A citation-based method for searching scientific literature

Xiaoping Han, Ziming Zhou, Lijiang Fei, Huiyu Sun, Renying Wang, Yao Chen, Haide Chen, Jingjing Wang, Huanna Tang, Wenhao Ge, Yincong Zhou, Fang Ye, Mengmeng Jiang, Junqing Wu, Yanyu Xiao, Xiaoning Jia, Tingyue Zhang, Xiaojie Ma, Qi Zhang, Xueli Bai, Shujing Lai, Chengxuan Yu, Lijun Zhu, Rui Lin, Yuchi Gao, Min Wang, Yiqing Wu, Jianming Zhang, Renya Zhan, Saiyong Zhu, Hailan Hu, Changchun Wang, Ming Chen, He Huang, Tingbo Liang, Jianghua Chen, Weilin Wang, Dan Zhang, Guoji Guo. Nature 2020
Times Cited: 256







List of co-cited articles
556 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
26


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
513
18

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

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
114
15

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
14

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
14

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
827
12

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
458
11

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
696
11

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

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
673
10

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor.
Markus Hoffmann, Hannah Kleine-Weber, Simon Schroeder, Nadine Krüger, Tanja Herrler, Sandra Erichsen, Tobias S Schiergens, Georg Herrler, Nai-Huei Wu, Andreas Nitsche,[...]. Cell 2020
9

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
9

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
9

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
660
9

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
8

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
758
8

scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation.
E Madissoon, A Wilbrey-Clark, R J Miragaia, K Saeb-Parsy, K T Mahbubani, N Georgakopoulos, P Harding, K Polanski, N Huang, K Nowicki-Osuch,[...]. Genome Biol 2019
129
8

A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure.
Maayan Baron, Adrian Veres, Samuel L Wolock, Aubrey L Faust, Renaud Gaujoux, Amedeo Vetere, Jennifer Hyoje Ryu, Bridget K Wagner, Shai S Shen-Orr, Allon M Klein,[...]. Cell Syst 2016
485
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
600
8

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
8

A molecular cell atlas of the human lung from single-cell RNA sequencing.
Kyle J Travaglini, Ahmad N Nabhan, Lolita Penland, Rahul Sinha, Astrid Gillich, Rene V Sit, Stephen Chang, Stephanie D Conley, Yasuo Mori, Jun Seita,[...]. Nature 2020
278
8

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
211
8

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
919
7

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes.
Waradon Sungnak, Ni Huang, Christophe Bécavin, Marijn Berg, Rachel Queen, Monika Litvinukova, Carlos Talavera-López, Henrike Maatz, Daniel Reichart, Fotios Sampaziotis,[...]. Nat Med 2020
7

Proteomics. Tissue-based map of the human proteome.
Mathias Uhlén, Linn Fagerberg, Björn M Hallström, Cecilia Lindskog, Per Oksvold, Adil Mardinoglu, Åsa Sivertsson, Caroline Kampf, Evelina Sjöstedt, Anna Asplund,[...]. Science 2015
7


GSVA: gene set variation analysis for microarray and RNA-seq data.
Sonja Hänzelmann, Robert Castelo, Justin Guinney. BMC Bioinformatics 2013
7

Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes.
Åsa Segerstolpe, Athanasia Palasantza, Pernilla Eliasson, Eva-Marie Andersson, Anne-Christine Andréasson, Xiaoyan Sun, Simone Picelli, Alan Sabirsh, Maryam Clausen, Magnus K Bjursell,[...]. Cell Metab 2016
623
7

A cellular census of human lungs identifies novel cell states in health and in asthma.
Felipe A Vieira Braga, Gozde Kar, Marijn Berg, Orestes A Carpaij, Krzysztof Polanski, Lukas M Simon, Sharon Brouwer, Tomás Gomes, Laura Hesse, Jian Jiang,[...]. Nat Med 2019
291
7

Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations.
Sonya A MacParland, Jeff C Liu, Xue-Zhong Ma, Brendan T Innes, Agata M Bartczak, Blair K Gage, Justin Manuel, Nicholas Khuu, Juan Echeverri, Ivan Linares,[...]. Nat Commun 2018
439
7

Deep generative modeling for single-cell transcriptomics.
Romain Lopez, Jeffrey Regier, Michael B Cole, Michael I Jordan, Nir Yosef. Nat Methods 2018
325
7

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
290
7

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods.
Jiarui Ding, Xian Adiconis, Sean K Simmons, Monika S Kowalczyk, Cynthia C Hession, Nemanja D Marjanovic, Travis K Hughes, Marc H Wadsworth, Tyler Burks, Lan T Nguyen,[...]. Nat Biotechnol 2020
187
7


Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis.
Paul A Reyfman, James M Walter, Nikita Joshi, Kishore R Anekalla, Alexandra C McQuattie-Pimentel, Stephen Chiu, Ramiro Fernandez, Mahzad Akbarpour, Ching-I Chen, Ziyou Ren,[...]. Am J Respir Crit Care Med 2019
424
7

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
7

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
7


Single-Cell Transcriptome Atlas of Murine Endothelial Cells.
Joanna Kalucka, Laura P M H de Rooij, Jermaine Goveia, Katerina Rohlenova, Sébastien J Dumas, Elda Meta, Nadine V Conchinha, Federico Taverna, Laure-Anne Teuwen, Koen Veys,[...]. Cell 2020
271
7

Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs.
Shuai He, Lin-He Wang, Yang Liu, Yi-Qi Li, Hai-Tian Chen, Jing-Hong Xu, Wan Peng, Guo-Wang Lin, Pan-Pan Wei, Bo Li,[...]. Genome Biol 2020
33
21

Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns.
Martin Enge, H Efsun Arda, Marco Mignardi, John Beausang, Rita Bottino, Seung K Kim, Stephen R Quake. Cell 2017
207
6

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
530
6

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
386
6

SARS-CoV-2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells.
Soeren Lukassen, Robert Lorenz Chua, Timo Trefzer, Nicolas C Kahn, Marc A Schneider, Thomas Muley, Hauke Winter, Michael Meister, Carmen Veith, Agnes W Boots,[...]. EMBO J 2020
557
6

Phenotype molding of stromal cells in the lung tumor microenvironment.
Diether Lambrechts, Els Wauters, Bram Boeckx, Sara Aibar, David Nittner, Oliver Burton, Ayse Bassez, Herbert Decaluwé, Andreas Pircher, Kathleen Van den Eynde,[...]. Nat Med 2018
553
6

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
897
6

A comparison of single-cell trajectory inference methods.
Wouter Saelens, Robrecht Cannoodt, Helena Todorov, Yvan Saeys. Nat Biotechnol 2019
400
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.