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Bioinformatics for spatial metabolomics

Deliverables

Evaluation of the online engine

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).

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Publications

Meta-mass shift chemical profiling of metabolomes from coral reefs

Author(s): 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
Published in: Proceedings of the National Academy of Sciences, Issue 114/44, 2017, Page(s) 11685-11690, ISSN 0027-8424
DOI: 10.1073/pnas.1710248114

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

Author(s): 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
Published in: eLife, Issue 6, 2017, ISSN 2050-084X
DOI: 10.7554/eLife.24214

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

Author(s): 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
Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322
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

Author(s): 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
Published in: Cell Metabolism, Issue 25/6, 2017, Page(s) 1334-1347.e4, ISSN 1550-4131
DOI: 10.1016/j.cmet.2017.04.012

Translational utility of a hierarchical classification strategy in biomolecular data analytics

Author(s): Dieter Galea, Paolo Inglese, Lidia Cammack, Nicole Strittmatter, Monica Rebec, Reza Mirnezami, Ivan Laponogov, James Kinross, Jeremy Nicholson, Zoltan Takats, Kirill A. Veselkov
Published in: Scientific Reports, Issue 7/1, 2017, ISSN 2045-2322
DOI: 10.1038/s41598-017-14092-7

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

Author(s): 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
Published in: Journal of Natural Products, Issue 81/4, 2018, Page(s) 758-767, ISSN 0163-3864
DOI: 10.1021/acs.jnatprod.7b00737

ChemDistiller: an engine for metabolite annotation in mass spectrometry

Author(s): Ivan Laponogov, Noureddin Sadawi, Dieter Galea, Reza Mirnezami, Kirill A Veselkov
Published in: Bioinformatics, Issue 34/12, 2018, Page(s) 2096-2102, ISSN 1367-4803
DOI: 10.1093/bioinformatics/bty080

Bi-clustering of metabolic data using matrix factorization tools

Author(s): Quan Gu, Kirill Veselkov
Published in: Methods, 2018, ISSN 1046-2023
DOI: 10.1016/j.ymeth.2018.02.004

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

Author(s): Dieter Galea, Ivan Laponogov, Kirill Veselkov
Published in: Bioinformatics, Issue 34/14, 2018, Page(s) 2474-2482, ISSN 1367-4803
DOI: 10.1093/bioinformatics/bty152

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

Author(s): 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
Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322
DOI: 10.1038/s41598-018-22499-z

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

Author(s): 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.
Published in: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Issue Volume 1864, Issue 9, 2016, ISSN 1570-9639
DOI: 10.1016/j.bbapap.2016.08.018

Where imaging mass spectrometry stands: here are the numbers

Author(s): Palmer, A., Trede, D., Alexandrov, T.
Published in: Metabolomics, Issue 12: 107, 2016, Page(s) 107, ISSN 1573-3882
DOI: 10.1007/s11306-016-1047-0

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

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

Lifestyle chemistries from phones for individual profiling

Author(s): 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
Published in: PNAS, Issue vol 113 no 48, 2016, Page(s) E7645–E7654, ISSN 0027-8424
DOI: 10.1073/pnas.1610019113

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

Author(s): John H.R. Burns, Theodore Alexandrov, Ekaterina Ovchinnikova, Ruth D. Gates, Misaki Takabayashi
Published in: Journal of Invertebrate Pathology, Issue Volume 140, 2016, Page(s) 51-57, ISSN 0022-2011
DOI: 10.1016/j.jip.2016.08.007

Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats

Author(s): 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
Published in: Analytical Chemistry, Issue 2, 2016, Page(s) 10775–10784, ISSN 0003-2700
DOI: 10.1021/acs.analchem.6b03456

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

Author(s): 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
Published in: Cancer Research, Issue 76/19, 2016, Page(s) 5647-5656, ISSN 0008-5472
DOI: 10.1158/0008-5472.CAN-16-0699

Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen

Author(s): 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
Published in: mSystems, Issue Volume 1 Issue 6, 2016, ISSN 2379-5077
DOI: 10.1128/mSystems.00139-16

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

Author(s): Misaki Takabayashi; Burns, John H.R.; Ruth D. Gates; Theodore Alexandrov; Katya Ovchinnikova
Published in: Data in Brief, Issue 1, 2016, ISSN 2352-3409
DOI: 10.1016/j.dib.2016.09.009

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

Author(s): Daniel Petras, Alan K Jarmusch, Pieter C Dorrestein
Published in: Current Opinion in Chemical Biology, Issue Volume 36, 2017, Page(s) 24-31, ISSN 1367-5931
DOI: 10.1016/j.cbpa.2016.12.018