A citation-based method for searching scientific literature

Jamie L Marshall, Benjamin R Doughty, Vidya Subramanian, Philine Guckelberger, Qingbo Wang, Linlin M Chen, Samuel G Rodriques, Kaite Zhang, Charles P Fulco, Joseph Nasser, Elizabeth J Grinkevich, Teia Noel, Sarah Mangiameli, Drew T Bergman, Anna Greka, Eric S Lander, Fei Chen, Jesse M Engreitz. Proc Natl Acad Sci U S A 2020
Times Cited: 5







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



Times Cited
  Times     Co-cited
Similarity


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
80

Comparative Analysis of Single-Cell RNA Sequencing Methods.
Christoph Ziegenhain, Beate Vieth, Swati Parekh, Björn Reinius, Amy Guillaumet-Adkins, Martha Smets, Heinrich Leonhardt, Holger Heyn, Ines Hellmann, Wolfgang Enard. Mol Cell 2017
553
40

CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification.
Tamar Hashimshony, Florian Wagner, Noa Sher, Itai Yanai. Cell Rep 2012
624
40

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
826
40

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
40

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
431
40

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
40

Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways.
Evan Der, Hemant Suryawanshi, Pavel Morozov, Manjunath Kustagi, Beatrice Goilav, Saritha Ranabothu, Peter Izmirly, Robert Clancy, H Michael Belmont, Mordecai Koenigsberg,[...]. Nat Immunol 2019
118
40

Smart-seq2 for sensitive full-length transcriptome profiling in single cells.
Simone Picelli, Åsa K Björklund, Omid R Faridani, Sven Sagasser, Gösta Winberg, Rickard Sandberg. Nat Methods 2013
40


Frequencies of dendritic cells (myeloid DC and plasmacytoid DC) and their ratio reduced in pregnant women: comparison with umbilical cord blood and normal healthy adults.
Yoko Ueda, Masao Hagihara, Ayako Okamoto, Ayako Higuchi, Akiko Tanabe, Kaori Hirabayashi, Shunichiro Izumi, Tsunehisa Makino, Shunichi Kato, Tomomitsu Hotta. Hum Immunol 2003
54
20

Development and applications of single-cell transcriptome analysis.
Fuchou Tang, Kaiqin Lao, M Azim Surani. Nat Methods 2011
200
20

A multi-laboratory comparison of blood dendritic cell populations.
Phillip Dieter Fromm, Fiona Kupresanin, Anna Elizabeth Stella Brooks, Peter Rodney Dunbar, Muzifilla Haniffa, Derek Nigel John Hart, Georgina Jane Clark. Clin Transl Immunology 2016
14
20

Activation of tonsil dendritic cells with immuno-adjuvants.
Marta E Polak, Nicola J Borthwick, Francis G Gabriel, Martine J Jager, Ian A Cree. BMC Immunol 2008
10
20

Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries.
Kent A Riemondy, Monica Ransom, Christopher Alderman, Austin E Gillen, Rui Fu, Jessica Finlay-Schultz, Gregory D Kirkpatrick, Jorge Di Paola, Peter Kabos, Carol A Sartorius,[...]. Nucleic Acids Res 2019
5
20

Droplet scRNA-seq is not zero-inflated.
Valentine Svensson. Nat Biotechnol 2020
56
20


The control of immunity and tolerance by dendritic cell.
R M Steinman. Pathol Biol (Paris) 2003
120
20

Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells.
Mridusmita Saikia, Philip Burnham, Sara H Keshavjee, Michael F Z Wang, Michael Heyang, Pablo Moral-Lopez, Meleana M Hinchman, Charles G Danko, John S L Parker, Iwijn De Vlaminck. Nat Methods 2019
32
20

Droplet-based single cell RNAseq tools: a practical guide.
Robert Salomon, Dominik Kaczorowski, Fatima Valdes-Mora, Robert E Nordon, Adrian Neild, Nona Farbehi, Nenad Bartonicek, David Gallego-Ortega. Lab Chip 2019
29
20

Intestinal CD103(+)CD11b(-) dendritic cells restrain colitis via IFN-γ-induced anti-inflammatory response in epithelial cells.
A R B M Muzaki, P Tetlak, J Sheng, S C Loh, Y A Setiagani, M Poidinger, F Zolezzi, K Karjalainen, C Ruedl. Mucosal Immunol 2016
76
20

Design and computational analysis of single-cell RNA-sequencing experiments.
Rhonda Bacher, Christina Kendziorski. Genome Biol 2016
210
20

Normalizing single-cell RNA sequencing data: challenges and opportunities.
Catalina A Vallejos, Davide Risso, Antonio Scialdone, Sandrine Dudoit, John C Marioni. Nat Methods 2017
166
20

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors.
Alexandra-Chloé Villani, Rahul Satija, Gary Reynolds, Siranush Sarkizova, Karthik Shekhar, James Fletcher, Morgane Griesbeck, Andrew Butler, Shiwei Zheng, Suzan Lazo,[...]. Science 2017
960
20

Human tissues contain CD141hi cross-presenting dendritic cells with functional homology to mouse CD103+ nonlymphoid dendritic cells.
Muzlifah Haniffa, Amanda Shin, Venetia Bigley, Naomi McGovern, Pearline Teo, Peter See, Pavandip Singh Wasan, Xiao-Nong Wang, Frano Malinarich, Benoit Malleret,[...]. Immunity 2012
499
20

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
171
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
739
20

Recent Insights into Kidney Injury and Repair from Transcriptomic Analyses.
Yuhei Kirita, Monica Chang-Panesso, Benjamin D Humphreys. Nephron 2019
4
25

Decoding myofibroblast origins in human kidney fibrosis.
Christoph Kuppe, Mahmoud M Ibrahim, Jennifer Kranz, Xiaoting Zhang, Susanne Ziegler, Javier Perales-Patón, Jitske Jansen, Katharina C Reimer, James R Smith, Ross Dobie,[...]. Nature 2021
65
20

Single-cell RNA sequencing of human kidney.
Jinling Liao, Zhenyuan Yu, Yang Chen, Mengying Bao, Chunlin Zou, Haiying Zhang, Deyun Liu, Tianyu Li, Qingyun Zhang, Jiaping Li,[...]. Sci Data 2020
50
20

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
20


Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility.
Caleb A Lareau, Fabiana M Duarte, Jennifer G Chew, Vinay K Kartha, Zach D Burkett, Andrew S Kohlway, Dmitry Pokholok, Martin J Aryee, Frank J Steemers, Ronald Lebofsky,[...]. Nat Biotechnol 2019
97
20

RNA-sequencing from single nuclei.
Rashel V Grindberg, Joyclyn L Yee-Greenbaum, Michael J McConnell, Mark Novotny, Andy L O'Shaughnessy, Georgina M Lambert, Marcos J Araúzo-Bravo, Jun Lee, Max Fishman, Gillian E Robbins,[...]. Proc Natl Acad Sci U S A 2013
149
20

The epigenetic basis of cellular heterogeneity.
Benjamin Carter, Keji Zhao. Nat Rev Genet 2021
18
20

Fluid-electrolyte homeostasis requires histone deacetylase function.
Kelly A Hyndman, Joshua S Speed, Luciano D Mendoza, John M Allan, Jackson Colson, Randee Sedaka, Chunhua Jin, Hyun Jun Jung, Samir El-Dahr, David M Pollock,[...]. JCI Insight 2020
5
20

Single-cell transcriptome conservation in cryopreserved cells and tissues.
Amy Guillaumet-Adkins, Gustavo Rodríguez-Esteban, Elisabetta Mereu, Maria Mendez-Lago, Diego A Jaitin, Alberto Villanueva, August Vidal, Alex Martinez-Marti, Enriqueta Felip, Ana Vivancos,[...]. Genome Biol 2017
84
20

Single-Cell Transcriptomics Reveal Immune Mechanisms of the Onset and Progression of IgA Nephropathy.
Ying Zheng, Ping Lu, Yiyao Deng, Lu Wen, Yong Wang, Xin Ma, Zhongxin Wang, Lingling Wu, Quan Hong, Shuwei Duan,[...]. Cell Rep 2020
9
20

A Single-Cell Transcriptome Atlas of the Mouse Glomerulus.
Nikos Karaiskos, Mahdieh Rahmatollahi, Anastasiya Boltengagen, Haiyue Liu, Martin Hoehne, Markus Rinschen, Bernhard Schermer, Thomas Benzing, Nikolaus Rajewsky, Christine Kocks,[...]. J Am Soc Nephrol 2018
72
20

The orchestrated cellular and molecular responses of the kidney to endotoxin define a precise sepsis timeline.
Danielle Janosevic, Jered Myslinski, Thomas W McCarthy, Amy Zollman, Farooq Syed, Xiaoling Xuei, Hongyu Gao, Yun-Long Liu, Kimberly S Collins, Ying-Hua Cheng,[...]. Elife 2021
7
20

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
316
20

Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies.
Atefeh Lafzi, Catia Moutinho, Simone Picelli, Holger Heyn. Nat Protoc 2018
60
20

Single-Cell Transcriptome Profiling of the Kidney Glomerulus Identifies Key Cell Types and Reactions to Injury.
Jun-Jae Chung, Leonard Goldstein, Ying-Jiun J Chen, Jiyeon Lee, Joshua D Webster, Merone Roose-Girma, Sharad C Paudyal, Zora Modrusan, Anwesha Dey, Andrey S Shaw. J Am Soc Nephrol 2020
24
20

Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors.
Matthew D Young, Thomas J Mitchell, Felipe A Vieira Braga, Maxine G B Tran, Benjamin J Stewart, John R Ferdinand, Grace Collord, Rachel A Botting, Dorin-Mirel Popescu, Kevin W Loudon,[...]. Science 2018
223
20

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
185
20

The single-cell transcriptomic landscape of early human diabetic nephropathy.
Parker C Wilson, Haojia Wu, Yuhei Kirita, Kohei Uchimura, Nicolas Ledru, Helmut G Rennke, Paul A Welling, Sushrut S Waikar, Benjamin D Humphreys. Proc Natl Acad Sci U S A 2019
97
20

A microfluidic device for preparing next generation DNA sequencing libraries and for automating other laboratory protocols that require one or more column chromatography steps.
Swee Jin Tan, Huan Phan, Benjamin Michael Gerry, Alexandre Kuhn, Lewis Zuocheng Hong, Yao Min Ong, Polly Suk Yean Poon, Marc Alexander Unger, Robert C Jones, Stephen R Quake,[...]. PLoS One 2013
23
20

Single-cell genomics and gene editing: implications for nephrology.
Parker C Wilson, Benjamin D Humphreys. Nat Rev Nephrol 2019
5
20


Cell fixation and preservation for droplet-based single-cell transcriptomics.
Jonathan Alles, Nikos Karaiskos, Samantha D Praktiknjo, Stefanie Grosswendt, Philipp Wahle, Pierre-Louis Ruffault, Salah Ayoub, Luisa Schreyer, Anastasiya Boltengagen, Carmen Birchmeier,[...]. BMC Biol 2017
100
20


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.