Chemically informed analyses of metabolomics mass spectrometry data with Qemistree
暂无分享,去创建一个
Justin J. J. van der Hooft | Mingxun Wang | Pieter C. Dorrestein | Rob Knight | Qiyun Zhu | Sebastian Böcker | Madeleine Ernst | Markus Fleischauer | Anupriya Tripathi | Yoshiki Vázquez-Baeza | Mélissa Nothias-Esposito | Daniel McDonald | Kai Dührkop | Louis-Félix Nothias | Julia M. Gauglitz | Marcus Ludwig | Deepa D. Acharya | Asker D. Brejnrod | Antonio Gonzalez | Jo Handelsman | R. Knight | S. Böcker | P. Dorrestein | Kai Dührkop | J. Handelsman | Antonio Gonzalez | A. Tripathi | Y. Vázquez-Baeza | Qiyun Zhu | M. Ludwig | A. Brejnrod | J. V. D. van der Hooft | Madeleine Ernst | L. Nothias | Mingxun Wang | Deepa Acharya | Mélissa Nothias-Esposito | J. Gauglitz | Markus Fleischauer | Daniel McDonald | Sebastian Böcker | R. Knight
[1] Habtom W. Ressom,et al. Metabolite Identification Using Artificial Neural Network , 2019, 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
[2] Natalie I. Tasman,et al. A Cross-platform Toolkit for Mass Spectrometry and Proteomics , 2012, Nature Biotechnology.
[3] Lennart Martens,et al. mzML—a Community Standard for Mass Spectrometry Data* , 2010, Molecular & Cellular Proteomics.
[4] Jian Wang,et al. Assembling the Community-Scale Discoverable Human Proteome , 2018, Cell systems.
[5] S Joseph Wright,et al. Sources of variation in foliar secondary chemistry in a tropical forest tree community. , 2017, Ecology.
[6] Lawrence A. David,et al. Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets , 2017, PeerJ.
[7] Kristian Fog Nielsen,et al. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking , 2016, Nature Biotechnology.
[8] Rob Knight,et al. Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs , 2019, mSystems.
[9] Juho Rousu,et al. Critical Assessment of Small Molecule Identification 2016: automated methods , 2017, Journal of Cheminformatics.
[10] Robert R Junker. A biosynthetically informed distance measure to compare secondary metabolite profiles , 2017, Chemoecology.
[11] Matej Oresic,et al. MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data , 2010, BMC Bioinformatics.
[12] R. Knight,et al. Species divergence and the measurement of microbial diversity. , 2008, FEMS microbiology reviews.
[13] Nuno Bandeira,et al. Mass spectral molecular networking of living microbial colonies , 2012, Proceedings of the National Academy of Sciences.
[14] Rick L. Stevens,et al. A communal catalogue reveals Earth’s multiscale microbial diversity , 2017, Nature.
[15] Rob Knight,et al. American Gut: an Open Platform for Citizen Science Microbiome Research , 2018, mSystems.
[16] Sebastian Böcker,et al. Fragmentation trees reloaded , 2014, Journal of Cheminformatics.
[17] Rob Knight,et al. Striped UniFrac: enabling microbiome analysis at unprecedented scale , 2018, Nature Methods.
[18] Thomas Zichner,et al. Identifying the unknowns by aligning fragmentation trees. , 2012, Analytical chemistry.
[19] Peer Bork,et al. Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features , 2019, bioRxiv.
[20] Juho Rousu,et al. Metabolite identification and molecular fingerprint prediction through machine learning , 2012, Bioinform..
[21] P. Bork,et al. Interactive Tree Of Life (iTOL) v4: recent updates and new developments , 2019, Nucleic Acids Res..
[22] Rob Knight,et al. Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information , 2018, mSystems.
[23] Simon Rogers,et al. Feature-Based Molecular Networking in the GNPS Analysis Environment , 2019, Nature Methods.
[24] R. Knight,et al. Microbial community resemblance methods differ in their ability to detect biologically relevant patterns , 2010, Nature Methods.
[25] Nuno Bandeira,et al. Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages. , 2020, Food chemistry.
[26] Sebastian Böcker,et al. Molecular Formula Identification Using Isotope Pattern Analysis and Calculation of Fragmentation Trees. , 2014, Mass spectrometry.
[27] Evan Bolton,et al. ClassyFire: automated chemical classification with a comprehensive, computable taxonomy , 2016, Journal of Cheminformatics.
[28] Stephen E. Stein,et al. Metabolite profiling of a NIST Standard Reference Material for human plasma (SRM 1950): GC-MS, LC-MS, NMR, and clinical laboratory analyses, libraries, and web-based resources. , 2013, Analytical chemistry.
[29] J. T. Curtis,et al. An Ordination of the Upland Forest Communities of Southern Wisconsin , 1957 .
[30] Mingxun Wang,et al. Qiita: rapid, web-enabled microbiome meta-analysis , 2018, Nature Methods.
[31] Noureddin Sadawi,et al. ChemDistiller: an engine for metabolite annotation in mass spectrometry , 2018, Bioinform..
[32] Pierre Champy,et al. Natural products targeting strategies involving molecular networking: different manners, one goal. , 2019, Natural product reports.
[33] Joe Wandy,et al. Topic modeling for untargeted substructure exploration in metabolomics , 2016, Proceedings of the National Academy of Sciences.
[34] Andrea Porzel,et al. Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies. , 2016, Analytical chemistry.
[35] S. Böcker,et al. Searching molecular structure databases with tandem mass spectra using CSI:FingerID , 2015, Proceedings of the National Academy of Sciences.
[36] C. Huttenhower,et al. The microbiome quality control project: baseline study design and future directions , 2015, Genome Biology.
[37] T. Garland,et al. Procedures for the Analysis of Comparative Data Using Phylogenetically Independent Contrasts , 1992 .
[38] Pieter C. Dorrestein,et al. Database-independent molecular formula annotation using Gibbs sampling through ZODIAC , 2020, Nature Machine Intelligence.
[39] Juho Rousu,et al. SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information , 2019, Nature Methods.
[40] D. Faith. Conservation evaluation and phylogenetic diversity , 1992 .
[41] Shiv Meka,et al. Hierarchical clustering of MS/MS spectra from the firefly metabolome identifies new lucibufagin compounds , 2020, Scientific Reports.
[42] Tobias Depke,et al. Clustering of MS2 spectra using unsupervised methods to aid the identification of secondary metabolites from Pseudomonas aeruginosa. , 2017, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.
[43] Francesco Asnicar,et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 , 2019, Nature Biotechnology.
[44] Peter Willett,et al. Similarity-based virtual screening using 2D fingerprints. , 2006, Drug discovery today.
[45] Károly Héberger,et al. Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations? , 2015, Journal of Cheminformatics.
[46] Nigel W. Hardy,et al. Proposed minimum reporting standards for chemical analysis , 2007, Metabolomics.