A citation-based method for searching scientific literature

Rasa Elmentaite, Alexander D B Ross, Kenny Roberts, Kylie R James, Daniel Ortmann, Tomás Gomes, Komal Nayak, Liz Tuck, Sophie Pritchard, Omer Ali Bayraktar, Robert Heuschkel, Ludovic Vallier, Sarah A Teichmann, Matthias Zilbauer. Dev Cell 2020
Times Cited: 35







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



Times Cited
  Times     Co-cited
Similarity


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
288
34

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
201
34

Spatiotemporal analysis of human intestinal development at single-cell resolution.
David Fawkner-Corbett, Agne Antanaviciute, Kaushal Parikh, Marta Jagielowicz, Ana Sousa Gerós, Tarun Gupta, Neil Ashley, Doran Khamis, Darren Fowler, Edward Morrissey,[...]. Cell 2021
44
28

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
197
25

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
589
25

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
22

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
210
22

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
77
22

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
32
25

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
22

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
20

Cells of the human intestinal tract mapped across space and time.
Rasa Elmentaite, Natsuhiko Kumasaka, Kenny Roberts, Aaron Fleming, Emma Dann, Hamish W King, Vitalii Kleshchevnikov, Monika Dabrowska, Sophie Pritchard, Liam Bolt,[...]. Nature 2021
26
26

Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro.
Jason R Spence, Christopher N Mayhew, Scott A Rankin, Matthew F Kuhar, Jefferson E Vallance, Kathryn Tolle, Elizabeth E Hoskins, Vladimir V Kalinichenko, Susanne I Wells, Aaron M Zorn,[...]. Nature 2011
17

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
17

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
17

Lgr5+ telocytes are a signaling source at the intestinal villus tip.
Keren Bahar Halpern, Hassan Massalha, Rachel K Zwick, Andreas E Moor, David Castillo-Azofeifa, Milena Rozenberg, Lydia Farack, Adi Egozi, Dan R Miller, Inna Averbukh,[...]. Nat Commun 2020
40
17

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
17

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
17

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
17

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
14

PDGFRα+ pericryptal stromal cells are the critical source of Wnts and RSPO3 for murine intestinal stem cells in vivo.
Gediminas Greicius, Zahra Kabiri, Kristmundur Sigmundsson, Chao Liang, Ralph Bunte, Manvendra K Singh, David M Virshup. Proc Natl Acad Sci U S A 2018
134
14

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
14

Cellular and molecular architecture of the intestinal stem cell niche.
Neil McCarthy, Judith Kraiczy, Ramesh A Shivdasani. Nat Cell Biol 2020
34
14

CD34+ mesenchymal cells are a major component of the intestinal stem cells niche at homeostasis and after injury.
Igor Stzepourginski, Giulia Nigro, Jean-Marie Jacob, Sophie Dulauroy, Philippe J Sansonetti, Gérard Eberl, Lucie Peduto. Proc Natl Acad Sci U S A 2017
142
14

Mucosal Profiling of Pediatric-Onset Colitis and IBD Reveals Common Pathogenics and Therapeutic Pathways.
Bing Huang, Zhanghua Chen, Lanlan Geng, Jun Wang, Huiying Liang, Yujie Cao, Huan Chen, Wanming Huang, Meiling Su, Hanqing Wang,[...]. Cell 2019
53
14

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
14

A human cell atlas of fetal gene expression.
Junyue Cao, Diana R O'Day, Hannah A Pliner, Paul D Kingsley, Mei Deng, Riza M Daza, Michael A Zager, Kimberly A Aldinger, Ronnie Blecher-Gonen, Fan Zhang,[...]. Science 2020
100
14

Construction of a human cell landscape at single-cell level.
Xiaoping Han, Ziming Zhou, Lijiang Fei, Huiyu Sun, Renying Wang, Yao Chen, Haide Chen, Jingjing Wang, Huanna Tang, Wenhao Ge,[...]. Nature 2020
232
14

Parasitic helminths induce fetal-like reversion in the intestinal stem cell niche.
Ysbrand M Nusse, Adam K Savage, Pauline Marangoni, Axel K M Rosendahl-Huber, Tyler A Landman, Frederic J de Sauvage, Richard M Locksley, Ophir D Klein. Nature 2018
104
14

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
14

Transcriptome-wide Analysis Reveals Hallmarks of Human Intestine Development and Maturation In Vitro and In Vivo.
Stacy R Finkbeiner, David R Hill, Christopher H Altheim, Priya H Dedhia, Matthew J Taylor, Yu-Hwai Tsai, Alana M Chin, Maxime M Mahe, Carey L Watson, Jennifer J Freeman,[...]. Stem Cell Reports 2015
134
11

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
11

The emergent landscape of the mouse gut endoderm at single-cell resolution.
Sonja Nowotschin, Manu Setty, Ying-Yi Kuo, Vincent Liu, Vidur Garg, Roshan Sharma, Claire S Simon, Nestor Saiz, Rui Gardner, Stéphane C Boutet,[...]. Nature 2019
100
11

Transplantation of expanded fetal intestinal progenitors contributes to colon regeneration after injury.
Robert P Fordham, Shiro Yui, Nicholas R F Hannan, Christoffer Soendergaard, Alison Madgwick, Pawel J Schweiger, Ole H Nielsen, Ludovic Vallier, Roger A Pedersen, Tetsuya Nakamura,[...]. Cell Stem Cell 2013
222
11

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
11

GLI1-expressing mesenchymal cells form the essential Wnt-secreting niche for colon stem cells.
Bahar Degirmenci, Tomas Valenta, Slavica Dimitrieva, George Hausmann, Konrad Basler. Nature 2018
151
11

Paracrine orchestration of intestinal tumorigenesis by a mesenchymal niche.
Manolis Roulis, Aimilios Kaklamanos, Marina Schernthanner, Piotr Bielecki, Jun Zhao, Eleanna Kaffe, Laura-Sophie Frommelt, Rihao Qu, Marlene S Knapp, Ana Henriques,[...]. Nature 2020
86
11

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
84
11

Cell fate specification and differentiation in the adult mammalian intestine.
Joep Beumer, Hans Clevers. Nat Rev Mol Cell Biol 2021
65
11

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
169
11

High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells.
Joep Beumer, Jens Puschhof, Julia Bauzá-Martinez, Adriana Martínez-Silgado, Rasa Elmentaite, Kylie R James, Alexander Ross, Delilah Hendriks, Benedetta Artegiani, Georg A Busslinger,[...]. Cell 2020
35
11

PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells.
F Alexander Wolf, Fiona K Hamey, Mireya Plass, Jordi Solana, Joakim S Dahlin, Berthold Göttgens, Nikolaus Rajewsky, Lukas Simon, Fabian J Theis. Genome Biol 2019
276
11

Fast, sensitive and accurate integration of single-cell data with Harmony.
Ilya Korsunsky, Nghia Millard, Jean Fan, Kamil Slowikowski, Fan Zhang, Kevin Wei, Yuriy Baglaenko, Michael Brenner, Po-Ru Loh, Soumya Raychaudhuri. Nat Methods 2019
613
11

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
148
11

Identification of Lgr5-independent spheroid-generating progenitors of the mouse fetal intestinal epithelium.
Roxana C Mustata, Gabriela Vasile, Valeria Fernandez-Vallone, Sandra Strollo, Anne Lefort, Frédérick Libert, Daniel Monteyne, David Pérez-Morga, Gilbert Vassart, Marie-Isabelle Garcia. Cell Rep 2013
122
11

Tracing the origin of adult intestinal stem cells.
Jordi Guiu, Edouard Hannezo, Shiro Yui, Samuel Demharter, Svetlana Ulyanchenko, Martti Maimets, Anne Jørgensen, Signe Perlman, Lene Lundvall, Linn Salto Mamsen,[...]. Nature 2019
57
11

Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
Luke Jostins, Stephan Ripke, Rinse K Weersma, Richard H Duerr, Dermot P McGovern, Ken Y Hui, James C Lee, L Philip Schumm, Yashoda Sharma, Carl A Anderson,[...]. Nature 2012
11

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
11

Exponential scaling of single-cell RNA-seq in the past decade.
Valentine Svensson, Roser Vento-Tormo, Sarah A Teichmann. Nat Protoc 2018
299
11

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
11


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.