A citation-based method for searching scientific literature

Paul A Reyfman, James M Walter, Nikita Joshi, Kishore R Anekalla, Alexandra C McQuattie-Pimentel, Stephen Chiu, Ramiro Fernandez, Mahzad Akbarpour, Ching-I Chen, Ziyou Ren, Rohan Verma, Hiam Abdala-Valencia, Kiwon Nam, Monica Chi, SeungHye Han, Francisco J Gonzalez-Gonzalez, Saul Soberanes, Satoshi Watanabe, Kinola J N Williams, Annette S Flozak, Trevor T Nicholson, Vince K Morgan, Deborah R Winter, Monique Hinchcliff, Cara L Hrusch, Robert D Guzy, Catherine A Bonham, Anne I Sperling, Remzi Bag, Robert B Hamanaka, Gökhan M Mutlu, Anjana V Yeldandi, Stacy A Marshall, Ali Shilatifard, Luis A N Amaral, Harris Perlman, Jacob I Sznajder, A Christine Argento, Colin T Gillespie, Jane Dematte, Manu Jain, Benjamin D Singer, Karen M Ridge, Anna P Lam, Ankit Bharat, Sangeeta M Bhorade, Cara J Gottardi, G R Scott Budinger, Alexander V Misharin. Am J Respir Crit Care Med 2019
Times Cited: 496







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



Times Cited
  Times     Co-cited
Similarity


Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis.
Taylor S Adams, Jonas C Schupp, Sergio Poli, Ehab A Ayaub, Nir Neumark, Farida Ahangari, Sarah G Chu, Benjamin A Raby, Giuseppe DeIuliis, Michael Januszyk,[...]. Sci Adv 2020
268
41

Single-cell RNA sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis.
Arun C Habermann, Austin J Gutierrez, Linh T Bui, Stephanie L Yahn, Nichelle I Winters, Carla L Calvi, Lance Peter, Mei-I Chung, Chase J Taylor, Christopher Jetter,[...]. Sci Adv 2020
235
38

Proliferating SPP1/MERTK-expressing macrophages in idiopathic pulmonary fibrosis.
Christina Morse, Tracy Tabib, John Sembrat, Kristina L Buschur, Humberto Trejo Bittar, Eleanor Valenzi, Yale Jiang, Daniel J Kass, Kevin Gibson, Wei Chen,[...]. Eur Respir J 2019
181
28

A molecular cell atlas of the human lung from single-cell RNA sequencing.
Kyle J Travaglini, Ahmad N Nabhan, Lolita Penland, Rahul Sinha, Astrid Gillich, Rene V Sit, Stephen Chang, Stephanie D Conley, Yasuo Mori, Jun Seita,[...]. Nature 2020
370
22

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage.
Dvir Aran, Agnieszka P Looney, Leqian Liu, Esther Wu, Valerie Fong, Austin Hsu, Suzanna Chak, Ram P Naikawadi, Paul J Wolters, Adam R Abate,[...]. Nat Immunol 2019
881
19

Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis.
Maximilian Strunz, Lukas M Simon, Meshal Ansari, Jaymin J Kathiriya, Ilias Angelidis, Christoph H Mayr, George Tsidiridis, Marius Lange, Laura F Mattner, Min Yee,[...]. Nat Commun 2020
141
19

Monocyte-derived alveolar macrophages drive lung fibrosis and persist in the lung over the life span.
Alexander V Misharin, Luisa Morales-Nebreda, Paul A Reyfman, Carla M Cuda, James M Walter, Alexandra C McQuattie-Pimentel, Ching-I Chen, Kishore R Anekalla, Nikita Joshi, Kinola J N Williams,[...]. J Exp Med 2017
468
18

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
16

Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19.
Mingfeng Liao, Yang Liu, Jing Yuan, Yanling Wen, Gang Xu, Juanjuan Zhao, Lin Cheng, Jinxiu Li, Xin Wang, Fuxiang Wang,[...]. Nat Med 2020
16

Idiopathic Pulmonary Fibrosis.
David J Lederer, Fernando J Martinez. N Engl J Med 2018
670
15

Single-cell RNA sequencing identifies diverse roles of epithelial cells in idiopathic pulmonary fibrosis.
Yan Xu, Takako Mizuno, Anusha Sridharan, Yina Du, Minzhe Guo, Jie Tang, Kathryn A Wikenheiser-Brokamp, Anne-Karina T Perl, Vincent A Funari, Jason J Gokey,[...]. JCI Insight 2016
309
15

Senescence of Alveolar Type 2 Cells Drives Progressive Pulmonary Fibrosis.
Changfu Yao, Xiangrong Guan, Gianni Carraro, Tanyalak Parimon, Xue Liu, Guanling Huang, Apoorva Mulay, Harmik J Soukiasian, Gregory David, Stephen S Weigt,[...]. Am J Respir Crit Care Med 2021
93
15

Persistence of a regeneration-associated, transitional alveolar epithelial cell state in pulmonary fibrosis.
Yoshihiko Kobayashi, Aleksandra Tata, Arvind Konkimalla, Hiroaki Katsura, Rebecca F Lee, Jianhong Ou, Nicholas E Banovich, Jonathan A Kropski, Purushothama Rao Tata. Nat Cell Biol 2020
123
13

Efficacy and safety of nintedanib in idiopathic pulmonary fibrosis.
Luca Richeldi, Roland M du Bois, Ganesh Raghu, Arata Azuma, Kevin K Brown, Ulrich Costabel, Vincent Cottin, Kevin R Flaherty, David M Hansell, Yoshikazu Inoue,[...]. N Engl J Med 2014
13

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
12

A spatially restricted fibrotic niche in pulmonary fibrosis is sustained by M-CSF/M-CSFR signalling in monocyte-derived alveolar macrophages.
Nikita Joshi, Satoshi Watanabe, Rohan Verma, Renea P Jablonski, Ching-I Chen, Paul Cheresh, Nikolay S Markov, Paul A Reyfman, Alexandra C McQuattie-Pimentel, Lango Sichizya,[...]. Eur Respir J 2020
90
13

A phase 3 trial of pirfenidone in patients with idiopathic pulmonary fibrosis.
Talmadge E King, Williamson Z Bradford, Socorro Castro-Bernardini, Elizabeth A Fagan, Ian Glaspole, Marilyn K Glassberg, Eduard Gorina, Peter M Hopkins, David Kardatzke, Lisa Lancaster,[...]. N Engl J Med 2014
12

Diagnosis of Idiopathic Pulmonary Fibrosis. An Official ATS/ERS/JRS/ALAT Clinical Practice Guideline.
Ganesh Raghu, Martine Remy-Jardin, Jeffrey L Myers, Luca Richeldi, Christopher J Ryerson, David J Lederer, Juergen Behr, Vincent Cottin, Sonye K Danoff, Ferran Morell,[...]. Am J Respir Crit Care Med 2018
11

Progressive Pulmonary Fibrosis Is Caused by Elevated Mechanical Tension on Alveolar Stem Cells.
Huijuan Wu, Yuanyuan Yu, Huanwei Huang, Yucheng Hu, Siling Fu, Zheng Wang, Mengting Shi, Xi Zhao, Jie Yuan, Jiao Li,[...]. Cell 2020
137
11

Regeneration of the lung alveolus by an evolutionarily conserved epithelial progenitor.
William J Zacharias, David B Frank, Jarod A Zepp, Michael P Morley, Farrah A Alkhaleel, Jun Kong, Su Zhou, Edward Cantu, Edward E Morrisey. Nature 2018
325
11

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
955
10

Inflammatory Signals Induce AT2 Cell-Derived Damage-Associated Transient Progenitors that Mediate Alveolar Regeneration.
Jinwook Choi, Jong-Eun Park, Georgia Tsagkogeorga, Motoko Yanagita, Bon-Kyoung Koo, Namshik Han, Joo-Hyeon Lee. Cell Stem Cell 2020
122
10

Single-cell Wnt signaling niches maintain stemness of alveolar type 2 cells.
Ahmad N Nabhan, Douglas G Brownfield, Pehr B Harbury, Mark A Krasnow, Tushar J Desai. Science 2018
332
10

Type 2 alveolar cells are stem cells in adult lung.
Christina E Barkauskas, Michael J Cronce, Craig R Rackley, Emily J Bowie, Douglas R Keene, Barry R Stripp, Scott H Randell, Paul W Noble, Brigid L M Hogan. J Clin Invest 2013
888
10

Idiopathic pulmonary fibrosis.
Fernando J Martinez, Harold R Collard, Annie Pardo, Ganesh Raghu, Luca Richeldi, Moises Selman, Jeffrey J Swigris, Hiroyuki Taniguchi, Athol U Wells. Nat Rev Dis Primers 2017
461
10

An official ATS/ERS/JRS/ALAT statement: idiopathic pulmonary fibrosis: evidence-based guidelines for diagnosis and management.
Ganesh Raghu, Harold R Collard, Jim J Egan, Fernando J Martinez, Juergen Behr, Kevin K Brown, Thomas V Colby, Jean-François Cordier, Kevin R Flaherty, Joseph A Lasky,[...]. Am J Respir Crit Care Med 2011
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

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
8

Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia.
Rogan A Grant, Luisa Morales-Nebreda, Nikolay S Markov, Suchitra Swaminathan, Melissa Querrey, Estefany R Guzman, Darryl A Abbott, Helen K Donnelly, Alvaro Donayre, Isaac A Goldberg,[...]. Nature 2021
273
8

A Single-Cell Atlas of the Human Healthy Airways.
Marie Deprez, Laure-Emmanuelle Zaragosi, Marin Truchi, Christophe Becavin, Sandra Ruiz García, Marie-Jeanne Arguel, Magali Plaisant, Virginie Magnone, Kevin Lebrigand, Sophie Abelanet,[...]. Am J Respir Crit Care Med 2020
98
8

Multiple stromal populations contribute to pulmonary fibrosis without evidence for epithelial to mesenchymal transition.
Jason R Rock, Christina E Barkauskas, Michael J Cronce, Yan Xue, Jeffrey R Harris, Jiurong Liang, Paul W Noble, Brigid L M Hogan. Proc Natl Acad Sci U S A 2011
652
8

COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets.
Toni M Delorey, Carly G K Ziegler, Graham Heimberg, Rachelly Normand, Yiming Yang, Åsa Segerstolpe, Domenic Abbondanza, Stephen J Fleming, Ayshwarya Subramanian, Daniel T Montoro,[...]. Nature 2021
211
8

Distinct Mesenchymal Lineages and Niches Promote Epithelial Self-Renewal and Myofibrogenesis in the Lung.
Jarod A Zepp, William J Zacharias, David B Frank, Christina A Cavanaugh, Su Zhou, Michael P Morley, Edward E Morrisey. Cell 2017
263
8

Two distinct interstitial macrophage populations coexist across tissues in specific subtissular niches.
Svetoslav Chakarov, Hwee Ying Lim, Leonard Tan, Sheau Yng Lim, Peter See, Josephine Lum, Xiao-Meng Zhang, Shihui Foo, Satoshi Nakamizo, Kaibo Duan,[...]. Science 2019
351
8

A common MUC5B promoter polymorphism and pulmonary fibrosis.
Max A Seibold, Anastasia L Wise, Marcy C Speer, Mark P Steele, Kevin K Brown, James E Loyd, Tasha E Fingerlin, Weiming Zhang, Gunnar Gudmundsson, Steve D Groshong,[...]. N Engl J Med 2011
690
8

Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis.
Tatsuya Tsukui, Kai-Hui Sun, Joseph B Wetter, John R Wilson-Kanamori, Lisa A Hazelwood, Neil C Henderson, Taylor S Adams, Jonas C Schupp, Sergio D Poli, Ivan O Rosas,[...]. Nat Commun 2020
135
8

Alveolar macrophages develop from fetal monocytes that differentiate into long-lived cells in the first week of life via GM-CSF.
Martin Guilliams, Ismé De Kleer, Sandrine Henri, Sijranke Post, Leen Vanhoutte, Sofie De Prijck, Kim Deswarte, Bernard Malissen, Hamida Hammad, Bart N Lambrecht. J Exp Med 2013
716
8

Cellular senescence mediates fibrotic pulmonary disease.
Marissa J Schafer, Thomas A White, Koji Iijima, Andrew J Haak, Giovanni Ligresti, Elizabeth J Atkinson, Ann L Oberg, Jodie Birch, Hanna Salmonowicz, Yi Zhu,[...]. Nat Commun 2017
665
8

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor.
Markus Hoffmann, Hannah Kleine-Weber, Simon Schroeder, Nadine Krüger, Tanja Herrler, Sandra Erichsen, Tobias S Schiergens, Georg Herrler, Nai-Huei Wu, Andreas Nitsche,[...]. Cell 2020
8

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
8

limma powers differential expression analyses for RNA-sequencing and microarray studies.
Matthew E Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, Gordon K Smyth. Nucleic Acids Res 2015
8

Nintedanib in Progressive Fibrosing Interstitial Lung Diseases.
Kevin R Flaherty, Athol U Wells, Vincent Cottin, Anand Devaraj, Simon L F Walsh, Yoshikazu Inoue, Luca Richeldi, Martin Kolb, Kay Tetzlaff, Susanne Stowasser,[...]. N Engl J Med 2019
669
8

Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China.
Chaolin Huang, Yeming Wang, Xingwang Li, Lili Ren, Jianping Zhao, Yi Hu, Li Zhang, Guohui Fan, Jiuyang Xu, Xiaoying Gu,[...]. Lancet 2020
7

Integrated analysis of multimodal single-cell data.
Yuhan Hao, Stephanie Hao, Erica Andersen-Nissen, William M Mauck, Shiwei Zheng, Andrew Butler, Maddie J Lee, Aaron J Wilk, Charlotte Darby, Michael Zager,[...]. Cell 2021
7

A molecular single-cell lung atlas of lethal COVID-19.
Johannes C Melms, Jana Biermann, Huachao Huang, Yiping Wang, Ajay Nair, Somnath Tagore, Igor Katsyv, André F Rendeiro, Amit Dipak Amin, Denis Schapiro,[...]. Nature 2021
137
7

Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis.
Tasha E Fingerlin, Elissa Murphy, Weiming Zhang, Anna L Peljto, Kevin K Brown, Mark P Steele, James E Loyd, Gregory P Cosgrove, David Lynch, Steve Groshong,[...]. Nat Genet 2013
475
7

A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte.
Lindsey W Plasschaert, Rapolas Žilionis, Rayman Choo-Wing, Virginia Savova, Judith Knehr, Guglielmo Roma, Allon M Klein, Aron B Jaffe. Nature 2018
463
7

Ineffectual Type 2-to-Type 1 Alveolar Epithelial Cell Differentiation in Idiopathic Pulmonary Fibrosis: Persistence of the KRT8hi Transitional State.
Peng Jiang, Rafael Gil de Rubio, Steven M Hrycaj, Stephen J Gurczynski, Kent A Riemondy, Bethany B Moore, M Bishr Omary, Karen M Ridge, Rachel L Zemans. Am J Respir Crit Care Med 2020
51
13

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes.
Daniel T Montoro, Adam L Haber, Moshe Biton, Vladimir Vinarsky, Brian Lin, Susan E Birket, Feng Yuan, Sijia Chen, Hui Min Leung, Jorge Villoria,[...]. Nature 2018
522
7

The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease.
Herbert B Schiller, Daniel T Montoro, Lukas M Simon, Emma L Rawlins, Kerstin B Meyer, Maximilian Strunz, Felipe A Vieira Braga, Wim Timens, Gerard H Koppelman, G R Scott Budinger,[...]. Am J Respir Cell Mol Biol 2019
87
8


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.