A citation-based method for searching scientific literature

David Fawkner-Corbett, Agne Antanaviciute, Kaushal Parikh, Marta Jagielowicz, Ana Sousa Gerós, Tarun Gupta, Neil Ashley, Doran Khamis, Darren Fowler, Edward Morrissey, Chris Cunningham, Paul R V Johnson, Hashem Koohy, Alison Simmons. Cell 2021
Times Cited: 25







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



Times Cited
  Times     Co-cited
Similarity


Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease.
James Kinchen, Hannah H Chen, Kaushal Parikh, Agne Antanaviciute, Marta Jagielowicz, David Fawkner-Corbett, Neil Ashley, Laura Cubitt, Esther Mellado-Gomez, Moustafa Attar,[...]. Cell 2018
171
40

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
32

Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn's Disease.
Rasa Elmentaite, Alexander D B Ross, Kenny Roberts, Kylie R James, Daniel Ortmann, Tomás Gomes, Komal Nayak, Liz Tuck, Sophie Pritchard, Omer Ali Bayraktar,[...]. Dev Cell 2020
24
29

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis.
Christopher S Smillie, Moshe Biton, Jose Ordovas-Montanes, Keri M Sullivan, Grace Burgin, Daniel B Graham, Rebecca H Herbst, Noga Rogel, Michal Slyper, Julia Waldman,[...]. Cell 2019
237
24

Mapping Development of the Human Intestinal Niche at Single-Cell Resolution.
Emily M Holloway, Michael Czerwinski, Yu-Hwai Tsai, Joshua H Wu, Angeline Wu, Charlie J Childs, Katherine D Walton, Caden W Sweet, Qianhui Yu, Ian Glass,[...]. Cell Stem Cell 2021
21
28

Spatial Reconstruction of Single Enterocytes Uncovers Broad Zonation along the Intestinal Villus Axis.
Andreas E Moor, Yotam Harnik, Shani Ben-Moshe, Efi E Massasa, Milena Rozenberg, Raya Eilam, Keren Bahar Halpern, Shalev Itzkovitz. Cell 2018
112
24

Colonic epithelial cell diversity in health and inflammatory bowel disease.
Kaushal Parikh, Agne Antanaviciute, David Fawkner-Corbett, Marta Jagielowicz, Anna Aulicino, Christoffer Lagerholm, Simon Davis, James Kinchen, Hannah H Chen, Nasullah Khalid Alham,[...]. Nature 2019
151
20

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
20

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
20

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
20

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
20

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
16

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
16

Subepithelial telocytes are an important source of Wnts that supports intestinal crypts.
Michal Shoshkes-Carmel, Yue J Wang, Kirk J Wangensteen, Beáta Tóth, Ayano Kondo, Efi E Massasa, Shalev Itzkovitz, Klaus H Kaestner. Nature 2018
190
16

A single-cell survey of the small intestinal epithelium.
Adam L Haber, Moshe Biton, Noga Rogel, Rebecca H Herbst, Karthik Shekhar, Christopher Smillie, Grace Burgin, Toni M Delorey, Michael R Howitt, Yarden Katz,[...]. Nature 2017
530
16

The Human and Mouse Enteric Nervous System at Single-Cell Resolution.
Eugene Drokhlyansky, Christopher S Smillie, Nicholas Van Wittenberghe, Maria Ericsson, Gabriel K Griffin, Gokcen Eraslan, Danielle Dionne, Michael S Cuoco, Max N Goder-Reiser, Tatyana Sharova,[...]. Cell 2020
57
16

Single-Cell Analysis of Crohn's Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy.
Jerome C Martin, Christie Chang, Gilles Boschetti, Ryan Ungaro, Mamta Giri, John A Grout, Kyle Gettler, Ling-Shiang Chuang, Shikha Nayar, Alexander J Greenstein,[...]. Cell 2019
162
16

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
16

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
16

Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics.
Marlon Stoeckius, Shiwei Zheng, Brian Houck-Loomis, Stephanie Hao, Bertrand Z Yeung, William M Mauck, Peter Smibert, Rahul Satija. Genome Biol 2018
209
12

Tyrosine kinase receptor RET is a key regulator of Peyer's patch organogenesis.
Henrique Veiga-Fernandes, Mark C Coles, Katie E Foster, Amisha Patel, Adam Williams, Dipa Natarajan, Amanda Barlow, Vassilis Pachnis, Dimitris Kioussis. Nature 2007
185
12

Lineage-dependent spatial and functional organization of the mammalian enteric nervous system.
Reena Lasrado, Werend Boesmans, Jens Kleinjung, Carmen Pin, Donald Bell, Leena Bhaw, Sarah McCallum, Hui Zong, Liqun Luo, Hans Clevers,[...]. Science 2017
68
12

Identification of Enteroendocrine Regulators by Real-Time Single-Cell Differentiation Mapping.
Helmuth Gehart, Johan H van Es, Karien Hamer, Joep Beumer, Kai Kretzschmar, Johanna F Dekkers, Anne Rios, Hans Clevers. Cell 2019
83
12

SCENIC: single-cell regulatory network inference and clustering.
Sara Aibar, Carmen Bravo González-Blas, Thomas Moerman, Vân Anh Huynh-Thu, Hana Imrichova, Gert Hulselmans, Florian Rambow, Jean-Christophe Marine, Pierre Geurts, Jan Aerts,[...]. Nat Methods 2017
698
12

Decoding human fetal liver haematopoiesis.
Dorin-Mirel Popescu, Rachel A Botting, Emily Stephenson, Kile Green, Simone Webb, Laura Jardine, Emily F Calderbank, Krzysztof Polanski, Issac Goh, Mirjana Efremova,[...]. Nature 2019
141
12

Reversed graph embedding resolves complex single-cell trajectories.
Xiaojie Qiu, Qi Mao, Ying Tang, Li Wang, Raghav Chawla, Hannah A Pliner, Cole Trapnell. Nat Methods 2017
792
12

Human Fetal TNF-α-Cytokine-Producing CD4+ Effector Memory T Cells Promote Intestinal Development and Mediate Inflammation Early in Life.
Renée R C E Schreurs, Martin E Baumdick, Adrian F Sagebiel, Max Kaufmann, Michal Mokry, Paul L Klarenbeek, Nicola Schaltenberg, Fenja L Steinert, Jorik M van Rijn, Agata Drewniak,[...]. Immunity 2019
64
12

Distinct Mesenchymal Cell Populations Generate the Essential Intestinal BMP Signaling Gradient.
Neil McCarthy, Elisa Manieri, Elaine E Storm, Assieh Saadatpour, Adrienne M Luoma, Varun N Kapoor, Shariq Madha, Liam T Gaynor, Christian Cox, Shilpa Keerthivasan,[...]. Cell Stem Cell 2020
57
12

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors.
Alexandra-Chloé Villani, Rahul Satija, Gary Reynolds, Siranush Sarkizova, Karthik Shekhar, James Fletcher, Morgane Griesbeck, Andrew Butler, Shiwei Zheng, Suzan Lazo,[...]. Science 2017
960
12

Distinct microbial and immune niches of the human colon.
Kylie R James, Tomas Gomes, Rasa Elmentaite, Nitin Kumar, Emily L Gulliver, Hamish W King, Mark D Stares, Bethany R Bareham, John R Ferdinand, Velislava N Petrova,[...]. Nat Immunol 2020
58
12

Single-cell atlas of colonic CD8+ T cells in ulcerative colitis.
Daniele Corridoni, Agne Antanaviciute, Tarun Gupta, David Fawkner-Corbett, Anna Aulicino, Marta Jagielowicz, Kaushal Parikh, Emmanouela Repapi, Steve Taylor, Dai Ishikawa,[...]. Nat Med 2020
28
12

Fixation and Spread of Somatic Mutations in Adult Human Colonic Epithelium.
Anna M Nicholson, Cora Olpe, Alice Hoyle, Ann-Sofie Thorsen, Teja Rus, Mathilde Colombé, Roxanne Brunton-Sim, Richard Kemp, Kate Marks, Phil Quirke,[...]. Cell Stem Cell 2018
48
12

Dimensionality reduction for visualizing single-cell data using UMAP.
Etienne Becht, Leland McInnes, John Healy, Charles-Antoine Dutertre, Immanuel W H Kwok, Lai Guan Ng, Florent Ginhoux, Evan W Newell. Nat Biotechnol 2018
918
12

Gene expression cartography.
Mor Nitzan, Nikos Karaiskos, Nir Friedman, Nikolaus Rajewsky. Nature 2019
70
12

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.
Laleh Haghverdi, Aaron T L Lun, Michael D Morgan, John C Marioni. Nat Biotechnol 2018
511
12

Identification of stem cells in small intestine and colon by marker gene Lgr5.
Nick Barker, Johan H van Es, Jeroen Kuipers, Pekka Kujala, Maaike van den Born, Miranda Cozijnsen, Andrea Haegebarth, Jeroen Korving, Harry Begthel, Peter J Peters,[...]. Nature 2007
12

Dynamic Reorganization of Chromatin Accessibility Signatures during Dedifferentiation of Secretory Precursors into Lgr5+ Intestinal Stem Cells.
Unmesh Jadhav, Madhurima Saxena, Nicholas K O'Neill, Assieh Saadatpour, Guo-Cheng Yuan, Zachary Herbert, Kazutaka Murata, Ramesh A Shivdasani. Cell Stem Cell 2017
115
12

Single-cell transcriptomes of the regenerating intestine reveal a revival stem cell.
Arshad Ayyaz, Sandeep Kumar, Bruno Sangiorgi, Bibaswan Ghoshal, Jessica Gosio, Shaida Ouladan, Mardi Fink, Seda Barutcu, Daniel Trcka, Jess Shen,[...]. Nature 2019
126
12

T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation.
Moshe Biton, Adam L Haber, Noga Rogel, Grace Burgin, Semir Beyaz, Alexandra Schnell, Orr Ashenberg, Chien-Wen Su, Christopher Smillie, Karthik Shekhar,[...]. Cell 2018
155
12

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
12

Spatial transcriptomics: paving the way for tissue-level systems biology.
Andreas E Moor, Shalev Itzkovitz. Curr Opin Biotechnol 2017
59
12

The Drosophila embryo at single-cell transcriptome resolution.
Nikos Karaiskos, Philipp Wahle, Jonathan Alles, Anastasiya Boltengagen, Salah Ayoub, Claudia Kipar, Christine Kocks, Nikolaus Rajewsky, Robert P Zinzen. Science 2017
171
12

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
12

Single-cell in situ RNA profiling by sequential hybridization.
Eric Lubeck, Ahmet F Coskun, Timur Zhiyentayev, Mubhij Ahmad, Long Cai. Nat Methods 2014
343
12

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.
Itay Tirosh, Benjamin Izar, Sanjay M Prakadan, Marc H Wadsworth, Daniel Treacy, John J Trombetta, Asaf Rotem, Christopher Rodman, Christine Lian, George Murphy,[...]. Science 2016
12

Deciphering cell-cell interactions and communication from gene expression.
Erick Armingol, Adam Officer, Olivier Harismendy, Nathan E Lewis. Nat Rev Genet 2021
63
12

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
12

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
12

mRNA-Seq whole-transcriptome analysis of a single cell.
Fuchou Tang, Catalin Barbacioru, Yangzhou Wang, Ellen Nordman, Clarence Lee, Nanlan Xu, Xiaohui Wang, John Bodeau, Brian B Tuch, Asim Siddiqui,[...]. Nat Methods 2009
12

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
68
12


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.