A citation-based method for searching scientific literature

Rachel Spicer, Reza M Salek, Pablo Moreno, Daniel Cañueto, Christoph Steinbeck. Metabolomics 2017
Times Cited: 117







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



Times Cited
  Times     Co-cited
Similarity


MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data.
Tomás Pluskal, Sandra Castillo, Alejandro Villar-Briones, Matej Oresic. BMC Bioinformatics 2010
25

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
23

Proposed minimum reporting standards for chemical analysis Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI).
Lloyd W Sumner, Alexander Amberg, Dave Barrett, Michael H Beale, Richard Beger, Clare A Daykin, Teresa W-M Fan, Oliver Fiehn, Royston Goodacre, Julian L Griffin,[...]. Metabolomics 2007
23

XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification.
Colin A Smith, Elizabeth J Want, Grace O'Maille, Ruben Abagyan, Gary Siuzdak. Anal Chem 2006
23

XCMS Online: a web-based platform to process untargeted metabolomic data.
Ralf Tautenhahn, Gary J Patti, Duane Rinehart, Gary Siuzdak. Anal Chem 2012
699
22

HMDB 4.0: the human metabolome database for 2018.
David S Wishart, Yannick Djoumbou Feunang, Ana Marcu, An Chi Guo, Kevin Liang, Rosa Vázquez-Fresno, Tanvir Sajed, Daniel Johnson, Carin Li, Naama Karu,[...]. Nucleic Acids Res 2018
20

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis.
Hiroshi Tsugawa, Tomas Cajka, Tobias Kind, Yan Ma, Brendan Higgins, Kazutaka Ikeda, Mitsuhiro Kanazawa, Jean VanderGheynst, Oliver Fiehn, Masanori Arita. Nat Methods 2015
19

Identifying small molecules via high resolution mass spectrometry: communicating confidence.
Emma L Schymanski, Junho Jeon, Rebekka Gulde, Kathrin Fenner, Matthias Ruff, Heinz P Singer, Juliane Hollender. Environ Sci Technol 2014
18

Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics.
Ivana Blaženović, Tobias Kind, Jian Ji, Oliver Fiehn. Metabolites 2018
244
17

CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets.
Carsten Kuhl, Ralf Tautenhahn, Christoph Böttcher, Tony R Larson, Steffen Neumann. Anal Chem 2012
599
17

MassBank: a public repository for sharing mass spectral data for life sciences.
Hisayuki Horai, Masanori Arita, Shigehiko Kanaya, Yoshito Nihei, Tasuku Ikeda, Kazuhiro Suwa, Yuya Ojima, Kenichi Tanaka, Satoshi Tanaka, Ken Aoshima,[...]. J Mass Spectrom 2010
16

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics.
Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob,[...]. Bioinformatics 2015
209
15

Guidelines and considerations for the use of system suitability and quality control samples in mass spectrometry assays applied in untargeted clinical metabolomic studies.
David Broadhurst, Royston Goodacre, Stacey N Reinke, Julia Kuligowski, Ian D Wilson, Matthew R Lewis, Warwick B Dunn. Metabolomics 2018
310
14

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.
Mingxun Wang, Jeremy J Carver, Vanessa V Phelan, Laura M Sanchez, Neha Garg, Yao Peng, Don Duy Nguyen, Jeramie Watrous, Clifford A Kapono, Tal Luzzatto-Knaan,[...]. Nat Biotechnol 2016
14

Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools.
Manish Sud, Eoin Fahy, Dawn Cotter, Kenan Azam, Ilango Vadivelu, Charles Burant, Arthur Edison, Oliver Fiehn, Richard Higashi, K Sreekumaran Nair,[...]. Nucleic Acids Res 2016
289
14

Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy.
Ralf J M Weber, Thomas N Lawson, Reza M Salek, Timothy M D Ebbels, Robert C Glen, Royston Goodacre, Julian L Griffin, Kenneth Haug, Albert Koulman, Pablo Moreno,[...]. Metabolomics 2017
46
30

Highly sensitive feature detection for high resolution LC/MS.
Ralf Tautenhahn, Christoph Böttcher, Steffen Neumann. BMC Bioinformatics 2008
631
13

Analytical methods in untargeted metabolomics: state of the art in 2015.
Arnald Alonso, Sara Marsal, Antonio Julià. Front Bioeng Biotechnol 2015
333
13

Updates in metabolomics tools and resources: 2014-2015.
Biswapriya B Misra, Justin J J van der Hooft. Electrophoresis 2016
74
14

METLIN: A Technology Platform for Identifying Knowns and Unknowns.
Carlos Guijas, J Rafael Montenegro-Burke, Xavier Domingo-Almenara, Amelia Palermo, Benedikt Warth, Gerrit Hermann, Gunda Koellensperger, Tao Huan, Winnie Uritboonthai, Aries E Aisporna,[...]. Anal Chem 2018
431
11

New tools and resources in metabolomics: 2016-2017.
Biswapriya B Misra. Electrophoresis 2018
32
34

Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics.
Zijuan Lai, Hiroshi Tsugawa, Gert Wohlgemuth, Sajjan Mehta, Matthew Mueller, Yuxuan Zheng, Atsushi Ogiwara, John Meissen, Megan Showalter, Kohei Takeuchi,[...]. Nat Methods 2018
197
11

Predicting network activity from high throughput metabolomics.
Shuzhao Li, Youngja Park, Sai Duraisingham, Frederick H Strobel, Nooruddin Khan, Quinlyn A Soltow, Dean P Jones, Bali Pulendran. PLoS Comput Biol 2013
454
11

Metabolomics: beyond biomarkers and towards mechanisms.
Caroline H Johnson, Julijana Ivanisevic, Gary Siuzdak. Nat Rev Mol Cell Biol 2016
997
11

NMR Spectroscopy for Metabolomics Research.
Abdul-Hamid Emwas, Raja Roy, Ryan T McKay, Leonardo Tenori, Edoardo Saccenti, G A Nagana Gowda, Daniel Raftery, Fatimah Alahmari, Lukasz Jaremko, Mariusz Jaremko,[...]. Metabolites 2019
303
11


HMDB 3.0--The Human Metabolome Database in 2013.
David S Wishart, Timothy Jewison, An Chi Guo, Michael Wilson, Craig Knox, Yifeng Liu, Yannick Djoumbou, Rupasri Mandal, Farid Aziat, Edison Dong,[...]. Nucleic Acids Res 2013
10


Quality assurance procedures for mass spectrometry untargeted metabolomics. a review.
Danuta Dudzik, Cecilia Barbas-Bernardos, Antonia García, Coral Barbas. J Pharm Biomed Anal 2018
146
9

MetFrag relaunched: incorporating strategies beyond in silico fragmentation.
Christoph Ruttkies, Emma L Schymanski, Sebastian Wolf, Juliane Hollender, Steffen Neumann. J Cheminform 2016
397
9

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
9

KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
9

Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data.
Robert L Davidson, Ralf J M Weber, Haoyu Liu, Archana Sharma-Oates, Mark R Viant. Gigascience 2016
54
16

Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online.
Erica M Forsberg, Tao Huan, Duane Rinehart, H Paul Benton, Benedikt Warth, Brian Hilmers, Gary Siuzdak. Nat Protoc 2018
125
9

IPO: a tool for automated optimization of XCMS parameters.
Gunnar Libiseller, Michaela Dvorzak, Ulrike Kleb, Edgar Gander, Tobias Eisenberg, Frank Madeo, Steffen Neumann, Gert Trausinger, Frank Sinner, Thomas Pieber,[...]. BMC Bioinformatics 2015
157
9



METLIN: a metabolite mass spectral database.
Colin A Smith, Grace O'Maille, Elizabeth J Want, Chuan Qin, Sunia A Trauger, Theodore R Brandon, Darlene E Custodio, Ruben Abagyan, Gary Siuzdak. Ther Drug Monit 2005
8

Untargeted Metabolomics Strategies-Challenges and Emerging Directions.
Alexandra C Schrimpe-Rutledge, Simona G Codreanu, Stacy D Sherrod, John A McLean. J Am Soc Mass Spectrom 2016
402
8

Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry.
Warwick B Dunn, David Broadhurst, Paul Begley, Eva Zelena, Sue Francis-McIntyre, Nadine Anderson, Marie Brown, Joshau D Knowles, Antony Halsall, John N Haselden,[...]. Nat Protoc 2011
8

Analysis of metabolomic data: tools, current strategies and future challenges for omics data integration.
Alice Cambiaghi, Manuela Ferrario, Marco Masseroli. Brief Bioinform 2017
88
9


SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information.
Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Alexander A Aksenov, Alexey V Melnik, Marvin Meusel, Pieter C Dorrestein, Juho Rousu, Sebastian Böcker. Nat Methods 2019
309
8

The metaRbolomics Toolbox in Bioconductor and beyond.
Jan Stanstrup, Corey D Broeckling, Rick Helmus, Nils Hoffmann, Ewy Mathé, Thomas Naake, Luca Nicolotti, Kristian Peters, Johannes Rainer, Reza M Salek,[...]. Metabolites 2019
41
19



Dereplication of microbial metabolites through database search of mass spectra.
Hosein Mohimani, Alexey Gurevich, Alexander Shlemov, Alla Mikheenko, Anton Korobeynikov, Liu Cao, Egor Shcherbin, Louis-Felix Nothias, Pieter C Dorrestein, Pavel A Pevzner. Nat Commun 2018
106
7

Challenges, progress and promises of metabolite annotation for LC-MS-based metabolomics.
Romanas Chaleckis, Isabel Meister, Pei Zhang, Craig E Wheelock. Curr Opin Biotechnol 2019
131
7

Review of emerging metabolomic tools and resources: 2015-2016.
Biswapriya B Misra, Johannes F Fahrmann, Dmitry Grapov. Electrophoresis 2017
27
25

Identification of small molecules using accurate mass MS/MS search.
Tobias Kind, Hiroshi Tsugawa, Tomas Cajka, Yan Ma, Zijuan Lai, Sajjan S Mehta, Gert Wohlgemuth, Dinesh Kumar Barupal, Megan R Showalter, Masanori Arita,[...]. Mass Spectrom Rev 2018
163
7


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.