A citation-based method for searching scientific literature

Yinlei Hu, Bin Li, Wen Zhang, Nianping Liu, Pengfei Cai, Falai Chen, Kun Qu. Brief Bioinform 2021
Times Cited: 2







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



Times Cited
  Times     Co-cited
Similarity


SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
812
100

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
100

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells.
Liying Yan, Mingyu Yang, Hongshan Guo, Lu Yang, Jun Wu, Rong Li, Ping Liu, Ying Lian, Xiaoying Zheng, Jie Yan,[...]. Nat Struct Mol Biol 2013
804
100

SAVER: gene expression recovery for single-cell RNA sequencing.
Mo Huang, Jingshu Wang, Eduardo Torre, Hannah Dueck, Sydney Shaffer, Roberto Bonasio, John I Murray, Arjun Raj, Mingyao Li, Nancy R Zhang. Nat Methods 2018
186
100

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
100

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
100

Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq.
Amit Zeisel, Ana B Muñoz-Manchado, Simone Codeluppi, Peter Lönnerberg, Gioele La Manno, Anna Juréus, Sueli Marques, Hermany Munguba, Liqun He, Christer Betsholtz,[...]. Science 2015
100

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
474
100


Reconstructing cell cycle pseudo time-series via single-cell transcriptome data.
Zehua Liu, Huazhe Lou, Kaikun Xie, Hao Wang, Ning Chen, Oscar M Aparicio, Michael Q Zhang, Rui Jiang, Ting Chen. Nat Commun 2017
44
50

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database.
Luke Zappia, Belinda Phipson, Alicia Oshlack. PLoS Comput Biol 2018
91
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

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq.
Barbara Treutlein, Doug G Brownfield, Angela R Wu, Norma F Neff, Gary L Mantalas, F Hernan Espinoza, Tushar J Desai, Mark A Krasnow, Stephen R Quake. Nature 2014
752
50


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
380
50


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

Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq.
Michael B Cole, Davide Risso, Allon Wagner, David DeTomaso, John Ngai, Elizabeth Purdom, Sandrine Dudoit, Nir Yosef. Cell Syst 2019
43
50

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation.
Aleksandra A Kolodziejczyk, Jong Kyoung Kim, Jason C H Tsang, Tomislav Ilicic, Johan Henriksson, Kedar N Natarajan, Alex C Tuck, Xuefei Gao, Marc Bühler, Pentao Liu,[...]. Cell Stem Cell 2015
241
50

Identification of cancer subtypes from single-cell RNA-seq data using a consensus clustering method.
Yanglan Gan, Ning Li, Guobing Zou, Yongchang Xin, Jihong Guan. BMC Med Genomics 2018
9
50

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer.
Lei Zhang, Xin Yu, Liangtao Zheng, Yuanyuan Zhang, Yansen Li, Qiao Fang, Ranran Gao, Boxi Kang, Qiming Zhang, Julie Y Huang,[...]. Nature 2018
251
50

Detection of high variability in gene expression from single-cell RNA-seq profiling.
Hung-I Harry Chen, Yufang Jin, Yufei Huang, Yidong Chen. BMC Genomics 2016
21
50

Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells.
Qiaolin Deng, Daniel Ramsköld, Björn Reinius, Rickard Sandberg. Science 2014
605
50

Identification of Differential Gene Groups From Single-Cell Transcriptomes Using Network Entropy.
Yanglan Gan, Shanshan Liang, Qingting Wei, Guobing Zou. Front Cell Dev Biol 2020
1
100


Comparison of Scanpy-based algorithms to remove the batch effect from single-cell RNA-seq data.
Jiaqi Li, Chengxuan Yu, Lifeng Ma, Jingjing Wang, Guoji Guo. Cell Regen 2020
2
50

Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments.
Luyi Tian, Xueyi Dong, Saskia Freytag, Kim-Anh Lê Cao, Shian Su, Abolfazl JalalAbadi, Daniela Amann-Zalcenstein, Tom S Weber, Azadeh Seidi, Jafar S Jabbari,[...]. Nat Methods 2019
89
50

PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells.
F Alexander Wolf, Fiona K Hamey, Mireya Plass, Jordi Solana, Joakim S Dahlin, Berthold Göttgens, Nikolaus Rajewsky, Lukas Simon, Fabian J Theis. Genome Biol 2019
222
50

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
50

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors.
Huipeng Li, Elise T Courtois, Debarka Sengupta, Yuliana Tan, Kok Hao Chen, Jolene Jie Lin Goh, Say Li Kong, Clarinda Chua, Lim Kiat Hon, Wah Siew Tan,[...]. Nat Genet 2017
397
50

CVXPY: A Python-Embedded Modeling Language for Convex Optimization.
Steven Diamond, Stephen Boyd. J Mach Learn Res 2016
42
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

Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq.
Bo Li, Joshua Gould, Yiming Yang, Siranush Sarkizova, Marcin Tabaka, Orr Ashenberg, Yanay Rosen, Michal Slyper, Monika S Kowalczyk, Alexandra-Chloé Villani,[...]. Nat Methods 2020
24
50

Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos.
Mubeen Goolam, Antonio Scialdone, Sarah J L Graham, Iain C Macaulay, Agnieszka Jedrusik, Anna Hupalowska, Thierry Voet, John C Marioni, Magdalena Zernicka-Goetz. Cell 2016
183
50

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

Spectral Mesh Segmentation via l0 Gradient Minimization.
Weihua Tong, Xiankang Yang, Maodong Pan, Falai Chen. IEEE Trans Vis Comput Graph 2020
1
100

A survey of human brain transcriptome diversity at the single cell level.
Spyros Darmanis, Steven A Sloan, Ye Zhang, Martin Enge, Christine Caneda, Lawrence M Shuer, Melanie G Hayden Gephart, Ben A Barres, Stephen R Quake. Proc Natl Acad Sci U S A 2015
571
50

Structural absorption by barbule microstructures of super black bird of paradise feathers.
Dakota E McCoy, Teresa Feo, Todd Alan Harvey, Richard O Prum. Nat Commun 2018
50


Dimensionality reduction for visualizing single-cell data using UMAP.
Etienne Becht, Leland McInnes, John Healy, Charles-Antoine Dutertre, Immanuel W H Kwok, Lai Guan Ng, Florent Ginhoux, Evan W Newell. Nat Biotechnol 2018
918
50

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
50

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
50


scLRTD : A novel low rank tensor decomposition method for imputing missing values in single-cell multi-omics sequencing data.
Zhijie Ni, Xiaoying Zheng, Xiao Zheng, Xiufen Zou. IEEE/ACM Trans Comput Biol Bioinform 2020
1
100

False signals induced by single-cell imputation.
Tallulah S Andrews, Martin Hemberg. F1000Res 2018
47
50

scRMD: imputation for single cell RNA-seq data via robust matrix decomposition.
Chong Chen, Changjing Wu, Linjie Wu, Xiaochen Wang, Minghua Deng, Ruibin Xi. Bioinformatics 2020
11
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

scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses.
Juexin Wang, Anjun Ma, Yuzhou Chang, Jianting Gong, Yuexu Jiang, Ren Qi, Cankun Wang, Hongjun Fu, Qin Ma, Dong Xu. Nat Commun 2021
10
50

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