A citation-based method for searching scientific literature

Aaron T L Lun, Karsten Bach, John C Marioni. Genome Biol 2016
Times Cited: 359







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



Times Cited
  Times     Co-cited
Similarity


Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R.
Davis J McCarthy, Kieran R Campbell, Aaron T L Lun, Quin F Wills. Bioinformatics 2017
382
35

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
33

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
32

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
428
31

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
29

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
28

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
27

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
26

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
575
23

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
123
23

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
22

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
623
21


SC3: consensus clustering of single-cell RNA-seq data.
Vladimir Yu Kiselev, Kristina Kirschner, Michael T Schaub, Tallulah Andrews, Andrew Yiu, Tamir Chandra, Kedar N Natarajan, Wolf Reik, Mauricio Barahona, Anthony R Green,[...]. Nat Methods 2017
441
18

Normalizing single-cell RNA sequencing data: challenges and opportunities.
Catalina A Vallejos, Davide Risso, Antonio Scialdone, Sandrine Dudoit, John C Marioni. Nat Methods 2017
151
18


Bayesian approach to single-cell differential expression analysis.
Peter V Kharchenko, Lev Silberstein, David T Scadden. Nat Methods 2014
529
17

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
17

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
17


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
502
16

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
580
15

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
961
15

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
310
15

EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data.
Aaron T L Lun, Samantha Riesenfeld, Tallulah Andrews, The Phuong Dao, Tomas Gomes, John C Marioni. Genome Biol 2019
117
15

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
107
15

Computational and analytical challenges in single-cell transcriptomics.
Oliver Stegle, Sarah A Teichmann, John C Marioni. Nat Rev Genet 2015
518
14

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data.
Catalina A Vallejos, John C Marioni, Sylvia Richardson. PLoS Comput Biol 2015
128
14

Differential expression analysis for sequence count data.
Simon Anders, Wolfgang Huber. Genome Biol 2010
14

Current best practices in single-cell RNA-seq analysis: a tutorial.
Malte D Luecken, Fabian J Theis. Mol Syst Biol 2019
269
14

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
14

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
212
13

Challenges in unsupervised clustering of single-cell RNA-seq data.
Vladimir Yu Kiselev, Tallulah S Andrews, Martin Hemberg. Nat Rev Genet 2019
190
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
339
13

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
12

limma powers differential expression analyses for RNA-sequencing and microarray studies.
Matthew E Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, Gordon K Smyth. Nucleic Acids Res 2015
12

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
12

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
12

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
396
12


M3Drop: dropout-based feature selection for scRNASeq.
Tallulah S Andrews, Martin Hemberg. Bioinformatics 2019
66
16

SAVER: gene expression recovery for single-cell RNA sequencing.
Mo Huang, Jingshu Wang, Eduardo Torre, Hannah Dueck, Sydney Shaffer, Roberto Bonasio, John I Murray, Arjun Raj, Mingyao Li, Nancy R Zhang. Nat Methods 2018
162
11

Missing data and technical variability in single-cell RNA-sequencing experiments.
Stephanie C Hicks, F William Townes, Mingxiang Teng, Rafael A Irizarry. Biostatistics 2018
133
11

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion.
David van Dijk, Roshan Sharma, Juozas Nainys, Kristina Yim, Pooja Kathail, Ambrose J Carr, Cassandra Burdziak, Kevin R Moon, Christine L Chaffer, Diwakar Pattabiraman,[...]. Cell 2018
328
11


Orchestrating single-cell analysis with Bioconductor.
Robert A Amezquita, Aaron T L Lun, Etienne Becht, Vince J Carey, Lindsay N Carpp, Ludwig Geistlinger, Federico Marini, Kevin Rue-Albrecht, Davide Risso, Charlotte Soneson,[...]. Nat Methods 2020
57
19

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
632
11

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
341
11

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
738
11

Near-optimal probabilistic RNA-seq quantification.
Nicolas L Bray, Harold Pimentel, Páll Melsted, Lior Pachter. Nat Biotechnol 2016
11


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.