A citation-based method for searching scientific literature

Shiquan Sun, Jiaqiang Zhu, Ying Ma, Xiang Zhou. Genome Biol 2019
Times Cited: 37







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



Times Cited
  Times     Co-cited
Similarity




A global geometric framework for nonlinear dimensionality reduction.
J B Tenenbaum, V de Silva, J C Langford. Science 2000
8

Single-cell mRNA quantification and differential analysis with Census.
Xiaojie Qiu, Andrew Hill, Jonathan Packer, Dejun Lin, Yi-An Ma, Cole Trapnell. Nat Methods 2017
398
8


Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning.
Yue Deng, Feng Bao, Qionghai Dai, Lani F Wu, Steven J Altschuler. Nat Methods 2019
41
8

Valid Post-clustering Differential Analysis for Single-Cell RNA-Seq.
Jesse M Zhang, Govinda M Kamath, David N Tse. Cell Syst 2019
11
27

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.
Hannah A Pliner, Jonathan S Packer, José L McFaline-Figueroa, Darren A Cusanovich, Riza M Daza, Delasa Aghamirzaie, Sanjay Srivatsan, Xiaojie Qiu, Dana Jackson, Anna Minkina,[...]. Mol Cell 2018
134
8

False signals induced by single-cell imputation.
Tallulah S Andrews, Martin Hemberg. F1000Res 2018
43
8



Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding.
Alexander B Rosenberg, Charles M Roco, Richard A Muscat, Anna Kuchina, Paul Sample, Zizhen Yao, Lucas T Graybuck, David J Peeler, Sumit Mukherjee, Wei Chen,[...]. Science 2018
370
8

SpatialDE: identification of spatially variable genes.
Valentine Svensson, Sarah A Teichmann, Oliver Stegle. Nat Methods 2018
66
8

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
329
8

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data.
Catalina A Vallejos, John C Marioni, Sylvia Richardson. PLoS Comput Biol 2015
130
8

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
445
8

Design and computational analysis of single-cell RNA-sequencing experiments.
Rhonda Bacher, Christina Kendziorski. Genome Biol 2016
204
8


Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity.
Christof Angermueller, Stephen J Clark, Heather J Lee, Iain C Macaulay, Mabel J Teng, Tim Xiaoming Hu, Felix Krueger, Sebastien Smallwood, Chris P Ponting, Thierry Voet,[...]. Nat Methods 2016
313
8

AutoImpute: Autoencoder based imputation of single-cell RNA-seq data.
Divyanshu Talwar, Aanchal Mongia, Debarka Sengupta, Angshul Majumdar. Sci Rep 2018
37
8

Tackling the widespread and critical impact of batch effects in high-throughput data.
Jeffrey T Leek, Robert B Scharpf, Héctor Corrada Bravo, David Simcha, Benjamin Langmead, W Evan Johnson, Donald Geman, Keith Baggerly, Rafael A Irizarry. Nat Rev Genet 2010
957
8

bayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing data.
Wenhao Tang, François Bertaux, Philipp Thomas, Claire Stefanelli, Malika Saint, Samuel Marguerat, Vahid Shahrezaei. Bioinformatics 2020
14
21

powsimR: power analysis for bulk and single cell RNA-seq experiments.
Beate Vieth, Christoph Ziegenhain, Swati Parekh, Wolfgang Enard, Ines Hellmann. Bioinformatics 2017
48
8

Comparison of Computational Methods for Imputing Single-Cell RNA-Sequencing Data.
Lihua Zhang, Shihua Zhang. IEEE/ACM Trans Comput Biol Bioinform 2020
42
8

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
303
8

From Louvain to Leiden: guaranteeing well-connected communities.
V A Traag, L Waltman, N J van Eck. Sci Rep 2019
259
8

SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation.
Hirotaka Matsumoto, Hisanori Kiryu, Chikara Furusawa, Minoru S H Ko, Shigeru B H Ko, Norio Gouda, Tetsutaro Hayashi, Itoshi Nikaido. Bioinformatics 2017
86
8

Functional interpretation of single cell similarity maps.
David DeTomaso, Matthew G Jones, Meena Subramaniam, Tal Ashuach, Chun J Ye, Nir Yosef. Nat Commun 2019
34
8


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
464
8


Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis.
Jean Fan, Neeraj Salathia, Rui Liu, Gwendolyn E Kaeser, Yun C Yung, Joseph L Herman, Fiona Kaper, Jian-Bing Fan, Kun Zhang, Jerold Chun,[...]. Nat Methods 2016
182
8

Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics.
Marlon Stoeckius, Shiwei Zheng, Brian Houck-Loomis, Stephanie Hao, Bertrand Z Yeung, William M Mauck, Peter Smibert, Rahul Satija. Genome Biol 2018
188
8

Near-optimal probabilistic RNA-seq quantification.
Nicolas L Bray, Harold Pimentel, Páll Melsted, Lior Pachter. Nat Biotechnol 2016
8

Visualizing structure and transitions in high-dimensional biological data.
Kevin R Moon, David van Dijk, Zheng Wang, Scott Gigante, Daniel B Burkhardt, William S Chen, Kristina Yim, Antonia van den Elzen, Matthew J Hirn, Ronald R Coifman,[...]. Nat Biotechnol 2019
96
8

Supervised classification enables rapid annotation of cell atlases.
Hannah A Pliner, Jay Shendure, Cole Trapnell. Nat Methods 2019
88
8

Salmon provides fast and bias-aware quantification of transcript expression.
Rob Patro, Geet Duggal, Michael I Love, Rafael A Irizarry, Carl Kingsford. Nat Methods 2017
8

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama.
Brian Hie, Bryan Bryson, Bonnie Berger. Nat Biotechnol 2019
123
8

The sva package for removing batch effects and other unwanted variation in high-throughput experiments.
Jeffrey T Leek, W Evan Johnson, Hilary S Parker, Andrew E Jaffe, John D Storey. Bioinformatics 2012
8

Fast, sensitive and accurate integration of single-cell data with Harmony.
Ilya Korsunsky, Nghia Millard, Jean Fan, Kamil Slowikowski, Fan Zhang, Kevin Wei, Yuriy Baglaenko, Michael Brenner, Po-Ru Loh, Soumya Raychaudhuri. Nat Methods 2019
400
8

Assessment of computational methods for the analysis of single-cell ATAC-seq data.
Huidong Chen, Caleb Lareau, Tommaso Andreani, Michael E Vinyard, Sara P Garcia, Kendell Clement, Miguel A Andrade-Navarro, Jason D Buenrostro, Luca Pinello. Genome Biol 2019
54
8

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics.
Bosiljka Tasic, Vilas Menon, Thuc Nghi Nguyen, Tae Kyung Kim, Tim Jarsky, Zizhen Yao, Boaz Levi, Lucas T Gray, Staci A Sorensen, Tim Dolbeare,[...]. Nat Neurosci 2016
715
8

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
75
8

Normalization of RNA-seq data using factor analysis of control genes or samples.
Davide Risso, John Ngai, Terence P Speed, Sandrine Dudoit. Nat Biotechnol 2014
686
8

Comparative Analysis of Droplet-Based Ultra-High-Throughput Single-Cell RNA-Seq Systems.
Xiannian Zhang, Tianqi Li, Feng Liu, Yaqi Chen, Jiacheng Yao, Zeyao Li, Yanyi Huang, Jianbin Wang. Mol Cell 2019
100
8

Benchmark and Parameter Sensitivity Analysis of Single-Cell RNA Sequencing Clustering Methods.
Monika Krzak, Yordan Raykov, Alexis Boukouvalas, Luisa Cutillo, Claudia Angelini. Front Genet 2019
8
37

GSVA: gene set variation analysis for microarray and RNA-seq data.
Sonja Hänzelmann, Robert Castelo, Justin Guinney. BMC Bioinformatics 2013
8

Single-cell RNA counting at allele and isoform resolution using Smart-seq3.
Michael Hagemann-Jensen, Christoph Ziegenhain, Ping Chen, Daniel Ramsköld, Gert-Jan Hendriks, Anton J M Larsson, Omid R Faridani, Rickard Sandberg. Nat Biotechnol 2020
70
8

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis.
Jacob H Levine, Erin F Simonds, Sean C Bendall, Kara L Davis, El-ad D Amir, Michelle D Tadmor, Oren Litvin, Harris G Fienberg, Astraea Jager, Eli R Zunder,[...]. Cell 2015
678
8



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.