A citation-based method for searching scientific literature

Lingxue Zhu, Jing Lei, Lambertus Klei, Bernie Devlin, Kathryn Roeder. Proc Natl Acad Sci U S A 2019
Times Cited: 21







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



Times Cited
  Times     Co-cited
Similarity


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
66

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
52

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
192
52

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
47

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
42


Challenges in unsupervised clustering of single-cell RNA-seq data.
Vladimir Yu Kiselev, Tallulah S Andrews, Martin Hemberg. Nat Rev Genet 2019
202
33

SAFE-clustering: Single-cell Aggregated (from Ensemble) clustering for single-cell RNA-seq data.
Yuchen Yang, Ruth Huh, Houston W Culpepper, Yuan Lin, Michael I Love, Yun Li. Bioinformatics 2019
30
33

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
670
33

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
33

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
28

A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure.
Maayan Baron, Adrian Veres, Samuel L Wolock, Aubrey L Faust, Renaud Gaujoux, Amedeo Vetere, Jennifer Hyoje Ryu, Bridget K Wagner, Shai S Shen-Orr, Allon M Klein,[...]. Cell Syst 2016
379
28

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
28

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity.
Joshua D Welch, Velina Kozareva, Ashley Ferreira, Charles Vanderburg, Carly Martin, Evan Z Macosko. Cell 2019
195
28

The technology and biology of single-cell RNA sequencing.
Aleksandra A Kolodziejczyk, Jong Kyoung Kim, Valentine Svensson, John C Marioni, Sarah A Teichmann. Mol Cell 2015
445
23

Single-cell messenger RNA sequencing reveals rare intestinal cell types.
Dominic Grün, Anna Lyubimova, Lennart Kester, Kay Wiebrands, Onur Basak, Nobuo Sasaki, Hans Clevers, Alexander van Oudenaarden. Nature 2015
568
23



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
23

Deep generative modeling for single-cell transcriptomics.
Romain Lopez, Jeffrey Regier, Michael B Cole, Michael I Jordan, Nir Yosef. Nat Methods 2018
209
23

Splatter: simulation of single-cell RNA sequencing data.
Luke Zappia, Belinda Phipson, Alicia Oshlack. Genome Biol 2017
177
23

Bayesian approach to single-cell differential expression analysis.
Peter V Kharchenko, Lev Silberstein, David T Scadden. Nat Methods 2014
532
23


De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data.
Dominic Grün, Mauro J Muraro, Jean-Charles Boisset, Kay Wiebrands, Anna Lyubimova, Gitanjali Dharmadhikari, Maaike van den Born, Johan van Es, Erik Jansen, Hans Clevers,[...]. Cell Stem Cell 2016
216
23

SAME-clustering: Single-cell Aggregated Clustering via Mixture Model Ensemble.
Ruth Huh, Yuchen Yang, Yuchao Jiang, Yin Shen, Yun Li. Nucleic Acids Res 2020
13
38

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
19

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
414
19

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
19

The Human Cell Atlas: from vision to reality.
Orit Rozenblatt-Rosen, Michael J T Stubbington, Aviv Regev, Sarah A Teichmann. Nature 2017
205
19

A general and flexible method for signal extraction from single-cell RNA-seq data.
Davide Risso, Fanny Perraudeau, Svetlana Gribkova, Sandrine Dudoit, Jean-Philippe Vert. Nat Commun 2018
178
19

Reversed graph embedding resolves complex single-cell trajectories.
Xiaojie Qiu, Qi Mao, Ying Tang, Li Wang, Raghav Chawla, Hannah A Pliner, Cole Trapnell. Nat Methods 2017
709
19

scmap: projection of single-cell RNA-seq data across data sets.
Vladimir Yu Kiselev, Andrew Yiu, Martin Hemberg. Nat Methods 2018
170
19

A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation.
Sonia Nestorowa, Fiona K Hamey, Blanca Pijuan Sala, Evangelia Diamanti, Mairi Shepherd, Elisa Laurenti, Nicola K Wilson, David G Kent, Berthold Göttgens. Blood 2016
233
19

Data denoising with transfer learning in single-cell transcriptomics.
Jingshu Wang, Divyansh Agarwal, Mo Huang, Gang Hu, Zilu Zhou, Chengzhong Ye, Nancy R Zhang. Nat Methods 2019
39
19

Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations.
Zhana Duren, Xi Chen, Mahdi Zamanighomi, Wanwen Zeng, Ansuman T Satpathy, Howard Y Chang, Yong Wang, Wing Hung Wong. Proc Natl Acad Sci U S A 2018
49
19

pcaReduce: hierarchical clustering of single cell transcriptional profiles.
Justina Žurauskienė, Christopher Yau. BMC Bioinformatics 2016
100
19

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
424
19

DIMM-SC: a Dirichlet mixture model for clustering droplet-based single cell transcriptomic data.
Zhe Sun, Ting Wang, Ke Deng, Xiao-Feng Wang, Robert Lafyatis, Ying Ding, Ming Hu, Wei Chen. Bioinformatics 2018
17
23

A Single-Cell Transcriptome Atlas of the Human Pancreas.
Mauro J Muraro, Gitanjali Dharmadhikari, Dominic Grün, Nathalie Groen, Tim Dielen, Erik Jansen, Leon van Gurp, Marten A Engelse, Francoise Carlotti, Eelco J P de Koning,[...]. Cell Syst 2016
354
19

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
19

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
120
19

SCALE method for single-cell ATAC-seq analysis via latent feature extraction.
Lei Xiong, Kui Xu, Kang Tian, Yanqiu Shao, Lei Tang, Ge Gao, Michael Zhang, Tao Jiang, Qiangfeng Cliff Zhang. Nat Commun 2019
34
19

Single-cell sequencing-based technologies will revolutionize whole-organism science.
Ehud Shapiro, Tamir Biezuner, Sten Linnarsson. Nat Rev Genet 2013
580
14

GiniClust: detecting rare cell types from single-cell gene expression data with Gini index.
Lan Jiang, Huidong Chen, Luca Pinello, Guo-Cheng Yuan. Genome Biol 2016
96
14

AutoImpute: Autoencoder based imputation of single-cell RNA-seq data.
Divyanshu Talwar, Aanchal Mongia, Debarka Sengupta, Angshul Majumdar. Sci Rep 2018
33
14

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
976
14

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors.
Huipeng Li, Elise T Courtois, Debarka Sengupta, Yuliana Tan, Kok Hao Chen, Jolene Jie Lin Goh, Say Li Kong, Clarinda Chua, Lim Kiat Hon, Wah Siew Tan,[...]. Nat Genet 2017
361
14

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
326
14


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
14


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.