A citation-based method for searching scientific literature

Jacob H Levine, Erin F Simonds, Sean C Bendall, Kara L Davis, El-ad D Amir, Michelle D Tadmor, Oren Litvin, Harris G Fienberg, Astraea Jager, Eli R Zunder, Rachel Finck, Amanda L Gedman, Ina Radtke, James R Downing, Dana Pe'er, Garry P Nolan. Cell 2015
Times Cited: 657







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



Times Cited
  Times     Co-cited
Similarity


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
775
17

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
17

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
17

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia.
El-ad David Amir, Kara L Davis, Michelle D Tadmor, Erin F Simonds, Jacob H Levine, Sean C Bendall, Daniel K Shenfeld, Smita Krishnaswamy, Garry P Nolan, Dana Pe'er. Nat Biotechnol 2013
916
16

FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data.
Sofie Van Gassen, Britt Callebaut, Mary J Van Helden, Bart N Lambrecht, Piet Demeester, Tom Dhaene, Yvan Saeys. Cytometry A 2015
431
16

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
13

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
670
13

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
13

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
650
10

Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum.
Sean C Bendall, Erin F Simonds, Peng Qiu, El-ad D Amir, Peter O Krutzik, Rachel Finck, Robert V Bruggner, Rachel Melamed, Angelica Trejo, Olga I Ornatsky,[...]. Science 2011
10

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
443
10

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
10

Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline.
Hao Chen, Mai Chan Lau, Michael Thomas Wong, Evan W Newell, Michael Poidinger, Jinmiao Chen. PLoS Comput Biol 2016
144
9

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
9


Mass Cytometry: Single Cells, Many Features.
Matthew H Spitzer, Garry P Nolan. Cell 2016
492
8


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
338
8

Automated mapping of phenotype space with single-cell data.
Nikolay Samusik, Zinaida Good, Matthew H Spitzer, Kara L Davis, Garry P Nolan. Nat Methods 2016
137
8

Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators.
Bernd Bodenmiller, Eli R Zunder, Rachel Finck, Tiffany J Chen, Erica S Savig, Robert V Bruggner, Erin F Simonds, Sean C Bendall, Karen Sachs, Peter O Krutzik,[...]. Nat Biotechnol 2012
327
7

Challenges in unsupervised clustering of single-cell RNA-seq data.
Vladimir Yu Kiselev, Tallulah S Andrews, Martin Hemberg. Nat Rev Genet 2019
202
7

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
7

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
369
7

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
7

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
447
7

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
7

Deep generative modeling for single-cell transcriptomics.
Romain Lopez, Jeffrey Regier, Michael B Cole, Michael I Jordan, Nir Yosef. Nat Methods 2018
209
7


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
364
7

Single-cell RNA sequencing technologies and bioinformatics pipelines.
Byungjin Hwang, Ji Hyun Lee, Duhee Bang. Exp Mol Med 2018
364
7

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
6

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
6

Robust enumeration of cell subsets from tissue expression profiles.
Aaron M Newman, Chih Long Liu, Michael R Green, Andrew J Gentles, Weiguo Feng, Yue Xu, Chuong D Hoang, Maximilian Diehn, Ash A Alizadeh. Nat Methods 2015
6

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
M Ashburner, C A Ball, J A Blake, D Botstein, H Butler, J M Cherry, A P Davis, K Dolinski, S S Dwight, J T Eppig,[...]. Nat Genet 2000
6

Single-cell RNA-seq denoising using a deep count autoencoder.
Gökcen Eraslan, Lukas M Simon, Maria Mircea, Nikola S Mueller, Fabian J Theis. Nat Commun 2019
162
6

Automated identification of stratifying signatures in cellular subpopulations.
Robert V Bruggner, Bernd Bodenmiller, David L Dill, Robert J Tibshirani, Garry P Nolan. Proc Natl Acad Sci U S A 2014
235
6

Critical assessment of automated flow cytometry data analysis techniques.
Nima Aghaeepour, Greg Finak, Holger Hoos, Tim R Mosmann, Ryan Brinkman, Raphael Gottardo, Richard H Scheuermann. Nat Methods 2013
272
6

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma.
Anoop P Patel, Itay Tirosh, John J Trombetta, Alex K Shalek, Shawn M Gillespie, Hiroaki Wakimoto, Daniel P Cahill, Brian V Nahed, William T Curry, Robert L Martuza,[...]. Science 2014
6


The end of gating? An introduction to automated analysis of high dimensional cytometry data.
Florian Mair, Felix J Hartmann, Dunja Mrdjen, Vinko Tosevski, Carsten Krieg, Burkhard Becher. Eur J Immunol 2016
120
6

Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development.
Sean C Bendall, Kara L Davis, El-Ad David Amir, Michelle D Tadmor, Erin F Simonds, Tiffany J Chen, Daniel K Shenfeld, Garry P Nolan, Dana Pe'er. Cell 2014
481
6

Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE.
Peng Qiu, Erin F Simonds, Sean C Bendall, Kenneth D Gibbs, Robert V Bruggner, Michael D Linderman, Karen Sachs, Garry P Nolan, Sylvia K Plevritis. Nat Biotechnol 2011
577
6

Mass cytometry: technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry.
Dmitry R Bandura, Vladimir I Baranov, Olga I Ornatsky, Alexei Antonov, Robert Kinach, Xudong Lou, Serguei Pavlov, Sergey Vorobiev, John E Dick, Scott D Tanner. Anal Chem 2009
643
6

From Louvain to Leiden: guaranteeing well-connected communities.
V A Traag, L Waltman, N J van Eck. Sci Rep 2019
231
6

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry.
Charlotte Giesen, Hao A O Wang, Denis Schapiro, Nevena Zivanovic, Andrea Jacobs, Bodo Hattendorf, Peter J Schüffler, Daniel Grolimund, Joachim M Buhmann, Simone Brandt,[...]. Nat Methods 2014
658
5

Bayesian approach to single-cell differential expression analysis.
Peter V Kharchenko, Lev Silberstein, David T Scadden. Nat Methods 2014
532
5

Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq.
Amit Zeisel, Ana B Muñoz-Manchado, Simone Codeluppi, Peter Lönnerberg, Gioele La Manno, Anna Juréus, Sueli Marques, Hermany Munguba, Liqun He, Christer Betsholtz,[...]. Science 2015
5

pcaReduce: hierarchical clustering of single cell transcriptional profiles.
Justina Žurauskienė, Christopher Yau. BMC Bioinformatics 2016
100
5

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
586
5

Adjusting batch effects in microarray expression data using empirical Bayes methods.
W Evan Johnson, Cheng Li, Ariel Rabinovic. Biostatistics 2007
5


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.