A citation-based method for searching scientific literature

Jingshu Wang, Mo Huang, Eduardo Torre, Hannah Dueck, Sydney Shaffer, John Murray, Arjun Raj, Mingyao Li, Nancy R Zhang. Proc Natl Acad Sci U S A 2018
Times Cited: 32







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



Times Cited
  Times     Co-cited
Similarity


Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH.
Eduardo Torre, Hannah Dueck, Sydney Shaffer, Janko Gospocic, Rohit Gupte, Roberto Bonasio, Junhyong Kim, John Murray, Arjun Raj. Cell Syst 2018
49
9



Renal compartment-specific genetic variation analyses identify new pathways in chronic kidney disease.
Chengxiang Qiu, Shizheng Huang, Jihwan Park, YoSon Park, Yi-An Ko, Matthew J Seasock, Joshua S Bryer, Xiang-Xi Xu, Wen-Chao Song, Matthew Palmer,[...]. Nat Med 2018
83
9

RNA-Seq: a revolutionary tool for transcriptomics.
Zhong Wang, Mark Gerstein, Michael Snyder. Nat Rev Genet 2009
9

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
205
9

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
9

Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease.
Jihwan Park, Rojesh Shrestha, Chengxiang Qiu, Ayano Kondo, Shizheng Huang, Max Werth, Mingyao Li, Jonathan Barasch, Katalin Suszták. Science 2018
363
9

Bulk tissue cell type deconvolution with multi-subject single-cell expression reference.
Xuran Wang, Jihwan Park, Katalin Susztak, Nancy R Zhang, Mingyao Li. Nat Commun 2019
142
9

From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing.
Georgi K Marinov, Brian A Williams, Ken McCue, Gary P Schroth, Jason Gertz, Richard M Myers, Barbara J Wold. Genome Res 2014
286
9

Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data.
Aaron T L Lun, Fernando J Calero-Nieto, Liora Haim-Vilmovsky, Berthold Göttgens, John C Marioni. Genome Res 2017
27
11


Synthetic spike-in standards for RNA-seq experiments.
Lichun Jiang, Felix Schlesinger, Carrie A Davis, Yu Zhang, Renhua Li, Marc Salit, Thomas R Gingeras, Brian Oliver. Genome Res 2011
353
9

Moderated statistical tests for assessing differences in tag abundance.
Mark D Robinson, Gordon K Smyth. Bioinformatics 2007
487
9

Accounting for technical noise in differential expression analysis of single-cell RNA sequencing data.
Cheng Jia, Yu Hu, Derek Kelly, Junhyong Kim, Mingyao Li, Nancy R Zhang. Nucleic Acids Res 2017
23
13

Analytical distributions for stochastic gene expression.
Vahid Shahrezaei, Peter S Swain. Proc Natl Acad Sci U S A 2008
364
9

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
174
9

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nat Protoc 2009
9


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
676
9

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.
Florian Buettner, Kedar N Natarajan, F Paolo Casale, Valentina Proserpio, Antonio Scialdone, Fabian J Theis, Sarah A Teichmann, John C Marioni, Oliver Stegle. Nat Biotechnol 2015
561
9

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning.
Bo Wang, Junjie Zhu, Emma Pierson, Daniele Ramazzotti, Serafim Batzoglou. Nat Methods 2017
199
9

Design and computational analysis of single-cell RNA-sequencing experiments.
Rhonda Bacher, Christina Kendziorski. Genome Biol 2016
204
9

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.
Alex K Shalek, Rahul Satija, Joe Shuga, John J Trombetta, Dave Gennert, Diana Lu, Peilin Chen, Rona S Gertner, Jellert T Gaublomme, Nir Yosef,[...]. Nature 2014
516
9


Tackling the widespread and critical impact of batch effects in high-throughput data.
Jeffrey T Leek, Robert B Scharpf, Héctor Corrada Bravo, David Simcha, Benjamin Langmead, W Evan Johnson, Donald Geman, Keith Baggerly, Rafael A Irizarry. Nat Rev Genet 2010
957
9

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
88
9

Adjusting batch effects in microarray expression data using empirical Bayes methods.
W Evan Johnson, Cheng Li, Ariel Rabinovic. Biostatistics 2007
9

Normalization of RNA-seq data using factor analysis of control genes or samples.
Davide Risso, John Ngai, Terence P Speed, Sandrine Dudoit. Nat Biotechnol 2014
686
9

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
474
9

Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing.
Chunhong Zheng, Liangtao Zheng, Jae-Kwang Yoo, Huahu Guo, Yuanyuan Zhang, Xinyi Guo, Boxi Kang, Ruozhen Hu, Julie Y Huang, Qiming Zhang,[...]. Cell 2017
657
9

voom: Precision weights unlock linear model analysis tools for RNA-seq read counts.
Charity W Law, Yunshun Chen, Wei Shi, Gordon K Smyth. Genome Biol 2014
9

Current best practices in single-cell RNA-seq analysis: a tutorial.
Malte D Luecken, Fabian J Theis. Mol Syst Biol 2019
308
9

Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments.
Quin F Wills, Kenneth J Livak, Alex J Tipping, Tariq Enver, Andrew J Goldson, Darren W Sexton, Chris Holmes. Nat Biotechnol 2013
148
6

Ancient DNA and the rewriting of human history: be sparing with Occam's razor.
Marc Haber, Massimo Mezzavilla, Yali Xue, Chris Tyler-Smith. Genome Biol 2016
248
6

Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex.
Sinisa Hrvatin, Daniel R Hochbaum, M Aurel Nagy, Marcelo Cicconet, Keiramarie Robertson, Lucas Cheadle, Rapolas Zilionis, Alex Ratner, Rebeca Borges-Monroy, Allon M Klein,[...]. Nat Neurosci 2018
174
6

Single-Cell RNA-Seq Reveals Hypothalamic Cell Diversity.
Renchao Chen, Xiaoji Wu, Lan Jiang, Yi Zhang. Cell Rep 2017
199
6

Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells.
Gioele La Manno, Daniel Gyllborg, Simone Codeluppi, Kaneyasu Nishimura, Carmen Salto, Amit Zeisel, Lars E Borm, Simon R W Stott, Enrique M Toledo, J Carlos Villaescusa,[...]. Cell 2016
312
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
482
6


Human cerebral organoids recapitulate gene expression programs of fetal neocortex development.
J Gray Camp, Farhath Badsha, Marta Florio, Sabina Kanton, Tobias Gerber, Michaela Wilsch-Bräuninger, Eric Lewitus, Alex Sykes, Wulf Hevers, Madeline Lancaster,[...]. Proc Natl Acad Sci U S A 2015
439
6

A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex.
Suijuan Zhong, Shu Zhang, Xiaoying Fan, Qian Wu, Liying Yan, Ji Dong, Haofeng Zhang, Long Li, Le Sun, Na Pan,[...]. Nature 2018
217
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
715
6

Splatter: simulation of single-cell RNA sequencing data.
Luke Zappia, Belinda Phipson, Alicia Oshlack. Genome Biol 2017
184
6

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
337
6

A survey of human brain transcriptome diversity at the single cell level.
Spyros Darmanis, Steven A Sloan, Ye Zhang, Martin Enge, Christine Caneda, Lawrence M Shuer, Melanie G Hayden Gephart, Ben A Barres, Stephen R Quake. Proc Natl Acad Sci U S A 2015
549
6

Genetic effects on gene expression across human tissues.
Alexis Battle, Christopher D Brown, Barbara E Engelhardt, Stephen B Montgomery. Nature 2017
6

Hallmarks of cancer: the next generation.
Douglas Hanahan, Robert A Weinberg. Cell 2011
6

Molecular insights into genome-wide association studies of chronic kidney disease-defining traits.
Xiaoguang Xu, James M Eales, Artur Akbarov, Hui Guo, Lorenz Becker, David Talavera, Fehzan Ashraf, Jabran Nawaz, Sanjeev Pramanik, John Bowes,[...]. Nat Commun 2018
27
7

Precision Medicine Approaches to Diabetic Kidney Disease: Tissue as an Issue.
Caroline Gluck, Yi-An Ko, Katalin Susztak. Curr Diab Rep 2017
15
13


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.