A citation-based method for searching scientific literature

Floris Imhann, Arnau Vich Vila, Marc Jan Bonder, Jingyuan Fu, Dirk Gevers, Marijn C Visschedijk, Lieke M Spekhorst, Rudi Alberts, Lude Franke, Hendrik M van Dullemen, Rinze W F Ter Steege, Curtis Huttenhower, Gerard Dijkstra, Ramnik J Xavier, Eleonora A M Festen, Cisca Wijmenga, Alexandra Zhernakova, Rinse K Weersma. Gut 2018
Times Cited: 325







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



Times Cited
  Times     Co-cited
Similarity


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
21

Gut microbiome structure and metabolic activity in inflammatory bowel disease.
Eric A Franzosa, Alexandra Sirota-Madi, Julian Avila-Pacheco, Nadine Fornelos, Henry J Haiser, Stefan Reinker, Tommi Vatanen, A Brantley Hall, Himel Mallick, Lauren J McIver,[...]. Nat Microbiol 2019
422
20

The treatment-naive microbiome in new-onset Crohn's disease.
Dirk Gevers, Subra Kugathasan, Lee A Denson, Yoshiki Vázquez-Baeza, Will Van Treuren, Boyu Ren, Emma Schwager, Dan Knights, Se Jin Song, Moran Yassour,[...]. Cell Host Microbe 2014
18

Gut microbiota and IBD: causation or correlation?
Josephine Ni, Gary D Wu, Lindsey Albenberg, Vesselin T Tomov. Nat Rev Gastroenterol Hepatol 2017
532
17

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment.
Xochitl C Morgan, Timothy L Tickle, Harry Sokol, Dirk Gevers, Kathryn L Devaney, Doyle V Ward, Joshua A Reyes, Samir A Shah, Neal LeLeiko, Scott B Snapper,[...]. Genome Biol 2012
16

Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients.
Harry Sokol, Bénédicte Pigneur, Laurie Watterlot, Omar Lakhdari, Luis G Bermúdez-Humarán, Jean-Jacques Gratadoux, Sébastien Blugeon, Chantal Bridonneau, Jean-Pierre Furet, Gérard Corthier,[...]. Proc Natl Acad Sci U S A 2008
16

The microbiome in inflammatory bowel disease: current status and the future ahead.
Aleksandar D Kostic, Ramnik J Xavier, Dirk Gevers. Gastroenterology 2014
911
14

A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis.
Kathleen Machiels, Marie Joossens, João Sabino, Vicky De Preter, Ingrid Arijs, Venessa Eeckhaut, Vera Ballet, Karolien Claes, Filip Van Immerseel, Kristin Verbeke,[...]. Gut 2014
813
14

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
14

Differences in Gut Microbiota in Patients With vs Without Inflammatory Bowel Diseases: A Systematic Review.
Rapat Pittayanon, Jennifer T Lau, Grigorios I Leontiadis, Frances Tse, Yuhong Yuan, Michael Surette, Paul Moayyedi. Gastroenterology 2020
118
13

Dynamics of the human gut microbiome in inflammatory bowel disease.
Jonas Halfvarson, Colin J Brislawn, Regina Lamendella, Yoshiki Vázquez-Baeza, William A Walters, Lisa M Bramer, Mauro D'Amato, Ferdinando Bonfiglio, Daniel McDonald, Antonio Gonzalez,[...]. Nat Microbiol 2017
454
13

Gut microbiota-derived metabolites as key actors in inflammatory bowel disease.
Aonghus Lavelle, Harry Sokol. Nat Rev Gastroenterol Hepatol 2020
276
13

A microbial signature for Crohn's disease.
Victoria Pascal, Marta Pozuelo, Natalia Borruel, Francesc Casellas, David Campos, Alba Santiago, Xavier Martinez, Encarna Varela, Guillaume Sarrabayrouse, Kathleen Machiels,[...]. Gut 2017
336
12

Fungal microbiota dysbiosis in IBD.
Harry Sokol, Valentin Leducq, Hugues Aschard, Hang-Phuong Pham, Sarah Jegou, Cecilia Landman, David Cohen, Giuseppina Liguori, Anne Bourrier, Isabelle Nion-Larmurier,[...]. Gut 2017
493
11

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease.
James D Lewis, Eric Z Chen, Robert N Baldassano, Anthony R Otley, Anne M Griffiths, Dale Lee, Kyle Bittinger, Aubrey Bailey, Elliot S Friedman, Christian Hoffmann,[...]. Cell Host Microbe 2015
384
11

Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases.
Daniel N Frank, Allison L St Amand, Robert A Feldman, Edgar C Boedeker, Noam Harpaz, Norman R Pace. Proc Natl Acad Sci U S A 2007
11

Diet rapidly and reproducibly alters the human gut microbiome.
Lawrence A David, Corinne F Maurice, Rachel N Carmody, David B Gootenberg, Julie E Button, Benjamin E Wolfe, Alisha V Ling, A Sloan Devlin, Yug Varma, Michael A Fischbach,[...]. Nature 2014
11

Microbial genes and pathways in inflammatory bowel disease.
Melanie Schirmer, Ashley Garner, Hera Vlamakis, Ramnik J Xavier. Nat Rev Microbiol 2019
162
10

Microbial network disturbances in relapsing refractory Crohn's disease.
Bahtiyar Yilmaz, Pascal Juillerat, Ove Øyås, Charlotte Ramon, Francisco Damian Bravo, Yannick Franc, Nicolas Fournier, Pierre Michetti, Christoph Mueller, Markus Geuking,[...]. Nat Med 2019
129
9

Disease-specific alterations in the enteric virome in inflammatory bowel disease.
Jason M Norman, Scott A Handley, Megan T Baldridge, Lindsay Droit, Catherine Y Liu, Brian C Keller, Amal Kambal, Cynthia L Monaco, Guoyan Zhao, Phillip Fleshner,[...]. Cell 2015
600
9

Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives.
Marie Joossens, Geert Huys, Margo Cnockaert, Vicky De Preter, Kristin Verbeke, Paul Rutgeerts, Peter Vandamme, Severine Vermeire. Gut 2011
579
9

Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells.
Yukihiro Furusawa, Yuuki Obata, Shinji Fukuda, Takaho A Endo, Gaku Nakato, Daisuke Takahashi, Yumiko Nakanishi, Chikako Uetake, Keiko Kato, Tamotsu Kato,[...]. Nature 2013
9

Connecting dysbiosis, bile-acid dysmetabolism and gut inflammation in inflammatory bowel diseases.
Henri Duboc, Sylvie Rajca, Dominique Rainteau, David Benarous, Marie-Anne Maubert, Elodie Quervain, Ginette Thomas, Véronique Barbu, Lydie Humbert, Guillaume Despras,[...]. Gut 2013
380
9

A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes.
Ben P Willing, Johan Dicksved, Jonas Halfvarson, Anders F Andersson, Marianna Lucio, Zongli Zheng, Gunnar Järnerot, Curt Tysk, Janet K Jansson, Lars Engstrand. Gastroenterology 2010
650
9

A human gut microbial gene catalogue established by metagenomic sequencing.
Junjie Qin, Ruiqiang Li, Jeroen Raes, Manimozhiyan Arumugam, Kristoffer Solvsten Burgdorf, Chaysavanh Manichanh, Trine Nielsen, Nicolas Pons, Florence Levenez, Takuji Yamada,[...]. Nature 2010
9

Human genetics shape the gut microbiome.
Julia K Goodrich, Jillian L Waters, Angela C Poole, Jessica L Sutter, Omry Koren, Ran Blekhman, Michelle Beaumont, William Van Treuren, Rob Knight, Jordana T Bell,[...]. Cell 2014
9

Alteration of Gut Microbiota in Inflammatory Bowel Disease (IBD): Cause or Consequence? IBD Treatment Targeting the Gut Microbiome.
Israr Khan, Naeem Ullah, Lajia Zha, Yanrui Bai, Ashiq Khan, Tang Zhao, Tuanjie Che, Chunjiang Zhang. Pathogens 2019
180
9

Fecal Microbiota Transplantation Induces Remission in Patients With Active Ulcerative Colitis in a Randomized Controlled Trial.
Paul Moayyedi, Michael G Surette, Peter T Kim, Josie Libertucci, Melanie Wolfe, Catherine Onischi, David Armstrong, John K Marshall, Zain Kassam, Walter Reinisch,[...]. Gastroenterology 2015
758
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

Short Chain Fatty Acids (SCFAs)-Mediated Gut Epithelial and Immune Regulation and Its Relevance for Inflammatory Bowel Diseases.
Daniela Parada Venegas, Marjorie K De la Fuente, Glauben Landskron, María Julieta González, Rodrigo Quera, Gerard Dijkstra, Hermie J M Harmsen, Klaas Nico Faber, Marcela A Hermoso. Front Immunol 2019
703
8

Colonisation by Faecalibacterium prausnitzii and maintenance of clinical remission in patients with ulcerative colitis.
E Varela, C Manichanh, M Gallart, A Torrejón, N Borruel, F Casellas, F Guarner, M Antolin. Aliment Pharmacol Ther 2013
132
8

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
8

The microbiome and inflammatory bowel disease.
Kerri L Glassner, Bincy P Abraham, Eamonn M M Quigley. J Allergy Clin Immunol 2020
120
8

Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome.
Arnau Vich Vila, Floris Imhann, Valerie Collij, Soesma A Jankipersadsing, Thomas Gurry, Zlatan Mujagic, Alexander Kurilshikov, Marc Jan Bonder, Xiaofang Jiang, Ettje F Tigchelaar,[...]. Sci Transl Med 2018
148
7

Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria.
Chin Wen Png, Sara K Lindén, Kristen S Gilshenan, Erwin G Zoetendal, Chris S McSweeney, Lindsay I Sly, Michael A McGuckin, Timothy H J Florin. Am J Gastroenterol 2010
716
7

Increased proportions of Bifidobacterium and the Lactobacillus group and loss of butyrate-producing bacteria in inflammatory bowel disease.
Wei Wang, Liping Chen, Rui Zhou, Xiaobing Wang, Lu Song, Sha Huang, Ge Wang, Bing Xia. J Clin Microbiol 2014
226
7


DADA2: High-resolution sample inference from Illumina amplicon data.
Benjamin J Callahan, Paul J McMurdie, Michael J Rosen, Andrew W Han, Amy Jo A Johnson, Susan P Holmes. Nat Methods 2016
7

Genetics and pathogenesis of inflammatory bowel disease.
Bernard Khor, Agnès Gardet, Ramnik J Xavier. Nature 2011
7



Host-microbiota interactions in inflammatory bowel disease.
Roberta Caruso, Bernard C Lo, Gabriel Núñez. Nat Rev Immunol 2020
118
7

Human gut microbiome viewed across age and geography.
Tanya Yatsunenko, Federico E Rey, Mark J Manary, Indi Trehan, Maria Gloria Dominguez-Bello, Monica Contreras, Magda Magris, Glida Hidalgo, Robert N Baldassano, Andrey P Anokhin,[...]. Nature 2012
7

Gut microbiota in the pathogenesis of inflammatory bowel disease.
Atsushi Nishida, Ryo Inoue, Osamu Inatomi, Shigeki Bamba, Yuji Naito, Akira Andoh. Clin J Gastroenterol 2018
378
7

Metagenomic biomarker discovery and explanation.
Nicola Segata, Jacques Izard, Levi Waldron, Dirk Gevers, Larisa Miropolsky, Wendy S Garrett, Curtis Huttenhower. Genome Biol 2011
7

The gut microbiota and inflammatory bowel disease.
Katsuyoshi Matsuoka, Takanori Kanai. Semin Immunopathol 2015
337
7

Ranking microbiome variance in inflammatory bowel disease: a large longitudinal intercontinental study.
Adam G Clooney, Julia Eckenberger, Emilio Laserna-Mendieta, Kathryn A Sexton, Matthew T Bernstein, Kathy Vagianos, Michael Sargent, Feargal J Ryan, Carthage Moran, Donal Sheehan,[...]. Gut 2021
43
16

Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels.
Mohammad Tauqeer Alam, Gregory C A Amos, Andrew R J Murphy, Simon Murch, Elizabeth M H Wellington, Ramesh P Arasaradnam. Gut Pathog 2020
84
8

Adherent-invasive Escherichia coli in inflammatory bowel disease.
Carolina Palmela, Caroline Chevarin, Zhilu Xu, Joana Torres, Gwladys Sevrin, Robert Hirten, Nicolas Barnich, Siew C Ng, Jean-Frederic Colombel. Gut 2018
177
6

Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease.
Adam G Clooney, Thomas D S Sutton, Andrey N Shkoporov, Ross K Holohan, Karen M Daly, Orla O'Regan, Feargal J Ryan, Lorraine A Draper, Scott E Plevy, R Paul Ross,[...]. Cell Host Microbe 2019
89
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.