Bioinformatics for spatial metabolomics

Rezultaty

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).

Publikacje

Meta-mass shift chemical profiling of metabolomes from coral reefs

Autorzy: 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
Opublikowane w: Proceedings of the National Academy of Sciences, Numer 114/44, 2017, Strona(/y) 11685-11690, ISSN 0027-8424
Wydawca: 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

Autorzy: 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
Opublikowane w: eLife, Numer 6, 2017, ISSN 2050-084X
Wydawca: eLife Sciences Publications
DOI: 10.7554/eLife.24214

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

Autorzy: 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
Opublikowane w: Scientific Reports, Numer 8/1, 2018, ISSN 2045-2322
Wydawca: 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

Autorzy: 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
Opublikowane w: Cell Metabolism, Numer 25/6, 2017, Strona(/y) 1334-1347.e4, ISSN 1550-4131
Wydawca: Cell Press
DOI: 10.1016/j.cmet.2017.04.012

Translational utility of a hierarchical classification strategy in biomolecular data analytics

Autorzy: Dieter Galea, Paolo Inglese, Lidia Cammack, Nicole Strittmatter, Monica Rebec, Reza Mirnezami, Ivan Laponogov, James Kinross, Jeremy Nicholson, Zoltan Takats, Kirill A. Veselkov
Opublikowane w: Scientific Reports, Numer 7/1, 2017, ISSN 2045-2322
Wydawca: 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

Autorzy: 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
Opublikowane w: Journal of Natural Products, Numer 81/4, 2018, Strona(/y) 758-767, ISSN 0163-3864
Wydawca: American Chemical Society
DOI: 10.1021/acs.jnatprod.7b00737

ChemDistiller: an engine for metabolite annotation in mass spectrometry

Autorzy: Ivan Laponogov, Noureddin Sadawi, Dieter Galea, Reza Mirnezami, Kirill A Veselkov
Opublikowane w: Bioinformatics, Numer 34/12, 2018, Strona(/y) 2096-2102, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/bty080

Bi-clustering of metabolic data using matrix factorization tools

Autorzy: Quan Gu, Kirill Veselkov
Opublikowane w: Methods, 2018, ISSN 1046-2023
Wydawca: Academic Press
DOI: 10.1016/j.ymeth.2018.02.004

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

Autorzy: Dieter Galea, Ivan Laponogov, Kirill Veselkov
Opublikowane w: Bioinformatics, Numer 34/14, 2018, Strona(/y) 2474-2482, ISSN 1367-4803
Wydawca: 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

Autorzy: 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
Opublikowane w: Scientific Reports, Numer 8/1, 2018, ISSN 2045-2322
Wydawca: 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

Autorzy: 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.
Opublikowane w: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Numer Volume 1864, Numer 9, 2016, ISSN 1570-9639
Wydawca: Elsevier BV
DOI: 10.1016/j.bbapap.2016.08.018

Where imaging mass spectrometry stands: here are the numbers

Autorzy: Palmer, A., Trede, D., Alexandrov, T.
Opublikowane w: Metabolomics, Numer 12: 107, 2016, Strona(/y) 107, ISSN 1573-3882
Wydawca: Springer Verlag
DOI: 10.1007/s11306-016-1047-0

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

Autorzy: Andrew Palmer, Prasad Phapale, Ilya Chernyavsky, Regis Lavigne, Dominik Fay, Artem Tarasov, Vitaly Kovalev, Jens Fuchser, Sergey Nikolenko, Charles Pineau, Michael Becker, Theodore Alexandrov
Opublikowane w: Nature Methods, Numer 14/1, 2016, Strona(/y) 57-60, ISSN 1548-7091
Wydawca: Nature Publishing Group
DOI: 10.1038/nmeth.4072

Lifestyle chemistries from phones for individual profiling

Autorzy: 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
Opublikowane w: PNAS, Numer vol 113 no 48, 2016, Strona(/y) E7645–E7654, ISSN 0027-8424
Wydawca: 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

Autorzy: John H.R. Burns, Theodore Alexandrov, Ekaterina Ovchinnikova, Ruth D. Gates, Misaki Takabayashi
Opublikowane w: Journal of Invertebrate Pathology, Numer Volume 140, 2016, Strona(/y) 51-57, ISSN 0022-2011
Wydawca: Academic Press
DOI: 10.1016/j.jip.2016.08.007

Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats

Autorzy: 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
Opublikowane w: Analytical Chemistry, Numer 2, 2016, Strona(/y) 10775–10784, ISSN 0003-2700
Wydawca: American Chemical Society
DOI: 10.1021/acs.analchem.6b03456

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

Autorzy: 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
Opublikowane w: Cancer Research, Numer 76/19, 2016, Strona(/y) 5647-5656, ISSN 0008-5472
Wydawca: American Association for Cancer Research
DOI: 10.1158/0008-5472.CAN-16-0699

Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen

Autorzy: 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
Opublikowane w: mSystems, Numer Volume 1 Numer 6, 2016, ISSN 2379-5077
Wydawca: 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

Autorzy: Misaki Takabayashi; Burns, John H.R.; Ruth D. Gates; Theodore Alexandrov; Katya Ovchinnikova
Opublikowane w: Data in Brief, Numer 1, 2016, ISSN 2352-3409
Wydawca: 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

Autorzy: Daniel Petras, Alan K Jarmusch, Pieter C Dorrestein
Opublikowane w: Current Opinion in Chemical Biology, Numer Volume 36, 2017, Strona(/y) 24-31, ISSN 1367-5931
Wydawca: Elsevier BV
DOI: 10.1016/j.cbpa.2016.12.018

Rezultaty

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