A citation-based method for searching scientific literature

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, Gerald F M Watts, A Helena Jonsson, Javier Rangel-Moreno, Nida Meednu, Cristina Rozo, William Apruzzese, Thomas M Eisenhaure, David J Lieb, David L Boyle, Arthur M Mandelin, Brendan F Boyce, Edward DiCarlo, Ellen M Gravallese, Peter K Gregersen, Larry Moreland, Gary S Firestein, Nir Hacohen, Chad Nusbaum, James A Lederer, Harris Perlman, Costantino Pitzalis, Andrew Filer, V Michael Holers, Vivian P Bykerk, Laura T Donlin, Jennifer H Anolik, Michael B Brenner, Soumya Raychaudhuri. Nat Immunol 2019
Times Cited: 393







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



Times Cited
  Times     Co-cited
Similarity


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
293
35

Functionally distinct disease-associated fibroblast subsets in rheumatoid arthritis.
Fumitaka Mizoguchi, Kamil Slowikowski, Kevin Wei, Jennifer L Marshall, Deepak A Rao, Sook Kyung Chang, Hung N Nguyen, Erika H Noss, Jason D Turner, Brandon E Earp,[...]. Nat Commun 2018
222
32

Distinct synovial tissue macrophage subsets regulate inflammation and remission in rheumatoid arthritis.
Stefano Alivernini, Lucy MacDonald, Aziza Elmesmari, Samuel Finlay, Barbara Tolusso, Maria Rita Gigante, Luca Petricca, Clara Di Mario, Laura Bui, Simone Perniola,[...]. Nat Med 2020
122
30

Notch signalling drives synovial fibroblast identity and arthritis pathology.
Kevin Wei, Ilya Korsunsky, Jennifer L Marshall, Anqi Gao, Gerald F M Watts, Triin Major, Adam P Croft, Jordan Watts, Philip E Blazar, Jeffrey K Lange,[...]. Nature 2020
121
29

Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation.
William Stephenson, Laura T Donlin, Andrew Butler, Cristina Rozo, Bernadette Bracken, Ali Rashidfarrokhi, Susan M Goodman, Lionel B Ivashkiv, Vivian P Bykerk, Dana E Orange,[...]. Nat Commun 2018
156
18

Molecular Portraits of Early Rheumatoid Arthritis Identify Clinical and Treatment Response Phenotypes.
Myles J Lewis, Michael R Barnes, Kevin Blighe, Katriona Goldmann, Sharmila Rana, Jason A Hackney, Nandhini Ramamoorthi, Christopher R John, David S Watson, Sarah K Kummerfeld,[...]. Cell Rep 2019
107
18

Pathologically expanded peripheral T helper cell subset drives B cells in rheumatoid arthritis.
Deepak A Rao, Michael F Gurish, Jennifer L Marshall, Kamil Slowikowski, Chamith Y Fonseka, Yanyan Liu, Laura T Donlin, Lauren A Henderson, Kevin Wei, Fumitaka Mizoguchi,[...]. Nature 2017
461
16

Locally renewing resident synovial macrophages provide a protective barrier for the joint.
Stephan Culemann, Anika Grüneboom, José Ángel Nicolás-Ávila, Daniela Weidner, Katrin Franziska Lämmle, Tobias Rothe, Juan A Quintana, Philipp Kirchner, Branislav Krljanac, Martin Eberhardt,[...]. Nature 2019
198
16

The pathogenesis of rheumatoid arthritis.
Iain B McInnes, Georg Schett. N Engl J Med 2011
14


Rheumatoid arthritis.
Josef S Smolen, Daniel Aletaha, Anne Barton, Gerd R Burmester, Paul Emery, Gary S Firestein, Arthur Kavanaugh, Iain B McInnes, Daniel H Solomon, Vibeke Strand,[...]. Nat Rev Dis Primers 2018
739
13

HBEGF+ macrophages in rheumatoid arthritis induce fibroblast invasiveness.
David Kuo, Jennifer Ding, Ian S Cohn, Fan Zhang, Kevin Wei, Deepak A Rao, Cristina Rozo, Upneet K Sokhi, Sara Shanaj, David J Oliver,[...]. Sci Transl Med 2019
80
16

Synovial cellular and molecular signatures stratify clinical response to csDMARD therapy and predict radiographic progression in early rheumatoid arthritis patients.
Frances Humby, Myles Lewis, Nandhini Ramamoorthi, Jason A Hackney, Michael R Barnes, Michele Bombardieri, A Francesca Setiadi, Stephen Kelly, Fabiola Bene, Maria DiCicco,[...]. Ann Rheum Dis 2019
107
12

Synovial phenotypes in rheumatoid arthritis correlate with response to biologic therapeutics.
Glynn Dennis, Cécile T J Holweg, Sarah K Kummerfeld, David F Choy, A Francesca Setiadi, Jason A Hackney, Peter M Haverty, Houston Gilbert, Wei Yu Lin, Lauri Diehl,[...]. Arthritis Res Ther 2014
213
12

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
11

Methods for high-dimensional analysis of cells dissociated from cryopreserved synovial tissue
Laura T Donlin, Deepak A Rao, Kevin Wei, Kamil Slowikowski, Mandy J McGeachy, Jason D Turner, Nida Meednu, Fumitaka Mizoguchi, Maria Gutierrez-Arcelus, David J Lieb,[...]. Arthritis Res Ther 2018
62
17

The immune cell landscape in kidneys of patients with lupus nephritis.
Arnon Arazi, Deepak A Rao, Celine C Berthier, Anne Davidson, Yanyan Liu, Paul J Hoover, Adam Chicoine, Thomas M Eisenhaure, A Helena Jonsson, Shuqiang Li,[...]. Nat Immunol 2019
267
10

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


Rituximab versus tocilizumab in anti-TNF inadequate responder patients with rheumatoid arthritis (R4RA): 16-week outcomes of a stratified, biopsy-driven, multicentre, open-label, phase 4 randomised controlled trial.
Frances Humby, Patrick Durez, Maya H Buch, Myles J Lewis, Hasan Rizvi, Felice Rivellese, Alessandra Nerviani, Giovanni Giorli, Arti Mahto, Carlomaurizio Montecucco,[...]. Lancet 2021
52
17

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
792
9

2010 Rheumatoid arthritis classification criteria: an American College of Rheumatology/European League Against Rheumatism collaborative initiative.
Daniel Aletaha, Tuhina Neogi, Alan J Silman, Julia Funovits, David T Felson, Clifton O Bingham, Neal S Birnbaum, Gerd R Burmester, Vivian P Bykerk, Marc D Cohen,[...]. Arthritis Rheum 2010
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

Specific autoantibodies precede the symptoms of rheumatoid arthritis: a study of serial measurements in blood donors.
Markus M J Nielen, Dirkjan van Schaardenburg, Henk W Reesink, Rob J van de Stadt, Irene E van der Horst-Bruinsma, Margret H M T de Koning, Moud R Habibuw, Jan P Vandenbroucke, Ben A C Dijkmans. Arthritis Rheum 2004
8

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
8

RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares.
Dana E Orange, Vicky Yao, Kirsty Sawicka, John Fak, Mayu O Frank, Salina Parveen, Nathalie E Blachere, Caryn Hale, Fan Zhang, Soumya Raychaudhuri,[...]. N Engl J Med 2020
52
15

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
8

EULAR recommendations for the management of rheumatoid arthritis with synthetic and biological disease-modifying antirheumatic drugs: 2019 update.
Josef S Smolen, Robert B M Landewé, Johannes W J Bijlsma, Gerd R Burmester, Maxime Dougados, Andreas Kerschbaumer, Iain B McInnes, Alexandre Sepriano, Ronald F van Vollenhoven, Maarten de Wit,[...]. Ann Rheum Dis 2020
938
8

Immunopathogenesis of Rheumatoid Arthritis.
Gary S Firestein, Iain B McInnes. Immunity 2017
458
8

Nonclassical Ly6C(-) monocytes drive the development of inflammatory arthritis in mice.
Alexander V Misharin, Carla M Cuda, Rana Saber, Jason D Turner, Angelica K Gierut, G Kenneth Haines, Sergejs Berdnikovs, Andrew Filer, Andrew R Clark, Christopher D Buckley,[...]. Cell Rep 2014
185
7

Cross-tissue organization of the fibroblast lineage.
Matthew B Buechler, Rachana N Pradhan, Akshay T Krishnamurty, Christian Cox, Aslihan Karabacak Calviello, Amber W Wang, Yeqing Angela Yang, Lucinda Tam, Roger Caothien, Merone Roose-Girma,[...]. Nature 2021
98
7

Rheumatoid arthritis.
Josef S Smolen, Daniel Aletaha, Iain B McInnes. Lancet 2016
7

Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways.
Evan Der, Hemant Suryawanshi, Pavel Morozov, Manjunath Kustagi, Beatrice Goilav, Saritha Ranabothu, Peter Izmirly, Robert Clancy, H Michael Belmont, Mordecai Koenigsberg,[...]. Nat Immunol 2019
175
6

B Cell Synovitis and Clinical Phenotypes in Rheumatoid Arthritis: Relationship to Disease Stages and Drug Exposure.
F Rivellese, F Humby, S Bugatti, L Fossati-Jimack, H Rizvi, D Lucchesi, G Lliso-Ribera, A Nerviani, R E Hands, G Giorli,[...]. Arthritis Rheumatol 2020
25
24

A Pauci-Immune Synovial Pathotype Predicts Inadequate Response to TNFα-Blockade in Rheumatoid Arthritis Patients.
Alessandra Nerviani, Maria Di Cicco, Arti Mahto, Gloria Lliso-Ribera, Felice Rivellese, Georgina Thorborn, Rebecca Hands, Mattia Bellan, Daniele Mauro, Marie-Astrid Boutet,[...]. Front Immunol 2020
29
20

NETs are a source of citrullinated autoantigens and stimulate inflammatory responses in rheumatoid arthritis.
Ritika Khandpur, Carmelo Carmona-Rivera, Anuradha Vivekanandan-Giri, Alison Gizinski, Srilakshmi Yalavarthi, Jason S Knight, Sean Friday, Sam Li, Rajiv M Patel, Venkataraman Subramanian,[...]. Sci Transl Med 2013
709
6

Synovial tissue research: a state-of-the-art review.
Carl Orr, Elsa Vieira-Sousa, David L Boyle, Maya H Buch, Christopher D Buckley, Juan D Cañete, Anca I Catrina, Ernest H S Choy, Paul Emery, Ursula Fearon,[...]. Nat Rev Rheumatol 2017
109
6

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.
Patrik L Ståhl, Fredrik Salmén, Sanja Vickovic, Anna Lundmark, José Fernández Navarro, Jens Magnusson, Stefania Giacomello, Michaela Asp, Jakub O Westholm, Mikael Huss,[...]. Science 2016
812
6

NicheNet: modeling intercellular communication by linking ligands to target genes.
Robin Browaeys, Wouter Saelens, Yvan Saeys. Nat Methods 2020
258
6

Single-cell sequencing reveals clonal expansions of pro-inflammatory synovial CD8 T cells expressing tissue-homing receptors in psoriatic arthritis.
Frank Penkava, Martin Del Castillo Velasco-Herrera, Matthew D Young, Nicole Yager, Lilian N Nwosu, Arthur G Pratt, Alicia Lledo Lara, Charlotte Guzzo, Ash Maroof, Lira Mamanova,[...]. Nat Commun 2020
42
14

Epigenetically-driven anatomical diversity of synovial fibroblasts guides joint-specific fibroblast functions.
Mojca Frank-Bertoncelj, Michelle Trenkmann, Kerstin Klein, Emmanuel Karouzakis, Hubert Rehrauer, Anna Bratus, Christoph Kolling, Maria Armaka, Andrew Filer, Beat A Michel,[...]. Nat Commun 2017
83
7

The normal synovium.
Malcolm D Smith. Open Rheumatol J 2011
187
6

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.
Cole Trapnell, Davide Cacchiarelli, Jonna Grimsby, Prapti Pokharel, Shuqiang Li, Michael Morse, Niall J Lennon, Kenneth J Livak, Tarjei S Mikkelsen, John L Rinn. Nat Biotechnol 2014
6

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
219
6

New learnings on the pathophysiology of RA from synovial biopsies.
Costantino Pitzalis, Stephen Kelly, Frances Humby. Curr Opin Rheumatol 2013
146
6

Synovitis score: discrimination between chronic low-grade and high-grade synovitis.
V Krenn, L Morawietz, G-R Burmester, R W Kinne, U Mueller-Ladner, B Muller, T Haupl. Histopathology 2006
354
6

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
335
6

Mapping systemic lupus erythematosus heterogeneity at the single-cell level.
Djamel Nehar-Belaid, Seunghee Hong, Radu Marches, Guo Chen, Mohan Bolisetty, Jeanine Baisch, Lynnette Walters, Marilynn Punaro, Robert J Rossi, Cheng-Han Chung,[...]. Nat Immunol 2020
69
8

Fibroblasts as immune regulators in infection, inflammation and cancer.
Sarah Davidson, Mark Coles, Tom Thomas, George Kollias, Burkhard Ludewig, Shannon Turley, Michael Brenner, Christopher D Buckley. Nat Rev Immunol 2021
52
11

Mixed-effects association of single cells identifies an expanded effector CD4+ T cell subset in rheumatoid arthritis.
Chamith Y Fonseka, Deepak A Rao, Nikola C Teslovich, Ilya Korsunsky, Susan K Hannes, Kamil Slowikowski, Michael F Gurish, Laura T Donlin, James A Lederer, Michael E Weinblatt,[...]. Sci Transl Med 2018
63
7


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.