A citation-based method for searching scientific literature

Jurrian K de Kanter, Philip Lijnzaad, Tito Candelli, Thanasis Margaritis, Frank C P Holstege. Nucleic Acids Res 2019
Times Cited: 44







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



Times Cited
  Times     Co-cited
Similarity


powsimR: power analysis for bulk and single cell RNA-seq experiments.
Beate Vieth, Christoph Ziegenhain, Swati Parekh, Wolfgang Enard, Ines Hellmann. Bioinformatics 2017
51
6

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution.
Samuel G Rodriques, Robert R Stickels, Aleksandrina Goeva, Carly A Martin, Evan Murray, Charles R Vanderburg, Joshua Welch, Linlin M Chen, Fei Chen, Evan Z Macosko. Science 2019
419
6

Validation of noise models for single-cell transcriptomics.
Dominic Grün, Lennart Kester, Alexander van Oudenaarden. Nat Methods 2014
331
6

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
6

cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes.
Erica A K DePasquale, Daniel Schnell, Phillip Dexheimer, Kyle Ferchen, Stuart Hay, Kashish Chetal, Íñigo Valiente-Alandí, Burns C Blaxall, H Leighton Grimes, Nathan Salomonis. Nucleic Acids Res 2019
25
12

Joint profiling of chromatin accessibility and gene expression in thousands of single cells.
Junyue Cao, Darren A Cusanovich, Vijay Ramani, Delasa Aghamirzaie, Hannah A Pliner, Andrew J Hill, Riza M Daza, Jose L McFaline-Figueroa, Jonathan S Packer, Lena Christiansen,[...]. Science 2018
252
6

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
680
6

Massively parallel single-nucleus RNA-seq with DroNc-seq.
Naomi Habib, Inbal Avraham-Davidi, Anindita Basu, Tyler Burks, Karthik Shekhar, Matan Hofree, Sourav R Choudhury, François Aguet, Ellen Gelfand, Kristin Ardlie,[...]. Nat Methods 2017
342
6

A test metric for assessing single-cell RNA-seq batch correction.
Maren Büttner, Zhichao Miao, F Alexander Wolf, Sarah A Teichmann, Fabian J Theis. Nat Methods 2019
90
6


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
77
6

Phenotype molding of stromal cells in the lung tumor microenvironment.
Diether Lambrechts, Els Wauters, Bram Boeckx, Sara Aibar, David Nittner, Oliver Burton, Ayse Bassez, Herbert Decaluwé, Andreas Pircher, Kathleen Van den Eynde,[...]. Nat Med 2018
432
6

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
6

Multiplexed quantification of proteins and transcripts in single cells.
Vanessa M Peterson, Kelvin Xi Zhang, Namit Kumar, Jerelyn Wong, Lixia Li, Douglas C Wilson, Renee Moore, Terrill K McClanahan, Svetlana Sadekova, Joel A Klappenbach. Nat Biotechnol 2017
307
6

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
6

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
598
6

CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes.
Mirjana Efremova, Miquel Vento-Tormo, Sarah A Teichmann, Roser Vento-Tormo. Nat Protoc 2020
283
6

The origin and evolution of cell types.
Detlev Arendt, Jacob M Musser, Clare V H Baker, Aviv Bergman, Connie Cepko, Douglas H Erwin, Mihaela Pavlicev, Gerhard Schlosser, Stefanie Widder, Manfred D Laubichler,[...]. Nat Rev Genet 2016
229
6

A human liver cell atlas reveals heterogeneity and epithelial progenitors.
Nadim Aizarani, Antonio Saviano, Sagar, Laurent Mailly, Sarah Durand, Josip S Herman, Patrick Pessaux, Thomas F Baumert, Dominic Grün. Nature 2019
272
6

Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations.
Sonya A MacParland, Jeff C Liu, Xue-Zhong Ma, Brendan T Innes, Agata M Bartczak, Blair K Gage, Justin Manuel, Nicholas Khuu, Juan Echeverri, Ivan Linares,[...]. Nat Commun 2018
331
6

Evaluating measures of association for single-cell transcriptomics.
Michael A Skinnider, Jordan W Squair, Leonard J Foster. Nat Methods 2019
31
9

Impact of similarity metrics on single-cell RNA-seq data clustering.
Taiyun Kim, Irene Rui Chen, Yingxin Lin, Andy Yi-Yang Wang, Jean Yee Hwa Yang, Pengyi Yang. Brief Bioinform 2019
30
10

Droplet scRNA-seq is not zero-inflated.
Valentine Svensson. Nat Biotechnol 2020
55
6

Adjusting batch effects in microarray expression data using empirical Bayes methods.
W Evan Johnson, Cheng Li, Ariel Rabinovic. Biostatistics 2007
6


A revised airway epithelial hierarchy includes CFTR-expressing ionocytes.
Daniel T Montoro, Adam L Haber, Moshe Biton, Vladimir Vinarsky, Brian Lin, Susan E Birket, Feng Yuan, Sijia Chen, Hui Min Leung, Jorge Villoria,[...]. Nature 2018
374
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
317
6

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex.
Alex A Pollen, Tomasz J Nowakowski, Joe Shuga, Xiaohui Wang, Anne A Leyrat, Jan H Lui, Nianzhen Li, Lukasz Szpankowski, Brian Fowler, Peilin Chen,[...]. Nat Biotechnol 2014
467
6


SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis.
Minzhe Guo, Hui Wang, S Steven Potter, Jeffrey A Whitsett, Yan Xu. PLoS Comput Biol 2015
144
6

xCell: digitally portraying the tissue cellular heterogeneity landscape.
Dvir Aran, Zicheng Hu, Atul J Butte. Genome Biol 2017
681
6

An ontology for cell types.
Jonathan Bard, Seung Y Rhee, Michael Ashburner. Genome Biol 2005
224
6

Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models.
Chenling Xu, Romain Lopez, Edouard Mehlman, Jeffrey Regier, Michael I Jordan, Nir Yosef. Mol Syst Biol 2021
14
21

scClassify: sample size estimation and multiscale classification of cells using single and multiple reference.
Yingxin Lin, Yue Cao, Hani Jieun Kim, Agus Salim, Terence P Speed, David M Lin, Pengyi Yang, Jean Yee Hwa Yang. Mol Syst Biol 2020
9
33

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
30
10

A curated database reveals trends in single-cell transcriptomics.
Valentine Svensson, Eduardo da Veiga Beltrame, Lior Pachter. Database (Oxford) 2020
27
11

Hierarchical progressive learning of cell identities in single-cell data.
Lieke Michielsen, Marcel J T Reinders, Ahmed Mahfouz. Nat Commun 2021
3
100


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
17

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
19
15

scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets.
Yingxin Lin, Shila Ghazanfar, Kevin Y X Wang, Johann A Gagnon-Bartsch, Kitty K Lo, Xianbin Su, Ze-Guang Han, John T Ormerod, Terence P Speed, Pengyi Yang,[...]. Proc Natl Acad Sci U S A 2019
44
4

Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes.
Timothy R Hammond, Connor Dufort, Lasse Dissing-Olesen, Stefanie Giera, Adam Young, Alec Wysoker, Alec J Walker, Frederick Gergits, Michael Segel, James Nemesh,[...]. Immunity 2019
475
4

The Human Cell Atlas bone marrow single-cell interactive web portal.
Stuart B Hay, Kyle Ferchen, Kashish Chetal, H Leighton Grimes, Nathan Salomonis. Exp Hematol 2018
53
4

Identifying cell populations with scRNASeq.
Tallulah S Andrews, Martin Hemberg. Mol Aspects Med 2018
94
4

Cell type discovery using single-cell transcriptomics: implications for ontological representation.
Brian D Aevermann, Mark Novotny, Trygve Bakken, Jeremy A Miller, Alexander D Diehl, David Osumi-Sutherland, Roger S Lasken, Ed S Lein, Richard H Scheuermann. Hum Mol Genet 2018
28
7

Cell type discovery and representation in the era of high-content single cell phenotyping.
Trygve Bakken, Lindsay Cowell, Brian D Aevermann, Mark Novotny, Rebecca Hodge, Jeremy A Miller, Alexandra Lee, Ivan Chang, Jamison McCorrison, Bali Pulendran,[...]. BMC Bioinformatics 2017
25
8

Dhaka: Variational Autoencoder for Unmasking Tumor Heterogeneity from Single Cell Genomic Data.
Sabrina Rashid, Sohrab Shah, Ziv Bar-Joseph, Ravi Pandya. Bioinformatics 2019
13
15

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
240
4

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing.
Xinyi Guo, Yuanyuan Zhang, Liangtao Zheng, Chunhong Zheng, Jintao Song, Qiming Zhang, Boxi Kang, Zhouzerui Liu, Liang Jin, Rui Xing,[...]. Nat Med 2018
360
4



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.