Evan Z Macosko, Anindita Basu, Rahul Satija, James Nemesh, Karthik Shekhar, Melissa Goldman, Itay Tirosh, Allison R Bialas, Nolan Kamitaki, Emily M Martersteck, John J Trombetta, David A Weitz, Joshua R Sanes, Alex K Shalek, Aviv Regev, Steven A McCarroll. Cell 2015
Times Cited: 2582
Times Cited: 2582
Times Cited
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Similarity
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
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Comprehensive Integration of Single-Cell Data.
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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
Allon M Klein, Linas Mazutis, Ilke Akartuna, Naren Tallapragada, Adrian Veres, Victor Li, Leonid Peshkin, David A Weitz, Marc W Kirschner. Cell 2015
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Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
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mRNA-Seq whole-transcriptome analysis of a single cell.
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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
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Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
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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
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
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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
Laleh Haghverdi, Aaron T L Lun, Michael D Morgan, John C Marioni. Nat Biotechnol 2018
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Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding.
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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
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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
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Reversed graph embedding resolves complex single-cell trajectories.
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Comprehensive single-cell transcriptional profiling of a multicellular organism.
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Simultaneous epitope and transcriptome measurement in single cells.
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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
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Full-length RNA-seq from single cells using Smart-seq2.
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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
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Current best practices in single-cell RNA-seq analysis: a tutorial.
Malte D Luecken, Fabian J Theis. Mol Syst Biol 2019
Malte D Luecken, Fabian J Theis. Mol Syst Biol 2019
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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
Etienne Becht, Leland McInnes, John Healy, Charles-Antoine Dutertre, Immanuel W H Kwok, Lai Guan Ng, Florent Ginhoux, Evan W Newell. Nat Biotechnol 2018
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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
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Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.
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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
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Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells.
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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
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
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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
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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
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Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression.
Christoph Hafemeister, Rahul Satija. Genome Biol 2019
Christoph Hafemeister, Rahul Satija. Genome Biol 2019
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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
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edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
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Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.
Aaron T L Lun, Karsten Bach, John C Marioni. Genome Biol 2016
Aaron T L Lun, Karsten Bach, John C Marioni. Genome Biol 2016
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Exponential scaling of single-cell RNA-seq in the past decade.
Valentine Svensson, Roser Vento-Tormo, Sarah A Teichmann. Nat Protoc 2018
Valentine Svensson, Roser Vento-Tormo, Sarah A Teichmann. Nat Protoc 2018
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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
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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
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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
Simone Picelli, Åsa K Björklund, Omid R Faridani, Sven Sagasser, Gösta Winberg, Rickard Sandberg. Nat Methods 2013
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Comparative Analysis of Droplet-Based Ultra-High-Throughput Single-Cell RNA-Seq Systems.
Xiannian Zhang, Tianqi Li, Feng Liu, Yaqi Chen, Jiacheng Yao, Zeyao Li, Yanyi Huang, Jianbin Wang. Mol Cell 2019
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Single-cell RNA sequencing technologies and bioinformatics pipelines.
Byungjin Hwang, Ji Hyun Lee, Duhee Bang. Exp Mol Med 2018
Byungjin Hwang, Ji Hyun Lee, Duhee Bang. Exp Mol Med 2018
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SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
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Quantitative single-cell RNA-seq with unique molecular identifiers.
Saiful Islam, Amit Zeisel, Simon Joost, Gioele La Manno, Pawel Zajac, Maria Kasper, Peter Lönnerberg, Sten Linnarsson. Nat Methods 2014
Saiful Islam, Amit Zeisel, Simon Joost, Gioele La Manno, Pawel Zajac, Maria Kasper, Peter Lönnerberg, Sten Linnarsson. Nat Methods 2014
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Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex.
Alex A Pollen, Tomasz J Nowakowski, Joe Shuga, Xiaohui Wang, Anne A Leyrat, Jan H Lui, Nianzhen Li, Lukasz Szpankowski, Brian Fowler, Peilin Chen,[...]. Nat Biotechnol 2014
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Validation of noise models for single-cell transcriptomics.
Dominic Grün, Lennart Kester, Alexander van Oudenaarden. Nat Methods 2014
Dominic Grün, Lennart Kester, Alexander van Oudenaarden. Nat Methods 2014
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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
Marlon Stoeckius, Shiwei Zheng, Brian Houck-Loomis, Stephanie Hao, Bertrand Z Yeung, William M Mauck, Peter Smibert, Rahul Satija. Genome Biol 2018
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A benchmark of batch-effect correction methods for single-cell RNA sequencing data.
Hoa Thi Nhu Tran, Kok Siong Ang, Marion Chevrier, Xiaomeng Zhang, Nicole Yee Shin Lee, Michelle Goh, Jinmiao Chen. Genome Biol 2020
Hoa Thi Nhu Tran, Kok Siong Ang, Marion Chevrier, Xiaomeng Zhang, Nicole Yee Shin Lee, Michelle Goh, Jinmiao Chen. Genome Biol 2020
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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
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Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data.
Samuel L Wolock, Romain Lopez, Allon M Klein. Cell Syst 2019
Samuel L Wolock, Romain Lopez, Allon M Klein. Cell Syst 2019
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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
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CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification.
Tamar Hashimshony, Florian Wagner, Noa Sher, Itai Yanai. Cell Rep 2012
Tamar Hashimshony, Florian Wagner, Noa Sher, Itai Yanai. Cell Rep 2012
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Single-Cell RNA-Seq Technologies and Related Computational Data Analysis.
Geng Chen, Baitang Ning, Tieliu Shi. Front Genet 2019
Geng Chen, Baitang Ning, Tieliu Shi. Front Genet 2019
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A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications.
Ashraful Haque, Jessica Engel, Sarah A Teichmann, Tapio Lönnberg. Genome Med 2017
Ashraful Haque, Jessica Engel, Sarah A Teichmann, Tapio Lönnberg. Genome Med 2017
7
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.