A citation-based method for searching scientific literature

Bijay Jassal, Lisa Matthews, Guilherme Viteri, Chuqiao Gong, Pascual Lorente, Antonio Fabregat, Konstantinos Sidiropoulos, Justin Cook, Marc Gillespie, Robin Haw, Fred Loney, Bruce May, Marija Milacic, Karen Rothfels, Cristoffer Sevilla, Veronica Shamovsky, Solomon Shorser, Thawfeek Varusai, Joel Weiser, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio. Nucleic Acids Res 2020
Times Cited: 543







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



Times Cited
  Times     Co-cited
Similarity



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
14

KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
14

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


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
11

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
11

KEGG: new perspectives on genomes, pathways, diseases and drugs.
Minoru Kanehisa, Miho Furumichi, Mao Tanabe, Yoko Sato, Kanae Morishima. Nucleic Acids Res 2017
9

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
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

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
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

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
7

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
7

Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study.
Fei Zhou, Ting Yu, Ronghui Du, Guohui Fan, Ying Liu, Zhibo Liu, Jie Xiang, Yeming Wang, Bin Song, Xiaoying Gu,[...]. Lancet 2020
6

Proteomics of SARS-CoV-2-infected host cells reveals therapy targets.
Denisa Bojkova, Kevin Klann, Benjamin Koch, Marek Widera, David Krause, Sandra Ciesek, Jindrich Cinatl, Christian Münch. Nature 2020
344
6

The PRIDE database and related tools and resources in 2019: improving support for quantification data.
Yasset Perez-Riverol, Attila Csordas, Jingwen Bai, Manuel Bernal-Llinares, Suresh Hewapathirana, Deepti J Kundu, Avinash Inuganti, Johannes Griss, Gerhard Mayer, Martin Eisenacher,[...]. Nucleic Acids Res 2019
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

Expression Atlas update: from tissues to single cells.
Irene Papatheodorou, Pablo Moreno, Jonathan Manning, Alfonso Muñoz-Pomer Fuentes, Nancy George, Silvie Fexova, Nuno A Fonseca, Anja Füllgrabe, Matthew Green, Ni Huang,[...]. Nucleic Acids Res 2020
102
5

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nat Protoc 2009
5


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
793
5

Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes.
Birgit H M Meldal, Hema Bye-A-Jee, Lukáš Gajdoš, Zuzana Hammerová, Aneta Horácková, Filip Melicher, Livia Perfetto, Daniel Pokorný, Milagros Rodriguez Lopez, Alžbeta Türková,[...]. Nucleic Acids Res 2019
36
11

KEGG as a reference resource for gene and protein annotation.
Minoru Kanehisa, Yoko Sato, Masayuki Kawashima, Miho Furumichi, Mao Tanabe. Nucleic Acids Res 2016
4

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium.
Sandra Orchard, Samuel Kerrien, Sara Abbani, Bruno Aranda, Jignesh Bhate, Shelby Bidwell, Alan Bridge, Leonardo Briganti, Fiona S L Brinkman, Gianni Cesareni,[...]. Nat Methods 2012
293
4

Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries.
Freddie Bray, Jacques Ferlay, Isabelle Soerjomataram, Rebecca L Siegel, Lindsey A Torre, Ahmedin Jemal. CA Cancer J Clin 2018
4

Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.
Jianjiong Gao, Bülent Arman Aksoy, Ugur Dogrusoz, Gideon Dresdner, Benjamin Gross, S Onur Sumer, Yichao Sun, Anders Jacobsen, Rileen Sinha, Erik Larsson,[...]. Sci Signal 2013
4

PANTHER: a library of protein families and subfamilies indexed by function.
Paul D Thomas, Michael J Campbell, Anish Kejariwal, Huaiyu Mi, Brian Karlak, Robin Daverman, Karen Diemer, Anushya Muruganujan, Apurva Narechania. Genome Res 2003
4

New approach for understanding genome variations in KEGG.
Minoru Kanehisa, Yoko Sato, Miho Furumichi, Kanae Morishima, Mao Tanabe. Nucleic Acids Res 2019
789
4

Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients.
Yong Xiong, Yuan Liu, Liu Cao, Dehe Wang, Ming Guo, Ao Jiang, Dong Guo, Wenjia Hu, Jiayi Yang, Zhidong Tang,[...]. Emerg Microbes Infect 2020
479
4

The DisGeNET knowledge platform for disease genomics: 2019 update.
Janet Piñero, Juan Manuel Ramírez-Anguita, Josep Saüch-Pitarch, Francesco Ronzano, Emilio Centeno, Ferran Sanz, Laura I Furlong. Nucleic Acids Res 2020
273
4

The ChEMBL database in 2017.
Anna Gaulton, Anne Hersey, Michał Nowotka, A Patrícia Bento, Jon Chambers, David Mendez, Prudence Mutowo, Francis Atkinson, Louisa J Bellis, Elena Cibrián-Uhalte,[...]. Nucleic Acids Res 2017
736
4

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019.
Annalisa Buniello, Jacqueline A L MacArthur, Maria Cerezo, Laura W Harris, James Hayhurst, Cinzia Malangone, Aoife McMahon, Joannella Morales, Edward Mountjoy, Elliot Sollis,[...]. Nucleic Acids Res 2019
885
4

Ensembl 2020.
Andrew D Yates, Premanand Achuthan, Wasiu Akanni, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Andrey G Azov, Ruth Bennett,[...]. Nucleic Acids Res 2020
462
4

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
4

OmniPath: guidelines and gateway for literature-curated signaling pathway resources.
Dénes Türei, Tamás Korcsmáros, Julio Saez-Rodriguez. Nat Methods 2016
137
4

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools.
Huaiyu Mi, Anushya Muruganujan, Dustin Ebert, Xiaosong Huang, Paul D Thomas. Nucleic Acids Res 2019
916
4

Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0).
Huaiyu Mi, Anushya Muruganujan, Xiaosong Huang, Dustin Ebert, Caitlin Mills, Xinyu Guo, Paul D Thomas. Nat Protoc 2019
340
4

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
4

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
4

Adjusting batch effects in microarray expression data using empirical Bayes methods.
W Evan Johnson, Cheng Li, Ariel Rabinovic. Biostatistics 2007
4

WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs.
Yuxing Liao, Jing Wang, Eric J Jaehnig, Zhiao Shi, Bing Zhang. Nucleic Acids Res 2019
551
4

KEGG: integrating viruses and cellular organisms.
Minoru Kanehisa, Miho Furumichi, Yoko Sato, Mari Ishiguro-Watanabe, Mao Tanabe. Nucleic Acids Res 2021
260
4

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
4

ChEBI in 2016: Improved services and an expanding collection of metabolites.
Janna Hastings, Gareth Owen, Adriano Dekker, Marcus Ennis, Namrata Kale, Venkatesh Muthukrishnan, Steve Turner, Neil Swainston, Pedro Mendes, Christoph Steinbeck. Nucleic Acids Res 2016
259
3

PubChem 2019 update: improved access to chemical data.
Sunghwan Kim, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li, Benjamin A Shoemaker, Paul A Thiessen, Bo Yu,[...]. Nucleic Acids Res 2019
865
3

COSMIC: the Catalogue Of Somatic Mutations In Cancer.
John G Tate, Sally Bamford, Harry C Jubb, Zbyslaw Sondka, David M Beare, Nidhi Bindal, Harry Boutselakis, Charlotte G Cole, Celestino Creatore, Elisabeth Dawson,[...]. Nucleic Acids Res 2019
3

The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.
Ethan Cerami, Jianjiong Gao, Ugur Dogrusoz, Benjamin E Gross, Selcuk Onur Sumer, Bülent Arman Aksoy, Anders Jacobsen, Caitlin J Byrne, Michael L Heuer, Erik Larsson,[...]. Cancer Discov 2012
3

The BioGRID interaction database: 2019 update.
Rose Oughtred, Chris Stark, Bobby-Joe Breitkreutz, Jennifer Rust, Lorrie Boucher, Christie Chang, Nadine Kolas, Lara O'Donnell, Genie Leung, Rochelle McAdam,[...]. Nucleic Acids Res 2019
440
3

The promise and peril of chemical probes.
Cheryl H Arrowsmith, James E Audia, Christopher Austin, Jonathan Baell, Jonathan Bennett, Julian Blagg, Chas Bountra, Paul E Brennan, Peter J Brown, Mark E Bunnage,[...]. Nat Chem Biol 2015
433
3


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.