A citation-based method for searching scientific literature

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, Jenny S Sauk, Robin G Wilson, Betsy W Stevens, Justin M Scott, Kerry Pierce, Amy A Deik, Kevin Bullock, Floris Imhann, Jeffrey A Porter, Alexandra Zhernakova, Jingyuan Fu, Rinse K Weersma, Cisca Wijmenga, Clary B Clish, Hera Vlamakis, Curtis Huttenhower, Ramnik J Xavier. Nat Microbiol 2019
Times Cited: 422







List of co-cited articles
827 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
36

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
18

Gut microbiota-derived metabolites as key actors in inflammatory bowel disease.
Aonghus Lavelle, Harry Sokol. Nat Rev Gastroenterol Hepatol 2020
276
18

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
15

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
14

Bile acid metabolites control TH17 and Treg cell differentiation.
Saiyu Hang, Donggi Paik, Lina Yao, Eunha Kim, Jamma Trinath, Jingping Lu, Soyoung Ha, Brandon N Nelson, Samantha P Kelly, Lin Wu,[...]. Nature 2019
260
13

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
13

The microbiome in inflammatory bowel disease: current status and the future ahead.
Aleksandar D Kostic, Ramnik J Xavier, Dirk Gevers. Gastroenterology 2014
911
12

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
12

Microbial bile acid metabolites modulate gut RORγ+ regulatory T cell homeostasis.
Xinyang Song, Ximei Sun, Sungwhan F Oh, Meng Wu, Yanbo Zhang, Wen Zheng, Naama Geva-Zatorsky, Ray Jupp, Diane Mathis, Christophe Benoist,[...]. Nature 2020
233
11

Dysbiosis-Induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation.
Sidhartha R Sinha, Yeneneh Haileselassie, Linh P Nguyen, Carolina Tropini, Min Wang, Laren S Becker, Davis Sim, Karolin Jarr, Estelle T Spear, Gulshan Singh,[...]. Cell Host Microbe 2020
110
11

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

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
10

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
10

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
10

A Disease-Associated Microbial and Metabolomics State in Relatives of Pediatric Inflammatory Bowel Disease Patients.
Jonathan P Jacobs, Maryam Goudarzi, Namita Singh, Maomeng Tong, Ian H McHardy, Paul Ruegger, Miro Asadourian, Bo-Hyun Moon, Allyson Ayson, James Borneman,[...]. Cell Mol Gastroenterol Hepatol 2016
99
10

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
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

Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease.
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,[...]. Gut 2018
325
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
9

Gut microbiota, metabolites and host immunity.
Michelle G Rooks, Wendy S Garrett. Nat Rev Immunol 2016
9

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
9

Microbial tryptophan catabolites in health and disease.
Henrik M Roager, Tine R Licht. Nat Commun 2018
482
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
8

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
8

Gut microbiota and IBD: causation or correlation?
Josephine Ni, Gary D Wu, Lindsey Albenberg, Vesselin T Tomov. Nat Rev Gastroenterol Hepatol 2017
532
8

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients.
Andrew Brantley Hall, Moran Yassour, Jenny Sauk, Ashley Garner, Xiaofang Jiang, Timothy Arthur, Georgia K Lagoudas, Tommi Vatanen, Nadine Fornelos, Robin Wilson,[...]. Genome Med 2017
216
8

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
8

Species-level functional profiling of metagenomes and metatranscriptomes.
Eric A Franzosa, Lauren J McIver, Gholamali Rahnavard, Luke R Thompson, Melanie Schirmer, George Weingart, Karen Schwarzberg Lipson, Rob Knight, J Gregory Caporaso, Nicola Segata,[...]. Nat Methods 2018
521
8

QIIME allows analysis of high-throughput community sequencing data.
J Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D Bushman, Elizabeth K Costello, Noah Fierer, Antonio Gonzalez Peña, Julia K Goodrich, Jeffrey I Gordon,[...]. Nat Methods 2010
8

The global burden of IBD: from 2015 to 2025.
Gilaad G Kaplan. Nat Rev Gastroenterol Hepatol 2015
888
8

Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites.
William R Wikoff, Andrew T Anfora, Jun Liu, Peter G Schultz, Scott A Lesley, Eric C Peters, Gary Siuzdak. Proc Natl Acad Sci U S A 2009
8

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
8

Population-level analysis of gut microbiome variation.
Gwen Falony, Marie Joossens, Sara Vieira-Silva, Jun Wang, Youssef Darzi, Karoline Faust, Alexander Kurilshikov, Marc Jan Bonder, Mireia Valles-Colomer, Doris Vandeputte,[...]. Science 2016
973
7

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
7

Gut Microbiota Regulation of Tryptophan Metabolism in Health and Disease.
Allison Agus, Julien Planchais, Harry Sokol. Cell Host Microbe 2018
592
7

Specific Bacteria and Metabolites Associated With Response to Fecal Microbiota Transplantation in Patients With Ulcerative Colitis.
Sudarshan Paramsothy, Shaun Nielsen, Michael A Kamm, Nandan P Deshpande, Jeremiah J Faith, Jose C Clemente, Ramesh Paramsothy, Alissa J Walsh, Johan van den Bogaerde, Douglas Samuel,[...]. Gastroenterology 2019
137
7

Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial.
Sudarshan Paramsothy, Michael A Kamm, Nadeem O Kaakoush, Alissa J Walsh, Johan van den Bogaerde, Douglas Samuel, Rupert W L Leong, Susan Connor, Watson Ng, Ramesh Paramsothy,[...]. Lancet 2017
557
7

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites.
Ara Koh, Filipe De Vadder, Petia Kovatcheva-Datchary, Fredrik Bäckhed. Cell 2016
7


Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis.
Eric M Brown, Xiaobo Ke, Daniel Hitchcock, Sarah Jeanfavre, Julian Avila-Pacheco, Toru Nakata, Timothy D Arthur, Nadine Fornelos, Cortney Heim, Eric A Franzosa,[...]. Cell Host Microbe 2019
97
7

Increased Tryptophan Metabolism Is Associated With Activity of Inflammatory Bowel Diseases.
Susanna Nikolaus, Berenice Schulte, Natalie Al-Massad, Florian Thieme, Dominik M Schulte, Johannes Bethge, Ateequr Rehman, Florian Tran, Konrad Aden, Robert Häsler,[...]. Gastroenterology 2017
158
7

Metabolomics reveals metabolic biomarkers of Crohn's disease.
Janet Jansson, Ben Willing, Marianna Lucio, Ages Fekete, Johan Dicksved, Jonas Halfvarson, Curt Tysk, Philippe Schmitt-Kopplin. PLoS One 2009
341
7

Dysbiotic gut microbiota causes transmissible Crohn's disease-like ileitis independent of failure in antimicrobial defence.
Monika Schaubeck, Thomas Clavel, Jelena Calasan, Ilias Lagkouvardos, Sven Bastiaan Haange, Nico Jehmlich, Marijana Basic, Aline Dupont, Mathias Hornef, Martin von Bergen,[...]. Gut 2016
192
7

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
7

CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands.
Bruno Lamas, Mathias L Richard, Valentin Leducq, Hang-Phuong Pham, Marie-Laure Michel, Gregory Da Costa, Chantal Bridonneau, Sarah Jegou, Thomas W Hoffmann, Jane M Natividad,[...]. Nat Med 2016
587
7


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
7

Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease.
Kyohei Nishino, Atsushi Nishida, Ryo Inoue, Yuki Kawada, Masashi Ohno, Shigeki Sakai, Osamu Inatomi, Shigeki Bamba, Mitsushige Sugimoto, Masahiro Kawahara,[...]. J Gastroenterol 2018
127
6

A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites.
Dylan Dodd, Matthew H Spitzer, William Van Treuren, Bryan D Merrill, Andrew J Hryckowian, Steven K Higginbottom, Anthony Le, Tina M Cowan, Garry P Nolan, Michael A Fischbach,[...]. Nature 2017
362
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.