A citation-based method for searching scientific literature

Dylan M Cable, Evan Murray, Luli S Zou, Aleksandrina Goeva, Evan Z Macosko, Fei Chen, Rafael A Irizarry. Nat Biotechnol 2021
Times Cited: 18







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



Times Cited
  Times     Co-cited
Similarity


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
576
72

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
402
72

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
61


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
21
55

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
679
50

SpatialDE: identification of spatially variable genes.
Valentine Svensson, Sarah A Teichmann, Oliver Stegle. Nat Methods 2018
66
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
303
50

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
97
44

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
177
44

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
100
44

Single-cell in situ RNA profiling by sequential hybridization.
Eric Lubeck, Ahmet F Coskun, Timur Zhiyentayev, Mubhij Ahmad, Long Cai. Nat Methods 2014
322
44

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
44

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
30
44

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
22
44

Spatially Resolved Transcriptomics Enables Dissection of Genetic Heterogeneity in Stage III Cutaneous Malignant Melanoma.
Kim Thrane, Hanna Eriksson, Jonas Maaskola, Johan Hansson, Joakim Lundeberg. Cancer Res 2018
61
38

Identification of spatial expression trends in single-cell gene expression data.
Daniel Edsgärd, Per Johnsson, Rickard Sandberg. Nat Methods 2018
65
38

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue.
Yang Liu, Mingyu Yang, Yanxiang Deng, Graham Su, Archibald Enninful, Cindy C Guo, Toma Tebaldi, Di Zhang, Dongjoo Kim, Zhiliang Bai,[...]. Cell 2020
43
38

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma.
Andrew L Ji, Adam J Rubin, Kim Thrane, Sizun Jiang, David L Reynolds, Robin M Meyers, Margaret G Guo, Benson M George, Annelie Mollbrink, Joseph Bergenstråhle,[...]. Cell 2020
59
38

Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity.
Emelie Berglund, Jonas Maaskola, Niklas Schultz, Stefanie Friedrich, Maja Marklund, Joseph Bergenstråhle, Firas Tarish, Anna Tanoglidi, Sanja Vickovic, Ludvig Larsson,[...]. Nat Commun 2018
113
33

The Human Cell Atlas.
Aviv Regev, Sarah A Teichmann, Eric S Lander, Ido Amit, Christophe Benoist, Ewan Birney, Bernd Bodenmiller, Peter Campbell, Piero Carninci, Menna Clatworthy,[...]. Elife 2017
668
33



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
33

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2.
Robert R Stickels, Evan Murray, Pawan Kumar, Jilong Li, Jamie L Marshall, Daniela J Di Bella, Paola Arlotta, Evan Z Macosko, Fei Chen. Nat Biotechnol 2021
33
33

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis.
Silas Maniatis, Tarmo Äijö, Sanja Vickovic, Catherine Braine, Kristy Kang, Annelie Mollbrink, Delphine Fagegaltier, Žaneta Andrusivová, Sami Saarenpää, Gonzalo Saiz-Castro,[...]. Science 2019
102
27

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
212
27

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
265
27

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
27

Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging.
Yury Goltsev, Nikolay Samusik, Julia Kennedy-Darling, Salil Bhate, Matthew Hale, Gustavo Vazquez, Sarah Black, Garry P Nolan. Cell 2018
266
27

Spatially Resolved Transcriptomes-Next Generation Tools for Tissue Exploration.
Michaela Asp, Joseph Bergenstråhle, Joakim Lundeberg. Bioessays 2020
47
27

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.
Itay Tirosh, Benjamin Izar, Sanjay M Prakadan, Marc H Wadsworth, Daniel Treacy, John J Trombetta, Asaf Rotem, Christopher Rodman, Christine Lian, George Murphy,[...]. Science 2016
27

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
24
27

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
215
27

Deciphering cell-cell interactions and communication from gene expression.
Erick Armingol, Adam Officer, Olivier Harismendy, Nathan E Lewis. Nat Rev Genet 2021
48
27

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
27

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
118
27

Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems.
Shahar Alon, Daniel R Goodwin, Anubhav Sinha, Asmamaw T Wassie, Fei Chen, Evan R Daugharthy, Yosuke Bando, Atsushi Kajita, Andrew G Xue, Karl Marrett,[...]. Science 2021
27
27

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
31
27


Seamless integration of image and molecular analysis for spatial transcriptomics workflows.
Joseph Bergenstråhle, Ludvig Larsson, Joakim Lundeberg. BMC Genomics 2020
14
35

The single-cell transcriptional landscape of mammalian organogenesis.
Junyue Cao, Malte Spielmann, Xiaojie Qiu, Xingfan Huang, Daniel M Ibrahim, Andrew J Hill, Fan Zhang, Stefan Mundlos, Lena Christiansen, Frank J Steemers,[...]. Nature 2019
444
22

Determining cell type abundance and expression from bulk tissues with digital cytometry.
Aaron M Newman, Chloé B Steen, Chih Long Liu, Andrew J Gentles, Aadel A Chaudhuri, Florian Scherer, Michael S Khodadoust, Mohammad S Esfahani, Bogdan A Luca, David Steiner,[...]. Nat Biotechnol 2019
415
22

Bulk tissue cell type deconvolution with multi-subject single-cell expression reference.
Xuran Wang, Jihwan Park, Katalin Susztak, Nancy R Zhang, Mingyao Li. Nat Commun 2019
142
22

Genome-wide atlas of gene expression in the adult mouse brain.
Ed S Lein, Michael J Hawrylycz, Nancy Ao, Mikael Ayres, Amy Bensinger, Amy Bernard, Andrew F Boe, Mark S Boguski, Kevin S Brockway, Emi J Byrnes,[...]. Nature 2007
22

Molecular Architecture of the Mouse Nervous System.
Amit Zeisel, Hannah Hochgerner, Peter Lönnerberg, Anna Johnsson, Fatima Memic, Job van der Zwan, Martin Häring, Emelie Braun, Lars E Borm, Gioele La Manno,[...]. Cell 2018
706
22

Gene expression cartography.
Mor Nitzan, Nikos Karaiskos, Nir Friedman, Nikolaus Rajewsky. Nature 2019
65
22

Spatial organization of the somatosensory cortex revealed by osmFISH.
Simone Codeluppi, Lars E Borm, Amit Zeisel, Gioele La Manno, Josina A van Lunteren, Camilla I Svensson, Sten Linnarsson. Nat Methods 2018
106
22

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
459
22

In situ sequencing for RNA analysis in preserved tissue and cells.
Rongqin Ke, Marco Mignardi, Alexandra Pacureanu, Jessica Svedlund, Johan Botling, Carolina Wählby, Mats Nilsson. Nat Methods 2013
289
22


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.