A citation-based method for searching scientific literature

Christian M Schürch, Salil S Bhate, Graham L Barlow, Darci J Phillips, Luca Noti, Inti Zlobec, Pauline Chu, Sarah Black, Janos Demeter, David R McIlwain, Shigemi Kinoshita, Nikolay Samusik, Yury Goltsev, Garry P Nolan. Cell 2020
Times Cited: 167







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



Times Cited
  Times     Co-cited
Similarity


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
464
56

The single-cell pathology landscape of breast cancer.
Hartland W Jackson, Jana R Fischer, Vito R T Zanotelli, H Raza Ali, Robert Mechera, Savas D Soysal, Holger Moch, Simone Muenst, Zsuzsanna Varga, Walter P Weber,[...]. Nature 2020
305
44

A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging.
Leeat Keren, Marc Bosse, Diana Marquez, Roshan Angoshtari, Samir Jain, Sushama Varma, Soo-Ryum Yang, Allison Kurian, David Van Valen, Robert West,[...]. Cell 2018
397
39

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
862
36

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
555
32

Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes.
Jia-Ren Lin, Benjamin Izar, Shu Wang, Clarence Yapp, Shaolin Mei, Parin M Shah, Sandro Santagata, Peter K Sorger. Elife 2018
231
24

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
236
19

Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue.
Michael J Gerdes, Christopher J Sevinsky, Anup Sood, Sudeshna Adak, Musodiq O Bello, Alexander Bordwell, Ali Can, Alex Corwin, Sean Dinn, Robert J Filkins,[...]. Proc Natl Acad Sci U S A 2013
380
19

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
158
18

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
674
18

CODEX multiplexed tissue imaging with DNA-conjugated antibodies.
Sarah Black, Darci Phillips, John W Hickey, Julia Kennedy-Darling, Vishal G Venkataraaman, Nikolay Samusik, Yury Goltsev, Christian M Schürch, Garry P Nolan. Nat Protoc 2021
49
36

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
925
17

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
205
17

Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method.
Jia-Ren Lin, Mohammad Fallahi-Sichani, Peter K Sorger. Nat Commun 2015
264
16

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
558
15

Understanding the tumor immune microenvironment (TIME) for effective therapy.
Mikhail Binnewies, Edward W Roberts, Kelly Kersten, Vincent Chan, Douglas F Fearon, Miriam Merad, Lisa M Coussens, Dmitry I Gabrilovich, Suzanne Ostrand-Rosenberg, Catherine C Hedrick,[...]. Nat Med 2018
14

CytoMAP: A Spatial Analysis Toolbox Reveals Features of Myeloid Cell Organization in Lymphoid Tissues.
Caleb R Stoltzfus, Jakub Filipek, Benjamin H Gern, Brandy E Olin, Joseph M Leal, Yajun Wu, Miranda R Lyons-Cohen, Jessica Y Huang, Clarissa L Paz-Stoltzfus, Courtney R Plumlee,[...]. Cell Rep 2020
68
20

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
950
14

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution.
Orit Rozenblatt-Rosen, Aviv Regev, Philipp Oberdoerffer, Tal Nawy, Anna Hupalowska, Jennifer E Rood, Orr Ashenberg, Ethan Cerami, Robert J Coffey, Emek Demir,[...]. Cell 2020
161
13

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
342
13

ilastik: interactive machine learning for (bio)image analysis.
Stuart Berg, Dominik Kutra, Thorben Kroeger, Christoph N Straehle, Bernhard X Kausler, Carsten Haubold, Martin Schiegg, Janez Ales, Thorsten Beier, Markus Rudy,[...]. Nat Methods 2019
663
13

QuPath: Open source software for digital pathology image analysis.
Peter Bankhead, Maurice B Loughrey, José A Fernández, Yvonne Dombrowski, Darragh G McArt, Philip D Dunne, Stephen McQuaid, Ronan T Gray, Liam J Murray, Helen G Coleman,[...]. Sci Rep 2017
13

Imaging mass cytometry and multiplatform genomics define the phenogenomic landscape of breast cancer.
H Raza Ali, Hartland W Jackson, Vito R T Zanotelli, Esther Danenberg, Jana R Fischer, Helen Bardwell, Elena Provenzano, Oscar M Rueda, Suet-Feung Chin, Samuel Aparicio,[...]. Nat Cancer 2020
74
17

CellProfiler 3.0: Next-generation image processing for biology.
Claire McQuin, Allen Goodman, Vasiliy Chernyshev, Lee Kamentsky, Beth A Cimini, Kyle W Karhohs, Minh Doan, Liya Ding, Susanne M Rafelski, Derek Thirstrup,[...]. PLoS Biol 2018
811
13


Cellpose: a generalist algorithm for cellular segmentation.
Carsen Stringer, Tim Wang, Michalis Michaelos, Marius Pachitariu. Nat Methods 2021
318
13

Multiplexed protein maps link subcellular organization to cellular states.
Gabriele Gut, Markus D Herrmann, Lucas Pelkmans. Science 2018
172
13

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
13

A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer.
Johanna Wagner, Maria Anna Rapsomaniki, Stéphane Chevrier, Tobias Anzeneder, Claus Langwieder, August Dykgers, Martin Rees, Annette Ramaswamy, Simone Muenst, Savas Deniz Soysal,[...]. Cell 2019
337
13

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
185
13

Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning.
Noah F Greenwald, Geneva Miller, Erick Moen, Alex Kong, Adam Kagel, Thomas Dougherty, Christine Camacho Fullaway, Brianna J McIntosh, Ke Xuan Leow, Morgan Sarah Schwartz,[...]. Nat Biotechnol 2022
57
21

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
949
12

Tertiary lymphoid structures improve immunotherapy and survival in melanoma.
Rita Cabrita, Martin Lauss, Adriana Sanna, Marco Donia, Mathilde Skaarup Larsen, Shamik Mitra, Iva Johansson, Bengt Phung, Katja Harbst, Johan Vallon-Christersson,[...]. Nature 2020
701
11

B cells and tertiary lymphoid structures promote immunotherapy response.
Beth A Helmink, Sangeetha M Reddy, Jianjun Gao, Shaojun Zhang, Rafet Basar, Rohit Thakur, Keren Yizhak, Moshe Sade-Feldman, Jorge Blando, Guangchun Han,[...]. Nature 2020
856
11

MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure.
Leeat Keren, Marc Bosse, Steve Thompson, Tyler Risom, Kausalia Vijayaragavan, Erin McCaffrey, Diana Marquez, Roshan Angoshtari, Noah F Greenwald, Harris Fienberg,[...]. Sci Adv 2019
110
11

Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging.
John W Hickey, Elizabeth K Neumann, Andrea J Radtke, Jeannie M Camarillo, Rebecca T Beuschel, Alexandre Albanese, Elizabeth McDonough, Julia Hatler, Anne E Wiblin, Jeremy Fisher,[...]. Nat Methods 2022
26
42

Spatial omics and multiplexed imaging to explore cancer biology.
Sabrina M Lewis, Marie-Liesse Asselin-Labat, Quan Nguyen, Jean Berthelet, Xiao Tan, Verena C Wimmer, Delphine Merino, Kelly L Rogers, Shalin H Naik. Nat Methods 2021
80
13

Hallmarks of cancer: the next generation.
Douglas Hanahan, Robert A Weinberg. Cell 2011
10

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
464
10

Overview of multiplex immunohistochemistry/immunofluorescence techniques in the era of cancer immunotherapy.
Wei Chang Colin Tan, Sanjna Nilesh Nerurkar, Hai Yun Cai, Harry Ho Man Ng, Duoduo Wu, Yu Ting Felicia Wee, Jeffrey Chun Tatt Lim, Joe Yeong, Tony Kiat Hon Lim. Cancer Commun (Lond) 2020
144
10

Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis.
Takahiro Tsujikawa, Sushil Kumar, Rohan N Borkar, Vahid Azimi, Guillaume Thibault, Young Hwan Chang, Ariel Balter, Rie Kawashima, Gina Choe, David Sauer,[...]. Cell Rep 2017
291
10

Immune cell topography predicts response to PD-1 blockade in cutaneous T cell lymphoma.
Darci Phillips, Magdalena Matusiak, Belén Rivero Gutierrez, Salil S Bhate, Graham L Barlow, Sizun Jiang, Janos Demeter, Kimberly S Smythe, Robert H Pierce, Steven P Fling,[...]. Nat Commun 2021
20
50

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
179
10

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
155
9

MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging.
Denis Schapiro, Artem Sokolov, Clarence Yapp, Yu-An Chen, Jeremy L Muhlich, Joshua Hess, Allison L Creason, Ajit J Nirmal, Gregory J Baker, Maulik K Nariya,[...]. Nat Methods 2022
29
31

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
255
9

A single-cell and spatially resolved atlas of human breast cancers.
Sunny Z Wu, Ghamdan Al-Eryani, Daniel Lee Roden, Simon Junankar, Kate Harvey, Alma Andersson, Aatish Thennavan, Chenfei Wang, James R Torpy, Nenad Bartonicek,[...]. Nat Genet 2021
103
9


Type, density, and location of immune cells within human colorectal tumors predict clinical outcome.
Jérôme Galon, Anne Costes, Fatima Sanchez-Cabo, Amos Kirilovsky, Bernhard Mlecnik, Christine Lagorce-Pagès, Marie Tosolini, Matthieu Camus, Anne Berger, Philippe Wind,[...]. Science 2006
8

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma.
Moshe Sade-Feldman, Keren Yizhak, Stacey L Bjorgaard, John P Ray, Carl G de Boer, Russell W Jenkins, David J Lieb, Jonathan H Chen, Dennie T Frederick, Michal Barzily-Rokni,[...]. Cell 2018
715
8


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.