Bioinformatics for spatial metabolomics

Livrables

A report on the expert evaluation of the online engine and individual deployable packages using gold standard datasets. A whitepaper with recommendations to users concerning the choice of the platform (workstation, server, cloud).

Publications

Meta-mass shift chemical profiling of metabolomes from coral reefs

Auteurs: Aaron C. Hartmann, Daniel Petras, Robert A. Quinn, Ivan Protsyuk, Frederick I. Archer, Emma Ransome, Gareth J. Williams, Barbara A. Bailey, Mark J. A. Vermeij, Theodore Alexandrov, Pieter C. Dorrestein, Forest L. Rohwer
Publié dans: Proceedings of the National Academy of Sciences, Numéro 114/44, 2017, Page(s) 11685-11690, ISSN 0027-8424
Éditeur: National Academy of Sciences
DOI: 10.1073/pnas.1710248114

Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae

Auteurs: Tal Luzzatto-Knaan, Neha Garg, Mingxun Wang, Evgenia Glukhov, Yao Peng, Gail Ackermann, Amnon Amir, Brendan M Duggan, Sergey Ryazanov, Lena Gerwick, Rob Knight, Theodore Alexandrov, Nuno Bandeira, William H Gerwick, Pieter C Dorrestein
Publié dans: eLife, Numéro 6, 2017, ISSN 2050-084X
Éditeur: eLife Sciences Publications
DOI: 10.7554/eLife.24214

Creating a 3D microbial and chemical snapshot of a human habitat

Auteurs: Clifford A. Kapono, James T. Morton, Amina Bouslimani, Alexey V. Melnik, Kayla Orlinsky, Tal Luzzatto Knaan, Neha Garg, Yoshiki Vázquez-Baeza, Ivan Protsyuk, Stefan Janssen, Qiyun Zhu, Theodore Alexandrov, Larry Smarr, Rob Knight, Pieter C. Dorrestein
Publié dans: Scientific Reports, Numéro 8/1, 2018, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-018-21541-4

N-acyl Taurines and Acylcarnitines Cause an Imbalance in Insulin Synthesis and Secretion Provoking β Cell Dysfunction in Type 2 Diabetes

Auteurs: Michaela Aichler, Daniela Borgmann, Jan Krumsiek, Achim Buck, Patrick E. MacDonald, Jocelyn E. Manning Fox, James Lyon, Peter E. Light, Susanne Keipert, Martin Jastroch, Annette Feuchtinger, Nikola S. Mueller, Na Sun, Andrew Palmer, Theodore Alexandrov, Martin Hrabe de Angelis, Susanne Neschen, Matthias H. Tschöp, Axel Walch
Publié dans: Cell Metabolism, Numéro 25/6, 2017, Page(s) 1334-1347.e4, ISSN 1550-4131
Éditeur: Cell Press
DOI: 10.1016/j.cmet.2017.04.012

Translational utility of a hierarchical classification strategy in biomolecular data analytics

Auteurs: Dieter Galea, Paolo Inglese, Lidia Cammack, Nicole Strittmatter, Monica Rebec, Reza Mirnezami, Ivan Laponogov, James Kinross, Jeremy Nicholson, Zoltan Takats, Kirill A. Veselkov
Publié dans: Scientific Reports, Numéro 7/1, 2017, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-017-14092-7

Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation

Auteurs: Louis-Félix Nothias, Mélissa Nothias-Esposito, Ricardo da Silva, Mingxun Wang, Ivan Protsyuk, Zheng Zhang, Abi Sarvepalli, Pieter Leyssen, David Touboul, Jean Costa, Julien Paolini, Theodore Alexandrov, Marc Litaudon, Pieter C. Dorrestein
Publié dans: Journal of Natural Products, Numéro 81/4, 2018, Page(s) 758-767, ISSN 0163-3864
Éditeur: American Chemical Society
DOI: 10.1021/acs.jnatprod.7b00737

ChemDistiller: an engine for metabolite annotation in mass spectrometry

Auteurs: Ivan Laponogov, Noureddin Sadawi, Dieter Galea, Reza Mirnezami, Kirill A Veselkov
Publié dans: Bioinformatics, Numéro 34/12, 2018, Page(s) 2096-2102, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/bty080

Bi-clustering of metabolic data using matrix factorization tools

Auteurs: Quan Gu, Kirill Veselkov
Publié dans: Methods, 2018, ISSN 1046-2023
Éditeur: Academic Press
DOI: 10.1016/j.ymeth.2018.02.004

Exploiting and assessing multi-source data for supervised biomedical named entity recognition

Auteurs: Dieter Galea, Ivan Laponogov, Kirill Veselkov
Publié dans: Bioinformatics, Numéro 34/14, 2018, Page(s) 2474-2482, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/bty152

BASIS: High-performance bioinformatics platform for processing of large-scale mass spectrometry imaging data in chemically augmented histology

Auteurs: Kirill Veselkov, Jonathan Sleeman, Emmanuelle Claude, Johannes P. C. Vissers, Dieter Galea, Anna Mroz, Ivan Laponogov, Mark Towers, Robert Tonge, Reza Mirnezami, Zoltan Takats, Jeremy K. Nicholson, James I. Langridge
Publié dans: Scientific Reports, Numéro 8/1, 2018, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-018-22499-z

Integration of 3D multimodal imaging data of a head and neck cancer and advanced feature recognition

Auteurs: Judith M. Lotz, Franziska Hoffmann, Johannes Lotz, Stefan Heldmann, Dennis Trede, Janina Oetjen, Michael Becker, Günther Ernst, Peter Maass, Theodore Alexandrov, Orlando Guntinas-Lichius, Herbert Thiele, Ferdinand von Eggeling.
Publié dans: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Numéro Volume 1864, Numéro 9, 2016, ISSN 1570-9639
Éditeur: Elsevier BV
DOI: 10.1016/j.bbapap.2016.08.018

Where imaging mass spectrometry stands: here are the numbers

Auteurs: Palmer, A., Trede, D., Alexandrov, T.
Publié dans: Metabolomics, Numéro 12: 107, 2016, Page(s) 107, ISSN 1573-3882
Éditeur: Springer Verlag
DOI: 10.1007/s11306-016-1047-0

FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry

Auteurs: Andrew Palmer, Prasad Phapale, Ilya Chernyavsky, Regis Lavigne, Dominik Fay, Artem Tarasov, Vitaly Kovalev, Jens Fuchser, Sergey Nikolenko, Charles Pineau, Michael Becker, Theodore Alexandrov
Publié dans: Nature Methods, Numéro 14/1, 2016, Page(s) 57-60, ISSN 1548-7091
Éditeur: Nature Publishing Group
DOI: 10.1038/nmeth.4072

Lifestyle chemistries from phones for individual profiling

Auteurs: Amina Bouslimani, Alexey V. Melnik, Zhenjiang Xu, Amnon Amir, Ricardo R. da Silva, Mingxun Wang, Nuno Bandeira, Theodore Alexandrov, Rob Knight, and Pieter C. Dorrestein
Publié dans: PNAS, Numéro vol 113 no 48, 2016, Page(s) E7645–E7654, ISSN 0027-8424
Éditeur: National Academy of Sciences
DOI: 10.1073/pnas.1610019113

Investigating the spatial distribution of growth anomalies affecting Montipora capitata corals in a 3-dimensional framework

Auteurs: John H.R. Burns, Theodore Alexandrov, Ekaterina Ovchinnikova, Ruth D. Gates, Misaki Takabayashi
Publié dans: Journal of Invertebrate Pathology, Numéro Volume 140, 2016, Page(s) 51-57, ISSN 0022-2011
Éditeur: Academic Press
DOI: 10.1016/j.jip.2016.08.007

Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats

Auteurs: Petras, Daniel; Wojnicz, Aneta; Morton, Jamie; McCall, Laura-Isobel; Hook, Vivian; Yang, Jin; Steffen, Dana; Quinn, Robert A.; Knight, Rob; Podvin, Sonia; Garg, Neha; Vargas, Fernando; Tuttle, Robert; Bouslimani, Amina; Dang, Tam; Kapono, Clifford A.; Ling, Tie-Jun; Sapp, Valerie; Luzzatto-Knaan, Tal; Meehan, Michael J; Shires, Sarah; Merritt, Jonathan K.; Jiang, Yike; Bandeira, Nuno; Todoric, Jel
Publié dans: Analytical Chemistry, Numéro 2, 2016, Page(s) 10775–10784, ISSN 0003-2700
Éditeur: American Chemical Society
DOI: 10.1021/acs.analchem.6b03456

Imaging of Esophageal Lymph Node Metastases by Desorption Electrospray Ionization Mass Spectrometry

Auteurs: Nima Abbassi-Ghadi, Ottmar Golf, Sacheen Kumar, Stefan Antonowicz, James S. McKenzie, Juzheng Huang, Nicole Strittmatter, Hiromi Kudo, Emrys A. Jones, Kirill Veselkov, Robert Goldin, Zoltan Takats, George B. Hanna
Publié dans: Cancer Research, Numéro 76/19, 2016, Page(s) 5647-5656, ISSN 0008-5472
Éditeur: American Association for Cancer Research
DOI: 10.1158/0008-5472.CAN-16-0699

Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen

Auteurs: Alexandrov, Theodore; Cichewicz, Robert H.; Sanchez, Laura M; Garg, Neha; Mohimani, Hosein; Zeng, Yi; Miao, Vivian; Edlund, Anna; Cai, Shengxin; Dorrestein, Pieter C.; Gurevich, Alexey; Luzzatto-Knaan, Tal; Lim, Yan Wei; Melnik, Alexey V; Rohwer, Forest; Pevzner, Pavel A.; Schiffler, Stefan
Publié dans: mSystems, Numéro Volume 1 Numéro 6, 2016, ISSN 2379-5077
Éditeur: American Society for Microbiology
DOI: 10.1128/mSystems.00139-16

Data for spatial analysis of growth anomaly lesions on Montipora capitata coral colonies using 3D reconstruction techniques

Auteurs: Misaki Takabayashi; Burns, John H.R.; Ruth D. Gates; Theodore Alexandrov; Katya Ovchinnikova
Publié dans: Data in Brief, Numéro 1, 2016, ISSN 2352-3409
Éditeur: Elsevier BV
DOI: 10.1016/j.dib.2016.09.009

From single cells to our planet—recent advances in using mass spectrometry for spatially resolved metabolomics

Auteurs: Daniel Petras, Alan K Jarmusch, Pieter C Dorrestein
Publié dans: Current Opinion in Chemical Biology, Numéro Volume 36, 2017, Page(s) 24-31, ISSN 1367-5931
Éditeur: Elsevier BV
DOI: 10.1016/j.cbpa.2016.12.018

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