A citation-based method for searching scientific literature

Shahar Alon, Daniel R Goodwin, Anubhav Sinha, Asmamaw T Wassie, Fei Chen, Evan R Daugharthy, Yosuke Bando, Atsushi Kajita, Andrew G Xue, Karl Marrett, Robert Prior, Yi Cui, Andrew C Payne, Chun-Chen Yao, Ho-Jun Suk, Ru Wang, Chih-Chieh Jay Yu, Paul Tillberg, Paul Reginato, Nikita Pak, Songlei Liu, Sukanya Punthambaker, Eswar P R Iyer, Richie E Kohman, Jeremy A Miller, Ed S Lein, Ana Lako, Nicole Cullen, Scott Rodig, Karla Helvie, Daniel L Abravanel, Nikhil Wagle, Bruce E Johnson, Johanna Klughammer, Michal Slyper, Julia Waldman, Judit Jané-Valbuena, Orit Rozenblatt-Rosen, Aviv Regev, George M Church, Adam H Marblestone, Edward S Boyden. Science 2021
Times Cited: 37







List of co-cited articles
428 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
625
43

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
43

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
40

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
40

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
40

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
37

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
35

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
35

Single-cell in situ RNA profiling by sequential hybridization.
Eric Lubeck, Ahmet F Coskun, Timur Zhiyentayev, Mubhij Ahmad, Long Cai. Nat Methods 2014
343
35


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
24

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
24

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues.
Je Hyuk Lee, Evan R Daugharthy, Jonathan Scheiman, Reza Kalhor, Thomas C Ferrante, Richard Terry, Brian M Turczyk, Joyce L Yang, Ho Suk Lee, John Aach,[...]. Nat Protoc 2015
218
21

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
21

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
21

Visualization of single RNA transcripts in situ.
A M Femino, F S Fay, K Fogarty, R H Singer. Science 1998
795
21

Multiplexed ion beam imaging of human breast tumors.
Michael Angelo, Sean C Bendall, Rachel Finck, Matthew B Hale, Chuck Hitzman, Alexander D Borowsky, Richard M Levenson, John B Lowe, Scot D Liu, Shuchun Zhao,[...]. Nat Med 2014
452
18

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
18

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
18


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
24

Optical imaging. Expansion microscopy.
Fei Chen, Paul W Tillberg, Edward S Boyden. Science 2015
487
16

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
16

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
16

Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy.
Guiping Wang, Jeffrey R Moffitt, Xiaowei Zhuang. Sci Rep 2018
76
16

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
16

Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer's Disease.
Wei-Ting Chen, Ashley Lu, Katleen Craessaerts, Benjamin Pavie, Carlo Sala Frigerio, Nikky Corthout, Xiaoyan Qian, Jana Laláková, Malte Kühnemund, Iryna Voytyuk,[...]. Cell 2020
101
16

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
710
16

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
24

From whole-mount to single-cell spatial assessment of gene expression in 3D.
Lisa N Waylen, Hieu T Nim, Luciano G Martelotto, Mirana Ramialison. Commun Biol 2020
31
19

Local protein synthesis is a ubiquitous feature of neuronal pre- and postsynaptic compartments.
Anne-Sophie Hafner, Paul G Donlin-Asp, Beulah Leitch, Etienne Herzog, Erin M Schuman. Science 2019
116
16


Gene expression cartography.
Mor Nitzan, Nikos Karaiskos, Nir Friedman, Nikolaus Rajewsky. Nature 2019
70
16


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
16

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
18

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization.
Jeffrey R Moffitt, Junjie Hao, Guiping Wang, Kok Hao Chen, Hazen P Babcock, Xiaowei Zhuang. Proc Natl Acad Sci U S A 2016
169
13

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
108
13

Simultaneous epitope and transcriptome measurement in single cells.
Marlon Stoeckius, Christoph Hafemeister, William Stephenson, Brian Houck-Loomis, Pratip K Chattopadhyay, Harold Swerdlow, Rahul Satija, Peter Smibert. Nat Methods 2017
739
13

Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues.
Sinem K Saka, Yu Wang, Jocelyn Y Kishi, Allen Zhu, Yitian Zeng, Wenxin Xie, Koray Kirli, Clarence Yapp, Marcelo Cicconet, Brian J Beliveau,[...]. Nat Biotechnol 2019
86
13

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry.
Charlotte Giesen, Hao A O Wang, Denis Schapiro, Nevena Zivanovic, Andrea Jacobs, Bodo Hattendorf, Peter J Schüffler, Daniel Grolimund, Joachim M Buhmann, Simone Brandt,[...]. Nat Methods 2014
693
13

ZipSeq: barcoding for real-time mapping of single cell transcriptomes.
Kenneth H Hu, John P Eichorst, Chris S McGinnis, David M Patterson, Eric D Chow, Kelly Kersten, Stephen C Jameson, Zev J Gartner, Arjun A Rao, Matthew F Krummel. Nat Methods 2020
21
23

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
14

Multiplex digital spatial profiling of proteins and RNA in fixed tissue.
Christopher R Merritt, Giang T Ong, Sarah E Church, Kristi Barker, Patrick Danaher, Gary Geiss, Margaret Hoang, Jaemyeong Jung, Yan Liang, Jill McKay-Fleisch,[...]. Nat Biotechnol 2020
80
13

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
44
13

Spatial transcriptomics: paving the way for tissue-level systems biology.
Andreas E Moor, Shalev Itzkovitz. Curr Opin Biotechnol 2017
59
13

Nanoscale imaging of RNA with expansion microscopy.
Fei Chen, Asmamaw T Wassie, Allison J Cote, Anubhav Sinha, Shahar Alon, Shoh Asano, Evan R Daugharthy, Jae-Byum Chang, Adam Marblestone, George M Church,[...]. Nat Methods 2016
150
13

Dynamic Axonal Translation in Developing and Mature Visual Circuits.
Toshiaki Shigeoka, Hosung Jung, Jane Jung, Benita Turner-Bridger, Jiyeon Ohk, Julie Qiaojin Lin, Paul S Amieux, Christine E Holt. Cell 2016
225
13

Spatially resolved transcriptomics and beyond.
Nicola Crosetto, Magda Bienko, Alexander van Oudenaarden. Nat Rev Genet 2015
232
13

Imaging individual mRNA molecules using multiple singly labeled probes.
Arjun Raj, Patrick van den Bogaard, Scott A Rifkin, Alexander van Oudenaarden, Sanjay Tyagi. Nat Methods 2008
13


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.