A citation-based method for searching scientific literature

Chen Shengquan, Zhang Boheng, Chen Xiaoyang, Zhang Xuegong, Jiang Rui. Bioinformatics 2021
Times Cited: 2







List of co-cited articles
46 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
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
780
100

SpaGE: Spatial Gene Enhancement using scRNA-seq.
Tamim Abdelaal, Soufiane Mourragui, Ahmed Mahfouz, Marcel J T Reinders. Nucleic Acids Res 2020
17
100

Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis.
Damien Arnol, Denis Schapiro, Bernd Bodenmiller, Julio Saez-Rodriguez, Oliver Stegle. Cell Rep 2019
43
100

SpatialDB: a database for spatially resolved transcriptomes.
Zhen Fan, Runsheng Chen, Xiaowei Chen. Nucleic Acids Res 2020
16
100


Super-resolved spatial transcriptomics by deep data fusion.
Ludvig Bergenstråhle, Bryan He, Joseph Bergenstråhle, Xesús Abalo, Reza Mirzazadeh, Kim Thrane, Andrew L Ji, Alma Andersson, Ludvig Larsson, Nathalie Stakenborg,[...]. Nat Biotechnol 2022
7
100


Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography.
Alma Andersson, Joseph Bergenstråhle, Michaela Asp, Ludvig Bergenstråhle, Aleksandra Jurek, José Fernández Navarro, Joakim Lundeberg. Commun Biol 2020
59
100

A draft network of ligand-receptor-mediated multicellular signalling in human.
Jordan A Ramilowski, Tatyana Goldberg, Jayson Harshbarger, Edda Kloppmann, Marina Lizio, Venkata P Satagopam, Masayoshi Itoh, Hideya Kawaji, Piero Carninci, Burkhard Rost,[...]. Nat Commun 2015
317
100

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
100


SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network.
Jian Hu, Xiangjie Li, Kyle Coleman, Amelia Schroeder, Nan Ma, David J Irwin, Edward B Lee, Russell T Shinohara, Mingyao Li. Nat Methods 2021
11
100

Spatially resolved transcriptomics and beyond.
Nicola Crosetto, Magda Bienko, Alexander van Oudenaarden. Nat Rev Genet 2015
246
100

The Drosophila embryo at single-cell transcriptome resolution.
Nikos Karaiskos, Philipp Wahle, Jonathan Alles, Anastasiya Boltengagen, Salah Ayoub, Claudia Kipar, Christine Kocks, Nikolaus Rajewsky, Robert P Zinzen. Science 2017
178
100

Spatially resolved transcriptomics adds a new dimension to genomics.
Ludvig Larsson, Jonas Frisén, Joakim Lundeberg. Nat Methods 2021
39
100

Deep generative modeling for single-cell transcriptomics.
Romain Lopez, Jeffrey Regier, Michael B Cole, Michael I Jordan, Nir Yosef. Nat Methods 2018
305
100

Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas.
Reuben Moncada, Dalia Barkley, Florian Wagner, Marta Chiodin, Joseph C Devlin, Maayan Baron, Cristina H Hajdu, Diane M Simeone, Itai Yanai. Nat Biotechnol 2020
158
100

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
144
100

The landscape of cell-cell communication through single-cell transcriptomics.
Axel A Almet, Zixuan Cang, Suoqin Jin, Qing Nie. Curr Opin Syst Biol 2021
14
100


High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin.
Kaia Achim, Jean-Baptiste Pettit, Luis R Saraiva, Daria Gavriouchkina, Tomas Larsson, Detlev Arendt, John C Marioni. Nat Biotechnol 2015
220
100

Gene expression cartography.
Mor Nitzan, Nikos Karaiskos, Nir Friedman, Nikolaus Rajewsky. Nature 2019
81
100

Probabilistic cell typing enables fine mapping of closely related cell types in situ.
Xiaoyan Qian, Kenneth D Harris, Thomas Hauling, Dimitris Nicoloutsopoulos, Ana B Muñoz-Manchado, Nathan Skene, Jens Hjerling-Leffler, Mats Nilsson. Nat Methods 2020
54
100


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
722
100

SpatialDE: identification of spatially variable genes.
Valentine Svensson, Sarah A Teichmann, Oliver Stegle. Nat Methods 2018
94
100

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.
Michaela Asp, Stefania Giacomello, Ludvig Larsson, Chenglin Wu, Daniel Fürth, Xiaoyan Qian, Eva Wärdell, Joaquin Custodio, Johan Reimegård, Fredrik Salmén,[...]. Cell 2019
150
100

Identification of spatial expression trends in single-cell gene expression data.
Daniel Edsgärd, Per Johnsson, Rickard Sandberg. Nat Methods 2018
87
100



High-definition spatial transcriptomics for in situ tissue profiling.
Sanja Vickovic, Gökcen Eraslan, Fredrik Salmén, Johanna Klughammer, Linnea Stenbeck, Denis Schapiro, Tarmo Äijö, Richard Bonneau, Ludvig Bergenstråhle, José Fernandéz Navarro,[...]. Nat Methods 2019
248
100

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
511
100


Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram.
Tommaso Biancalani, Gabriele Scalia, Lorenzo Buffoni, Raghav Avasthi, Ziqing Lu, Aman Sanger, Neriman Tokcan, Charles R Vanderburg, Åsa Segerstolpe, Meng Zhang,[...]. Nat Methods 2021
10
100

Spatial transcriptomics at subspot resolution with BayesSpace.
Edward Zhao, Matthew R Stone, Xing Ren, Jamie Guenthoer, Kimberly S Smythe, Thomas Pulliam, Stephen R Williams, Cedric R Uytingco, Sarah E B Taylor, Paul Nghiem,[...]. Nat Biotechnol 2021
22
100

Giotto: a toolbox for integrative analysis and visualization of spatial expression data.
Ruben Dries, Qian Zhu, Rui Dong, Chee-Huat Linus Eng, Huipeng Li, Kan Liu, Yuntian Fu, Tianxiao Zhao, Arpan Sarkar, Feng Bao,[...]. Genome Biol 2021
50
100

Toward a Common Coordinate Framework for the Human Body.
Jennifer E Rood, Tim Stuart, Shila Ghazanfar, Tommaso Biancalani, Eyal Fisher, Andrew Butler, Anna Hupalowska, Leslie Gaffney, William Mauck, Gökçen Eraslan,[...]. Cell 2019
27
100

SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes.
Marc Elosua-Bayes, Paula Nieto, Elisabetta Mereu, Ivo Gut, Holger Heyn. Nucleic Acids Res 2021
51
100

Integrating spatial gene expression and breast tumour morphology via deep learning.
Bryan He, Ludvig Bergenstråhle, Linnea Stenbeck, Abubakar Abid, Alma Andersson, Åke Borg, Jonas Maaskola, Joakim Lundeberg, James Zou. Nat Biomed Eng 2020
45
100

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
100


Mapping the physical network of cellular interactions.
Jean-Charles Boisset, Judith Vivié, Dominic Grün, Mauro J Muraro, Anna Lyubimova, Alexander van Oudenaarden. Nat Methods 2018
56
100

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
425
100

Robust decomposition of cell type mixtures in spatial transcriptomics.
Dylan M Cable, Evan Murray, Luli S Zou, Aleksandrina Goeva, Evan Z Macosko, Fei Chen, Rafael A Irizarry. Nat Biotechnol 2022
40
100

Seamless integration of image and molecular analysis for spatial transcriptomics workflows.
Joseph Bergenstråhle, Ludvig Larsson, Joakim Lundeberg. BMC Genomics 2020
28
100

Automated assignment of cell identity from single-cell multiplexed imaging and proteomic data.
Michael J Geuenich, Jinyu Hou, Sunyun Lee, Shanza Ayub, Hartland W Jackson, Kieran R Campbell. Cell Syst 2021
2
50

Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability.
Mojca Mattiazzi Usaj, Nil Sahin, Helena Friesen, Carles Pons, Matej Usaj, Myra Paz D Masinas, Ermira Shuteriqi, Aleksei Shkurin, Patrick Aloy, Quaid Morris,[...]. Mol Syst Biol 2020
15
50


Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis.
T Lohoff, S Ghazanfar, A Missarova, N Koulena, N Pierson, J A Griffiths, E S Bardot, C-H L Eng, R C V Tyser, R Argelaguet,[...]. Nat Biotechnol 2022
10
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.