A citation-based method for searching scientific literature

Irina Rusinova, Sam Forster, Simon Yu, Anitha Kannan, Marion Masse, Helen Cumming, Ross Chapman, Paul J Hertzog. Nucleic Acids Res 2013
Times Cited: 453







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



Times Cited
  Times     Co-cited
Similarity


Interferon-stimulated genes: a complex web of host defenses.
William M Schneider, Meike Dittmann Chevillotte, Charles M Rice. Annu Rev Immunol 2014
19

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
17

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
15

Regulation of type I interferon responses.
Lionel B Ivashkiv, Laura T Donlin. Nat Rev Immunol 2014
11

A diverse range of gene products are effectors of the type I interferon antiviral response.
John W Schoggins, Sam J Wilson, Maryline Panis, Mary Y Murphy, Christopher T Jones, Paul Bieniasz, Charles M Rice. Nature 2011
11

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
10

Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19.
Daniel Blanco-Melo, Benjamin E Nilsson-Payant, Wen-Chun Liu, Skyler Uhl, Daisy Hoagland, Rasmus Møller, Tristan X Jordan, Kohei Oishi, Maryline Panis, David Sachs,[...]. Cell 2020
10

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
9

Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients.
Jérôme Hadjadj, Nader Yatim, Laura Barnabei, Aurélien Corneau, Jeremy Boussier, Nikaïa Smith, Hélène Péré, Bruno Charbit, Vincent Bondet, Camille Chenevier-Gobeaux,[...]. Science 2020
872
9

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

Heightened Innate Immune Responses in the Respiratory Tract of COVID-19 Patients.
Zhuo Zhou, Lili Ren, Li Zhang, Jiaxin Zhong, Yan Xiao, Zhilong Jia, Li Guo, Jing Yang, Chun Wang, Shuai Jiang,[...]. Cell Host Microbe 2020
361
8

Interferon-Stimulated Genes: What Do They All Do?
John W Schoggins. Annu Rev Virol 2019
140
8


The Molecular Signatures Database (MSigDB) hallmark gene set collection.
Arthur Liberzon, Chet Birger, Helga Thorvaldsdóttir, Mahmoud Ghandi, Jill P Mesirov, Pablo Tamayo. Cell Syst 2015
7

Parsing the Interferon Transcriptional Network and Its Disease Associations.
Sara Mostafavi, Hideyuki Yoshida, Devapregasan Moodley, Hugo LeBoité, Katherine Rothamel, Towfique Raj, Chun Jimmie Ye, Nicolas Chevrier, Shen-Ying Zhang, Ting Feng,[...]. Cell 2016
120
7

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
7

Ten Strategies of Interferon Evasion by Viruses.
Adolfo García-Sastre. Cell Host Microbe 2017
173
7

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
7


Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.
Steffen Durinck, Paul T Spellman, Ewan Birney, Wolfgang Huber. Nat Protoc 2009
7

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
7

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
7

Autoantibodies against type I IFNs in patients with life-threatening COVID-19.
Paul Bastard, Lindsey B Rosen, Qian Zhang, Eleftherios Michailidis, Hans-Heinrich Hoffmann, Yu Zhang, Karim Dorgham, Quentin Philippot, Jérémie Rosain, Vivien Béziat,[...]. Science 2020
699
7

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.
Maxim V Kuleshov, Matthew R Jones, Andrew D Rouillard, Nicolas F Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L Jenkins, Kathleen M Jagodnik, Alexander Lachmann,[...]. Nucleic Acids Res 2016
7

Virus interference. I. The interferon.
A ISAACS, J LINDENMANN. Proc R Soc Lond B Biol Sci 1957
6

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.
David E Gordon, Gwendolyn M Jang, Mehdi Bouhaddou, Jiewei Xu, Kirsten Obernier, Kris M White, Matthew J O'Meara, Veronica V Rezelj, Jeffrey Z Guo, Danielle L Swaney,[...]. Nature 2020
6

Fiji: an open-source platform for biological-image analysis.
Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid,[...]. Nat Methods 2012
6

Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT-qPCR primer-probe sets.
Chantal B F Vogels, Anderson F Brito, Anne L Wyllie, Joseph R Fauver, Isabel M Ott, Chaney C Kalinich, Mary E Petrone, Arnau Casanovas-Massana, M Catherine Muenker, Adam J Moore,[...]. Nat Microbiol 2020
242
6

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets.
Yingyao Zhou, Bin Zhou, Lars Pache, Max Chang, Alireza Hadj Khodabakhshi, Olga Tanaseichuk, Christopher Benner, Sumit K Chanda. Nat Commun 2019
6

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Damian Szklarczyk, Annika L Gable, David Lyon, Alexander Junge, Stefan Wyder, Jaime Huerta-Cepas, Milan Simonovic, Nadezhda T Doncheva, John H Morris, Peer Bork,[...]. Nucleic Acids Res 2019
6

The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus.
Abraham L Brass, I-Chueh Huang, Yair Benita, Sinu P John, Manoj N Krishnan, Eric M Feeley, Bethany J Ryan, Jessica L Weyer, Louise van der Weyden, Erol Fikrig,[...]. Cell 2009
834
6

IRF-7 is the master regulator of type-I interferon-dependent immune responses.
Kenya Honda, Hideyuki Yanai, Hideo Negishi, Masataka Asagiri, Mitsuharu Sato, Tatsuaki Mizutani, Naoya Shimada, Yusuke Ohba, Akinori Takaoka, Nobuaki Yoshida,[...]. Nature 2005
5


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
5

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
5

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
M Ashburner, C A Ball, J A Blake, D Botstein, H Butler, J M Cherry, A P Davis, K Dolinski, S S Dwight, J T Eppig,[...]. Nat Genet 2000
5

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool.
Edward Y Chen, Christopher M Tan, Yan Kou, Qiaonan Duan, Zichen Wang, Gabriela Vaz Meirelles, Neil R Clark, Avi Ma'ayan. BMC Bioinformatics 2013
5

Interferon-stimulated genes and their antiviral effector functions.
John W Schoggins, Charles M Rice. Curr Opin Virol 2011
695
5

IFIT1 is an antiviral protein that recognizes 5'-triphosphate RNA.
Andreas Pichlmair, Caroline Lassnig, Carol-Ann Eberle, Maria W Górna, Christoph L Baumann, Thomas R Burkard, Tilmann Bürckstümmer, Adrijana Stefanovic, Sigurd Krieger, Keiryn L Bennett,[...]. Nat Immunol 2011
298
5

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
5

Longitudinal analyses reveal immunological misfiring in severe COVID-19.
Carolina Lucas, Patrick Wong, Jon Klein, Tiago B R Castro, Julio Silva, Maria Sundaram, Mallory K Ellingson, Tianyang Mao, Ji Eun Oh, Benjamin Israelow,[...]. Nature 2020
552
5

LY6E impairs coronavirus fusion and confers immune control of viral disease.
Stephanie Pfaender, Katrina B Mar, Eleftherios Michailidis, Annika Kratzel, Ian N Boys, Philip V'kovski, Wenchun Fan, Jenna N Kelly, Dagny Hirt, Nadine Ebert,[...]. Nat Microbiol 2020
54
9

The type I interferon response in COVID-19: implications for treatment.
Jeong Seok Lee, Eui-Cheol Shin. Nat Rev Immunol 2020
91
5

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
5

The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
5

Clinical Characteristics of Coronavirus Disease 2019 in China.
Wei-Jie Guan, Zheng-Yi Ni, Yu Hu, Wen-Hua Liang, Chun-Quan Ou, Jian-Xing He, Lei Liu, Hong Shan, Chun-Liang Lei, David S C Hui,[...]. N Engl J Med 2020
5

Shared and Distinct Functions of Type I and Type III Interferons.
Helen M Lazear, John W Schoggins, Michael S Diamond. Immunity 2019
257
5

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nucleic Acids Res 2009
5

Identification of Interferon-Stimulated Genes with Antiretroviral Activity.
Melissa Kane, Trinity M Zang, Suzannah J Rihn, Fengwen Zhang, Tonya Kueck, Mudathir Alim, John Schoggins, Charles M Rice, Sam J Wilson, Paul D Bieniasz. Cell Host Microbe 2016
103
5

COVID-19 severity correlates with airway epithelium-immune cell interactions identified by single-cell analysis.
Robert Lorenz Chua, Soeren Lukassen, Saskia Trump, Bianca P Hennig, Daniel Wendisch, Fabian Pott, Olivia Debnath, Loreen Thürmann, Florian Kurth, Maria Theresa Völker,[...]. Nat Biotechnol 2020
298
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.