A citation-based method for searching scientific literature

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, David Casero, Holly Courtney, Antonio Gonzalez, Thomas G Graeber, A Brantley Hall, Kathleen Lake, Carol J Landers, Himel Mallick, Damian R Plichta, Mahadev Prasad, Gholamali Rahnavard, Jenny Sauk, Dmitry Shungin, Yoshiki Vázquez-Baeza, Richard A White, Jonathan Braun, Lee A Denson, Janet K Jansson, Rob Knight, Subra Kugathasan, Dermot P B McGovern, Joseph F Petrosino, Thaddeus S Stappenbeck, Harland S Winter, Clary B Clish, Eric A Franzosa, Hera Vlamakis, Ramnik J Xavier, Curtis Huttenhower. Nature 2019
Times Cited: 667







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



Times Cited
  Times     Co-cited
Similarity


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
23

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
21


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
13

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
12

Gut microbiota-derived metabolites as key actors in inflammatory bowel disease.
Aonghus Lavelle, Harry Sokol. Nat Rev Gastroenterol Hepatol 2020
276
12

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
12

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
11

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

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
11

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
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

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

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

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
10


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
9

Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice.
Suzanne Devkota, Yunwei Wang, Mark W Musch, Vanessa Leone, Hannah Fehlner-Peach, Anuradha Nadimpalli, Dionysios A Antonopoulos, Bana Jabri, Eugene B Chang. Nature 2012
9

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
9

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
9

The global burden of IBD: from 2015 to 2025.
Gilaad G Kaplan. Nat Rev Gastroenterol Hepatol 2015
888
9

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.
Edoardo Pasolli, Francesco Asnicar, Serena Manara, Moreno Zolfo, Nicolai Karcher, Federica Armanini, Francesco Beghini, Paolo Manghi, Adrian Tett, Paolo Ghensi,[...]. Cell 2019
461
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
8

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile.
Charlie G Buffie, Vanni Bucci, Richard R Stein, Peter T McKenney, Lilan Ling, Asia Gobourne, Daniel No, Hui Liu, Melissa Kinnebrew, Agnes Viale,[...]. Nature 2015
936
8

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

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

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
8

Longitudinal multi-omics of host-microbe dynamics in prediabetes.
Wenyu Zhou, M Reza Sailani, Kévin Contrepois, Yanjiao Zhou, Sara Ahadi, Shana R Leopold, Martin J Zhang, Varsha Rao, Monika Avina, Tejaswini Mishra,[...]. Nature 2019
173
7

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
7

Muc2-deficient mice spontaneously develop colitis, indicating that MUC2 is critical for colonic protection.
Maria Van der Sluis, Barbara A E De Koning, Adrianus C J M De Bruijn, Anna Velcich, Jules P P Meijerink, Johannes B Van Goudoever, Hans A Büller, Jan Dekker, Isabelle Van Seuningen, Ingrid B Renes,[...]. Gastroenterology 2006
916
7

Mend Your Fences: The Epithelial Barrier and its Relationship With Mucosal Immunity in Inflammatory Bowel Disease.
Eva Martini, Susanne M Krug, Britta Siegmund, Markus F Neurath, Christoph Becker. Cell Mol Gastroenterol Hepatol 2017
218
7

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.
Jakob Wirbel, Paul Theodor Pyl, Ece Kartal, Konrad Zych, Alireza Kashani, Alessio Milanese, Jonas S Fleck, Anita Y Voigt, Albert Palleja, Ruby Ponnudurai,[...]. Nat Med 2019
296
7

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian C Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar,[...]. Nat Biotechnol 2019
7

Enterotypes of the human gut microbiome.
Manimozhiyan Arumugam, Jeroen Raes, Eric Pelletier, Denis Le Paslier, Takuji Yamada, Daniel R Mende, Gabriel R Fernandes, Julien Tap, Thomas Bruls, Jean-Michel Batto,[...]. Nature 2011
7

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility.
Mahesh S Desai, Anna M Seekatz, Nicole M Koropatkin, Nobuhiko Kamada, Christina A Hickey, Mathis Wolter, Nicholas A Pudlo, Sho Kitamoto, Nicolas Terrapon, Arnaud Muller,[...]. Cell 2016
984
7

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
7

Global chemical effects of the microbiome include new bile-acid conjugations.
Robert A Quinn, Alexey V Melnik, Alison Vrbanac, Ting Fu, Kathryn A Patras, Mitchell P Christy, Zsolt Bodai, Pedro Belda-Ferre, Anupriya Tripathi, Lawton K Chung,[...]. Nature 2020
115
7

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
Christian Quast, Elmar Pruesse, Pelin Yilmaz, Jan Gerken, Timmy Schweer, Pablo Yarza, Jörg Peplies, Frank Oliver Glöckner. Nucleic Acids Res 2013
7

Farnesoid X receptor activation inhibits inflammation and preserves the intestinal barrier in inflammatory bowel disease.
Raffaella M Gadaleta, Karel J van Erpecum, Bas Oldenburg, Ellen C L Willemsen, Willem Renooij, Stefania Murzilli, Leo W J Klomp, Peter D Siersema, Marguerite E I Schipper, Silvio Danese,[...]. Gut 2011
407
7


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
7

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
7

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

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses.
Claire Duvallet, Sean M Gibbons, Thomas Gurry, Rafael A Irizarry, Eric J Alm. Nat Commun 2017
369
6

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
6

Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn's disease, produces an inflammatory polysaccharide.
Matthew T Henke, Douglas J Kenny, Chelsi D Cassilly, Hera Vlamakis, Ramnik J Xavier, Jon Clardy. Proc Natl Acad Sci U S A 2019
154
6

Microbial genes and pathways in inflammatory bowel disease.
Melanie Schirmer, Ashley Garner, Hera Vlamakis, Ramnik J Xavier. Nat Rev Microbiol 2019
162
6

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

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
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.