A citation-based method for searching scientific literature

Thomas De Vijlder, Dirk Valkenborg, Filip Lemière, Edwin P Romijn, Kris Laukens, Filip Cuyckens. Mass Spectrom Rev 2018
Times Cited: 73







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



Times Cited
  Times     Co-cited
Similarity


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
16

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
158
16

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
13

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
13

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
12


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
10

Searching molecular structure databases with tandem mass spectra using CSI:FingerID.
Kai Dührkop, Huibin Shen, Marvin Meusel, Juho Rousu, Sebastian Böcker. Proc Natl Acad Sci U S A 2015
355
9


MetFrag relaunched: incorporating strategies beyond in silico fragmentation.
Christoph Ruttkies, Emma L Schymanski, Sebastian Wolf, Juliane Hollender, Steffen Neumann. J Cheminform 2016
391
9

Illuminating the dark matter in metabolomics.
Ricardo R da Silva, Pieter C Dorrestein, Robert A Quinn. Proc Natl Acad Sci U S A 2015
206
9

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
420
9

Propagating annotations of molecular networks using in silico fragmentation.
Ricardo R da Silva, Mingxun Wang, Louis-Félix Nothias, Justin J J van der Hooft, Andrés Mauricio Caraballo-Rodríguez, Evan Fox, Marcy J Balunas, Jonathan L Klassen, Norberto Peporine Lopes, Pieter C Dorrestein. PLoS Comput Biol 2018
119
9

CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra.
Felicity Allen, Allison Pon, Michael Wilson, Russ Greiner, David Wishart. Nucleic Acids Res 2014
242
8

Computational mass spectrometry for small molecules.
Kerstin Scheubert, Franziska Hufsky, Sebastian Böcker. J Cheminform 2013
82
8



Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics.
Ivana Blaženović, Tobias Kind, Jian Ji, Oliver Fiehn. Metabolites 2018
238
8

Hydrogen Rearrangement Rules: Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software.
Hiroshi Tsugawa, Tobias Kind, Ryo Nakabayashi, Daichi Yukihira, Wataru Tanaka, Tomas Cajka, Kazuki Saito, Oliver Fiehn, Masanori Arita. Anal Chem 2016
242
6


SIRIUS: decomposing isotope patterns for metabolite identification.
Sebastian Böcker, Matthias C Letzel, Zsuzsanna Lipták, Anton Pervukhin. Bioinformatics 2009
164
6


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
6


MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data.
Kenneth Haug, Reza M Salek, Pablo Conesa, Janna Hastings, Paula de Matos, Mark Rijnbeek, Tejasvi Mahendraker, Mark Williams, Steffen Neumann, Philippe Rocca-Serra,[...]. Nucleic Acids Res 2013
394
6

Topic modeling for untargeted substructure exploration in metabolomics.
Justin Johan Jozias van der Hooft, Joe Wandy, Michael P Barrett, Karl E V Burgess, Simon Rogers. Proc Natl Acad Sci U S A 2016
126
6

Mass spectral molecular networking of living microbial colonies.
Jeramie Watrous, Patrick Roach, Theodore Alexandrov, Brandi S Heath, Jane Y Yang, Roland D Kersten, Menno van der Voort, Kit Pogliano, Harald Gross, Jos M Raaijmakers,[...]. Proc Natl Acad Sci U S A 2012
509
6

Metabolic reaction network-based recursive metabolite annotation for untargeted metabolomics.
Xiaotao Shen, Ruohong Wang, Xin Xiong, Yandong Yin, Yuping Cai, Zaijun Ma, Nan Liu, Zheng-Jiang Zhu. Nat Commun 2019
106
6

MetFusion: integration of compound identification strategies.
Michael Gerlich, Steffen Neumann. J Mass Spectrom 2013
104
5


In silico fragmentation for computer assisted identification of metabolite mass spectra.
Sebastian Wolf, Stephan Schmidt, Matthias Müller-Hannemann, Steffen Neumann. BMC Bioinformatics 2010
379
5

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
5

Combined Liquid Chromatography-Infrared Ion Spectroscopy for Identification of Regioisomeric Drug Metabolites.
Jonathan Martens, Valerie Koppen, Giel Berden, Filip Cuyckens, Jos Oomens. Anal Chem 2017
27
14

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
191
5


MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics.
James G Jeffryes, Ricardo L Colastani, Mona Elbadawi-Sidhu, Tobias Kind, Thomas D Niehaus, Linda J Broadbelt, Andrew D Hanson, Oliver Fiehn, Keith E J Tyo, Christopher S Henry. J Cheminform 2015
119
5

RIKEN tandem mass spectral database (ReSpect) for phytochemicals: a plant-specific MS/MS-based data resource and database.
Yuji Sawada, Ryo Nakabayashi, Yutaka Yamada, Makoto Suzuki, Muneo Sato, Akane Sakata, Kenji Akiyama, Tetsuya Sakurai, Fumio Matsuda, Toshio Aoki,[...]. Phytochemistry 2012
162
5

Automatic Compound Annotation from Mass Spectrometry Data Using MAGMa.
Lars Ridder, Justin J J van der Hooft, Stefan Verhoeven. Mass Spectrom (Tokyo) 2014
38
10

Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication.
Pierre-Marie Allard, Tiphaine Péresse, Jonathan Bisson, Katia Gindro, Laurence Marcourt, Van Cuong Pham, Fanny Roussi, Marc Litaudon, Jean-Luc Wolfender. Anal Chem 2016
189
5

Critical Assessment of Small Molecule Identification 2016: automated methods.
Emma L Schymanski, Christoph Ruttkies, Martin Krauss, Céline Brouard, Tobias Kind, Kai Dührkop, Felicity Allen, Arpana Vaniya, Dries Verdegem, Sebastian Böcker,[...]. J Cheminform 2017
69
5

Dark matter in host-microbiome metabolomics: Tackling the unknowns-A review.
B Y Loulou Peisl, Emma L Schymanski, Paul Wilmes. Anal Chim Acta 2018
64
6

Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy.
Ivana Blaženović, Tobias Kind, Hrvoje Torbašinović, Slobodan Obrenović, Sajjan S Mehta, Hiroshi Tsugawa, Tobias Wermuth, Nicolas Schauer, Martina Jahn, Rebekka Biedendieck,[...]. J Cheminform 2017
53
7

Navigating freely-available software tools for metabolomics analysis.
Rachel Spicer, Reza M Salek, Pablo Moreno, Daniel Cañueto, Christoph Steinbeck. Metabolomics 2017
114
5

Significance estimation for large scale metabolomics annotations by spectral matching.
Kerstin Scheubert, Franziska Hufsky, Daniel Petras, Mingxun Wang, Louis-Félix Nothias, Kai Dührkop, Nuno Bandeira, Pieter C Dorrestein, Sebastian Böcker. Nat Commun 2017
81
5

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
5

Current approaches and challenges for the metabolite profiling of complex natural extracts.
Jean-Luc Wolfender, Guillaume Marti, Aurélien Thomas, Samuel Bertrand. J Chromatogr A 2015
234
5

Metabolite profiling: from diagnostics to systems biology.
Alisdair R Fernie, Richard N Trethewey, Arno J Krotzky, Lothar Willmitzer. Nat Rev Mol Cell Biol 2004
475
5

Molecular networking as a dereplication strategy.
Jane Y Yang, Laura M Sanchez, Christopher M Rath, Xueting Liu, Paul D Boudreau, Nicole Bruns, Evgenia Glukhov, Anne Wodtke, Rafael de Felicio, Amanda Fenner,[...]. J Nat Prod 2013
326
5

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
5

The WEIZMASS spectral library for high-confidence metabolite identification.
Nir Shahaf, Ilana Rogachev, Uwe Heinig, Sagit Meir, Sergey Malitsky, Maor Battat, Hilary Wyner, Shuning Zheng, Ron Wehrens, Asaph Aharoni. Nat Commun 2016
55
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.