A citation-based method for searching scientific literature

Xin Shao, Xiaoyan Lu, Jie Liao, Huajun Chen, Xiaohui Fan. Protein Cell 2020
Times Cited: 13







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



Times Cited
  Times     Co-cited
Similarity


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
308
46

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.
Evan Z Macosko, Anindita Basu, Rahul Satija, James Nemesh, Karthik Shekhar, Melissa Goldman, Itay Tirosh, Allison R Bialas, Nolan Kamitaki, Emily M Martersteck,[...]. Cell 2015
46

A draft network of ligand-receptor-mediated multicellular signalling in human.
Jordan A Ramilowski, Tatyana Goldberg, Jayson Harshbarger, Edda Kloppmann, Marina Lizio, Venkata P Satagopam, Masayoshi Itoh, Hideya Kawaji, Piero Carninci, Burkhard Rost,[...]. Nat Commun 2015
282
38

SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics.
Simon Cabello-Aguilar, Mélissa Alame, Fabien Kon-Sun-Tack, Caroline Fau, Matthieu Lacroix, Jacques Colinge. Nucleic Acids Res 2020
45
38

scCATCH: Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data.
Xin Shao, Jie Liao, Xiaoyan Lu, Rui Xue, Ni Ai, Xiaohui Fan. iScience 2020
31
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
625
30

Cell lineage and communication network inference via optimization for single-cell transcriptomics.
Shuxiong Wang, Matthew Karikomi, Adam L MacLean, Qing Nie. Nucleic Acids Res 2019
32
30

Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics.
Manu P Kumar, Jinyan Du, Georgia Lagoudas, Yang Jiao, Andrew Sawyer, Daryl C Drummond, Douglas A Lauffenburger, Andreas Raue. Cell Rep 2018
115
30

Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting.
Merav Cohen, Amir Giladi, Anna-Dorothea Gorki, Dikla Gelbard Solodkin, Mor Zada, Anastasiya Hladik, Andras Miklosi, Tomer-Meir Salame, Keren Bahar Halpern, Eyal David,[...]. Cell 2018
156
30


Single-cell reconstruction of the early maternal-fetal interface in humans.
Roser Vento-Tormo, Mirjana Efremova, Rachel A Botting, Margherita Y Turco, Miquel Vento-Tormo, Kerstin B Meyer, Jong-Eun Park, Emily Stephenson, Krzysztof Polański, Angela Goncalves,[...]. Nature 2018
570
30

NicheNet: modeling intercellular communication by linking ligands to target genes.
Robin Browaeys, Wouter Saelens, Yvan Saeys. Nat Methods 2020
136
30

Deciphering cell-cell interactions and communication from gene expression.
Erick Armingol, Adam Officer, Olivier Harismendy, Nathan E Lewis. Nat Rev Genet 2021
63
30

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
31
30

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
23

Mapping the Mouse Cell Atlas by Microwell-Seq.
Xiaoping Han, Renying Wang, Yincong Zhou, Lijiang Fei, Huiyu Sun, Shujing Lai, Assieh Saadatpour, Ziming Zhou, Haide Chen, Fang Ye,[...]. Cell 2018
433
23

Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.
Allon M Klein, Linas Mazutis, Ilke Akartuna, Naren Tallapragada, Adrian Veres, Victor Li, Leonid Peshkin, David A Weitz, Marc W Kirschner. Cell 2015
23

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
23

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.
Cole Trapnell, Davide Cacchiarelli, Jonna Grimsby, Prapti Pokharel, Shuqiang Li, Michael Morse, Niall J Lennon, Kenneth J Livak, Tarjei S Mikkelsen, John L Rinn. Nat Biotechnol 2014
23

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
23

A dream of single-cell proteomics.
Vivien Marx. Nat Methods 2019
89
23

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Damian Szklarczyk, Annika L Gable, David Lyon, Alexander Junge, Stefan Wyder, Jaime Huerta-Cepas, Milan Simonovic, Nadezhda T Doncheva, John H Morris, Peer Bork,[...]. Nucleic Acids Res 2019
23

A cellular census of human lungs identifies novel cell states in health and in asthma.
Felipe A Vieira Braga, Gozde Kar, Marijn Berg, Orestes A Carpaij, Krzysztof Polanski, Lukas M Simon, Sharon Brouwer, Tomás Gomes, Laura Hesse, Jian Jiang,[...]. Nat Med 2019
236
23

PyMINEr Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq.
Scott R Tyler, Pavana G Rotti, Xingshen Sun, Yaling Yi, Weiliang Xie, Michael C Winter, Miles J Flamme-Wiese, Budd A Tucker, Robert F Mullins, Andrew W Norris,[...]. Cell Rep 2019
17
23

Eleven grand challenges in single-cell data science.
David Lähnemann, Johannes Köster, Ewa Szczurek, Davis J McCarthy, Stephanie C Hicks, Mark D Robinson, Catalina A Vallejos, Kieran R Campbell, Niko Beerenwinkel, Ahmed Mahfouz,[...]. Genome Biol 2020
171
23

Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma.
Qiming Zhang, Yao He, Nan Luo, Shashank J Patel, Yanjie Han, Ranran Gao, Madhura Modak, Sebastian Carotta, Christian Haslinger, David Kind,[...]. Cell 2019
239
23

Dissecting cellular crosstalk by sequencing physically interacting cells.
Amir Giladi, Merav Cohen, Chiara Medaglia, Yael Baran, Baoguo Li, Mor Zada, Pierre Bost, Ronnie Blecher-Gonen, Tomer-Meir Salame, Johannes U Mayer,[...]. Nat Biotechnol 2020
51
23

Immune Landscape of Viral- and Carcinogen-Driven Head and Neck Cancer.
Anthony R Cillo, Cornelius H L Kürten, Tracy Tabib, Zengbiao Qi, Sayali Onkar, Ting Wang, Angen Liu, Umamaheswar Duvvuri, Seungwon Kim, Ryan J Soose,[...]. Immunity 2020
98
23

Reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly.
Xianwen Ren, Guojie Zhong, Qiming Zhang, Lei Zhang, Yujie Sun, Zemin Zhang. Cell Res 2020
26
23


Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling.
Allen W Zhang, Ciara O'Flanagan, Elizabeth A Chavez, Jamie L P Lim, Nicholas Ceglia, Andrew McPherson, Matt Wiens, Pascale Walters, Tim Chan, Brittany Hewitson,[...]. Nat Methods 2019
73
23

Polylox barcoding reveals haematopoietic stem cell fates realized in vivo.
Weike Pei, Thorsten B Feyerabend, Jens Rössler, Xi Wang, Daniel Postrach, Katrin Busch, Immanuel Rode, Kay Klapproth, Nikolaus Dietlein, Claudia Quedenau,[...]. Nature 2017
180
15

Molecular architecture of lineage allocation and tissue organization in early mouse embryo.
Guangdun Peng, Shengbao Suo, Guizhong Cui, Fang Yu, Ran Wang, Jun Chen, Shirui Chen, Zhiwen Liu, Guoyu Chen, Yun Qian,[...]. Nature 2019
51
15

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
15

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
15

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
15


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
15


Somatic autophagy of axonal mitochondria in ischemic neurons.
Yanrong Zheng, Xiangnan Zhang, Xiaoli Wu, Lei Jiang, Anil Ahsan, Shijia Ma, Ziyu Xiao, Feng Han, Zheng-Hong Qin, Weiwei Hu,[...]. J Cell Biol 2019
24
15

Spatially resolved transcriptome profiling in model plant species.
Stefania Giacomello, Fredrik Salmén, Barbara K Terebieniec, Sanja Vickovic, José Fernandez Navarro, Andrey Alexeyenko, Johan Reimegård, Lauren S McKee, Chanaka Mannapperuma, Vincent Bulone,[...]. Nat Plants 2017
46
15

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding.
Alexander B Rosenberg, Charles M Roco, Richard A Muscat, Anna Kuchina, Paul Sample, Zizhen Yao, Lucas T Graybuck, David J Peeler, Sumit Mukherjee, Wei Chen,[...]. Science 2018
393
15

A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex.
Suijuan Zhong, Shu Zhang, Xiaoying Fan, Qian Wu, Liying Yan, Ji Dong, Haofeng Zhang, Long Li, Le Sun, Na Pan,[...]. Nature 2018
229
15

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
112
15

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
15

Whole-organism lineage tracing by combinatorial and cumulative genome editing.
Aaron McKenna, Gregory M Findlay, James A Gagnon, Marshall S Horwitz, Alexander F Schier, Jay Shendure. Science 2016
320
15

Single-cell multimodal omics: the power of many.
Chenxu Zhu, Sebastian Preissl, Bing Ren. Nat Methods 2020
82
15

A Unique Microglia Type Associated with Restricting Development of Alzheimer's Disease.
Hadas Keren-Shaul, Amit Spinrad, Assaf Weiner, Orit Matcovitch-Natan, Raz Dvir-Szternfeld, Tyler K Ulland, Eyal David, Kuti Baruch, David Lara-Astaiso, Beata Toth,[...]. Cell 2017
15

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
15

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
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.