A citation-based method for searching scientific literature

Chia-Hao Chin, Shu-Hwa Chen, Hsin-Hung Wu, Chin-Wen Ho, Ming-Tat Ko, Chung-Yen Lin. BMC Syst Biol 2014
Times Cited: 1364







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



Times Cited
  Times     Co-cited
Similarity


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
44

clusterProfiler: an R package for comparing biological themes among gene clusters.
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. OMICS 2012
32

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
30

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
24

NCBI GEO: archive for functional genomics data sets--update.
Tanya Barrett, Stephen E Wilhite, Pierre Ledoux, Carlos Evangelista, Irene F Kim, Maxim Tomashevsky, Kimberly A Marshall, Katherine H Phillippy, Patti M Sherman, Michelle Holko,[...]. Nucleic Acids Res 2013
18


WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
16

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nat Protoc 2009
14

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
13

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 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
13

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
11

STRING v10: protein-protein interaction networks, integrated over the tree of life.
Damian Szklarczyk, Andrea Franceschini, Stefan Wyder, Kristoffer Forslund, Davide Heller, Jaime Huerta-Cepas, Milan Simonovic, Alexander Roth, Alberto Santos, Kalliopi P Tsafou,[...]. Nucleic Acids Res 2015
10


KEGG: new perspectives on genomes, pathways, diseases and drugs.
Minoru Kanehisa, Miho Furumichi, Mao Tanabe, Yoko Sato, Kanae Morishima. Nucleic Acids Res 2017
8

GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses.
Zefang Tang, Chenwei Li, Boxi Kang, Ge Gao, Cheng Li, Zemin Zhang. Nucleic Acids Res 2017
8

Cytoscape 2.8: new features for data integration and network visualization.
Michael E Smoot, Keiichiro Ono, Johannes Ruscheinski, Peng-Liang Wang, Trey Ideker. Bioinformatics 2011
8


The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.
Damian Szklarczyk, Annika L Gable, Katerina C Nastou, David Lyon, Rebecca Kirsch, Sampo Pyysalo, Nadezhda T Doncheva, Marc Legeay, Tao Fang, Peer Bork,[...]. Nucleic Acids Res 2021
518
8

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
Damian Szklarczyk, John H Morris, Helen Cook, Michael Kuhn, Stefan Wyder, Milan Simonovic, Alberto Santos, Nadezhda T Doncheva, Alexander Roth, Peer Bork,[...]. Nucleic Acids Res 2017
7

NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis.
Guangyan Zhou, Othman Soufan, Jessica Ewald, Robert E W Hancock, Niladri Basu, Jianguo Xia. Nucleic Acids Res 2019
450
6

HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
6

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.
Ron Edgar, Michael Domrachev, Alex E Lash. Nucleic Acids Res 2002
6

A general framework for weighted gene co-expression network analysis.
Bin Zhang, Steve Horvath. Stat Appl Genet Mol Biol 2005
6

Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries.
Hyuna Sung, Jacques Ferlay, Rebecca L Siegel, Mathieu Laversanne, Isabelle Soerjomataram, Ahmedin Jemal, Freddie Bray. CA Cancer J Clin 2021
6

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
6

DrugBank 5.0: a major update to the DrugBank database for 2018.
David S Wishart, Yannick D Feunang, An C Guo, Elvis J Lo, Ana Marcu, Jason R Grant, Tanvir Sajed, Daniel Johnson, Carin Li, Zinat Sayeeda,[...]. Nucleic Acids Res 2018
5

TCMSP: a database of systems pharmacology for drug discovery from herbal medicines.
Jinlong Ru, Peng Li, Jinan Wang, Wei Zhou, Bohui Li, Chao Huang, Pidong Li, Zihu Guo, Weiyang Tao, Yinfeng Yang,[...]. J Cheminform 2014
5

GeneCards Version 3: the human gene integrator.
Marilyn Safran, Irina Dalah, Justin Alexander, Naomi Rosen, Tsippi Iny Stein, Michael Shmoish, Noam Nativ, Iris Bahir, Tirza Doniger, Hagit Krug,[...]. Database (Oxford) 2010
670
5


STRING v9.1: protein-protein interaction networks, with increased coverage and integration.
Andrea Franceschini, Damian Szklarczyk, Sune Frankild, Michael Kuhn, Milan Simonovic, Alexander Roth, Jianyi Lin, Pablo Minguez, Peer Bork, Christian von Mering,[...]. Nucleic Acids Res 2013
5

GSVA: gene set variation analysis for microarray and RNA-seq data.
Sonja Hänzelmann, Robert Castelo, Justin Guinney. BMC Bioinformatics 2013
5

affy--analysis of Affymetrix GeneChip data at the probe level.
Laurent Gautier, Leslie Cope, Benjamin M Bolstad, Rafael A Irizarry. Bioinformatics 2004
5

Application of ggplot2 to Pharmacometric Graphics.
K Ito, D Murphy. CPT Pharmacometrics Syst Pharmacol 2013
189
5

Cytoscape Automation: empowering workflow-based network analysis.
David Otasek, John H Morris, Jorge Bouças, Alexander R Pico, Barry Demchak. Genome Biol 2019
326
4

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
4

CytoNCA: a cytoscape plugin for centrality analysis and evaluation of protein interaction networks.
Yu Tang, Min Li, Jianxin Wang, Yi Pan, Fang-Xiang Wu. Biosystems 2015
413
4

ChEA3: transcription factor enrichment analysis by orthogonal omics integration.
Alexandra B Keenan, Denis Torre, Alexander Lachmann, Ariel K Leong, Megan L Wojciechowicz, Vivian Utti, Kathleen M Jagodnik, Eryk Kropiwnicki, Zichen Wang, Avi Ma'ayan. Nucleic Acids Res 2019
122
4

PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes.
Vamsi K Mootha, Cecilia M Lindgren, Karl-Fredrik Eriksson, Aravind Subramanian, Smita Sihag, Joseph Lehar, Pere Puigserver, Emma Carlsson, Martin Ridderstråle, Esa Laurila,[...]. Nat Genet 2003
4

Complex heatmaps reveal patterns and correlations in multidimensional genomic data.
Zuguang Gu, Roland Eils, Matthias Schlesner. Bioinformatics 2016
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


iRegulon: from a gene list to a gene regulatory network using large motif and track collections.
Rekin's Janky, Annelien Verfaillie, Hana Imrichová, Bram Van de Sande, Laura Standaert, Valerie Christiaens, Gert Hulselmans, Koen Herten, Marina Naval Sanchez, Delphine Potier,[...]. PLoS Comput Biol 2014
446
4

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks.
Gabriela Bindea, Bernhard Mlecnik, Hubert Hackl, Pornpimol Charoentong, Marie Tosolini, Amos Kirilovsky, Wolf-Herman Fridman, Franck Pagès, Zlatko Trajanoski, Jérôme Galon. Bioinformatics 2009
4

pROC: an open-source package for R and S+ to analyze and compare ROC curves.
Xavier Robin, Natacha Turck, Alexandre Hainard, Natalia Tiberti, Frédérique Lisacek, Jean-Charles Sanchez, Markus Müller. BMC Bioinformatics 2011
4

GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis.
Zefang Tang, Boxi Kang, Chenwei Li, Tianxiang Chen, Zemin Zhang. Nucleic Acids Res 2019
937
4

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function.
David Warde-Farley, Sylva L Donaldson, Ovi Comes, Khalid Zuberi, Rashad Badrawi, Pauline Chao, Max Franz, Chris Grouios, Farzana Kazi, Christian Tannus Lopes,[...]. Nucleic Acids Res 2010
4

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
Cole Trapnell, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold, Lior Pachter. Nat Biotechnol 2010
4

miRWalk: An online resource for prediction of microRNA binding sites.
Carsten Sticht, Carolina De La Torre, Alisha Parveen, Norbert Gretz. PLoS One 2018
481
4


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.