A citation-based method for searching scientific literature

Jerome C Martin, Christie Chang, Gilles Boschetti, Ryan Ungaro, Mamta Giri, John A Grout, Kyle Gettler, Ling-Shiang Chuang, Shikha Nayar, Alexander J Greenstein, Marla Dubinsky, Laura Walker, Andrew Leader, Jay S Fine, Charles E Whitehurst, M Lamine Mbow, Subra Kugathasan, Lee A Denson, Jeffrey S Hyams, Joshua R Friedman, Prerak T Desai, Huaibin M Ko, Ilaria Laface, Guray Akturk, Eric E Schadt, Helene Salmon, Sacha Gnjatic, Adeeb H Rahman, Miriam Merad, Judy H Cho, Ephraim Kenigsberg. Cell 2019
Times Cited: 197







List of co-cited articles
1014 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
44

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
23

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
23

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
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
16

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
15

Prediction of complicated disease course for children newly diagnosed with Crohn's disease: a multicentre inception cohort study.
Subra Kugathasan, Lee A Denson, Thomas D Walters, Mi-Ok Kim, Urko M Marigorta, Melanie Schirmer, Kajari Mondal, Chunyan Liu, Anne Griffiths, Joshua D Noe,[...]. Lancet 2017
301
14

Crohn's disease.
Joana Torres, Saurabh Mehandru, Jean-Frédéric Colombel, Laurent Peyrin-Biroulet. Lancet 2017
744
12

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
11

Mucosal gene signatures to predict response to infliximab in patients with ulcerative colitis.
I Arijs, K Li, G Toedter, R Quintens, L Van Lommel, K Van Steen, P Leemans, G De Hertogh, K Lemaire, M Ferrante,[...]. Gut 2009
248
10

Ulcerative colitis.
Ryan Ungaro, Saurabh Mehandru, Patrick B Allen, Laurent Peyrin-Biroulet, Jean-Frédéric Colombel. Lancet 2017
9

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.
Jason Lloyd-Price, Cesar Arze, Ashwin N Ananthakrishnan, Melanie Schirmer, Julian Avila-Pacheco, Tiffany W Poon, Elizabeth Andrews, Nadim J Ajami, Kevin S Bonham, Colin J Brislawn,[...]. Nature 2019
667
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

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
9

Distinct fibroblast subsets drive inflammation and damage in arthritis.
Adam P Croft, Joana Campos, Kathrin Jansen, Jason D Turner, Jennifer Marshall, Moustafa Attar, Loriane Savary, Corinna Wehmeyer, Amy J Naylor, Samuel Kemble,[...]. Nature 2019
265
9

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

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
8

NicheNet: modeling intercellular communication by linking ligands to target genes.
Robin Browaeys, Wouter Saelens, Yvan Saeys. Nat Methods 2020
190
8

Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations.
Jimmy Z Liu, Suzanne van Sommeren, Hailiang Huang, Siew C Ng, Rudi Alberts, Atsushi Takahashi, Stephan Ripke, James C Lee, Luke Jostins, Tejas Shah,[...]. Nat Genet 2015
8

Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry.
Fan Zhang, Kevin Wei, Kamil Slowikowski, Chamith Y Fonseka, Deepak A Rao, Stephen Kelly, Susan M Goodman, Darren Tabechian, Laura B Hughes, Karen Salomon-Escoto,[...]. Nat Immunol 2019
337
8

Cytokine Networks in the Pathophysiology of Inflammatory Bowel Disease.
Matthias Friedrich, Mathilde Pohin, Fiona Powrie. Immunity 2019
178
7

Cell-centred meta-analysis reveals baseline predictors of anti-TNFα non-response in biopsy and blood of patients with IBD.
Renaud Gaujoux, Elina Starosvetsky, Naama Maimon, Francesco Vallania, Haggai Bar-Yoseph, Sigal Pressman, Roni Weisshof, Idan Goren, Keren Rabinowitz, Matti Waterman,[...]. Gut 2019
88
7

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
274
7

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
7

DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome.
Kate Joanne Howell, Judith Kraiczy, Komal M Nayak, Marco Gasparetto, Alexander Ross, Claire Lee, Tim N Mak, Bon-Kyoung Koo, Nitin Kumar, Trevor Lawley,[...]. Gastroenterology 2018
119
7

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
20

Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn's Disease.
Vanessa Mitsialis, Sarah Wall, Peng Liu, Jose Ordovas-Montanes, Tamar Parmet, Marko Vukovic, Dennis Spencer, Michael Field, Collin McCourt, Jessica Toothaker,[...]. Gastroenterology 2020
32
21

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
7

Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response.
Yael Haberman, Rebekah Karns, Phillip J Dexheimer, Melanie Schirmer, Judith Somekh, Ingrid Jurickova, Tzipi Braun, Elizabeth Novak, Laura Bauman, Margaret H Collins,[...]. Nat Commun 2019
97
7

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

Transcriptional and functional profiling defines human small intestinal macrophage subsets.
Anna Bujko, Nader Atlasy, Ole J B Landsverk, Lisa Richter, Sheraz Yaqub, Rune Horneland, Ole Øyen, Einar Martin Aandahl, Lars Aabakken, Hendrik G Stunnenberg,[...]. J Exp Med 2018
81
7

Unique CD14 intestinal macrophages contribute to the pathogenesis of Crohn disease via IL-23/IFN-gamma axis.
Nobuhiko Kamada, Tadakazu Hisamatsu, Susumu Okamoto, Hiroshi Chinen, Taku Kobayashi, Toshiro Sato, Atsushi Sakuraba, Mina T Kitazume, Akira Sugita, Kazutaka Koganei,[...]. J Clin Invest 2008
435
6

Inherited determinants of Crohn's disease and ulcerative colitis phenotypes: a genetic association study.
Isabelle Cleynen, Gabrielle Boucher, Luke Jostins, L Philip Schumm, Sebastian Zeissig, Tariq Ahmad, Vibeke Andersen, Jane M Andrews, Vito Annese, Stephan Brand,[...]. Lancet 2016
392
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

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
6

Paneth cells as a site of origin for intestinal inflammation.
Timon E Adolph, Michal F Tomczak, Lukas Niederreiter, Hyun-Jeong Ko, Janne Böck, Eduardo Martinez-Naves, Jonathan N Glickman, Markus Tschurtschenthaler, John Hartwig, Shuhei Hosomi,[...]. Nature 2013
429
6

The diagnostic approach to monogenic very early onset inflammatory bowel disease.
Holm H Uhlig, Tobias Schwerd, Sibylle Koletzko, Neil Shah, Jochen Kammermeier, Abdul Elkadri, Jodie Ouahed, David C Wilson, Simon P Travis, Dan Turner,[...]. Gastroenterology 2014
347
6

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
6

Low TREM1 expression in whole blood predicts anti-TNF response in inflammatory bowel disease.
Bram Verstockt, Sare Verstockt, Jonas Dehairs, Vera Ballet, Helene Blevi, Willem-Jan Wollants, Christine Breynaert, Gert Van Assche, Séverine Vermeire, Marc Ferrante. EBioMedicine 2019
59
10

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
6

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
6

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.
Greg Finak, Andrew McDavid, Masanao Yajima, Jingyuan Deng, Vivian Gersuk, Alex K Shalek, Chloe K Slichter, Hannah W Miller, M Juliana McElrath, Martin Prlic,[...]. Genome Biol 2015
766
6

Smart-seq2 for sensitive full-length transcriptome profiling in single cells.
Simone Picelli, Åsa K Björklund, Omid R Faridani, Sven Sagasser, Gösta Winberg, Rickard Sandberg. Nat Methods 2013
6

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
8

Expansion of IL-23 receptor bearing TNFR2+ T cells is associated with molecular resistance to anti-TNF therapy in Crohn's disease.
Heike Schmitt, Ulrike Billmeier, Walburga Dieterich, Timo Rath, Sophia Sonnewald, Stephen Reid, Simon Hirschmann, Kai Hildner, Maximilian J Waldner, Jonas Mudter,[...]. Gut 2019
68
8

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
6

Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt+ Regulatory T Cells and Exacerbate Colitis in Mice.
Graham J Britton, Eduardo J Contijoch, Ilaria Mogno, Olivia H Vennaro, Sean R Llewellyn, Ruby Ng, Zhihua Li, Arthur Mortha, Miriam Merad, Anuk Das,[...]. Immunity 2019
168
6

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
7

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
11

Cytokines in inflammatory bowel disease.
Markus F Neurath. Nat Rev Immunol 2014
5


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.