A citation-based method for searching scientific literature

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, Jason H Bielas, Raphael Gottardo. Nat Biotechnol 2021
Times Cited: 5







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



Times Cited
  Times     Co-cited
Similarity


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
714
80


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
52
80

Single-cell in situ RNA profiling by sequential hybridization.
Eric Lubeck, Ahmet F Coskun, Timur Zhiyentayev, Mubhij Ahmad, Long Cai. Nat Methods 2014
343
80

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
121
80

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
475
80

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
625
80

Identification of spatial expression trends in single-cell gene expression data.
Daniel Edsgärd, Per Johnsson, Rickard Sandberg. Nat Methods 2018
73
80

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
208
80

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
440
80

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
25
80

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 2021
20
80

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
370
80


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
326
80

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
60

RNA velocity of single cells.
Gioele La Manno, Ruslan Soldatov, Amit Zeisel, Emelie Braun, Hannah Hochgerner, Viktor Petukhov, Katja Lidschreiber, Maria E Kastriti, Peter Lönnerberg, Alessandro Furlan,[...]. Nature 2018
732
60

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
125
60

SpaCell: integrating tissue morphology and spatial gene expression to predict disease cells.
Xiao Tan, Andrew Su, Minh Tran, Quan Nguyen. Bioinformatics 2020
9
60

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
37
60


Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin.
Jun-Han Su, Pu Zheng, Seon S Kinrot, Bogdan Bintu, Xiaowei Zhuang. Cell 2020
66
60

Integrated spatial genomics reveals global architecture of single nuclei.
Yodai Takei, Jina Yun, Shiwei Zheng, Noah Ollikainen, Nico Pierson, Jonathan White, Sheel Shah, Julian Thomassie, Shengbao Suo, Chee-Huat Linus Eng,[...]. Nature 2021
31
60

NicheNet: modeling intercellular communication by linking ligands to target genes.
Robin Browaeys, Wouter Saelens, Yvan Saeys. Nat Methods 2020
136
60

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
35
60

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
115
60

Seamless integration of image and molecular analysis for spatial transcriptomics workflows.
Joseph Bergenstråhle, Ludvig Larsson, Joakim Lundeberg. BMC Genomics 2020
18
60

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
290
60

Spatially Resolved Transcriptomes-Next Generation Tools for Tissue Exploration.
Michaela Asp, Joseph Bergenstråhle, Joakim Lundeberg. Bioessays 2020
65
60

Microscopic examination of spatial transcriptome using Seq-Scope.
Chun-Seok Cho, Jingyue Xi, Yichen Si, Sung-Rye Park, Jer-En Hsu, Myungjin Kim, Goo Jun, Hyun Min Kang, Jun Hee Lee. Cell 2021
8
60

SpatialDE: identification of spatially variable genes.
Valentine Svensson, Sarah A Teichmann, Oliver Stegle. Nat Methods 2018
74
60

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
40
60

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
289
60

Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling.
Susanne Nichterwitz, Geng Chen, Julio Aguila Benitez, Marlene Yilmaz, Helena Storvall, Ming Cao, Rickard Sandberg, Qiaolin Deng, Eva Hedlund. Nat Commun 2016
123
40

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
489
40

The safety of lecithin diet supplementation in schizophrenic patients.
C F Yackulic, B G Anderson, D Reker, E Webb, J Volavka. Biol Psychiatry 1982
20
40

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
300
40

STARCH: copy number and clone inference from spatial transcriptomics data.
Rebecca Elyanow, Ron Zeira, Max Land, Benjamin J Raphael. Phys Biol 2021
6
40

Synthetic recording and in situ readout of lineage information in single cells.
Kirsten L Frieda, James M Linton, Sahand Hormoz, Joonhyuk Choi, Ke-Huan K Chow, Zakary S Singer, Mark W Budde, Michael B Elowitz, Long Cai. Nature 2017
191
40

histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data.
Denis Schapiro, Hartland W Jackson, Swetha Raghuraman, Jana R Fischer, Vito R T Zanotelli, Daniel Schulz, Charlotte Giesen, Raúl Catena, Zsuzsanna Varga, Bernd Bodenmiller. Nat Methods 2017
148
40

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.
Kelly Street, Davide Risso, Russell B Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom, Sandrine Dudoit. BMC Genomics 2018
374
40

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
812
40

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
242
40

In situ genome sequencing resolves DNA sequence and structure in intact biological samples.
Andrew C Payne, Zachary D Chiang, Paul L Reginato, Sarah M Mangiameli, Evan M Murray, Chun-Chen Yao, Styliani Markoulaki, Andrew S Earl, Ajay S Labade, Rudolf Jaenisch,[...]. Science 2021
25
40

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
126
40

Spatially resolved transcriptomics adds a new dimension to genomics.
Ludvig Larsson, Jonas Frisén, Joakim Lundeberg. Nat Methods 2021
21
40

3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing.
Huy Q Nguyen, Shyamtanu Chattoraj, David Castillo, Son C Nguyen, Guy Nir, Antonios Lioutas, Elliot A Hershberg, Nuno M C Martins, Paul L Reginato, Mohammed Hannan,[...]. Nat Methods 2020
27
40

Cellpose: a generalist algorithm for cellular segmentation.
Carsen Stringer, Tim Wang, Michalis Michaelos, Marius Pachitariu. Nat Methods 2021
89
40

Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq.
Jun Chen, Shengbao Suo, Patrick Pl Tam, Jing-Dong J Han, Guangdun Peng, Naihe Jing. Nat Protoc 2017
94
40

Integrative single-cell analysis.
Tim Stuart, Rahul Satija. Nat Rev Genet 2019
354
40


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.