Cognitive analysis of metabolomics data for systems biology
Abstract
Cognitive computing is revolutionizing the way big data are processed and integrated, with artificial intelligence (AI) natural language processing (NLP) platforms helping researchers to efficiently search and digest the vast scientific literature. Most available platforms have been developed for biomedical researchers, but new NLP tools are emerging for biologists in other fields and an important example is metabolomics. NLP provides literature-based contextualization of metabolic features that decreases the time and expert-level subject knowledge required during the prioritization, identification and interpretation steps in the metabolomics data analysis pipeline. Here, we describe and demonstrate four workflows that combine metabolomics data with NLP-based literature searches of scientific databases to aid in the analysis of metabolomics data and their biological interpretation. Additionally, the four procedures can be used in isolation or consecutively, depending on the research questions. The first, used for initial metabolite annotation and prioritization, creates a list of metabolites that would be interesting for follow-up. The second workflow finds literature evidence of the activity of metabolites and metabolic pathways in governing the biological condition on a systems biology level. The third is used to identify candidate biomarkers, and the fourth looks for metabolic conditions or drug-repurposing targets that the two diseases havemore »
- Authors:
-
[1];
[1];
[1];
[2];
[1];
[1];
[1];
[1];
[3];
[1]
- The Scripps Research Inst., La Jolla, CA (United States). Center for Mass Spectrometry and Metabolomics
- IBM Watson Health, Cambridge, MA (United States)
- Waters Corp., Milford, MA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)
- OSTI Identifier:
- 1774918
- Grant/Contract Number:
- AC02-05CH11231; RI2811/1-1; R35 GM130385; P30 MH062261; P01 DA026146; U01 CA235493
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Protocols
- Additional Journal Information:
- Journal Volume: 16; Journal Issue: 3; Journal ID: ISSN 1754-2189
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Literature mining; predictive markers; systems analysis
Citation Formats
Majumder, Erica L.-W., Billings, Elizabeth M., Benton, H. Paul, Martin, Richard L., Palermo, Amelia, Guijas, Carlos, Rinschen, Markus M., Domingo-Almenara, Xavier, Montenegro-Burke, J. Rafael, Tagtow, Bradley A., Plumb, Robert S., and Siuzdak, Gary. Cognitive analysis of metabolomics data for systems biology. United States: N. p., 2021.
Web. doi:10.1038/s41596-020-00455-4.
Majumder, Erica L.-W., Billings, Elizabeth M., Benton, H. Paul, Martin, Richard L., Palermo, Amelia, Guijas, Carlos, Rinschen, Markus M., Domingo-Almenara, Xavier, Montenegro-Burke, J. Rafael, Tagtow, Bradley A., Plumb, Robert S., & Siuzdak, Gary. Cognitive analysis of metabolomics data for systems biology. United States. https://doi.org/10.1038/s41596-020-00455-4
Majumder, Erica L.-W., Billings, Elizabeth M., Benton, H. Paul, Martin, Richard L., Palermo, Amelia, Guijas, Carlos, Rinschen, Markus M., Domingo-Almenara, Xavier, Montenegro-Burke, J. Rafael, Tagtow, Bradley A., Plumb, Robert S., and Siuzdak, Gary. Fri .
"Cognitive analysis of metabolomics data for systems biology". United States. https://doi.org/10.1038/s41596-020-00455-4. https://www.osti.gov/servlets/purl/1774918.
@article{osti_1774918,
title = {Cognitive analysis of metabolomics data for systems biology},
author = {Majumder, Erica L.-W. and Billings, Elizabeth M. and Benton, H. Paul and Martin, Richard L. and Palermo, Amelia and Guijas, Carlos and Rinschen, Markus M. and Domingo-Almenara, Xavier and Montenegro-Burke, J. Rafael and Tagtow, Bradley A. and Plumb, Robert S. and Siuzdak, Gary},
abstractNote = {Cognitive computing is revolutionizing the way big data are processed and integrated, with artificial intelligence (AI) natural language processing (NLP) platforms helping researchers to efficiently search and digest the vast scientific literature. Most available platforms have been developed for biomedical researchers, but new NLP tools are emerging for biologists in other fields and an important example is metabolomics. NLP provides literature-based contextualization of metabolic features that decreases the time and expert-level subject knowledge required during the prioritization, identification and interpretation steps in the metabolomics data analysis pipeline. Here, we describe and demonstrate four workflows that combine metabolomics data with NLP-based literature searches of scientific databases to aid in the analysis of metabolomics data and their biological interpretation. Additionally, the four procedures can be used in isolation or consecutively, depending on the research questions. The first, used for initial metabolite annotation and prioritization, creates a list of metabolites that would be interesting for follow-up. The second workflow finds literature evidence of the activity of metabolites and metabolic pathways in governing the biological condition on a systems biology level. The third is used to identify candidate biomarkers, and the fourth looks for metabolic conditions or drug-repurposing targets that the two diseases have in common. The protocol can take 1–4 h or more to complete, depending on the processing time of the various software used.},
doi = {10.1038/s41596-020-00455-4},
journal = {Nature Protocols},
number = 3,
volume = 16,
place = {United States},
year = {Fri Jan 22 00:00:00 EST 2021},
month = {Fri Jan 22 00:00:00 EST 2021}
}
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Works referenced in this record:
Integrating electronic health record genotype and phenotype datasets to transform patient care
journal, January 2016
- Roden, Dm; Denny, Jc
- Clinical Pharmacology & Therapeutics, Vol. 99, Issue 3
Metabolomics activity screening for identifying metabolites that modulate phenotype
journal, April 2018
- Guijas, Carlos; Montenegro-Burke, J. Rafael; Warth, Benedikt
- Nature Biotechnology, Vol. 36, Issue 4
Growth rates of modern science: A bibliometric analysis based on the number of publications and cited references: Growth Rates of Modern Science: A Bibliometric Analysis Based on the Number of Publications and Cited References
journal, April 2015
- Bornmann, Lutz; Mutz, Rüdiger
- Journal of the Association for Information Science and Technology, Vol. 66, Issue 11
Urine metabolome analysis by gas chromatography–mass spectrometry (GC–MS): Standardization and optimization of protocols for urea removal and short-term sample storage
journal, October 2018
- Palmas, Francesco; Mussap, Michele; Fattuoni, Claudia
- Clinica Chimica Acta, Vol. 485
Metabolite identification and molecular fingerprint prediction through machine learning
journal, July 2012
- Heinonen, M.; Shen, H.; Zamboni, N.
- Bioinformatics, Vol. 28, Issue 18
Oligodendrocyte precursor cells in the demyelinated multiple sclerosis spinal cord
journal, February 2002
- Wolswijk, Guus
- Brain, Vol. 125, Issue 2
Systems biology guided by XCMS Online metabolomics
journal, April 2017
- Huan, Tao; Forsberg, Erica M.; Rinehart, Duane
- Nature Methods, Vol. 14, Issue 5
Oligodendrocyte-specific expression and autoantigenicity of transaldolase in multiple sclerosis.
journal, November 1994
- Banki, K.; Colombo, E.; Sia, F.
- Journal of Experimental Medicine, Vol. 180, Issue 5
Plasma malonaldehyde levels during myocardial infarction
journal, April 1983
- Dousset, Jean-Claude; Trouilh, Maryse; Foglietti, Marie-José
- Clinica Chimica Acta, Vol. 129, Issue 3
Induction, titration, and maintenance dosing regimen in a phase 2 study of pegvaliase for control of blood phenylalanine in adults with phenylketonuria
journal, November 2018
- Zori, Roberto; Thomas, Janet A.; Shur, Natasha
- Molecular Genetics and Metabolism, Vol. 125, Issue 3
YMDB 2.0: a significantly expanded version of the yeast metabolome database
journal, November 2016
- Ramirez-Gaona, Miguel; Marcu, Ana; Pon, Allison
- Nucleic Acids Research, Vol. 45, Issue D1
Interactive XCMS Online: Simplifying Advanced Metabolomic Data Processing and Subsequent Statistical Analyses
journal, June 2014
- Gowda, Harsha; Ivanisevic, Julijana; Johnson, Caroline H.
- Analytical Chemistry, Vol. 86, Issue 14
The effects of iron dextran on the oxidative stress in cardiovascular tissues of rats with chronic renal failure
journal, May 2004
- Lim, Chun Soo; Vaziri, Nosratola D.
- Kidney International, Vol. 65, Issue 5
IBM Watson: How Cognitive Computing Can Be Applied to Big Data Challenges in Life Sciences Research
journal, April 2016
- Chen, Ying; Elenee Argentinis, Jd; Weber, Griff
- Clinical Therapeutics, Vol. 38, Issue 4
Metabolic rewiring of the hypertensive kidney
journal, December 2019
- Rinschen, Markus M.; Palygin, Oleg; Guijas, Carlos
- Science Signaling, Vol. 12, Issue 611
Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease
journal, February 2016
- Hyötyläinen, Tuulia; Jerby, Livnat; Petäjä, Elina M.
- Nature Communications, Vol. 7, Issue 1
Toward ‘Omic Scale Metabolite Profiling: A Dual Separation–Mass Spectrometry Approach for Coverage of Lipid and Central Carbon Metabolism
journal, July 2013
- Ivanisevic, Julijana; Zhu, Zheng-Jiang; Plate, Lars
- Analytical Chemistry, Vol. 85, Issue 14
ChemSpider: An Online Chemical Information Resource
journal, November 2010
- Pence, Harry E.; Williams, Antony
- Journal of Chemical Education, Vol. 87, Issue 11
A complete workflow for high-resolution spectral-stitching nanoelectrospray direct-infusion mass-spectrometry-based metabolomics and lipidomics
journal, January 2017
- Southam, Andrew D.; Weber, Ralf J. M.; Engel, Jasper
- Nature Protocols, Vol. 12, Issue 2
Global metabolomics reveals metabolic dysregulation in ischemic retinopathy
journal, November 2015
- Paris, Liliana P.; Johnson, Caroline H.; Aguilar, Edith
- Metabolomics, Vol. 12, Issue 1
Networks of Scientific Papers
journal, July 1965
- de Solla Price, D. J.
- Science, Vol. 149, Issue 3683
Chronic Kidney Disease and the Risks of Death, Cardiovascular Events, and Hospitalization
journal, September 2004
- Go, Alan S.; Chertow, Glenn M.; Fan, Dongjie
- New England Journal of Medicine, Vol. 351, Issue 13
Genomics and natural language processing
journal, August 2002
- Yandell, Mark D.; Majoros, William H.
- Nature Reviews Genetics, Vol. 3, Issue 8
Novel biomarkers for pre-eclampsia detected using metabolomics and machine learning
journal, July 2005
- Kenny, Louise C.; Dunn, Warwick B.; Ellis, David I.
- Metabolomics, Vol. 1, Issue 3
Software tools, databases and resources in metabolomics: updates from 2018 to 2019
journal, March 2020
- O’Shea, Keiron; Misra, Biswapriya B.
- Metabolomics, Vol. 16, Issue 3
XCMS Online: A Web-Based Platform to Process Untargeted Metabolomic Data
journal, June 2012
- Tautenhahn, Ralf; Patti, Gary J.; Rinehart, Duane
- Analytical Chemistry, Vol. 84, Issue 11
KEGG as a reference resource for gene and protein annotation
journal, October 2015
- Kanehisa, Minoru; Sato, Yoko; Kawashima, Masayuki
- Nucleic Acids Research, Vol. 44, Issue D1
Annotation: A Computational Solution for Streamlining Metabolomics Analysis
journal, November 2017
- Domingo-Almenara, Xavier; Montenegro-Burke, J. Rafael; Benton, H. Paul
- Analytical Chemistry, Vol. 90, Issue 1
Thalia: semantic search engine for biomedical abstracts
journal, October 2018
- Soto, Axel J.; Przybyła, Piotr; Ananiadou, Sophia
- Bioinformatics, Vol. 35, Issue 10
Literature information in PubChem: associations between PubChem records and scientific articles
journal, June 2016
- Kim, Sunghwan; Thiessen, Paul A.; Cheng, Tiejun
- Journal of Cheminformatics, Vol. 8, Issue 1
DrugBank 5.0: a major update to the DrugBank database for 2018
journal, November 2017
- Wishart, David S.; Feunang, Yannick D.; Guo, An C.
- Nucleic Acids Research, Vol. 46, Issue D1
MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis
journal, May 2018
- Chong, Jasmine; Soufan, Othman; Li, Carin
- Nucleic Acids Research, Vol. 46, Issue W1
Mining metabolites: extracting the yeast metabolome from the literature
journal, October 2010
- Nobata, Chikashi; Dobson, Paul D.; Iqbal, Syed A.
- Metabolomics, Vol. 7, Issue 1
Advances in natural language processing
journal, July 2015
- Hirschberg, J.; Manning, C. D.
- Science, Vol. 349, Issue 6245
COL4A3 Gene Variants and Diabetic Kidney Disease in MODY
journal, July 2018
- Wang, Yiting; Zhang, Junlin; Zhao, Yingwang
- Clinical Journal of the American Society of Nephrology, Vol. 13, Issue 8
Metabolomics-based discovery of a metabolite that enhances oligodendrocyte maturation
journal, November 2017
- Beyer, Brittney A.; Fang, Mingliang; Sadrian, Benjamin
- Nature Chemical Biology, Vol. 14, Issue 1
Literature-based automated discovery of tumor suppressor p53 phosphorylation and inhibition by NEK2
journal, September 2018
- Choi, Byung-Kwon; Dayaram, Tajhal; Parikh, Neha
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 42
Using MetaboAnalyst 4.0 for Comprehensive and Integrative Metabolomics Data Analysis
journal, September 2019
- Chong, Jasmine; Wishart, David S.; Xia, Jianguo
- Current Protocols in Bioinformatics, Vol. 68, Issue 1
Catecholamine production and tyrosine hydroxylase expression in peripheral blood mononuclear cells from multiple sclerosis patients: effect of cell stimulation and possible relevance for activation-induced apoptosis
journal, December 2002
- Cosentino, Marco; Zaffaroni, Mauro; Marino, Franca
- Journal of Neuroimmunology, Vol. 133, Issue 1-2
Cleavage of Transaldolase by Granzyme B Causes the Loss of Enzymatic Activity with Retention of Antigenicity for Multiple Sclerosis Patients
journal, March 2010
- Niland, Brian; Miklossy, Gabriella; Banki, Katalin
- The Journal of Immunology, Vol. 184, Issue 7
Design and rationale of a multicentre, randomised, double-blind, placebo-controlled clinical trial to evaluate the effect of vitamin D on ventricular remodelling in patients with anterior myocardial infarction: the VITamin D in Acute Myocardial Infarction (VITDAMI) trial
journal, August 2016
- Tuñón, José; González-Hernández, Ignacio; Llanos-Jiménez, Lucía
- BMJ Open, Vol. 6, Issue 8
The Pathogenic Role of the Adaptive Immune Response to Modified LDL in Diabetes
journal, January 2012
- Virella, Gabriel; Lopes-Virella, Maria F.
- Frontiers in Endocrinology, Vol. 3
Artificial intelligence in neurodegenerative disease research: use of IBM Watson to identify additional RNA-binding proteins altered in amyotrophic lateral sclerosis
journal, November 2017
- Bakkar, Nadine; Kovalik, Tina; Lorenzini, Ileana
- Acta Neuropathologica, Vol. 135, Issue 2
Current breathomics—a review on data pre-processing techniques and machine learning in metabolomics breath analysis
journal, April 2014
- Smolinska, A.; Hauschild, A-Ch; Fijten, R. R. R.
- Journal of Breath Research, Vol. 8, Issue 2
Fecal Microbiome and Volatile Organic Compound Metabolome in Obese Humans With Nonalcoholic Fatty Liver Disease
journal, July 2013
- Raman, Maitreyi; Ahmed, Iftikhar; Gillevet, Patrick M.
- Clinical Gastroenterology and Hepatology, Vol. 11, Issue 7
Toward mechanistic models for genotype–phenotype correlations in phenylketonuria using protein stability calculations
journal, January 2019
- Scheller, Rasmus; Stein, Amelie; Nielsen, Sofie V.
- Human Mutation, Vol. 40, Issue 4
Metabolism Links Bacterial Biofilms and Colon Carcinogenesis
journal, June 2015
- Johnson, Caroline H.; Dejea, Christine M.; Edler, David
- Cell Metabolism, Vol. 21, Issue 6
N -Acetylcysteine alleviates gut dysbiosis and glucose metabolic disorder in high-fat diet-fed mice: N-乙酰半胱氨酸改善高脂饮食小鼠的肠道菌群失衡和糖代谢紊乱
journal, July 2018
- Zheng, Junping; Yuan, Xubing; Zhang, Chen
- Journal of Diabetes, Vol. 11, Issue 1
Scholarly article seeking, reading, and use: a continuing evolution from print to electronic in the sciences and social sciences
journal, April 2015
- Tenopir, Carol; King, Donald W.; Christian, Lisa
- Learned Publishing, Vol. 28, Issue 2
Artificial Intelligence in Precision Cardiovascular Medicine
journal, May 2017
- Krittanawong, Chayakrit; Zhang, HongJu; Wang, Zhen
- Journal of the American College of Cardiology, Vol. 69, Issue 21
UniProt: a hub for protein information
journal, October 2014
- Consortium, UniPot
- Nucleic Acids Research, Vol. 43, Issue D1, p. D204-D212
Repurposing drugs to treat l-DOPA-induced dyskinesia in Parkinson's disease
journal, March 2019
- Johnston, Tom H.; Lacoste, Alix M. B.; Visanji, Naomi P.
- Neuropharmacology, Vol. 147
Metabolomics: beyond biomarkers and towards mechanisms
journal, March 2016
- Johnson, Caroline H.; Ivanisevic, Julijana; Siuzdak, Gary
- Nature Reviews Molecular Cell Biology, Vol. 17, Issue 7
A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms
journal, March 2019
- Tsugawa, Hiroshi; Nakabayashi, Ryo; Mori, Tetsuya
- Nature Methods, Vol. 16, Issue 4
Metabolite Structure Assignment Using In Silico NMR Techniques
journal, July 2020
- Das, Susanta; Edison, Arthur S.; Merz, Kenneth M.
- Analytical Chemistry, Vol. 92, Issue 15
Non-invasive prenatal testing of pregnancies at risk for phenylketonuria
journal, January 2018
- Duan, Huikun; Liu, Ning; Zhao, Zhenhua
- Archives of Disease in Childhood - Fetal and Neonatal Edition, Vol. 104, Issue 1
Dereplication of microbial metabolites through database search of mass spectra
journal, October 2018
- Mohimani, Hosein; Gurevich, Alexey; Shlemov, Alexander
- Nature Communications, Vol. 9, Issue 1
Alport's Syndrome, Goodpasture's Syndrome, and Type IV Collagen
journal, June 2003
- Hudson, Billy G.; Tryggvason, Karl; Sundaramoorthy, Munirathinam
- New England Journal of Medicine, Vol. 348, Issue 25
Navigating freely-available software tools for metabolomics analysis
journal, August 2017
- Spicer, Rachel; Salek, Reza M.; Moreno, Pablo
- Metabolomics, Vol. 13, Issue 9
PubTator central: automated concept annotation for biomedical full text articles
journal, May 2019
- Wei, Chih-Hsuan; Allot, Alexis; Leaman, Robert
- Nucleic Acids Research, Vol. 47, Issue W1
Boosting automatic event extraction from the literature using domain adaptation and coreference resolution
journal, April 2012
- Miwa, M.; Thompson, P.; Ananiadou, S.
- Bioinformatics, Vol. 28, Issue 13
KEGG: new perspectives on genomes, pathways, diseases and drugs
journal, November 2016
- Kanehisa, Minoru; Furumichi, Miho; Tanabe, Mao
- Nucleic Acids Research, Vol. 45, Issue D1
Metabolic adaptation to calorie restriction
journal, September 2020
- Guijas, Carlos; Montenegro-Burke, J. Rafael; Cintron-Colon, Rigo
- Science Signaling, Vol. 13, Issue 648
Metabolomics Identifies Perturbations in Human Disorders of Propionate Metabolism
journal, December 2007
- Wikoff, William R.; Gangoiti, Jon A.; Barshop, Bruce A.
- Clinical Chemistry, Vol. 53, Issue 12
Transcriptional profiling and biomarker identification reveal tissue specific effects of expanded ataxin-3 in a spinocerebellar ataxia type 3 mouse model
journal, June 2018
- Toonen, Lodewijk J. A.; Overzier, Maurice; Evers, Melvin M.
- Molecular Neurodegeneration, Vol. 13, Issue 1
Metabolomics and systems biology: making sense of the soup
journal, June 2004
- Kell, D.
- Current Opinion in Microbiology, Vol. 7, Issue 3
XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification
journal, February 2006
- Smith, Colin A.; Want, Elizabeth J.; O'Maille, Grace
- Analytical Chemistry, Vol. 78, Issue 3
Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database
journal, February 2013
- Zhu, Zheng-Jiang; Schultz, Andrew W.; Wang, Junhua
- Nature Protocols, Vol. 8, Issue 3
Autonomous METLIN-Guided In-source Fragment Annotation for Untargeted Metabolomics
journal, January 2019
- Domingo-Almenara, Xavier; Montenegro-Burke, J. Rafael; Guijas, Carlos
- Analytical Chemistry, Vol. 91, Issue 5
XCMS-MRM and METLIN-MRM: a cloud library and public resource for targeted analysis of small molecules
journal, August 2018
- Domingo-Almenara, Xavier; Montenegro-Burke, J. Rafael; Ivanisevic, Julijana
- Nature Methods, Vol. 15, Issue 9
Association between the phenylethanolamine N-methyltransferase gene and multiple sclerosis
journal, March 2002
- Mann, Michael B.; Wu, Shijuan; Rostamkhani, Massud
- Journal of Neuroimmunology, Vol. 124, Issue 1-2
MetaboAnalystR 2.0: From Raw Spectra to Biological Insights
journal, March 2019
- Chong, Jasmine; Yamamoto, Mai; Xia, Jianguo
- Metabolites, Vol. 9, Issue 3
Synthesis of multi-omic data and community metabolic models reveals insights into the role of hydrogen sulfide in colon cancer
journal, October 2018
- Hale, Vanessa L.; Jeraldo, Patricio; Mundy, Michael
- Methods, Vol. 149
Proposed minimum reporting standards for data analysis in metabolomics
journal, August 2007
- Goodacre, Royston; Broadhurst, David; Smilde, Age K.
- Metabolomics, Vol. 3, Issue 3
MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
journal, July 2010
- Pluskal, Tomáš; Castillo, Sandra; Villar-Briones, Alejandro
- BMC Bioinformatics, Vol. 11, Issue 1
A Cloud-Based Metabolite and Chemical Prioritization System for the Biology/Disease-Driven Human Proteome Project
journal, August 2018
- Yu, Kun-Hsing; Lee, Tsung-Lu Michael; Chen, Yu-Ju
- Journal of Proteome Research, Vol. 17, Issue 12
Type 3 Deiodinase Expression in Inflammatory Spinal Cord Lesions in Rat Experimental Autoimmune Encephalomyelitis
journal, December 2009
- Boelen, Anita; Mikita, Joanna; Boiziau, Claudine
- Thyroid, Vol. 19, Issue 12
Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics
journal, May 2018
- Blaženović, Ivana; Kind, Tobias; Ji, Jian
- Metabolites, Vol. 8, Issue 2
Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics
journal, January 2020
- Adams, Kendra J.; Pratt, Brian; Bose, Neelanjan
- Journal of Proteome Research, Vol. 19, Issue 4
Exposome-Scale Investigations Guided by Global Metabolomics, Pathway Analysis, and Cognitive Computing
journal, October 2017
- Warth, Benedikt; Spangler, Scott; Fang, Mingliang
- Analytical Chemistry, Vol. 89, Issue 21
PubTator: a web-based text mining tool for assisting biocuration
journal, May 2013
- Wei, Chih-Hsuan; Kao, Hung-Yu; Lu, Zhiyong
- Nucleic Acids Research, Vol. 41, Issue W1
STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data
journal, November 2015
- Szklarczyk, Damian; Santos, Alberto; von Mering, Christian
- Nucleic Acids Research, Vol. 44, Issue D1
SciFinder
journal, October 2018
- Gabrielson, Stephen Walter
- Journal of the Medical Library Association, Vol. 106, Issue 4
Visual and Semantic Enrichment of Analytical Chemistry Literature Searches by Combining Text Mining and Computational Chemistry
journal, February 2019
- Palmblad, Magnus
- Analytical Chemistry, Vol. 91, Issue 7
Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online
journal, March 2018
- Forsberg, Erica M.; Huan, Tao; Rinehart, Duane
- Nature Protocols, Vol. 13, Issue 4
Fully Automated Trimethylsilyl (TMS) Derivatisation Protocol for Metabolite Profiling by GC-MS
journal, December 2016
- Zarate, Erica; Boyle, Veronica; Rupprecht, Udo
- Metabolites, Vol. 7, Issue 1
Metabolite extraction for high-throughput FTICR-MS-based metabolomics of grapevine leaves
journal, September 2016
- Maia, Marisa; Monteiro, Filipa; Sebastiana, Mónica
- EuPA Open Proteomics, Vol. 12
Metabolomics Analysis for Biomarker Discovery: Advances and Challenges
journal, January 2013
- Monteiro, M. S.; Carvalho, M.; Bastos, M. L.
- Current Medicinal Chemistry, Vol. 20, Issue 2
Semantic Scholar
journal, January 2018
- Fricke, Suzanne
- Journal of the Medical Library Association, Vol. 106, Issue 1
Metabolic niche of a prominent sulfate-reducing human gut bacterium
journal, July 2013
- Rey, F. E.; Gonzalez, M. D.; Cheng, J.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 33
MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis
journal, May 2015
- Tsugawa, Hiroshi; Cajka, Tomas; Kind, Tobias
- Nature Methods, Vol. 12, Issue 6
Application of metabolomics to plant genotype discrimination using statistics and machine learning
journal, October 2002
- Taylor, J.; King, R. D.; Altmann, T.
- Bioinformatics, Vol. 18, Issue Suppl 2
Meta-analysis of untargeted metabolomic data from multiple profiling experiments
journal, February 2012
- Patti, Gary J.; Tautenhahn, Ralf; Siuzdak, Gary
- Nature Protocols, Vol. 7, Issue 3
Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics
journal, November 2017
- Lai, Zijuan; Tsugawa, Hiroshi; Wohlgemuth, Gert
- Nature Methods, Vol. 15, Issue 1
Metabolomics standards initiative: ontology working group work in progress
journal, September 2007
- Sansone, Susanna-Assunta; Schober, Daniel; Atherton, Helen J.
- Metabolomics, Vol. 3, Issue 3
METLIN: A Technology Platform for Identifying Knowns and Unknowns
journal, January 2018
- Guijas, Carlos; Montenegro-Burke, J. Rafael; Domingo-Almenara, Xavier
- Analytical Chemistry, Vol. 90, Issue 5
SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data
journal, January 2016
- Venkatesan, Aravind; Kim, Jee-Hyub; Talo, Francesco
- Wellcome Open Research, Vol. 1
Autoantibodies against aldehyde-modified collagen type IV are associated with risk of development of myocardial infarction
journal, September 2017
- Vallejo, J.; Dunér, P.; Fredrikson, G. N.
- Journal of Internal Medicine, Vol. 282, Issue 6
Metabolomics for biomarker discovery in the diagnosis, prognosis, survival and recurrence of colorectal cancer: a systematic review
journal, March 2017
- Zhang, Fan; Zhang, Yuanyuan; Zhao, Weiwei
- Oncotarget, Vol. 8, Issue 21
One-year follow-up of B vitamin and Iron status in patients with phenylketonuria provided tetrahydrobiopterin (BH4)
journal, October 2018
- Brantley, Kristen D.; Douglas, Teresa D.; Singh, Rani H.
- Orphanet Journal of Rare Diseases, Vol. 13, Issue 1
Proposed minimum reporting standards for chemical analysis: Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI)
journal, September 2007
- Sumner, Lloyd W.; Amberg, Alexander; Barrett, Dave
- Metabolomics, Vol. 3, Issue 3
HMDB 4.0: the human metabolome database for 2018
journal, November 2017
- Wishart, David S.; Feunang, Yannick Djoumbou; Marcu, Ana
- Nucleic Acids Research, Vol. 46, Issue D1
The MetaCyc database of metabolic pathways and enzymes
journal, October 2017
- Caspi, Ron; Billington, Richard; Fulcher, Carol A.
- Nucleic Acids Research, Vol. 46, Issue D1
High-throughput extraction and quantification method for targeted metabolomics in murine tissues
journal, December 2017
- Zukunft, Sven; Prehn, Cornelia; Röhring, Cornelia
- Metabolomics, Vol. 14, Issue 1
Evaluation of sample preparation protocols for quantitative NMR-based metabolomics
journal, May 2019
- Snytnikova, Olga A.; Khlichkina, Anastasiya A.; Sagdeev, Renad Z.
- Metabolomics, Vol. 15, Issue 6
Facilitating the development of controlled vocabularies for metabolomics technologies with text mining
journal, April 2008
- Spasić, Irena; Schober, Daniel; Sansone, Susanna-Assunta
- BMC Bioinformatics, Vol. 9, Issue S5
Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources
journal, May 2020
- Eicher, Tara; Kinnebrew, Garrett; Patt, Andrew
- Metabolites, Vol. 10, Issue 5
Transaldolase: From biochemistry to human disease
journal, July 2009
- Samland, Anne K.; Sprenger, Georg A.
- The International Journal of Biochemistry & Cell Biology, Vol. 41, Issue 7
NMR Metabolomics Protocols for Drug Discovery
book, January 2019
- Bhinderwala, Fatema; Powers, Robert
- NMR-Based Metabolomics
Works referencing / citing this record:
A Novel Heterozygous Mutation of the COL4A3 Gene Causes a Peculiar Phenotype without Hematuria and Renal Function Impairment in a Chinese Family
journal, February 2019
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- Disease Markers, Vol. 2019