A citation-based method for searching scientific literature

Yael Haberman, Timothy L Tickle, Phillip J Dexheimer, Mi-Ok Kim, Dora Tang, Rebekah Karns, Robert N Baldassano, Joshua D Noe, Joel Rosh, James Markowitz, Melvin B Heyman, Anne M Griffiths, Wallace V Crandall, David R Mack, Susan S Baker, Curtis Huttenhower, David J Keljo, Jeffrey S Hyams, Subra Kugathasan, Thomas D Walters, Bruce Aronow, Ramnik J Xavier, Dirk Gevers, Lee A Denson. J Clin Invest 2014
Times Cited: 281







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



Times Cited
  Times     Co-cited
Similarity


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
29

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
267
21

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
20

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
15

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
14

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
14

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
78
17

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
351
12

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
985
11

The microbiome in inflammatory bowel disease: current status and the future ahead.
Aleksandar D Kostic, Ramnik J Xavier, Dirk Gevers. Gastroenterology 2014
830
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
265
11

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
494
11

Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach.
C Manichanh, L Rigottier-Gois, E Bonnaud, K Gloux, E Pelletier, L Frangeul, R Nalin, C Jarrin, P Chardon, P Marteau,[...]. Gut 2006
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
289
10

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
236
10

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
358
9

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
9

Increasing incidence and prevalence of the inflammatory bowel diseases with time, based on systematic review.
Natalie A Molodecky, Ing Shian Soon, Doreen M Rabi, William A Ghali, Mollie Ferris, Greg Chernoff, Eric I Benchimol, Remo Panaccione, Subrata Ghosh, Herman W Barkema,[...]. Gastroenterology 2012
8

The global burden of IBD: from 2015 to 2025.
Gilaad G Kaplan. Nat Rev Gastroenterol Hepatol 2015
746
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
8

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
287
8

Extensive Modulation of the Fecal Metagenome in Children With Crohn's Disease During Exclusive Enteral Nutrition.
Christopher Quince, Umer Zeeshan Ijaz, Nick Loman, A Murat Eren, Delphine Saulnier, Julie Russell, Sarah J Haig, Szymon T Calus, Joshua Quick, Andrew Barclay,[...]. Am J Gastroenterol 2015
130
8

Gut microbiota and IBD: causation or correlation?
Josephine Ni, Gary D Wu, Lindsey Albenberg, Vesselin T Tomov. Nat Rev Gastroenterol Hepatol 2017
436
8

Ulcerative colitis.
Ryan Ungaro, Saurabh Mehandru, Patrick B Allen, Laurent Peyrin-Biroulet, Jean-Frédéric Colombel. Lancet 2017
826
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

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
146
8

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
309
8

Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease.
Kelly A Shaw, Madeline Bertha, Tatyana Hofmekler, Pankaj Chopra, Tommi Vatanen, Abhiram Srivatsa, Jarod Prince, Archana Kumar, Cary Sauer, Michael E Zwick,[...]. Genome Med 2016
125
7

Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases.
Ashwin N Ananthakrishnan, Chengwei Luo, Vijay Yajnik, Hamed Khalili, John J Garber, Betsy W Stevens, Thomas Cleland, Ramnik J Xavier. Cell Host Microbe 2017
143
7

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
394
7

Mucosal gene expression of antimicrobial peptides in inflammatory bowel disease before and after first infliximab treatment.
Ingrid Arijs, Gert De Hertogh, Katleen Lemaire, Roel Quintens, Leentje Van Lommel, Kristel Van Steen, Peter Leemans, Isabelle Cleynen, Gert Van Assche, Séverine Vermeire,[...]. PLoS One 2009
133
7

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
359
7



Crohn's disease.
Joana Torres, Saurabh Mehandru, Jean-Frédéric Colombel, Laurent Peyrin-Biroulet. Lancet 2017
596
7

Toward an integrated clinical, molecular and serological classification of inflammatory bowel disease: report of a Working Party of the 2005 Montreal World Congress of Gastroenterology.
Mark S Silverberg, Jack Satsangi, Tariq Ahmad, Ian D R Arnott, Charles N Bernstein, Steven R Brant, Renzo Caprilli, Jean-Frédéric Colombel, Christoph Gasche, Karel Geboes,[...]. Can J Gastroenterol 2005
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

ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems.
Vivek Kaimal, Eric E Bardes, Scott C Tabar, Anil G Jegga, Bruce J Aronow. Nucleic Acids Res 2010
211
6

Effect of faecal stream diversion on recurrence of Crohn's disease in the neoterminal ileum.
P Rutgeerts, K Goboes, M Peeters, M Hiele, F Penninckx, R Aerts, R Kerremans, G Vantrappen. Lancet 1991
536
6

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
6

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
75
8

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome.
Melanie Schirmer, Eric A Franzosa, Jason Lloyd-Price, Lauren J McIver, Randall Schwager, Tiffany W Poon, Ashwin N Ananthakrishnan, Elizabeth Andrews, Gildardo Barron, Kathleen Lake,[...]. Nat Microbiol 2018
165
6

Ustekinumab as Induction and Maintenance Therapy for Crohn's Disease.
Brian G Feagan, William J Sandborn, Christopher Gasink, Douglas Jacobstein, Yinghua Lang, Joshua R Friedman, Marion A Blank, Jewel Johanns, Long-Long Gao, Ye Miao,[...]. N Engl J Med 2016
700
6

Vedolizumab as induction and maintenance therapy for Crohn's disease.
William J Sandborn, Brian G Feagan, Paul Rutgeerts, Stephen Hanauer, Jean-Frédéric Colombel, Bruce E Sands, Milan Lukas, Richard N Fedorak, Scott Lee, Brian Bressler,[...]. N Engl J Med 2013
6

Increased Expression of DUOX2 Is an Epithelial Response to Mucosal Dysbiosis Required for Immune Homeostasis in Mouse Intestine.
Helmut Grasberger, Jun Gao, Hiroko Nagao-Kitamoto, Sho Kitamoto, Min Zhang, Nobuhiko Kamada, Kathryn A Eaton, Mohamad El-Zaatari, Andrew B Shreiner, Juanita L Merchant,[...]. Gastroenterology 2015
67
8

Ustekinumab induction and maintenance therapy in refractory Crohn's disease.
William J Sandborn, Christopher Gasink, Long-Long Gao, Marion A Blank, Jewel Johanns, Cynthia Guzzo, Bruce E Sands, Stephen B Hanauer, Stephan Targan, Paul Rutgeerts,[...]. N Engl J Med 2012
696
6

A functional genomics predictive network model identifies regulators of inflammatory bowel disease.
Lauren A Peters, Jacqueline Perrigoue, Arthur Mortha, Alina Iuga, Won-Min Song, Eric M Neiman, Sean R Llewellyn, Antonio Di Narzo, Brian A Kidd, Shannon E Telesco,[...]. Nat Genet 2017
80
7

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
215
6

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization.
Jing Chen, Eric E Bardes, Bruce J Aronow, Anil G Jegga. Nucleic Acids Res 2009
5

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
545
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.