Bioinformatics for spatial metabolomics

Resultado final

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).

Publicaciones

Meta-mass shift chemical profiling of metabolomes from coral reefs

Autores: 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
Publicado en: Proceedings of the National Academy of Sciences, Edición 114/44, 2017, Página(s) 11685-11690, ISSN 0027-8424
Editor: 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

Autores: 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
Publicado en: eLife, Edición 6, 2017, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/eLife.24214

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

Autores: 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
Publicado en: Scientific Reports, Edición 8/1, 2018, ISSN 2045-2322
Editor: 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

Autores: 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
Publicado en: Cell Metabolism, Edición 25/6, 2017, Página(s) 1334-1347.e4, ISSN 1550-4131
Editor: Cell Press
DOI: 10.1016/j.cmet.2017.04.012

Translational utility of a hierarchical classification strategy in biomolecular data analytics

Autores: Dieter Galea, Paolo Inglese, Lidia Cammack, Nicole Strittmatter, Monica Rebec, Reza Mirnezami, Ivan Laponogov, James Kinross, Jeremy Nicholson, Zoltan Takats, Kirill A. Veselkov
Publicado en: Scientific Reports, Edición 7/1, 2017, ISSN 2045-2322
Editor: 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

Autores: 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
Publicado en: Journal of Natural Products, Edición 81/4, 2018, Página(s) 758-767, ISSN 0163-3864
Editor: American Chemical Society
DOI: 10.1021/acs.jnatprod.7b00737

ChemDistiller: an engine for metabolite annotation in mass spectrometry

Autores: Ivan Laponogov, Noureddin Sadawi, Dieter Galea, Reza Mirnezami, Kirill A Veselkov
Publicado en: Bioinformatics, Edición 34/12, 2018, Página(s) 2096-2102, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/bty080

Bi-clustering of metabolic data using matrix factorization tools

Autores: Quan Gu, Kirill Veselkov
Publicado en: Methods, 2018, ISSN 1046-2023
Editor: Academic Press
DOI: 10.1016/j.ymeth.2018.02.004

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

Autores: Dieter Galea, Ivan Laponogov, Kirill Veselkov
Publicado en: Bioinformatics, Edición 34/14, 2018, Página(s) 2474-2482, ISSN 1367-4803
Editor: 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

Autores: 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
Publicado en: Scientific Reports, Edición 8/1, 2018, ISSN 2045-2322
Editor: 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

Autores: 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.
Publicado en: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Edición Volume 1864, Edición 9, 2016, ISSN 1570-9639
Editor: Elsevier BV
DOI: 10.1016/j.bbapap.2016.08.018

Where imaging mass spectrometry stands: here are the numbers

Autores: Palmer, A., Trede, D., Alexandrov, T.
Publicado en: Metabolomics, Edición 12: 107, 2016, Página(s) 107, ISSN 1573-3882
Editor: Springer Verlag
DOI: 10.1007/s11306-016-1047-0

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

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

Lifestyle chemistries from phones for individual profiling

Autores: 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
Publicado en: PNAS, Edición vol 113 no 48, 2016, Página(s) E7645–E7654, ISSN 0027-8424
Editor: 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

Autores: John H.R. Burns, Theodore Alexandrov, Ekaterina Ovchinnikova, Ruth D. Gates, Misaki Takabayashi
Publicado en: Journal of Invertebrate Pathology, Edición Volume 140, 2016, Página(s) 51-57, ISSN 0022-2011
Editor: Academic Press
DOI: 10.1016/j.jip.2016.08.007

Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats

Autores: 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
Publicado en: Analytical Chemistry, Edición 2, 2016, Página(s) 10775–10784, ISSN 0003-2700
Editor: American Chemical Society
DOI: 10.1021/acs.analchem.6b03456

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

Autores: 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
Publicado en: Cancer Research, Edición 76/19, 2016, Página(s) 5647-5656, ISSN 0008-5472
Editor: American Association for Cancer Research
DOI: 10.1158/0008-5472.CAN-16-0699

Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen

Autores: 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
Publicado en: mSystems, Edición Volume 1 Edición 6, 2016, ISSN 2379-5077
Editor: 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

Autores: Misaki Takabayashi; Burns, John H.R.; Ruth D. Gates; Theodore Alexandrov; Katya Ovchinnikova
Publicado en: Data in Brief, Edición 1, 2016, ISSN 2352-3409
Editor: 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

Autores: Daniel Petras, Alan K Jarmusch, Pieter C Dorrestein
Publicado en: Current Opinion in Chemical Biology, Edición Volume 36, 2017, Página(s) 24-31, ISSN 1367-5931
Editor: Elsevier BV
DOI: 10.1016/j.cbpa.2016.12.018

Resultado final

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