A citation-based method for searching scientific literature

Adam L Haber, Moshe Biton, Noga Rogel, Rebecca H Herbst, Karthik Shekhar, Christopher Smillie, Grace Burgin, Toni M Delorey, Michael R Howitt, Yarden Katz, Itay Tirosh, Semir Beyaz, Danielle Dionne, Mei Zhang, Raktima Raychowdhury, Wendy S Garrett, Orit Rozenblatt-Rosen, Hai Ning Shi, Omer Yilmaz, Ramnik J Xavier, Aviv Regev. Nature 2017
Times Cited: 589







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



Times Cited
  Times     Co-cited
Similarity


Tuft-cell-derived IL-25 regulates an intestinal ILC2-epithelial response circuit.
Jakob von Moltke, Ming Ji, Hong-Erh Liang, Richard M Locksley. Nature 2016
576
20

Intestinal epithelial tuft cells initiate type 2 mucosal immunity to helminth parasites.
François Gerbe, Emmanuelle Sidot, Danielle J Smyth, Makoto Ohmoto, Ichiro Matsumoto, Valérie Dardalhon, Pierre Cesses, Laure Garnier, Marie Pouzolles, Bénédicte Brulin,[...]. Nature 2016
434
18

Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche.
Toshiro Sato, Robert G Vries, Hugo J Snippert, Marc van de Wetering, Nick Barker, Daniel E Stange, Johan H van Es, Arie Abo, Pekka Kujala, Peter J Peters,[...]. Nature 2009
18

Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts.
Toshiro Sato, Johan H van Es, Hugo J Snippert, Daniel E Stange, Robert G Vries, Maaike van den Born, Nick Barker, Noah F Shroyer, Marc van de Wetering, Hans Clevers. Nature 2011
16

Tuft cells, taste-chemosensory cells, orchestrate parasite type 2 immunity in the gut.
Michael R Howitt, Sydney Lavoie, Monia Michaud, Arthur M Blum, Sara V Tran, Joel V Weinstock, Carey Ann Gallini, Kevin Redding, Robert F Margolskee, Lisa C Osborne,[...]. Science 2016
435
16

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
100
15

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
15

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
13

Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett's epithelium.
Toshiro Sato, Daniel E Stange, Marc Ferrante, Robert G J Vries, Johan H Van Es, Stieneke Van den Brink, Winan J Van Houdt, Apollo Pronk, Joost Van Gorp, Peter D Siersema,[...]. Gastroenterology 2011
12

Enteroendocrine cells switch hormone expression along the crypt-to-villus BMP signalling gradient.
Joep Beumer, Benedetta Artegiani, Yorick Post, Frank Reimann, Fiona Gribble, Thuc Nghi Nguyen, Hongkui Zeng, Maaike Van den Born, Johan H Van Es, Hans Clevers. Nat Cell Biol 2018
95
11

Detection of Succinate by Intestinal Tuft Cells Triggers a Type 2 Innate Immune Circuit.
Marija S Nadjsombati, John W McGinty, Miranda R Lyons-Cohen, James B Jaffe, Lucian DiPeso, Christoph Schneider, Corey N Miller, Joshua L Pollack, G A Nagana Gowda, Mary F Fontana,[...]. Immunity 2018
184
11

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
11

Requirement of Math1 for secretory cell lineage commitment in the mouse intestine.
Q Yang, N A Bermingham, M J Finegold, H Y Zoghbi. Science 2001
665
10

Distinct ATOH1 and Neurog3 requirements define tuft cells as a new secretory cell type in the intestinal epithelium.
François Gerbe, Johan H van Es, Leila Makrini, Bénédicte Brulin, Georg Mellitzer, Sylvie Robine, Béatrice Romagnolo, Noah F Shroyer, Jean-François Bourgaux, Christine Pignodel,[...]. J Cell Biol 2011
231
10


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
188
10

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
10

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
10

The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent '+4' cell markers.
Javier Muñoz, Daniel E Stange, Arnout G Schepers, Marc van de Wetering, Bon-Kyoung Koo, Shalev Itzkovitz, Richard Volckmann, Kevin S Kung, Jan Koster, Sorina Radulescu,[...]. EMBO J 2012
487
9

Stem cells, self-renewal, and differentiation in the intestinal epithelium.
Laurens G van der Flier, Hans Clevers. Annu Rev Physiol 2009
9

A Metabolite-Triggered Tuft Cell-ILC2 Circuit Drives Small Intestinal Remodeling.
Christoph Schneider, Claire E O'Leary, Jakob von Moltke, Hong-Erh Liang, Qi Yan Ang, Peter J Turnbaugh, Sridhar Radhakrishnan, Michael Pellizzon, Averil Ma, Richard M Locksley. Cell 2018
170
9

Tuft-Cell-Derived Leukotrienes Drive Rapid Anti-helminth Immunity in the Small Intestine but Are Dispensable for Anti-protist Immunity.
John W McGinty, Hung-An Ting, Tyler E Billipp, Marija S Nadjsombati, Danish M Khan, Nora A Barrett, Hong-Erh Liang, Ichiro Matsumoto, Jakob von Moltke. Immunity 2020
57
15

Tales from the crypt: new insights into intestinal stem cells.
Helmuth Gehart, Hans Clevers. Nat Rev Gastroenterol Hepatol 2019
272
8

Single-cell messenger RNA sequencing reveals rare intestinal cell types.
Dominic Grün, Anna Lyubimova, Lennart Kester, Kay Wiebrands, Onur Basak, Nobuo Sasaki, Hans Clevers, Alexander van Oudenaarden. Nature 2015
621
8

Redundant sources of Wnt regulate intestinal stem cells and promote formation of Paneth cells.
Henner F Farin, Johan H Van Es, Hans Clevers. Gastroenterology 2012
393
8

Function and mechanisms of enteroendocrine cells and gut hormones in metabolism.
Fiona M Gribble, Frank Reimann. Nat Rev Endocrinol 2019
164
8

Murine intestinal cells expressing Trpm5 are mostly brush cells and express markers of neuronal and inflammatory cells.
C Bezençon, A Fürholz, F Raymond, R Mansourian, S Métairon, J Le Coutre, S Damak. J Comp Neurol 2008
153
8

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
8

Enterochromaffin Cells Are Gut Chemosensors that Couple to Sensory Neural Pathways.
Nicholas W Bellono, James R Bayrer, Duncan B Leitch, Joel Castro, Chuchu Zhang, Tracey A O'Donnell, Stuart M Brierley, Holly A Ingraham, David Julius. Cell 2017
315
8

A gut-brain neural circuit for nutrient sensory transduction.
Melanie Maya Kaelberer, Kelly L Buchanan, Marguerita E Klein, Bradley B Barth, Marcia M Montoya, Xiling Shen, Diego V Bohórquez. Science 2018
262
8

Massively parallel digital transcriptional profiling of single cells.
Grace X Y Zheng, Jessica M Terry, Phillip Belgrader, Paul Ryvkin, Zachary W Bent, Ryan Wilson, Solongo B Ziraldo, Tobias D Wheeler, Geoff P McDermott, Junjie Zhu,[...]. Nat Commun 2017
8

Enteroendocrine Cells: Chemosensors in the Intestinal Epithelium.
Fiona M Gribble, Frank Reimann. Annu Rev Physiol 2016
255
8

Niche-independent high-purity cultures of Lgr5+ intestinal stem cells and their progeny.
Xiaolei Yin, Henner F Farin, Johan H van Es, Hans Clevers, Robert Langer, Jeffrey M Karp. Nat Methods 2014
298
7

Induced Quiescence of Lgr5+ Stem Cells in Intestinal Organoids Enables Differentiation of Hormone-Producing Enteroendocrine Cells.
Onur Basak, Joep Beumer, Kay Wiebrands, Hiroshi Seno, Alexander van Oudenaarden, Hans Clevers. Cell Stem Cell 2017
164
7

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes.
Daniel T Montoro, Adam L Haber, Moshe Biton, Vladimir Vinarsky, Brian Lin, Susan E Birket, Feng Yuan, Sijia Chen, Hui Min Leung, Jorge Villoria,[...]. Nature 2018
437
7

Human Intestinal Organoids Maintain Self-Renewal Capacity and Cellular Diversity in Niche-Inspired Culture Condition.
Masayuki Fujii, Mami Matano, Kohta Toshimitsu, Ai Takano, Yohei Mikami, Shingo Nishikori, Shinya Sugimoto, Toshiro Sato. Cell Stem Cell 2018
160
7

Distribution pattern and molecular signature of cholinergic tuft cells in human gastro-intestinal and pancreatic-biliary tract.
Burkhard Schütz, Anna-Lena Ruppert, Oliver Strobel, Michael Lazarus, Yoshihiro Urade, Markus W Büchler, Eberhard Weihe. Sci Rep 2019
35
20

Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine.
Yalong Wang, Wanlu Song, Jilian Wang, Ting Wang, Xiaochen Xiong, Zhen Qi, Wei Fu, Xuerui Yang, Ye-Guang Chen. J Exp Med 2020
74
9

Fiji: an open-source platform for biological-image analysis.
Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid,[...]. Nat Methods 2012
7

Cell fate specification and differentiation in the adult mammalian intestine.
Joep Beumer, Hans Clevers. Nat Rev Mol Cell Biol 2021
65
10

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
178
7

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
123
6

Tissue-specific and inducible Cre-mediated recombination in the gut epithelium.
Fatima el Marjou, Klaus-Peter Janssen, Benny Hung-Junn Chang, Mei Li, Valérie Hindie, Lawrence Chan, Daniel Louvard, Pierre Chambon, Daniel Metzger, Sylvie Robine. Genesis 2004
676
6

Neurogenin3 is differentially required for endocrine cell fate specification in the intestinal and gastric epithelium.
Marjorie Jenny, Céline Uhl, Colette Roche, Isabelle Duluc, Valérie Guillermin, Francois Guillemot, Jan Jensen, Michèle Kedinger, Gérard Gradwohl. EMBO J 2002
339
6

Regulation of immune responses by tuft cells.
Christoph Schneider, Claire E O'Leary, Richard M Locksley. Nat Rev Immunol 2019
65
9

Interplay between metabolic identities in the intestinal crypt supports stem cell function.
Maria J Rodríguez-Colman, Matthias Schewe, Maaike Meerlo, Edwin Stigter, Johan Gerrits, Mia Pras-Raves, Andrea Sacchetti, Marten Hornsveld, Koen C Oost, Hugo J Snippert,[...]. Nature 2017
224
6

Dll1+ secretory progenitor cells revert to stem cells upon crypt damage.
Johan H van Es, Toshiro Sato, Marc van de Wetering, Anna Lyubimova, Annie Ng Yee Nee, Alex Gregorieff, Nobuo Sasaki, Laura Zeinstra, Maaike van den Born, Jeroen Korving,[...]. Nat Cell Biol 2012
493
6

Sox4 Promotes Atoh1-Independent Intestinal Secretory Differentiation Toward Tuft and Enteroendocrine Fates.
Adam D Gracz, Leigh Ann Samsa, Matthew J Fordham, Danny C Trotier, Bailey Zwarycz, Yuan-Hung Lo, Katherine Bao, Joshua Starmer, Jesse R Raab, Noah F Shroyer,[...]. Gastroenterology 2018
33
18

Unsupervised Trajectory Analysis of Single-Cell RNA-Seq and Imaging Data Reveals Alternative Tuft Cell Origins in the Gut.
Charles A Herring, Amrita Banerjee, Eliot T McKinley, Alan J Simmons, Jie Ping, Joseph T Roland, Jeffrey L Franklin, Qi Liu, Michael J Gerdes, Robert J Coffey,[...]. Cell Syst 2018
86
6

The ets-domain transcription factor Spdef promotes maturation of goblet and paneth cells in the intestinal epithelium.
Alex Gregorieff, Daniel E Stange, Pekka Kujala, Harry Begthel, Maaike van den Born, Jeroen Korving, Peter J Peters, Hans Clevers. Gastroenterology 2009
161
6


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.