A citation-based method for searching scientific literature

Kiya W Govek, Emma C Troisi, Zhen Miao, Rachael G Aubin, Steven Woodhouse, Pablo G Camara. Sci Adv 2021
Times Cited: 13







List of co-cited articles
85 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
53

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
860
46

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
38

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
38

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
755
30

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
30

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
30

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
347
30

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
30

Comparison of Biomarker Modalities for Predicting Response to PD-1/PD-L1 Checkpoint Blockade: A Systematic Review and Meta-analysis.
Steve Lu, Julie E Stein, David L Rimm, Daphne W Wang, J Michael Bell, Douglas B Johnson, Jeffrey A Sosman, Kurt A Schalper, Robert A Anders, Hao Wang,[...]. JAMA Oncol 2019
204
23

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
491
23

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
82
23

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
151
23

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
23


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
23

Spatially resolved transcriptomics and beyond.
Nicola Crosetto, Magda Bienko, Alexander van Oudenaarden. Nat Rev Genet 2015
246
23


SpatialDE: identification of spatially variable genes.
Valentine Svensson, Sarah A Teichmann, Oliver Stegle. Nat Methods 2018
94
23

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
883
23

Multiplexed quantification of proteins and transcripts in single cells.
Vanessa M Peterson, Kelvin Xi Zhang, Namit Kumar, Jerelyn Wong, Lixia Li, Douglas C Wilson, Renee Moore, Terrill K McClanahan, Svetlana Sadekova, Joel A Klappenbach. Nat Biotechnol 2017
353
23

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
23

Integrated analysis of multimodal single-cell data.
Yuhan Hao, Stephanie Hao, Erica Andersen-Nissen, William M Mauck, Shiwei Zheng, Andrew Butler, Maddie J Lee, Aaron J Wilk, Charlotte Darby, Michael Zager,[...]. Cell 2021
345
23

CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes.
Mirjana Efremova, Miquel Vento-Tormo, Sarah A Teichmann, Roser Vento-Tormo. Nat Protoc 2020
420
23

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
23

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
81
23

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
312
23

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
23

Automated cell-type classification in intact tissues by single-cell molecular profiling.
Monica Nagendran, Daniel P Riordan, Pehr B Harbury, Tushar J Desai. Elife 2018
50
15

Quantitative Spatial Profiling of PD-1/PD-L1 Interaction and HLA-DR/IDO-1 Predicts Improved Outcomes of Anti-PD-1 Therapies in Metastatic Melanoma.
Douglas B Johnson, Jennifer Bordeaux, Ju Young Kim, Christine Vaupel, David L Rimm, Thai H Ho, Richard W Joseph, Adil I Daud, Robert M Conry, Elizabeth M Gaughan,[...]. Clin Cancer Res 2018
61
15

Immune contexture analysis in immuno-oncology: applications and challenges of multiplex fluorescent immunohistochemistry.
Reshma Shakya, Tam Hong Nguyen, Nigel Waterhouse, Rajiv Khanna. Clin Transl Immunology 2020
8
25

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
15

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
78
15

The Society for Immunotherapy of Cancer statement on best practices for multiplex immunohistochemistry (IHC) and immunofluorescence (IF) staining and validation.
Janis M Taube, Guray Akturk, Michael Angelo, Elizabeth L Engle, Sacha Gnjatic, Shirley Greenbaum, Noah F Greenwald, Cyrus V Hedvat, Travis J Hollmann, Jonathan Juco,[...]. J Immunother Cancer 2020
52
15

Spatial Heterogeneity in the Tumor Microenvironment.
Yinyin Yuan. Cold Spring Harb Perspect Med 2016
98
15

Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data.
Tallulah S Andrews, Vladimir Yu Kiselev, Davis McCarthy, Martin Hemberg. Nat Protoc 2021
31
15

Modular, efficient and constant-memory single-cell RNA-seq preprocessing.
Páll Melsted, A Sina Booeshaghi, Lauren Liu, Fan Gao, Lambda Lu, Kyung Hoi Joseph Min, Eduardo da Veiga Beltrame, Kristján Eldjárn Hjörleifsson, Jase Gehring, Lior Pachter. Nat Biotechnol 2021
37
15

Current best practices in single-cell RNA-seq analysis: a tutorial.
Malte D Luecken, Fabian J Theis. Mol Syst Biol 2019
419
15

Uncovering an Organ's Molecular Architecture at Single-Cell Resolution by Spatially Resolved Transcriptomics.
Jie Liao, Xiaoyan Lu, Xin Shao, Ling Zhu, Xiaohui Fan. Trends Biotechnol 2021
45
15

Gene expression cartography.
Mor Nitzan, Nikos Karaiskos, Nir Friedman, Nikolaus Rajewsky. Nature 2019
81
15



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
631
15

Multi-domain translation between single-cell imaging and sequencing data using autoencoders.
Karren Dai Yang, Anastasiya Belyaeva, Saradha Venkatachalapathy, Karthik Damodaran, Abigail Katcoff, Adityanarayanan Radhakrishnan, G V Shivashankar, Caroline Uhler. Nat Commun 2021
22
15

Spatially Resolved Transcriptomes-Next Generation Tools for Tissue Exploration.
Michaela Asp, Joseph Bergenstråhle, Joakim Lundeberg. Bioessays 2020
92
15

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
15

Joint probabilistic modeling of single-cell multi-omic data with totalVI.
Adam Gayoso, Zoë Steier, Romain Lopez, Jeffrey Regier, Kristopher L Nazor, Aaron Streets, Nir Yosef. Nat Methods 2021
28
15


Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.
Atray Dixit, Oren Parnas, Biyu Li, Jenny Chen, Charles P Fulco, Livnat Jerby-Arnon, Nemanja D Marjanovic, Danielle Dionne, Tyler Burks, Raktima Raychowdhury,[...]. Cell 2016
505
15

BREM-SC: a bayesian random effects mixture model for joint clustering single cell multi-omics data.
Xinjun Wang, Zhe Sun, Yanfu Zhang, Zhongli Xu, Hongyi Xin, Heng Huang, Richard H Duerr, Kong Chen, Ying Ding, Wei Chen. Nucleic Acids Res 2020
13
15


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.