A citation-based method for searching scientific literature

Tianyi Sun, Dongyuan Song, Wei Vivian Li, Jingyi Jessica Li. Genome Biol 2021
Times Cited: 10







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



Times Cited
  Times     Co-cited
Similarity


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

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
40

Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model.
F William Townes, Stephanie C Hicks, Martin J Aryee, Rafael A Irizarry. Genome Biol 2019
84
40

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
40

Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual.
Diana L Cousminer, Yadav Wagley, James A Pippin, Ahmed Elhakeem, Gregory P Way, Matthew C Pahl, Shana E McCormack, Alessandra Chesi, Jonathan A Mitchell, Joseph M Kindler,[...]. Genome Biol 2021
40
40

M3Drop: dropout-based feature selection for scRNASeq.
Tallulah S Andrews, Martin Hemberg. Bioinformatics 2019
90
30

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
219
30

A statistical simulator scDesign for rational scRNA-seq experimental design.
Wei Vivian Li, Jingyi Jessica Li. Bioinformatics 2019
16
30

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
30

Splatter: simulation of single-cell RNA sequencing data.
Luke Zappia, Belinda Phipson, Alicia Oshlack. Genome Biol 2017
241
30


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
30

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
177
30

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
219
30

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
527
30

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
114
20



SCMarker: Ab initio marker selection for single cell transcriptome profiling.
Fang Wang, Shaoheng Liang, Tapsi Kumar, Nicholas Navin, Ken Chen. PLoS Comput Biol 2019
8
25

Challenges in unsupervised clustering of single-cell RNA-seq data.
Vladimir Yu Kiselev, Tallulah S Andrews, Martin Hemberg. Nat Rev Genet 2019
271
20

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
505
20

Current best practices in single-cell RNA-seq analysis: a tutorial.
Malte D Luecken, Fabian J Theis. Mol Syst Biol 2019
419
20

Demystifying "drop-outs" in single-cell UMI data.
Tae Hyun Kim, Xiang Zhou, Mengjie Chen. Genome Biol 2020
19
20

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
940
20


Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
20

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
20


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
766
20


In situ click chemistry generation of cyclooxygenase-2 inhibitors.
Atul Bhardwaj, Jatinder Kaur, Melinda Wuest, Frank Wuest. Nat Commun 2017
20

Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications.
Koen Van den Berge, Fanny Perraudeau, Charlotte Soneson, Michael I Love, Davide Risso, Jean-Philippe Vert, Mark D Robinson, Sandrine Dudoit, Lieven Clement. Genome Biol 2018
77
20

A statistical approach for identifying differential distributions in single-cell RNA-seq experiments.
Keegan D Korthauer, Li-Fang Chu, Michael A Newton, Yuan Li, James Thomson, Ron Stewart, Christina Kendziorski. Genome Biol 2016
98
20


DEsingle for detecting three types of differential expression in single-cell RNA-seq data.
Zhun Miao, Ke Deng, Xiaowo Wang, Xuegong Zhang. Bioinformatics 2018
65
20

Simulating multiple faceted variability in single cell RNA sequencing.
Xiuwei Zhang, Chenling Xu, Nir Yosef. Nat Commun 2019
31
20

powsimR: power analysis for bulk and single cell RNA-seq experiments.
Beate Vieth, Christoph Ziegenhain, Swati Parekh, Wolfgang Enard, Ines Hellmann. Bioinformatics 2017
64
20

An entropy-based metric for assessing the purity of single cell populations.
Baolin Liu, Chenwei Li, Ziyi Li, Dongfang Wang, Xianwen Ren, Zemin Zhang. Nat Commun 2020
20
20

Droplet scRNA-seq is not zero-inflated.
Valentine Svensson. Nat Biotechnol 2020
83
20

Full-length RNA-seq from single cells using Smart-seq2.
Simone Picelli, Omid R Faridani, Asa K Björklund, Gösta Winberg, Sven Sagasser, Rickard Sandberg. Nat Protoc 2014
20

U1 snRNP regulates cancer cell migration and invasion in vitro.
Jung-Min Oh, Christopher C Venters, Chao Di, Anna Maria Pinto, Lili Wan, Ihab Younis, Zhiqiang Cai, Chie Arai, Byung Ran So, Jingqi Duan,[...]. Nat Commun 2020
759
20

Efficacy of continuous EGFR-inhibition and role of Hedgehog in EGFR acquired resistance in human lung cancer cells with activating mutation of EGFR.
Carminia Maria Della Corte, Umberto Malapelle, Elena Vigliar, Francesco Pepe, Giancarlo Troncone, Vincenza Ciaramella, Teresa Troiani, Erika Martinelli, Valentina Belli, Fortunato Ciardiello,[...]. Oncotarget 2017
21
10

Treating cancer with selective CDK4/6 inhibitors.
Ben O'Leary, Richard S Finn, Nicholas C Turner. Nat Rev Clin Oncol 2016
523
10


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
57
10

Selection of housekeeping genes for gene expression studies in human reticulocytes using real-time PCR.
Nicholas Silver, Steve Best, Jie Jiang, Swee Lay Thein. BMC Mol Biol 2006
828
10

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
282
10

Comparison of clustering tools in R for medium-sized 10x Genomics single-cell RNA-sequencing data.
Saskia Freytag, Luyi Tian, Ingrid Lönnstedt, Milica Ng, Melanie Bahlo. F1000Res 2018
69
10

Housekeeping genes as internal standards: use and limits.
O Thellin, W Zorzi, B Lakaye, B De Borman, B Coumans, G Hennen, T Grisar, A Igout, E Heinen. J Biotechnol 1999
10

Human housekeeping genes, revisited.
Eli Eisenberg, Erez Y Levanon. Trends Genet 2013
636
10


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.