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references.bib
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@incollection{2003,
title = {Random {{Effects}}: {{Generalized Linear Mixed Models}} for {{Categorical Responses}}},
shorttitle = {Random {{Effects}}},
booktitle = {Categorical {{Data Analysis}}},
year = {2003},
pages = {491--537},
publisher = {John Wiley \& Sons, Ltd},
doi = {10.1002/0471249688.ch12},
urldate = {2019-05-17},
copyright = {Copyright {\copyright} 2002 John Wiley \& Sons, Inc.},
isbn = {978-0-471-24968-9},
langid = {english},
keywords = {clustered data,Gauss--Hermite quadrature,logistic-normal model,mixed models,overdispersion,random effects,repeated measures,subject-specific}
}
@incollection{2005,
title = {Neutral {{Losses}} and {{Ion Series}}},
booktitle = {Understanding {{Mass Spectra}}: {{A Basic Approach}}},
year = {2005},
month = jan,
pages = {121--149},
publisher = {Wiley-Blackwell},
doi = {10.1002/0471479357.ch4},
urldate = {2018-03-26},
isbn = {978-0-471-47935-2},
langid = {english},
keywords = {aliphatic hydrocarbon spectra,arson analysis,benzoyl ion series,benzyl ion series,effect of chain branching,low-mass ion series,mass chromatography,Neutral losses,small molecule losses}
}
@misc{2014,
title = {What Is Principal Component Analysis?},
year = {2014},
month = may,
journal = {Bits of DNA},
urldate = {2017-09-14},
annotation = {00001}
}
@article{2016,
title = {維格納半圓分布},
year = {2016},
month = aug,
journal = {Wikipedia},
copyright = {Creative Commons Attribution-ShareAlike License},
langid = {english},
annotation = {00000 Page Version ID: 41047657}
}
@article{abdollahi,
title = {Is Nontargeted Data Acquisition for Target Analysis ({{nDATA}}) in Mass Spectrometry a Forward-Thinking Analytical Approach?},
author = {Abdollahi, Marzieh and Segura, Pedro A. and Beaudry, Francis},
journal = {Biomedical Chromatography},
publisher = {Wiley},
address = {Hoboken},
issn = {0269-3879},
doi = {10.1002/bmc.5531},
urldate = {2023-01-31},
langid = {english},
keywords = {bioanalysis,data-dependent acquisition,data-independent acquisition,gas-chromatography,high-resolution,human plasma,identification,ion library,mass spectrometry,metabolomics,protein,proteomics,quantification,swath-ms data,triple quadrupole},
annotation = {WOS:000875145000001}
}
@article{abrahamsson2023,
title = {Extracting {{Structural Information}} from {{Physicochemical Property Measurements Using Machine Learning}}-{{A New Approach}} for {{Structure Elucidation}} in {{Non-targeted Analysis}}},
author = {Abrahamsson, Dimitri and Brueck, Christopher L. and Prasse, Carsten and Lambropoulou, Dimitra A. and Koronaiou, Lelouda-Athanasia and Wang, Miaomiao and Park, June-Soo and Woodruff, Tracey J.},
year = {2023},
month = sep,
journal = {Environmental Science \& Technology},
publisher = {American Chemical Society},
issn = {0013-936X},
doi = {10.1021/acs.est.3c03003},
urldate = {2023-10-01}
}
@article{adams2020,
title = {Skyline for {{Small Molecules}}: {{A Unifying Software Package}} for {{Quantitative Metabolomics}}},
shorttitle = {Skyline for {{Small Molecules}}},
author = {Adams, Kendra J. and Pratt, Brian and Bose, Neelanjan and Dubois, Laura G. and {St John-Williams}, Lisa and Perrott, Kevin M. and Ky, Karina and Kapahi, Pankaj and Sharma, Vagisha and MacCoss, Michael J. and Moseley, M. Arthur and Colton, Carol A. and MacLean, Brendan X. and Schilling, Birgit and Thompson, J. Will and {Alzheimer's Disease Metabolomics Consortium}},
year = {2020},
month = apr,
journal = {Journal of Proteome Research},
volume = {19},
number = {4},
pages = {1447--1458},
issn = {1535-3907},
doi = {10.1021/acs.jproteome.9b00640},
langid = {english},
pmcid = {PMC7127945},
pmid = {31984744},
keywords = {data analysis,liquid chromatography,metabolite,metabolomics,quantitative,Skyline,small molecules,tandem mass spectrometry,targeted}
}
@article{aguilar-mogas2017,
title = {{{iMet}}: {{A Network-Based Computational Tool To Assist}} in the {{Annotation}} of {{Metabolites}} from {{Tandem Mass Spectra}}},
shorttitle = {{{iMet}}},
author = {{Aguilar-Mogas}, Antoni and {Sales-Pardo}, Marta and Navarro, Miriam and Guimer{\`a}, Roger and Yanes, Oscar},
year = {2017},
month = mar,
journal = {Analytical Chemistry},
volume = {89},
number = {6},
pages = {3474--3482},
issn = {0003-2700},
doi = {10.1021/acs.analchem.6b04512},
urldate = {2018-05-10}
}
@article{ahn2010,
title = {Link Communities Reveal Multiscale Complexity in Networks},
author = {Ahn, Yong-Yeol and Bagrow, James P. and Lehmann, Sune},
year = {2010},
month = aug,
journal = {Nature},
volume = {466},
number = {7307},
pages = {761--764},
issn = {1476-4687},
doi = {10.1038/nature09182},
urldate = {2019-01-02},
copyright = {2010 Nature Publishing Group},
langid = {english}
}
@article{al-salhi2022,
title = {Analytical Strategies to Profile the Internal Chemical Exposome and the Metabolome of Human Placenta},
author = {{Al-Salhi}, Raghad and Monfort, Christine and Bonvallot, Nathalie and David, Arthur},
year = {2022},
month = aug,
journal = {Analytica Chimica Acta},
volume = {1219},
pages = {339983},
issn = {0003-2670},
doi = {10.1016/j.aca.2022.339983},
urldate = {2023-01-31},
langid = {english},
keywords = {High-resolution mass spectrometry,Non-targeted analyses,Placenta,Sample preparation,Suspect screening}
}
@article{albreht2022,
title = {Structure {{Elucidation}} and {{Mitigation}} of {{Endogenous Interferences}} in {{LC-MS-Based Metabolic Profiling}} of {{Urine}}},
author = {Albreht, Alen and Hussain, Humma and Jim{\'e}nez, Beatriz and Yuen, Ada H. Y. and Whiley, Luke and Witt, Matthias and Lewis, Matthew R. and Chekmeneva, Elena},
year = {2022},
month = jan,
journal = {Analytical Chemistry},
volume = {94},
number = {3},
pages = {1760--1768},
publisher = {American Chemical Society},
issn = {0003-2700},
doi = {10.1021/acs.analchem.1c04378},
urldate = {2023-01-31}
}
@article{alden2017,
title = {Biologically {{Consistent Annotation}} of {{Metabolomics Data}}},
author = {Alden, Nicholas and Krishnan, Smitha and Porokhin, Vladimir and Raju, Ravali and McElearney, Kyle and Gilbert, Alan and Lee, Kyongbum},
year = {2017},
month = nov,
journal = {Analytical Chemistry},
issn = {0003-2700},
doi = {10.1021/acs.analchem.7b02162},
annotation = {00000}
}
@article{ali2019,
title = {Single-Cell Metabolomics by Mass Spectrometry: {{Advances}}, Challenges, and Future Applications},
shorttitle = {Single-Cell Metabolomics by Mass Spectrometry},
author = {Ali, Ahmed and Abouleila, Yasmine and Shimizu, Yoshihiro and Hiyama, Eiso and Emara, Samy and Mashaghi, Alireza and Hankemeier, Thomas},
year = {2019},
month = nov,
journal = {TrAC Trends in Analytical Chemistry},
volume = {120},
pages = {115436},
issn = {0165-9936},
doi = {10.1016/j.trac.2019.02.033},
urldate = {2020-12-27},
langid = {english},
keywords = {Cellular heterogeneity,Mass spectrometry,Metabolomics,Single-cell analysis,Single-cell isolation}
}
@incollection{alka2020,
title = {{{CHAPTER}} 6:{{OpenMS}} and {{KNIME}} for {{Mass Spectrometry Data Processing}}},
shorttitle = {{{CHAPTER}} 6},
booktitle = {Processing {{Metabolomics}} and {{Proteomics Data}} with {{Open Software}}},
author = {Alka, Oliver and Sachsenberg, Timo and Bichmann, Leon and Pfeuffer, Julianus and Weisser, Hendrik and Wein, Samuel and Netz, Eugen and Rurik, Marc and Kohlbacher, Oliver and R{\"o}st, Hannes},
year = {2020},
month = mar,
pages = {201--231},
doi = {10.1039/9781788019880-00201},
urldate = {2021-01-03},
langid = {english}
}
@article{alka2022,
title = {{{DIAMetAlyzer}} Allows Automated False-Discovery Rate-Controlled Analysis for Data-Independent Acquisition in Metabolomics},
author = {Alka, Oliver and Shanthamoorthy, Premy and Witting, Michael and Kleigrewe, Karin and Kohlbacher, Oliver and R{\"o}st, Hannes L.},
year = {2022},
month = mar,
journal = {Nature Communications},
volume = {13},
number = {1},
pages = {1347},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/s41467-022-29006-z},
urldate = {2022-04-08},
copyright = {2022 The Author(s)},
langid = {english},
keywords = {Metabolomics,Software}
}
@article{allam-ndoul2016,
title = {Association between {{Metabolite Profiles}}, {{Metabolic Syndrome}} and {{Obesity Status}}},
author = {{Allam-Ndoul}, B{\'e}n{\'e}dicte and Gu{\'e}nard, Fr{\'e}d{\'e}ric and Garneau, V{\'e}ronique and Cormier, Hubert and Barbier, Olivier and P{\'e}russe, Louis and Vohl, Marie-Claude},
year = {2016},
month = may,
journal = {Nutrients},
volume = {8},
number = {6},
pages = {324},
doi = {10.3390/nu8060324},
urldate = {2017-03-27},
copyright = {http://creativecommons.org/licenses/by/3.0/},
langid = {english},
keywords = {metabolic syndrome,metabolites,Obesity},
annotation = {00003}
}
@article{allard2017,
title = {Deep Metabolome Annotation in Natural Products Research: Towards a Virtuous Cycle in Metabolite Identification},
shorttitle = {Deep Metabolome Annotation in Natural Products Research},
author = {Allard, Pierre-Marie and {Genta-Jouve}, Gr{\'e}gory and Wolfender, Jean-Luc},
year = {2017},
month = feb,
journal = {Current Opinion in Chemical Biology},
series = {Omics},
volume = {36},
pages = {40--49},
issn = {1367-5931},
doi = {10.1016/j.cbpa.2016.12.022},
annotation = {00006}
}
@article{allen2014,
title = {{{CFM-ID}}: A Web Server for Annotation, Spectrum Prediction and Metabolite Identification from Tandem Mass Spectra},
shorttitle = {{{CFM-ID}}},
author = {Allen, Felicity and Pon, Allison and Wilson, Michael and Greiner, Russ and Wishart, David},
year = {2014},
month = jul,
journal = {Nucleic Acids Research},
volume = {42},
number = {W1},
pages = {W94-W99},
issn = {0305-1048},
doi = {10.1093/nar/gku436},
urldate = {2017-09-27},
annotation = {00066}
}
@article{alonso2015,
title = {Analytical {{Methods}} in {{Untargeted Metabolomics}}: {{State}} of the {{Art}} in 2015},
shorttitle = {Analytical {{Methods}} in {{Untargeted Metabolomics}}},
author = {Alonso, Arnald and Marsal, Sara and Juli{\`a}, Antonio},
year = {2015},
month = mar,
journal = {Frontiers in Bioengineering and Biotechnology},
volume = {3},
issn = {2296-4185},
doi = {10.3389/fbioe.2015.00023},
urldate = {2016-09-15},
pmcid = {PMC4350445},
pmid = {25798438},
annotation = {00058}
}
@article{alonso2017,
title = {Nontargeted {{Screening}} of {{Halogenated Organic Compounds}} in {{Bottlenose Dolphins}} ({{Tursiops}} Truncatus) from {{Rio}} de {{Janeiro}}, {{Brazil}}},
author = {Alonso, Mariana B. and Maruya, Keith A. and Dodder, Nathan G. and {Lailson-Brito}, Jos{\'e} and Azevedo, Alexandre and {Santos-Neto}, Elitieri and Torres, Joao P. M. and Malm, Olaf and Hoh, Eunha},
year = {2017},
month = jan,
journal = {Environmental Science \& Technology},
issn = {0013-936X},
doi = {10.1021/acs.est.6b04186},
urldate = {2017-01-30},
annotation = {00000}
}
@article{alseekh2021,
ids = {alseekh2021a},
title = {Mass Spectrometry-Based Metabolomics: A Guide for Annotation, Quantification and Best Reporting Practices},
shorttitle = {Mass Spectrometry-Based Metabolomics},
author = {Alseekh, Saleh and Aharoni, Asaph and Brotman, Yariv and Contrepois, K{\'e}vin and D'Auria, John and Ewald, Jan and Ewald, Jennifer C. and Fraser, Paul D. and Giavalisco, Patrick and Hall, Robert D. and Heinemann, Matthias and Link, Hannes and Luo, Jie and Neumann, Steffen and Nielsen, Jens and {\noopsort{souza}}de Souza, Leonardo Perez and Saito, Kazuki and Sauer, Uwe and Schroeder, Frank C. and Schuster, Stefan and Siuzdak, Gary and Skirycz, Aleksandra and Sumner, Lloyd W. and Snyder, Michael P. and Tang, Huiru and Tohge, Takayuki and Wang, Yulan and Wen, Weiwei and Wu, Si and Xu, Guowang and Zamboni, Nicola and Fernie, Alisdair R.},
year = {2021},
month = jul,
journal = {Nature Methods},
volume = {18},
number = {7},
pages = {747--756},
publisher = {Nature Publishing Group},
issn = {1548-7105},
doi = {10.1038/s41592-021-01197-1},
urldate = {2021-07-19},
copyright = {2021 Springer Nature America, Inc.},
langid = {english},
keywords = {Mass spectrometry,Metabolomics},
annotation = {Bandiera\_abtest: a Cg\_type: Nature Research Journals Primary\_atype: Reviews Subject\_term: Mass spectrometry;Metabolomics Subject\_term\_id: mass-spectrometry;metabolomics}
}
@article{alves2017,
title = {Case {{Study}} on {{Screening Emerging Pollutants}} in {{Urine}} and {{Nails}}},
author = {Alves, Andreia and Giovanoulis, Georgios and Nilsson, Ulrika and Erratico, Claudio and Lucattini, Luisa and Haug, Line S. and Jacobs, Griet and {\noopsort{wit}}{de Wit}, Cynthia A. and Leonards, Pim E. G. and Covaci, Adrian and Magner, J{\"o}rgen and Voorspoels, Stefan},
year = {2017},
month = mar,
journal = {Environmental Science \& Technology},
issn = {0013-936X},
doi = {10.1021/acs.est.6b05661},
urldate = {2017-03-27},
annotation = {00000}
}
@article{alzharani2020,
title = {Metabolomics Profiling of Plasma, Urine and Saliva after Short Term Training in Young Professional Football Players in {{Saudi Arabia}}},
author = {Alzharani, Mansour A. and Alshuwaier, Ghareeb O. and Aljaloud, Khalid S. and {Al-Tannak}, Naser F. and Watson, David G.},
year = {2020},
month = nov,
journal = {Scientific Reports},
volume = {10},
number = {1},
pages = {19759},
publisher = {Nature Publishing Group},
issn = {2045-2322},
doi = {10.1038/s41598-020-75755-6},
urldate = {2020-12-23},
copyright = {2020 The Author(s)},
langid = {english}
}
@article{anderson2021,
title = {Modifying {{Chromatography Conditions}} for {{Improved Unknown Feature Identification}} in {{Untargeted Metabolomics}}},
author = {Anderson, Brady G. and Raskind, Alexander and Habra, Hani and Kennedy, Robert T. and Evans, Charles R.},
year = {2021},
month = dec,
journal = {Analytical Chemistry},
volume = {93},
number = {48},
pages = {15840--15849},
publisher = {American Chemical Society},
issn = {0003-2700},
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copyright = {Copyright {\copyright} 2009 John Wiley \& Sons, Ltd.},
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copyright = {2022 The Author(s)},
langid = {english},
keywords = {Cheminformatics,Machine learning,Metabolomics}
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langid = {english},
keywords = {Adapted Marr wavelet,Continuous wavelet transform,Peak detection and quantification,Shape matching index}
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urldate = {2024-03-24},
copyright = {2023 The Author(s), under exclusive licence to Springer Nature America, Inc.},
langid = {english},
keywords = {Databases,Metabolomics}
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urldate = {2020-10-08},
chapter = {Physical Sciences},
copyright = {{\copyright} 2007 by The National Academy of Sciences of the USA},
langid = {english},
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copyright = {2021 The Author(s)},
langid = {english},
keywords = {Data processing,Metabolomics,Statistical methods}
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urldate = {2017-01-10},
langid = {english},
keywords = {data pre-processing,imaging metabolomics,isotopic labeling,Multivariate Analysis,pathway,univariate analysis},
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title = {Training in Metabolomics Research. {{I}}. {{Designing}} the Experiment, Collecting and Extracting Samples and Generating Metabolomics Data},
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langid = {english},
keywords = {CE-MS,GC-MS,LC-MS,Metabolomics,NMR,sample extraction,study design},
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title = {{{mWISE}}: {{An Algorithm}} for {{Context-Based Annotation}} of {{Liquid Chromatography}}--{{Mass Spectrometry Features}} through {{Diffusion}} in {{Graphs}}},
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author = {{Barranco-Altirriba}, Maria and {Sol{\`a}-Santos}, Pol and {Picart-Armada}, Sergio and {Kanaan-Izquierdo}, Samir and Fonollosa, Jordi and {Perera-Lluna}, Alexandre},
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title = {Sparse Network Modeling and Metscape-Based Visualization Methods for the Analysis of Large-Scale Metabolomics Data},
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title = {In {{Vitro Liquid Extraction Surface Analysis Mass Spectrometry}} ({{ivLESA-MS}}) for {{Direct Metabolic Analysis}} of {{Adherent Cells}} in {{Culture}}},
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title = {{{DeltaMS}}: A Tool to Track Isotopologues in {{GC-}} and {{LC-MS}} Data},
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journal = {Metabolomics},
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pages = {41},
issn = {1573-3890},
doi = {10.1007/s11306-018-1336-x},
urldate = {2019-01-02},
langid = {english},
keywords = {Computer-aided tool,DeltaMS,Isotope signature,Metallomics,Shiny,Stable isotope labeling}
}
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title = {Nontargeted {{Discovery}} of {{Novel Contaminants}} in the {{Great Lakes Region}}: {{A Comparison}} of {{Fish Fillets}} and {{Fish Consumers}}},
shorttitle = {Nontargeted {{Discovery}} of {{Novel Contaminants}} in the {{Great Lakes Region}}},
author = {Baygi, Sadjad Fakouri and Fernando, Sujan and Hopke, Philip K. and Holsen, Thomas M. and Crimmins, Bernard S.},
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title = {{{IDSL}}.{{UFA Assigns High-Confidence Molecular Formula Annotations}} for {{Untargeted LC}}/{{HRMS Data Sets}} in {{Metabolomics}} and {{Exposomics}}},
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publisher = {American Chemical Society},
issn = {0003-2700},
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urldate = {2022-12-14}
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title = {{{IDSL}}.{{CSA}}: {{Composite Spectra Analysis}} for {{Chemical Annotation}} of {{Untargeted Metabolomics Datasets}}},
author = {Baygi, Sadjad Fakouri and Kumar, Yashwant and Barupal, Dinesh Kumar},
year = {2023},
month = jun,
journal = {IDSL.CSA: Composite Spectra Analysis for Chemical Annotation of Untargeted Metabolomics Datasets},
publisher = {American Chemical Society},
doi = {10.1021/acs.analchem.3c00376},
copyright = {{\copyright} 2023 American Chemical Society},
langid = {american}
}
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title = {Review of Recent Developments in {{GC}}--{{MS}} Approaches to Metabolomics-Based Research},
author = {Beale, David J. and Pinu, Farhana R. and Kouremenos, Konstantinos A. and Poojary, Mahesha M. and Narayana, Vinod K. and Boughton, Berin A. and Kanojia, Komal and Dayalan, Saravanan and Jones, Oliver A. H. and Dias, Daniel A.},
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journal = {Metabolomics},
volume = {14},
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urldate = {2020-12-27},
langid = {english}
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title = {News {{Feature}}: {{Exposing}} the Exposome to Elucidate Disease},
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author = {Beans, Carolyn},
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doi = {10.1073/pnas.1817771115},
urldate = {2018-12-01},
copyright = {{\copyright} 2018 . Published under the PNAS license.},
langid = {english},
pmid = {30459267}
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title = {Nontarget {{Approach}} to {{Identify Complexing Agents}} in {{Atmospheric Aerosol}} and {{Rainwater Samples}}},
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title = {Hyphenated {{MS-based}} Targeted Approaches in Metabolomics},
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year = {2017},
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title = {Using {{Expert Driven Machine Learning}} to {{Enhance Dynamic Metabolomics Data Analysis}}},
author = {Beirnaert, Charlie and Peeters, Laura and Meysman, Pieter and Bittremieux, Wout and Foubert, Kenn and Custers, Deborah and {Van der Auwera}, Anastasia and Cuykx, Matthias and Pieters, Luc and Covaci, Adrian and Laukens, Kris},
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journal = {Metabolites},
volume = {9},
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publisher = {Multidisciplinary Digital Publishing Institute},
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urldate = {2021-01-03},
copyright = {http://creativecommons.org/licenses/by/3.0/},
langid = {english},
keywords = {data simulation,dynamic metabolomics,machine learning}
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title = {Investigation of Commercial Sorbents for the Analysis of Opioid Peptides in Human Plasma by On-Line {{SPE-CE}}},
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urldate = {2018-07-03},
copyright = {Copyright {\copyright} 2010 WILEY-VCH Verlag GmbH \& Co. KGaA, Weinheim},
langid = {english},
keywords = {MS,Neuropeptides,On-line,Plasma,Preconcentration,UV}
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title = {A Strategy to Incorporate Prior Knowledge into Correlation Network Cutoff Selection},
author = {Benedetti, Elisa and {Pu{\v c}i{\'c}-Bakovi{\'c}}, Maja and Keser, Toma and Gerstner, Nathalie and B{\"u}y{\"u}k{\"o}zkan, Mustafa and {\v S}tambuk, Tamara and Selman, Maurice H. J. and Rudan, Igor and Pola{\v s}ek, Ozren and Hayward, Caroline and {Al-Amin}, Hassen and Suhre, Karsten and Kastenm{\"u}ller, Gabi and Lauc, Gordan and Krumsiek, Jan},
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urldate = {2021-07-07},
copyright = {2020 The Author(s)},
langid = {english},
annotation = {Bandiera\_abtest: a Cc\_license\_type: cc\_by Cg\_type: Nature Research Journals Primary\_atype: Research Subject\_term: Biochemical reaction networks;Computational biology and bioinformatics;Computational models Subject\_term\_id: biochemical-reaction-networks;computational-biology-and-bioinformatics;computational-models}
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title = {New {{Approach}} for the {{Identification}} of {{Isobaric}} and {{Isomeric Metabolites}}},
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year = {2023},
month = may,
journal = {Analytical Chemistry},
volume = {95},
number = {18},
pages = {7118--7126},
issn = {1520-6882},
doi = {10.1021/acs.analchem.2c04962},
langid = {english},
pmcid = {PMC10173252},
pmid = {37119183},
keywords = {{Databases, Factual},Ion Mobility Spectrometry,Isomerism,Metabolomics}
}
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