento-Tormo, Kerstin B Meyer, Jong-Eun Park, Emily Stephenson, Krzysztof Polański, Angela Goncalves,[...]. Nature 2018
829
6

Integrative single-cell analysis.
Tim Stuart, Rahul Satija. Nat Rev Genet 2019
494
6

A comparison of single-cell trajectory inference methods.
Wouter Saelens, Robrecht Cannoodt, Helena Todorov, Yvan Saeys. Nat Biotechnol 2019
482
6

Molecular recording of mammalian embryogenesis.
Michelle M Chan, Zachary D Smith, Stefanie Grosswendt, Helene Kretzmer, Thomas M Norman, Britt Adamson, Marco Jost, Jeffrey J Quinn, Dian Yang, Matthew G Jones,[...]. Nature 2019
143
6

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
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.