A citation-based method for searching scientific literature

Liang Chen, Weinan Wang, Yuyao Zhai, Minghua Deng. NAR Genom Bioinform 2020
Times Cited: 6







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



Times Cited
  Times     Co-cited
Similarity


Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
100

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
189
83


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
482
66

Splatter: simulation of single-cell RNA sequencing data.
Luke Zappia, Belinda Phipson, Alicia Oshlack. Genome Biol 2017
202
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
66

Deep generative modeling for single-cell transcriptomics.
Romain Lopez, Jeffrey Regier, Michael B Cole, Michael I Jordan, Nir Yosef. Nat Methods 2018
252
66

Deep learning enables accurate clustering with batch effect removal in single-cell RNA-seq analysis.
Xiangjie Li, Kui Wang, Yafei Lyu, Huize Pan, Jingxiao Zhang, Dwight Stambolian, Katalin Susztak, Muredach P Reilly, Gang Hu, Mingyao Li. Nat Commun 2020
39
66

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
223
50

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
50

Challenges in unsupervised clustering of single-cell RNA-seq data.
Vladimir Yu Kiselev, Tallulah S Andrews, Martin Hemberg. Nat Rev Genet 2019
234
50

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
397
50



Clustering and classification methods for single-cell RNA-sequencing data.
Ren Qi, Anjun Ma, Qin Ma, Quan Zou. Brief Bioinform 2020
30
50

Integrating Deep Supervised, Self-Supervised and Unsupervised Learning for Single-Cell RNA-seq Clustering and Annotation.
Liang Chen, Yuyao Zhai, Qiuyan He, Weinan Wang, Minghua Deng. Genes (Basel) 2020
6
50

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
812
50

Mapping the Mouse Cell Atlas by Microwell-Seq.
Xiaoping Han, Renying Wang, Yincong Zhou, Lijiang Fei, Huiyu Sun, Shujing Lai, Assieh Saadatpour, Ziming Zhou, Haide Chen, Fang Ye,[...]. Cell 2018
433
50

Semisoft clustering of single-cell data.
Lingxue Zhu, Jing Lei, Lambertus Klei, Bernie Devlin, Kathryn Roeder. Proc Natl Acad Sci U S A 2019
24
50

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
50

scmap: projection of single-cell RNA-seq data across data sets.
Vladimir Yu Kiselev, Andrew Yiu, Martin Hemberg. Nat Methods 2018
191
33

Single-Cell RNA-Seq Reveals Hypothalamic Cell Diversity.
Renchao Chen, Xiaoji Wu, Lan Jiang, Yi Zhang. Cell Rep 2017
206
33

Iterative transfer learning with neural network for clustering and cell type classification in single-cell RNA-seq analysis.
Jian Hu, Xiangjie Li, Gang Hu, Yafei Lyu, Katalin Susztak, Mingyao Li. Nat Mach Intell 2020
9
33

Deep learning: new computational modelling techniques for genomics.
Gökcen Eraslan, Žiga Avsec, Julien Gagneur, Fabian J Theis. Nat Rev Genet 2019
226
33

A comparison of automatic cell identification methods for single-cell RNA sequencing data.
Tamim Abdelaal, Lieke Michielsen, Davy Cats, Dylan Hoogduin, Hailiang Mei, Marcel J T Reinders, Ahmed Mahfouz. Genome Biol 2019
105
33

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects.
Elisabetta Mereu, Atefeh Lafzi, Catia Moutinho, Christoph Ziegenhain, Davis J McCarthy, Adrián Álvarez-Varela, Eduard Batlle, Sagar, Dominic Grün, Julia K Lau,[...]. Nat Biotechnol 2020
87
33

Supervised classification enables rapid annotation of cell atlases.
Hannah A Pliner, Jay Shendure, Cole Trapnell. Nat Methods 2019
101
33

Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes.
Roman A Romanov, Amit Zeisel, Joanne Bakker, Fatima Girach, Arash Hellysaz, Raju Tomer, Alán Alpár, Jan Mulder, Frédéric Clotman, Erik Keimpema,[...]. Nat Neurosci 2017
177
33

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
475
33

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
208
33


Using transfer learning from prior reference knowledge to improve the clustering of single-cell RNA-Seq data.
Bettina Mieth, James R F Hockley, Nico Görnitz, Marina M-C Vidovic, Klaus-Robert Müller, Alex Gutteridge, Daniel Ziemek. Sci Rep 2019
7
33

Comprehensive single-cell transcriptional profiling of a multicellular organism.
Junyue Cao, Jonathan S Packer, Vijay Ramani, Darren A Cusanovich, Chau Huynh, Riza Daza, Xiaojie Qiu, Choli Lee, Scott N Furlan, Frank J Steemers,[...]. Science 2017
465
33

Scedar: A scalable Python package for single-cell RNA-seq exploratory data analysis.
Yuanchao Zhang, Man S Kim, Erin R Reichenberger, Ben Stear, Deanne M Taylor. PLoS Comput Biol 2020
3
66

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
592
33

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
489
33

scIGANs: single-cell RNA-seq imputation using generative adversarial networks.
Yungang Xu, Zhigang Zhang, Lei You, Jiajia Liu, Zhiwei Fan, Xiaobo Zhou. Nucleic Acids Res 2020
17
33

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
511
33

MARS: discovering novel cell types across heterogeneous single-cell experiments.
Maria Brbić, Marinka Zitnik, Sheng Wang, Angela O Pisco, Russ B Altman, Spyros Darmanis, Jure Leskovec. Nat Methods 2020
21
33

Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST.
Zhi-Jie Cao, Lin Wei, Shen Lu, De-Chang Yang, Ge Gao. Nat Commun 2020
17
16

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
16

Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing.
Dmitry Usoskin, Alessandro Furlan, Saiful Islam, Hind Abdo, Peter Lönnerberg, Daohua Lou, Jens Hjerling-Leffler, Jesper Haeggström, Olga Kharchenko, Peter V Kharchenko,[...]. Nat Neurosci 2015
909
16

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods.
Jiarui Ding, Xian Adiconis, Sean K Simmons, Monika S Kowalczyk, Cynthia C Hession, Nemanja D Marjanovic, Travis K Hughes, Marc H Wadsworth, Tyler Burks, Lan T Nguyen,[...]. Nat Biotechnol 2020
145
16

Machine learning and statistical methods for clustering single-cell RNA-sequencing data.
Raphael Petegrosso, Zhuliu Li, Rui Kuang. Brief Bioinform 2020
19
16

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.
Alexander D Diehl, Terrence F Meehan, Yvonne M Bradford, Matthew H Brush, Wasila M Dahdul, David S Dougall, Yongqun He, David Osumi-Sutherland, Alan Ruttenberg, Sirarat Sarntivijai,[...]. J Biomed Semantics 2016
80
16

Single-cell transcriptomes identify human islet cell signatures and reveal cell-type-specific expression changes in type 2 diabetes.
Nathan Lawlor, Joshy George, Mohan Bolisetty, Romy Kursawe, Lili Sun, V Sivakamasundari, Ina Kycia, Paul Robson, Michael L Stitzel. Genome Res 2017
170
16

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
421
16

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
41
16

Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns.
Martin Enge, H Efsun Arda, Marco Mignardi, John Beausang, Rita Bottino, Seung K Kim, Stephen R Quake. Cell 2017
188
16

From Louvain to Leiden: guaranteeing well-connected communities.
V A Traag, L Waltman, N J van Eck. Sci Rep 2019
300
16


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.