A citation-based method for searching scientific literature

Vladimir Yu Kiselev, Andrew Yiu, Martin Hemberg. Nat Methods 2018
Times Cited: 191







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



Times Cited
  Times     Co-cited
Similarity



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
8

Batch effects and the effective design of single-cell gene expression studies.
Po-Yuan Tung, John D Blischak, Chiaowen Joyce Hsiao, David A Knowles, Jonathan E Burnett, Jonathan K Pritchard, Yoav Gilad. Sci Rep 2017
133
8

scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets.
Yingxin Lin, Shila Ghazanfar, Kevin Y X Wang, Johann A Gagnon-Bartsch, Kitty K Lo, Xianbin Su, Ze-Guang Han, John T Ormerod, Terence P Speed, Pengyi Yang,[...]. Proc Natl Acad Sci U S A 2019
44
18

The Human Cell Atlas: from vision to reality.
Orit Rozenblatt-Rosen, Michael J T Stubbington, Aviv Regev, Sarah A Teichmann. Nature 2017
222
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

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
625
8

Shared and distinct transcriptomic cell types across neocortical areas.
Bosiljka Tasic, Zizhen Yao, Lucas T Graybuck, Kimberly A Smith, Thuc Nghi Nguyen, Darren Bertagnolli, Jeff Goldy, Emma Garren, Michael N Economo, Sarada Viswanathan,[...]. Nature 2018
440
8

Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model.
F William Townes, Stephanie C Hicks, Martin J Aryee, Rafael A Irizarry. Genome Biol 2019
71
11


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
465
8

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility.
Darren A Cusanovich, Andrew J Hill, Delasa Aghamirzaie, Riza M Daza, Hannah A Pliner, Joel B Berletch, Galina N Filippova, Xingfan Huang, Lena Christiansen, William S DeWitt,[...]. Cell 2018
222
8

Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.
Darren A Cusanovich, Riza Daza, Andrew Adey, Hannah A Pliner, Lena Christiansen, Kevin L Gunderson, Frank J Steemers, Cole Trapnell, Jay Shendure. Science 2015
486
7

Design and computational analysis of single-cell RNA-sequencing experiments.
Rhonda Bacher, Christina Kendziorski. Genome Biol 2016
210
7

A test metric for assessing single-cell RNA-seq batch correction.
Maren Büttner, Zhichao Miao, F Alexander Wolf, Sarah A Teichmann, Fabian J Theis. Nat Methods 2019
93
7

Droplet scRNA-seq is not zero-inflated.
Valentine Svensson. Nat Biotechnol 2020
56
12


Accounting for technical noise in single-cell RNA-seq experiments.
Philip Brennecke, Simon Anders, Jong Kyoung Kim, Aleksandra A Kołodziejczyk, Xiuwei Zhang, Valentina Proserpio, Bianka Baying, Vladimir Benes, Sarah A Teichmann, John C Marioni,[...]. Nat Methods 2013
509
7

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
342
7

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
137
7

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
216
7

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics.
Karthik Shekhar, Sylvain W Lapan, Irene E Whitney, Nicholas M Tran, Evan Z Macosko, Monika Kowalczyk, Xian Adiconis, Joshua Z Levin, James Nemesh, Melissa Goldman,[...]. Cell 2016
491
7

Single-Cell Multiomics: Multiple Measurements from Single Cells.
Iain C Macaulay, Chris P Ponting, Thierry Voet. Trends Genet 2017
227
7

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation.
Jason D Buenrostro, M Ryan Corces, Caleb A Lareau, Beijing Wu, Alicia N Schep, Martin J Aryee, Ravindra Majeti, Howard Y Chang, William J Greenleaf. Cell 2018
206
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
234
7

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
203
7

Single-cell RNA sequencing to explore immune cell heterogeneity.
Efthymia Papalexi, Rahul Satija. Nat Rev Immunol 2018
397
7

scCATCH: Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data.
Xin Shao, Jie Liao, Xiaoyan Lu, Rui Xue, Ni Ai, Xiaohui Fan. iScience 2020
31
22

A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa.
Huanan Zhang, Catherine A A Lee, Zhuliu Li, John R Garbe, Cindy R Eide, Raphael Petegrosso, Rui Kuang, Jakub Tolar. PLoS Comput Biol 2018
15
40

Multilineage communication regulates human liver bud development from pluripotency.
J Gray Camp, Keisuke Sekine, Tobias Gerber, Henry Loeffler-Wirth, Hans Binder, Malgorzata Gac, Sabina Kanton, Jorge Kageyama, Georg Damm, Daniel Seehofer,[...]. Nature 2017
225
6

Validation of noise models for single-cell transcriptomics.
Dominic Grün, Lennart Kester, Alexander van Oudenaarden. Nat Methods 2014
334
6

Comparison of Computational Methods for Imputing Single-Cell RNA-Sequencing Data.
Lihua Zhang, Shihua Zhang. IEEE/ACM Trans Comput Biol Bioinform 2020
44
13

Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells.
Qiaolin Deng, Daniel Ramsköld, Björn Reinius, Rickard Sandberg. Science 2014
605
6

False signals induced by single-cell imputation.
Tallulah S Andrews, Martin Hemberg. F1000Res 2018
47
12

SCnorm: robust normalization of single-cell RNA-seq data.
Rhonda Bacher, Li-Fang Chu, Ning Leng, Audrey P Gasch, James A Thomson, Ron M Stewart, Michael Newton, Christina Kendziorski. Nat Methods 2017
128
6


Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq.
Saiful Islam, Una Kjällquist, Annalena Moliner, Pawel Zajac, Jian-Bing Fan, Peter Lönnerberg, Sten Linnarsson. Genome Res 2011
494
6

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database.
Luke Zappia, Belinda Phipson, Alicia Oshlack. PLoS Comput Biol 2018
91
6

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
6

Classification of low quality cells from single-cell RNA-seq data.
Tomislav Ilicic, Jong Kyoung Kim, Aleksandra A Kolodziejczyk, Frederik Otzen Bagger, Davis James McCarthy, John C Marioni, Sarah A Teichmann. Genome Biol 2016
231
6

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
6

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations.
Susanne C van den Brink, Fanny Sage, Ábel Vértesy, Bastiaan Spanjaard, Josi Peterson-Maduro, Chloé S Baron, Catherine Robin, Alexander van Oudenaarden. Nat Methods 2017
316
6

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
714
6

Visualizing structure and transitions in high-dimensional biological data.
Kevin R Moon, David van Dijk, Zheng Wang, Scott Gigante, Daniel B Burkhardt, William S Chen, Kristina Yim, Antonia van den Elzen, Matthew J Hirn, Ronald R Coifman,[...]. Nat Biotechnol 2019
112
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
570
6

cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes.
Erica A K DePasquale, Daniel Schnell, Phillip Dexheimer, Kyle Ferchen, Stuart Hay, Kashish Chetal, Íñigo Valiente-Alandí, Burns C Blaxall, H Leighton Grimes, Nathan Salomonis. Nucleic Acids Res 2019
25
24

DrImpute: imputing dropout events in single cell RNA sequencing data.
Wuming Gong, Il-Youp Kwak, Pruthvi Pota, Naoko Koyano-Nakagawa, Daniel J Garry. BMC Bioinformatics 2018
96
6

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics.
Bosiljka Tasic, Vilas Menon, Thuc Nghi Nguyen, Tae Kyung Kim, Tim Jarsky, Zizhen Yao, Boaz Levi, Lucas T Gray, Staci A Sorensen, Tim Dolbeare,[...]. Nat Neurosci 2016
740
6

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region.
Jeffrey R Moffitt, Dhananjay Bambah-Mukku, Stephen W Eichhorn, Eric Vaughn, Karthik Shekhar, Julio D Perez, Nimrod D Rubinstein, Junjie Hao, Aviv Regev, Catherine Dulac,[...]. Science 2018
289
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.