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List of co-cited articles
173 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
28

The PRIDE database and related tools and resources in 2019: improving support for quantification data.
Yasset Perez-Riverol, Attila Csordas, Jingwen Bai, Manuel Bernal-Llinares, Suresh Hewapathirana, Deepti J Kundu, Avinash Inuganti, Johannes Griss, Gerhard Mayer, Martin Eisenacher,[...]. Nucleic Acids Res 2019
24

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
23

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
21

Universal sample preparation method for proteome analysis.
Jacek R Wiśniewski, Alexandre Zougman, Nagarjuna Nagaraj, Matthias Mann. Nat Methods 2009
13

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics.
Stefka Tyanova, Tikira Temu, Juergen Cox. Nat Protoc 2016
10

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
10

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
10

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
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
9

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
9

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
9


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


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


Ultrasensitive proteome analysis using paramagnetic bead technology.
Christopher S Hughes, Sophia Foehr, David A Garfield, Eileen E Furlong, Lars M Steinmetz, Jeroen Krijgsveld. Mol Syst Biol 2014
440
5

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
5

Visualization of LC-MS/MS proteomics data in MaxQuant.
Stefka Tyanova, Tikira Temu, Arthur Carlson, Pavel Sinitcyn, Matthias Mann, Juergen Cox. Proteomics 2015
125
5

Near-optimal probabilistic RNA-seq quantification.
Nicolas L Bray, Harold Pimentel, Páll Melsted, Lior Pachter. Nat Biotechnol 2016
4

Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells.
Nils A Kulak, Garwin Pichler, Igor Paron, Nagarjuna Nagaraj, Matthias Mann. Nat Methods 2014
889
4

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics.
Andy T Kong, Felipe V Leprevost, Dmitry M Avtonomov, Dattatreya Mellacheruvu, Alexey I Nesvizhskii. Nat Methods 2017
318
4

Comprehensive Single-Shot Proteomics with FAIMS on a Hybrid Orbitrap Mass Spectrometer.
Alexander S Hebert, Satendra Prasad, Michael W Belford, Derek J Bailey, Graeme C McAlister, Susan E Abbatiello, Romain Huguet, Eloy R Wouters, Jean-Jacques Dunyach, Dain R Brademan,[...]. Anal Chem 2018
103
4



WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit.
Jing Wang, Suhas Vasaikar, Zhiao Shi, Michael Greer, Bing Zhang. Nucleic Acids Res 2017
585
4

The Pfam protein families database: towards a more sustainable future.
Robert D Finn, Penelope Coggill, Ruth Y Eberhardt, Sean R Eddy, Jaina Mistry, Alex L Mitchell, Simon C Potter, Marco Punta, Matloob Qureshi, Amaia Sangrador-Vegas,[...]. Nucleic Acids Res 2016
4


BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes.
Florian Meier, Philipp E Geyer, Sebastian Virreira Winter, Juergen Cox, Matthias Mann. Nat Methods 2018
172
3

Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial.
Christina Ludwig, Ludovic Gillet, George Rosenberger, Sabine Amon, Ben C Collins, Ruedi Aebersold. Mol Syst Biol 2018
325
3

Online Parallel Accumulation-Serial Fragmentation (PASEF) with a Novel Trapped Ion Mobility Mass Spectrometer.
Florian Meier, Andreas-David Brunner, Scarlet Koch, Heiner Koch, Markus Lubeck, Michael Krause, Niels Goedecke, Jens Decker, Thomas Kosinski, Melvin A Park,[...]. Mol Cell Proteomics 2018
240
3


Single-pot, solid-phase-enhanced sample preparation for proteomics experiments.
Christopher S Hughes, Sophie Moggridge, Torsten Müller, Poul H Sorensen, Gregg B Morin, Jeroen Krijgsveld. Nat Protoc 2019
251
3

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
3

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

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
3

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
3


ProteomeXchange provides globally coordinated proteomics data submission and dissemination.
Juan A Vizcaíno, Eric W Deutsch, Rui Wang, Attila Csordas, Florian Reisinger, Daniel Ríos, José A Dianes, Zhi Sun, Terry Farrah, Nuno Bandeira,[...]. Nat Biotechnol 2014
3

The somatic genomic landscape of glioblastoma.
Cameron W Brennan, Roel G W Verhaak, Aaron McKenna, Benito Campos, Houtan Noushmehr, Sofie R Salama, Siyuan Zheng, Debyani Chakravarty, J Zachary Sanborn, Samuel H Berman,[...]. Cell 2013
3

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
3

RSeQC: quality control of RNA-seq experiments.
Liguo Wang, Shengqin Wang, Wei Li. Bioinformatics 2012
3


WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs.
Yuxing Liao, Jing Wang, Eric J Jaehnig, Zhiao Shi, Bing Zhang. Nucleic Acids Res 2019
838
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

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

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

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
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.