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: 3908







List of co-cited articles
154 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
16

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics.
Stefka Tyanova, Tikira Temu, Juergen Cox. Nat Protoc 2016
12

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
10

Universal sample preparation method for proteome analysis.
Jacek R Wiśniewski, Alexandre Zougman, Nagarjuna Nagaraj, Matthias Mann. Nat Methods 2009
9


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
7

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
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

Fiji: an open-source platform for biological-image analysis.
Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid,[...]. Nat Methods 2012
6

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
6


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
531
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

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

NIH Image to ImageJ: 25 years of image analysis.
Caroline A Schneider, Wayne S Rasband, Kevin W Eliceiri. Nat Methods 2012
5

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

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nat Protoc 2009
4

MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights.
Zhiqiang Pang, Jasmine Chong, Guangyan Zhou, David Anderson de Lima Morais, Le Chang, Michel Barrette, Carol Gauthier, Pierre-Étienne Jacques, Shuzhao Li, Jianguo Xia. Nucleic Acids Res 2021
509
4



Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics.
Shao-En Ong, Blagoy Blagoev, Irina Kratchmarova, Dan Bach Kristensen, Hanno Steen, Akhilesh Pandey, Matthias Mann. Mol Cell Proteomics 2002
4


Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues.
Roland Bruderer, Oliver M Bernhardt, Tejas Gandhi, Saša M Miladinović, Lin-Yang Cheng, Simon Messner, Tobias Ehrenberger, Vito Zanotelli, Yulia Butscheid, Claudia Escher,[...]. Mol Cell Proteomics 2015
443
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

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
4

KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
3

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nucleic Acids Res 2009
3

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists.
Eran Eden, Roy Navon, Israel Steinfeld, Doron Lipson, Zohar Yakhini. BMC Bioinformatics 2009
3

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
258
3

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
3


Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9.
John G Doench, Nicolo Fusi, Meagan Sullender, Mudra Hegde, Emma W Vaimberg, Katherine F Donovan, Ian Smith, Zuzana Tothova, Craig Wilen, Robert Orchard,[...]. Nat Biotechnol 2016
3

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments.
Brendan MacLean, Daniela M Tomazela, Nicholas Shulman, Matthew Chambers, Gregory L Finney, Barbara Frewen, Randall Kern, David L Tabb, Daniel C Liebler, Michael J MacCoss. Bioinformatics 2010
3

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
3


Semi-supervised learning for peptide identification from shotgun proteomics datasets.
Lukas Käll, Jesse D Canterbury, Jason Weston, William Stafford Noble, Michael J MacCoss. Nat Methods 2007
3

Efficient proximity labeling in living cells and organisms with TurboID.
Tess C Branon, Justin A Bosch, Ariana D Sanchez, Namrata D Udeshi, Tanya Svinkina, Steven A Carr, Jessica L Feldman, Norbert Perrimon, Alice Y Ting. Nat Biotechnol 2018
454
3

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update).
Uku Raudvere, Liis Kolberg, Ivan Kuzmin, Tambet Arak, Priit Adler, Hedi Peterson, Jaak Vilo. Nucleic Acids Res 2019
3

A brave new world of RNA-binding proteins.
Matthias W Hentze, Alfredo Castello, Thomas Schwarzl, Thomas Preiss. Nat Rev Mol Cell Biol 2018
607
3

SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software.
Guoci Teo, Guomin Liu, Jianping Zhang, Alexey I Nesvizhskii, Anne-Claude Gingras, Hyungwon Choi. J Proteomics 2014
282
3

Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis.
Ludovic C Gillet, Pedro Navarro, Stephen Tate, Hannes Röst, Nathalie Selevsek, Lukas Reiter, Ron Bonner, Ruedi Aebersold. Mol Cell Proteomics 2012
3

Enrichment map: a network-based method for gene-set enrichment visualization and interpretation.
Daniele Merico, Ruth Isserlin, Oliver Stueker, Andrew Emili, Gary D Bader. PLoS One 2010
3

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations.
Peter V Hornbeck, Bin Zhang, Beth Murray, Jon M Kornhauser, Vaughan Latham, Elzbieta Skrzypek. Nucleic Acids Res 2015
3

ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity.
T Xu, S K Park, J D Venable, J A Wohlschlegel, J K Diedrich, D Cociorva, B Lu, L Liao, J Hewel, X Han,[...]. J Proteomics 2015
266
3

A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients.
Dorte B Bekker-Jensen, Ana Martínez-Val, Sophia Steigerwald, Patrick Rüther, Kyle L Fort, Tabiwang N Arrey, Alexander Harder, Alexander Makarov, Jesper V Olsen. Mol Cell Proteomics 2020
79
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

The epidermal growth factor receptor (EGFR) promotes uptake of influenza A viruses (IAV) into host cells.
Thorsten Eierhoff, Eike R Hrincius, Ursula Rescher, Stephan Ludwig, Christina Ehrhardt. PLoS Pathog 2010
202
2

Fast, sensitive and accurate integration of single-cell data with Harmony.
Ilya Korsunsky, Nghia Millard, Jean Fan, Kamil Slowikowski, Fan Zhang, Kevin Wei, Yuriy Baglaenko, Michael Brenner, Po-Ru Loh, Soumya Raychaudhuri. Nat Methods 2019
792
2

MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.
Kai Wang, Darshan Singh, Zheng Zeng, Stephen J Coleman, Yan Huang, Gleb L Savich, Xiaping He, Piotr Mieczkowski, Sara A Grimm, Charles M Perou,[...]. Nucleic Acids Res 2010
678
2


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.