A citation-based method for searching scientific literature

Minzhe Zhang, Thomas Sheffield, Xiaowei Zhan, Qiwei Li, Donghan M Yang, Yunguan Wang, Shidan Wang, Yang Xie, Tao Wang, Guanghua Xiao. Brief Bioinform 2021
Times Cited: 2







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



Times Cited
  Times     Co-cited
Similarity


Single-cell in situ RNA profiling by sequential hybridization.
Eric Lubeck, Ahmet F Coskun, Timur Zhiyentayev, Mubhij Ahmad, Long Cai. Nat Methods 2014
312
100

RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells.
Kok Hao Chen, Alistair N Boettiger, Jeffrey R Moffitt, Siyuan Wang, Xiaowei Zhuang. Science 2015
655
100

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region.
Jeffrey R Moffitt, Dhananjay Bambah-Mukku, Stephen W Eichhorn, Eric Vaughn, Karthik Shekhar, Julio D Perez, Nimrod D Rubinstein, Junjie Hao, Aviv Regev, Catherine Dulac,[...]. Science 2018
242
100


Cell-specific network constructed by single-cell RNA sequencing data.
Hao Dai, Lin Li, Tao Zeng, Luonan Chen. Nucleic Acids Res 2019
24
50

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression.
Chenglong Xia, Jean Fan, George Emanuel, Junjie Hao, Xiaowei Zhuang. Proc Natl Acad Sci U S A 2019
100
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

Identifying signaling genes in spatial single-cell expression data.
Dongshunyi Li, Jun Ding, Ziv Bar-Joseph. Bioinformatics 2021
1
100

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
50

A general framework for weighted gene co-expression network analysis.
Bin Zhang, Steve Horvath. Stat Appl Genet Mol Biol 2005
50

Highly multiplexed subcellular RNA sequencing in situ.
Je Hyuk Lee, Evan R Daugharthy, Jonathan Scheiman, Reza Kalhor, Joyce L Yang, Thomas C Ferrante, Richard Terry, Sauveur S F Jeanty, Chao Li, Ryoji Amamoto,[...]. Science 2014
450
50

Learning from Co-expression Networks: Possibilities and Challenges.
Elise A R Serin, Harm Nijveen, Henk W M Hilhorst, Wilco Ligterink. Front Plant Sci 2016
114
50

A gene-coexpression network for global discovery of conserved genetic modules.
Joshua M Stuart, Eran Segal, Daphne Koller, Stuart K Kim. Science 2003
50

Gene co-expression network topology provides a framework for molecular characterization of cellular state.
Scott L Carter, Christian M Brechbühler, Michael Griffin, Andrew T Bond. Bioinformatics 2004
189
50

A molecular census of arcuate hypothalamus and median eminence cell types.
John N Campbell, Evan Z Macosko, Henning Fenselau, Tune H Pers, Anna Lyubetskaya, Danielle Tenen, Melissa Goldman, Anne M J Verstegen, Jon M Resch, Steven A McCarroll,[...]. Nat Neurosci 2017
290
50

The intellectual disability protein PAK3 regulates oligodendrocyte precursor cell differentiation.
Majistor Raj Luxman Maglorius Renkilaraj, Lucas Baudouin, Claire M Wells, Mohamed Doulazmi, Rosine Wehrlé, Vidjeacoumary Cannaya, Corinne Bachelin, Jean-Vianney Barnier, Zhengping Jia, Brahim Nait Oumesmar,[...]. Neurobiol Dis 2017
18
50

The Gene Ontology (GO) database and informatics resource.
M A Harris, J Clark, A Ireland, J Lomax, M Ashburner, R Foulger, K Eilbeck, S Lewis, B Marshall, C Mungall,[...]. Nucleic Acids Res 2004
50

A Bayesian model for single cell transcript expression analysis on MERFISH data.
Johannes Köster, Myles Brown, X Shirley Liu. Bioinformatics 2019
5
50

Single-Cell RNA-Seq Reveals Hypothalamic Cell Diversity.
Renchao Chen, Xiaoji Wu, Lan Jiang, Yi Zhang. Cell Rep 2017
188
50

c-CSN: Single-cell RNA Sequencing Data Analysis by Conditional Cell-specific Network.
Lin Li, Hao Dai, Zhaoyuan Fang, Luonan Chen. Genomics Proteomics Bioinformatics 2021
2
50



Differential expression analysis for RNAseq using Poisson mixed models.
Shiquan Sun, Michelle Hood, Laura Scott, Qinke Peng, Sayan Mukherjee, Jenny Tung, Xiang Zhou. Nucleic Acids Res 2017
32
50


Three-dimensional intact-tissue sequencing of single-cell transcriptional states.
Xiao Wang, William E Allen, Matthew A Wright, Emily L Sylwestrak, Nikolay Samusik, Sam Vesuna, Kathryn Evans, Cindy Liu, Charu Ramakrishnan, Jia Liu,[...]. Science 2018
280
50

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
50

ESCO: single cell expression simulation incorporating gene co-expression.
Jinjin Tian, Jiebiao Wang, Kathryn Roeder. Bioinformatics 2021
1
100


Gaussian processes for time-series modelling.
S Roberts, M Osborne, M Ebden, S Reece, N Gibson, S Aigrain. Philos Trans A Math Phys Eng Sci 2012
33
50

Detecting differential gene expression with a semiparametric hierarchical mixture method.
Michael A Newton, Amine Noueiry, Deepayan Sarkar, Paul Ahlquist. Biostatistics 2004
282
50


edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
50

Bayesian approach to single-cell differential expression analysis.
Peter V Kharchenko, Lev Silberstein, David T Scadden. Nat Methods 2014
529
50

Bayesian negative binomial mixture regression models for the analysis of sequence count and methylation data.
Qiwei Li, Alberto Cassese, Michele Guindani, Marina Vannucci. Biometrics 2019
3
50

GSEA-P: a desktop application for Gene Set Enrichment Analysis.
Aravind Subramanian, Heidi Kuehn, Joshua Gould, Pablo Tamayo, Jill P Mesirov. Bioinformatics 2007
675
50

Normalization, testing, and false discovery rate estimation for RNA-sequencing data.
Jun Li, Daniela M Witten, Iain M Johnstone, Robert Tibshirani. Biostatistics 2012
163
50

Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development.
Nick D L Owens, Ira L Blitz, Maura A Lane, Ilya Patrushev, John D Overton, Michael J Gilchrist, Ken W Y Cho, Mustafa K Khokha. Cell Rep 2016
86
50

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
359
50

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.
Patrik L Ståhl, Fredrik Salmén, Sanja Vickovic, Anna Lundmark, José Fernández Navarro, Jens Magnusson, Stefania Giacomello, Michaela Asp, Jakub O Westholm, Mikael Huss,[...]. Science 2016
535
50


SpatialDE: identification of spatially variable genes.
Valentine Svensson, Sarah A Teichmann, Oliver Stegle. Nat Methods 2018
62
50

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
50

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
575
50

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH.
Chee-Huat Linus Eng, Michael Lawson, Qian Zhu, Ruben Dries, Noushin Koulena, Yodai Takei, Jina Yun, Christopher Cronin, Christoph Karp, Guo-Cheng Yuan,[...]. Nature 2019
303
50


Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.
Maxim V Kuleshov, Matthew R Jones, Andrew D Rouillard, Nicolas F Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L Jenkins, Kathleen M Jagodnik, Alexander Lachmann,[...]. Nucleic Acids Res 2016
50

Identification of spatial expression trends in single-cell gene expression data.
Daniel Edsgärd, Per Johnsson, Rickard Sandberg. Nat Methods 2018
60
50

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.
John C Marioni, Christopher E Mason, Shrikant M Mane, Matthew Stephens, Yoav Gilad. Genome Res 2008
50

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
376
50



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.