A citation-based method for searching scientific literature

Yasset Perez-Riverol, Attila Csordas, Jingwen Bai, Manuel Bernal-Llinares, Suresh Hewapathirana, Deepti J Kundu, Avinash Inuganti, Johannes Griss, Gerhard Mayer, Martin Eisenacher, Enrique Pérez, Julian Uszkoreit, Julianus Pfeuffer, Timo Sachsenberg, Sule Yilmaz, Shivani Tiwary, Jürgen Cox, Enrique Audain, Mathias Walzer, Andrew F Jarnuczak, Tobias Ternent, Alvis Brazma, Juan Antonio Vizcaíno. Nucleic Acids Res 2019
Times Cited: 2494







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



Times Cited
  Times     Co-cited
Similarity



The Perseus computational platform for comprehensive analysis of (prote)omics data.
Stefka Tyanova, Tikira Temu, Pavel Sinitcyn, Arthur Carlson, Marco Y Hein, Tamar Geiger, Matthias Mann, Jürgen Cox. Nat Methods 2016
10



The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.
Eric W Deutsch, Nuno Bandeira, Vagisha Sharma, Yasset Perez-Riverol, Jeremy J Carver, Deepti J Kundu, David García-Seisdedos, Andrew F Jarnuczak, Suresh Hewapathirana, Benjamin S Pullman,[...]. Nucleic Acids Res 2020
118
6

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
5

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations.
Peter V Hornbeck, Bin Zhang, Beth Murray, Jon M Kornhauser, Vaughan Latham, Elzbieta Skrzypek. Nucleic Acids Res 2015
5

Global quantification of mammalian gene expression control.
Björn Schwanhäusser, Dorothea Busse, Na Li, Gunnar Dittmar, Johannes Schuchhardt, Jana Wolf, Wei Chen, Matthias Selbach. Nature 2011
5

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
5

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
5

Andromeda: a peptide search engine integrated into the MaxQuant environment.
Jürgen Cox, Nadin Neuhauser, Annette Michalski, Richard A Scheltema, Jesper V Olsen, Matthias Mann. J Proteome Res 2011
5

Increasing the multiplexing capacity of TMTs using reporter ion isotopologues with isobaric masses.
Graeme C McAlister, Edward L Huttlin, Wilhelm Haas, Lily Ting, Mark P Jedrychowski, John C Rogers, Karsten Kuhn, Ian Pike, Robert A Grothe, Justin D Blethrow,[...]. Anal Chem 2012
326
4

A cross-platform toolkit for mass spectrometry and proteomics.
Matthew C Chambers, Brendan Maclean, Robert Burke, Dario Amodei, Daniel L Ruderman, Steffen Neumann, Laurent Gatto, Bernd Fischer, Brian Pratt, Jarrett Egertson,[...]. Nat Biotechnol 2012
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

Universal sample preparation method for proteome analysis.
Jacek R Wiśniewski, Alexandre Zougman, Nagarjuna Nagaraj, Matthias Mann. Nat Methods 2009
4

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
4

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
4

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.
Eric W Deutsch, Attila Csordas, Zhi Sun, Andrew Jarnuczak, Yasset Perez-Riverol, Tobias Ternent, David S Campbell, Manuel Bernal-Llinares, Shujiro Okuda, Shin Kawano,[...]. Nucleic Acids Res 2017
457
4

Characteristics of a human cell line transformed by DNA from human adenovirus type 5.
F L Graham, J Smiley, W C Russell, R Nairn. J Gen Virol 1977
3

An improved smaller biotin ligase for BioID proximity labeling.
Dae In Kim, Samuel C Jensen, Kyle A Noble, Birendra Kc, Kenneth H Roux, Khatereh Motamedchaboki, Kyle J Roux. Mol Biol Cell 2016
240
3


Target-decoy search strategy for mass spectrometry-based proteomics.
Joshua E Elias, Steven P Gygi. Methods Mol Biol 2010
326
3

Quantitative mass spectrometry-based multiplexing compares the abundance of 5000 S. cerevisiae proteins across 10 carbon sources.
Joao A Paulo, Jeremy D O'Connell, Robert A Everley, Jonathon O'Brien, Micah A Gygi, Steven P Gygi. J Proteomics 2016
81
3

Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS.
Andrew Thompson, Jürgen Schäfer, Karsten Kuhn, Stefan Kienle, Josef Schwarz, Günter Schmidt, Thomas Neumann, R Johnstone, A Karim A Mohammed, Christian Hamon. Anal Chem 2003
3

A tissue-specific atlas of mouse protein phosphorylation and expression.
Edward L Huttlin, Mark P Jedrychowski, Joshua E Elias, Tapasree Goswami, Ramin Rad, Sean A Beausoleil, Judit Villén, Wilhelm Haas, Mathew E Sowa, Steven P Gygi. Cell 2010
3


Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nat Protoc 2009
3


UniProt: the universal protein knowledgebase.
The UniProt Consortium. Nucleic Acids Res 2018
790
3

MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes.
Oliver Thimm, Oliver Bläsing, Yves Gibon, Axel Nagel, Svenja Meyer, Peter Krüger, Joachim Selbig, Lukas A Müller, Seung Y Rhee, Mark Stitt. Plant J 2004
3

The Immune Epitope Database (IEDB): 2018 update.
Randi Vita, Swapnil Mahajan, James A Overton, Sandeep Kumar Dhanda, Sheridan Martini, Jason R Cantrell, Daniel K Wheeler, Alessandro Sette, Bjoern Peters. Nucleic Acids Res 2019
324
3

HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
3

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
3

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
3



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
3

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

Benchmarking common quantification strategies for large-scale phosphoproteomics.
Alexander Hogrebe, Louise von Stechow, Dorte B Bekker-Jensen, Brian T Weinert, Christian D Kelstrup, Jesper V Olsen. Nat Commun 2018
107
3

Transcriptomic and proteomic landscape of mitochondrial dysfunction reveals secondary coenzyme Q deficiency in mammals.
Inge Kühl, Maria Miranda, Ilian Atanassov, Irina Kuznetsova, Yvonne Hinze, Arnaud Mourier, Aleksandra Filipovska, Nils-Göran Larsson. Elife 2017
68
4


Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
3

KEGG: new perspectives on genomes, pathways, diseases and drugs.
Minoru Kanehisa, Miho Furumichi, Mao Tanabe, Yoko Sato, Kanae Morishima. Nucleic Acids Res 2017
3

A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics.
Jürgen Cox, Ivan Matic, Maximiliane Hilger, Nagarjuna Nagaraj, Matthias Selbach, Jesper V Olsen, Matthias Mann. Nat Protoc 2009
571
2

Interpretation of shotgun proteomic data: the protein inference problem.
Alexey I Nesvizhskii, Ruedi Aebersold. Mol Cell Proteomics 2005
670
2

Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data.
Nadezhda T Doncheva, John H Morris, Jan Gorodkin, Lars J Jensen. J Proteome Res 2019
256
2


A probability-based approach for high-throughput protein phosphorylation analysis and site localization.
Sean A Beausoleil, Judit Villén, Scott A Gerber, John Rush, Steven P Gygi. Nat Biotechnol 2006
2

Characterization and Optimization of Multiplexed Quantitative Analyses Using High-Field Asymmetric-Waveform Ion Mobility Mass Spectrometry.
Devin K Schweppe, Satendra Prasad, Michael W Belford, José Navarrete-Perea, Derek J Bailey, Romain Huguet, Mark P Jedrychowski, Ramin Rad, Graeme McAlister, Susan E Abbatiello,[...]. Anal Chem 2019
48
4

A Novel Differential Ion Mobility Device Expands the Depth of Proteome Coverage and the Sensitivity of Multiplex Proteomic Measurements.
Sibylle Pfammatter, Eric Bonneil, Francis P McManus, Satendra Prasad, Derek J Bailey, Michael Belford, Jean-Jacques Dunyach, Pierre Thibault. Mol Cell Proteomics 2018
49
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.