A citation-based method for searching scientific literature

Katja Luck, Dae-Kyum Kim, Luke Lambourne, Kerstin Spirohn, Bridget E Begg, Wenting Bian, Ruth Brignall, Tiziana Cafarelli, Francisco J Campos-Laborie, Benoit Charloteaux, Dongsic Choi, Atina G Coté, Meaghan Daley, Steven Deimling, Alice Desbuleux, Amélie Dricot, Marinella Gebbia, Madeleine F Hardy, Nishka Kishore, Jennifer J Knapp, István A Kovács, Irma Lemmens, Miles W Mee, Joseph C Mellor, Carl Pollis, Carles Pons, Aaron D Richardson, Sadie Schlabach, Bridget Teeking, Anupama Yadav, Mariana Babor, Dawit Balcha, Omer Basha, Christian Bowman-Colin, Suet-Feung Chin, Soon Gang Choi, Claudia Colabella, Georges Coppin, Cassandra D'Amata, David De Ridder, Steffi De Rouck, Miquel Duran-Frigola, Hanane Ennajdaoui, Florian Goebels, Liana Goehring, Anjali Gopal, Ghazal Haddad, Elodie Hatchi, Mohamed Helmy, Yves Jacob, Yoseph Kassa, Serena Landini, Roujia Li, Natascha van Lieshout, Andrew MacWilliams, Dylan Markey, Joseph N Paulson, Sudharshan Rangarajan, John Rasla, Ashyad Rayhan, Thomas Rolland, Adriana San-Miguel, Yun Shen, Dayag Sheykhkarimli, Gloria M Sheynkman, Eyal Simonovsky, Murat Taşan, Alexander Tejeda, Vincent Tropepe, Jean-Claude Twizere, Yang Wang, Robert J Weatheritt, Jochen Weile, Yu Xia, Xinping Yang, Esti Yeger-Lotem, Quan Zhong, Patrick Aloy, Gary D Bader, Javier De Las Rivas, Suzanne Gaudet, Tong Hao, Janusz Rak, Jan Tavernier, David E Hill, Marc Vidal, Frederick P Roth, Michael A Calderwood. Nature 2020
Times Cited: 259







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



Times Cited
  Times     Co-cited
Similarity


Architecture of the human interactome defines protein communities and disease networks.
Edward L Huttlin, Raphael J Bruckner, Joao A Paulo, Joe R Cannon, Lily Ting, Kurt Baltier, Greg Colby, Fana Gebreab, Melanie P Gygi, Hannah Parzen,[...]. Nature 2017
692
15

A proteome-scale map of the human interactome network.
Thomas Rolland, Murat Taşan, Benoit Charloteaux, Samuel J Pevzner, Quan Zhong, Nidhi Sahni, Song Yi, Irma Lemmens, Celia Fontanillo, Roberto Mosca,[...]. Cell 2014
775
14

Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
Edward L Huttlin, Raphael J Bruckner, Jose Navarrete-Perea, Joe R Cannon, Kurt Baltier, Fana Gebreab, Melanie P Gygi, Alexandra Thornock, Gabriela Zarraga, Stanley Tam,[...]. Cell 2021
85
16

The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.
Sandra Orchard, Mais Ammari, Bruno Aranda, Lionel Breuza, Leonardo Briganti, Fiona Broackes-Carter, Nancy H Campbell, Gayatri Chavali, Carol Chen, Noemi del-Toro,[...]. Nucleic Acids Res 2014
984
14

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
12

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
655
11

The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions.
Rose Oughtred, Jennifer Rust, Christie Chang, Bobby-Joe Breitkreutz, Chris Stark, Andrew Willems, Lorrie Boucher, Genie Leung, Nadine Kolas, Frederick Zhang,[...]. Protein Sci 2021
167
11

Highly accurate protein structure prediction with AlphaFold.
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko,[...]. Nature 2021
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
10


The Database of Interacting Proteins: 2004 update.
Lukasz Salwinski, Christopher S Miller, Adam J Smith, Frank K Pettit, James U Bowie, David Eisenberg. Nucleic Acids Res 2004
8

The mutational constraint spectrum quantified from variation in 141,456 humans.
Konrad J Karczewski, Laurent C Francioli, Grace Tiao, Beryl B Cummings, Jessica Alföldi, Qingbo Wang, Ryan L Collins, Kristen M Laricchia, Andrea Ganna, Daniel P Birnbaum,[...]. Nature 2020
7

HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks.
Gregorio Alanis-Lobato, Miguel A Andrade-Navarro, Martin H Schaefer. Nucleic Acids Res 2017
180
7

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
7

The reactome pathway knowledgebase.
Bijay Jassal, Lisa Matthews, Guilherme Viteri, Chuqiao Gong, Pascual Lorente, Antonio Fabregat, Konstantinos Sidiropoulos, Justin Cook, Marc Gillespie, Robin Haw,[...]. Nucleic Acids Res 2020
991
7

Interactome3D: adding structural details to protein networks.
Roberto Mosca, Arnaud Céol, Patrick Aloy. Nat Methods 2013
266
7

MINT, the molecular interaction database: 2012 update.
Luana Licata, Leonardo Briganti, Daniele Peluso, Livia Perfetto, Marta Iannuccelli, Eugenia Galeota, Francesca Sacco, Anita Palma, Aurelio Pio Nardozza, Elena Santonico,[...]. Nucleic Acids Res 2012
638
6

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
6

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
6

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
6

The BioPlex Network: A Systematic Exploration of the Human Interactome.
Edward L Huttlin, Lily Ting, Raphael J Bruckner, Fana Gebreab, Melanie P Gygi, John Szpyt, Stanley Tam, Gabriela Zarraga, Greg Colby, Kurt Baltier,[...]. Cell 2015
814
6

Network propagation: a universal amplifier of genetic associations.
Lenore Cowen, Trey Ideker, Benjamin J Raphael, Roded Sharan. Nat Rev Genet 2017
231
6

Widespread macromolecular interaction perturbations in human genetic disorders.
Nidhi Sahni, Song Yi, Mikko Taipale, Juan I Fuxman Bass, Jasmin Coulombe-Huntington, Fan Yang, Jian Peng, Jochen Weile, Georgios I Karras, Yang Wang,[...]. Cell 2015
298
6

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
6

WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
6


Structure-based prediction of protein-protein interactions on a genome-wide scale.
Qiangfeng Cliff Zhang, Donald Petrey, Lei Deng, Li Qiang, Yu Shi, Chan Aye Thu, Brygida Bisikirska, Celine Lefebvre, Domenico Accili, Tony Hunter,[...]. Nature 2012
404
6

Towards a proteome-scale map of the human protein-protein interaction network.
Jean-François Rual, Kavitha Venkatesan, Tong Hao, Tomoko Hirozane-Kishikawa, Amélie Dricot, Ning Li, Gabriel F Berriz, Francis D Gibbons, Matija Dreze, Nono Ayivi-Guedehoussou,[...]. Nature 2005
6

Accurate prediction of protein structures and interactions using a three-track neural network.
Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Qian Cong, Lisa N Kinch, R Dustin Schaeffer,[...]. Science 2021
512
6

A human interactome in three quantitative dimensions organized by stoichiometries and abundances.
Marco Y Hein, Nina C Hubner, Ina Poser, Jürgen Cox, Nagarjuna Nagaraj, Yusuke Toyoda, Igor A Gak, Ina Weisswange, Jörg Mansfeld, Frank Buchholz,[...]. Cell 2015
721
6


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
516
5

Disease networks. Uncovering disease-disease relationships through the incomplete interactome.
Jörg Menche, Amitabh Sharma, Maksim Kitsak, Susan Dina Ghiassian, Marc Vidal, Joseph Loscalzo, Albert-László Barabási. Science 2015
663
5

Understanding multicellular function and disease with human tissue-specific networks.
Casey S Greene, Arjun Krishnan, Aaron K Wong, Emanuela Ricciotti, Rene A Zelaya, Daniel S Himmelstein, Ran Zhang, Boris M Hartmann, Elena Zaslavsky, Stuart C Sealfon,[...]. Nat Genet 2015
427
5


iRefIndex: a consolidated protein interaction database with provenance.
Sabry Razick, George Magklaras, Ian M Donaldson. BMC Bioinformatics 2008
362
5

APID database: redefining protein-protein interaction experimental evidences and binary interactomes.
Diego Alonso-López, Francisco J Campos-Laborie, Miguel A Gutiérrez, Luke Lambourne, Michael A Calderwood, Marc Vidal, Javier De Las Rivas. Database (Oxford) 2019
58
8

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
631
5

A proximity-dependent biotinylation map of a human cell.
Christopher D Go, James D R Knight, Archita Rajasekharan, Bhavisha Rathod, Geoffrey G Hesketh, Kento T Abe, Ji-Young Youn, Payman Samavarchi-Tehrani, Hui Zhang, Lucie Y Zhu,[...]. Nature 2021
62
8

High-quality binary protein interaction map of the yeast interactome network.
Haiyuan Yu, Pascal Braun, Muhammed A Yildirim, Irma Lemmens, Kavitha Venkatesan, Julie Sahalie, Tomoko Hirozane-Kishikawa, Fana Gebreab, Na Li, Nicolas Simonis,[...]. Science 2008
888
5

Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging.
Hyun-Woo Rhee, Peng Zou, Namrata D Udeshi, Jeffrey D Martell, Vamsi K Mootha, Steven A Carr, Alice Y Ting. Science 2013
669
5


Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.
Ron Edgar, Michael Domrachev, Alex E Lash. Nucleic Acids Res 2002
4


LD Score regression distinguishes confounding from polygenicity in genome-wide association studies.
Brendan K Bulik-Sullivan, Po-Ru Loh, Hilary K Finucane, Stephan Ripke, Jian Yang, Nick Patterson, Mark J Daly, Alkes L Price, Benjamin M Neale. Nat Genet 2015
4

Transient protein-protein interactions: structural, functional, and network properties.
James R Perkins, Ilhem Diboun, Benoit H Dessailly, Jon G Lees, Christine Orengo. Structure 2010
325
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

The IntAct molecular interaction database in 2012.
Samuel Kerrien, Bruno Aranda, Lionel Breuza, Alan Bridge, Fiona Broackes-Carter, Carol Chen, Margaret Duesbury, Marine Dumousseau, Marc Feuermann, Ursula Hinz,[...]. Nucleic Acids Res 2012
696
4

KEGG: integrating viruses and cellular organisms.
Minoru Kanehisa, Miho Furumichi, Yoko Sato, Mari Ishiguro-Watanabe, Mao Tanabe. Nucleic Acids Res 2021
811
4

The CRAPome: a contaminant repository for affinity purification-mass spectrometry data.
Dattatreya Mellacheruvu, Zachary Wright, Amber L Couzens, Jean-Philippe Lambert, Nicole A St-Denis, Tuo Li, Yana V Miteva, Simon Hauri, Mihaela E Sardiu, Teck Yew Low,[...]. Nat Methods 2013
852
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.