A citation-based method for searching scientific literature

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, Malika Sud, Elizabeth Andrews, Gabriella Velonias, Adam L Haber, Karthik Jagadeesh, Sanja Vickovic, Junmei Yao, Christine Stevens, Danielle Dionne, Lan T Nguyen, Alexandra-Chloé Villani, Matan Hofree, Elizabeth A Creasey, Hailiang Huang, Orit Rozenblatt-Rosen, John J Garber, Hamed Khalili, A Nicole Desch, Mark J Daly, Ashwin N Ananthakrishnan, Alex K Shalek, Ramnik J Xavier, Aviv Regev. Cell 2019
Times Cited: 288







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



Times Cited
  Times     Co-cited
Similarity


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
28

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
21

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
18

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
18

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
14

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
13

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

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
12

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
12

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
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

Oncostatin M drives intestinal inflammation and predicts response to tumor necrosis factor-neutralizing therapy in patients with inflammatory bowel disease.
Nathaniel R West, Ahmed N Hegazy, Benjamin M J Owens, Samuel J Bullers, Bryan Linggi, Sofia Buonocore, Margherita Coccia, Dieter Görtz, Sébastien This, Krista Stockenhuber,[...]. Nat Med 2017
313
10

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
9

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
9

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
9

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
9

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
10

Cytokine Networks in the Pathophysiology of Inflammatory Bowel Disease.
Matthias Friedrich, Mathilde Pohin, Fiona Powrie. Immunity 2019
178
8

Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker. Genome Res 2003
8

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
8

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
8

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
8

Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease.
Katrina M de Lange, Loukas Moutsianas, James C Lee, Christopher A Lamb, Yang Luo, Nicholas A Kennedy, Luke Jostins, Daniel L Rice, Javier Gutierrez-Achury, Sun-Gou Ji,[...]. Nat Genet 2017
418
8

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
15

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
8

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

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
35
22

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
9


Crohn's disease.
Joana Torres, Saurabh Mehandru, Jean-Frédéric Colombel, Laurent Peyrin-Biroulet. Lancet 2017
744
7

Ulcerative colitis.
Ryan Ungaro, Saurabh Mehandru, Patrick B Allen, Laurent Peyrin-Biroulet, Jean-Frédéric Colombel. Lancet 2017
7

Proteomics. Tissue-based map of the human proteome.
Mathias Uhlén, Linn Fagerberg, Björn M Hallström, Cecilia Lindskog, Per Oksvold, Adil Mardinoglu, Åsa Sivertsson, Caroline Kampf, Evelina Sjöstedt, Anna Asplund,[...]. Science 2015
7

Full-length RNA-seq from single cells using Smart-seq2.
Simone Picelli, Omid R Faridani, Asa K Björklund, Gösta Winberg, Sven Sagasser, Rickard Sandberg. Nat Protoc 2014
7

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

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
7

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
7

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
7

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
72
9


Worldwide incidence and prevalence of inflammatory bowel disease in the 21st century: a systematic review of population-based studies.
Siew C Ng, Hai Yun Shi, Nima Hamidi, Fox E Underwood, Whitney Tang, Eric I Benchimol, Remo Panaccione, Subrata Ghosh, Justin C Y Wu, Francis K L Chan,[...]. Lancet 2017
7

Anti-commensal IgG Drives Intestinal Inflammation and Type 17 Immunity in Ulcerative Colitis.
Tomas Castro-Dopico, Thomas W Dennison, John R Ferdinand, Rebeccah J Mathews, Aaron Fleming, Dean Clift, Benjamin J Stewart, Chenzhi Jing, Konstantina Strongili, Larisa I Labzin,[...]. Immunity 2019
66
9

Microanatomical dissection of human intestinal T-cell immunity reveals site-specific changes in gut-associated lymphoid tissues over life.
Takashi Senda, Pranay Dogra, Tomer Granot, Kazuhiro Furuhashi, Mark E Snyder, Dustin J Carpenter, Peter A Szabo, Puspa Thapa, Michelle Miron, Donna L Farber. Mucosal Immunol 2019
42
14

Genetics and pathogenesis of inflammatory bowel disease.
Bernard Khor, Agnès Gardet, Ramnik J Xavier. Nature 2011
6

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
844
6

Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer.
Lei Zhang, Ziyi Li, Katarzyna M Skrzypczynska, Qiao Fang, Wei Zhang, Sarah A O'Brien, Yao He, Lynn Wang, Qiming Zhang, Aeryon Kim,[...]. Cell 2020
199
6

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
644
6

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
6

Genome-wide association study identifies distinct genetic contributions to prognosis and susceptibility in Crohn's disease.
James C Lee, Daniele Biasci, Rebecca Roberts, Richard B Gearry, John C Mansfield, Tariq Ahmad, Natalie J Prescott, Jack Satsangi, David C Wilson, Luke Jostins,[...]. Nat Genet 2017
132
6

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
6

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
7


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.