A citation-based method for searching scientific literature

G Joshi-Tope, M Gillespie, I Vastrik, P D'Eustachio, E Schmidt, B de Bono, B Jassal, G R Gopinath, G R Wu, L Matthews, S Lewis, E Birney, L Stein. Nucleic Acids Res 2005
Times Cited: 776







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



Times Cited
  Times     Co-cited
Similarity


KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
25

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
24

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
22

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
16

KEGG: Kyoto Encyclopedia of Genes and Genomes.
H Ogata, S Goto, K Sato, W Fujibuchi, H Bono, M Kanehisa. Nucleic Acids Res 1999
11

Ten years of pathway analysis: current approaches and outstanding challenges.
Purvesh Khatri, Marina Sirota, Atul J Butte. PLoS Comput Biol 2012
869
8

PID: the Pathway Interaction Database.
Carl F Schaefer, Kira Anthony, Shiva Krupa, Jeffrey Buchoff, Matthew Day, Timo Hannay, Kenneth H Buetow. Nucleic Acids Res 2009
932
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

KEGG as a reference resource for gene and protein annotation.
Minoru Kanehisa, Yoko Sato, Masayuki Kawashima, Miho Furumichi, Mao Tanabe. Nucleic Acids Res 2016
7

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
7

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
6

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
6

KEGG: new perspectives on genomes, pathways, diseases and drugs.
Minoru Kanehisa, Miho Furumichi, Mao Tanabe, Yoko Sato, Kanae Morishima. Nucleic Acids Res 2017
6

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
6

WikiPathways: pathway editing for the people.
Alexander R Pico, Thomas Kelder, Martijn P van Iersel, Kristina Hanspers, Bruce R Conklin, Chris Evelo. PLoS Biol 2008
369
6

Proteomics. Tissue-based map of the human proteome.
Mathias Uhlén, Linn Fagerberg, Björn M Hallström, Cecilia Lindskog, Per Oksvold, Adil Mardinoglu, Åsa Sivertsson, Caroline Kampf, Evelina Sjöstedt, Anna Asplund,[...]. Science 2015
5

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis.
Jasmine Chong, Othman Soufan, Carin Li, Iurie Caraus, Shuzhao Li, Guillaume Bourque, David S Wishart, Jianguo Xia. Nucleic Acids Res 2018
5


WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research.
Denise N Slenter, Martina Kutmon, Kristina Hanspers, Anders Riutta, Jacob Windsor, Nuno Nunes, Jonathan Mélius, Elisa Cirillo, Susan L Coort, Daniela Digles,[...]. Nucleic Acids Res 2018
399
5



A novel signaling pathway impact analysis.
Adi Laurentiu Tarca, Sorin Draghici, Purvesh Khatri, Sonia S Hassan, Pooja Mittal, Jung-Sun Kim, Chong Jai Kim, Juan Pedro Kusanovic, Roberto Romero. Bioinformatics 2009
611
5

Pathway Commons, a web resource for biological pathway data.
Ethan G Cerami, Benjamin E Gross, Emek Demir, Igor Rodchenkov, Ozgün Babur, Nadia Anwar, Nikolaus Schultz, Gary D Bader, Chris Sander. Nucleic Acids Res 2011
658
5

Hallmarks of cancer: the next generation.
Douglas Hanahan, Robert A Weinberg. Cell 2011
5

Reactome: a database of reactions, pathways and biological processes.
David Croft, Gavin O'Kelly, Guanming Wu, Robin Haw, Marc Gillespie, Lisa Matthews, Michael Caudy, Phani Garapati, Gopal Gopinath, Bijay Jassal,[...]. Nucleic Acids Res 2011
979
5


Robust enumeration of cell subsets from tissue expression profiles.
Aaron M Newman, Chih Long Liu, Michael R Green, Andrew J Gentles, Weiguo Feng, Yue Xu, Chuong D Hoang, Maximilian Diehn, Ash A Alizadeh. Nat Methods 2015
4

InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation.
Karin Breuer, Amir K Foroushani, Matthew R Laird, Carol Chen, Anastasia Sribnaia, Raymond Lo, Geoffrey L Winsor, Robert E W Hancock, Fiona S L Brinkman, David J Lynn. Nucleic Acids Res 2013
619
4

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly,[...]. Genome Res 2010
4

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations.
Peter V Hornbeck, Bin Zhang, Beth Murray, Jon M Kornhauser, Vaughan Latham, Elzbieta Skrzypek. Nucleic Acids Res 2015
4

REVIGO summarizes and visualizes long lists of gene ontology terms.
Fran Supek, Matko Bošnjak, Nives Škunca, Tomislav Šmuc. PLoS One 2011
4

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
4

Molecular signatures database (MSigDB) 3.0.
Arthur Liberzon, Aravind Subramanian, Reid Pinchback, Helga Thorvaldsdóttir, Pablo Tamayo, Jill P Mesirov. Bioinformatics 2011
4

The BioPAX community standard for pathway data sharing.
Emek Demir, Michael P Cary, Suzanne Paley, Ken Fukuda, Christian Lemer, Imre Vastrik, Guanming Wu, Peter D'Eustachio, Carl Schaefer, Joanne Luciano,[...]. Nat Biotechnol 2010
379
4


Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ.
Jürgen Cox, Marco Y Hein, Christian A Luber, Igor Paron, Nagarjuna Nagaraj, Matthias Mann. Mol Cell Proteomics 2014
4

The KEGG resource for deciphering the genome.
Minoru Kanehisa, Susumu Goto, Shuichi Kawashima, Yasushi Okuno, Masahiro Hattori. Nucleic Acids Res 2004
4

WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
4

Multi-omics approaches to disease.
Yehudit Hasin, Marcus Seldin, Aldons Lusis. Genome Biol 2017
631
4

Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver.
Xia Yang, Bin Zhang, Cliona Molony, Eugene Chudin, Ke Hao, Jun Zhu, Andrea Gaedigk, Christine Suver, Hua Zhong, J Steven Leeder,[...]. Genome Res 2010
181
4

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.
Ron Edgar, Michael Domrachev, Alex E Lash. Nucleic Acids Res 2002
3

Integrated Omics: Tools, Advances, and Future Approaches.
Biswapriya B Misra, Carl D Langefeld, Michael Olivier, Laura A Cox. J Mol Endocrinol 2018
121
3

The FAIR Guiding Principles for scientific data management and stewardship.
Mark D Wilkinson, Michel Dumontier, I Jsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, Jan-Willem Boiten, Luiz Bonino da Silva Santos, Philip E Bourne,[...]. Sci Data 2016
3

Human Protein Reference Database--2009 update.
T S Keshava Prasad, Renu Goel, Kumaran Kandasamy, Shivakumar Keerthikumar, Sameer Kumar, Suresh Mathivanan, Deepthi Telikicherla, Rajesh Raju, Beema Shafreen, Abhilash Venugopal,[...]. Nucleic Acids Res 2009
3

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
3

Supervised risk predictor of breast cancer based on intrinsic subtypes.
Joel S Parker, Michael Mullins, Maggie C U Cheang, Samuel Leung, David Voduc, Tammi Vickery, Sherri Davies, Christiane Fauron, Xiaping He, Zhiyuan Hu,[...]. J Clin Oncol 2009
3

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1.
David A Barbie, Pablo Tamayo, Jesse S Boehm, So Young Kim, Susan E Moody, Ian F Dunn, Anna C Schinzel, Peter Sandy, Etienne Meylan, Claudia Scholl,[...]. Nature 2009
3

The Cancer Genome Atlas Pan-Cancer analysis project.
John N Weinstein, Eric A Collisson, Gordon B Mills, Kenna R Mills Shaw, Brad A Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, Joshua M Stuart. Nat Genet 2013
3

What is flux balance analysis?
Jeffrey D Orth, Ines Thiele, Bernhard Ø Palsson. Nat Biotechnol 2010
3

Network medicine: a network-based approach to human disease.
Albert-László Barabási, Natali Gulbahce, Joseph Loscalzo. Nat Rev Genet 2011
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.