Metabolism of a cell pictured by single-cell approach

Project Information

METACELL

Grant agreement ID: 773089

DOI

10.3030/773089

Project closed

EC signature date 12 February 2018

Start date 1 July 2018

End date 30 April 2024

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 330 628,00

EU contribution

€ 2 330 628,00

Coordinated by

EUROPEAN MOLECULAR BIOLOGY LABORATORY
Germany

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (22)

Single-cell analyses reveal SARS-CoV-2 interference with intrinsic immune response in the human gut.

Author(s): Sergio Triana; Camila Metz-Zumaran; Carlos A Ramírez; Carmon Kee; Carmon Kee; Patricio Doldan; Patricio Doldan; Mohammed Shahraz; Daniel Schraivogel; Andreas R Gschwind; Ashwini Kumar Sharma; Ashwini Kumar Sharma; Lars M. Steinmetz; Carl Herrmann; Theodore Alexandrov; Theodore Alexandrov; Steeve Boulant; Steeve Boulant; Megan L. Stanifer
Published in: Molecular Systems Biology, Vol 17, Iss 4, Pp n/a-n/a (2021), Issue 1, 2021, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.202110232

Increasing quantitation in spatial single-cell metabolomics by using fluorescence as ground truth

Author(s): Martijn R Molenaar, Mohammed Shahraz, Jeany Delafiori, Andreas Eisenbarth, Måns Ekelöf, Luca Rappez, Theodore Alexandrov
Published in: Front Mol Biosci, Issue 9, 2022, ISSN 2296-889X
Publisher: Frontiers

Spatial Metabolomics and Imaging Mass Spectrometry in the Age of Artificial Intelligence

Author(s): Theodore Alexandrov
Published in: Annual Review of Biomedical Data Science, Issue 3:61-87, 2020
Publisher: 2574-3414

Enablers and challenges of spatial omics, a melting pot of technologies

Author(s): Theodore Alexandrov, Julio Saez‐Rodriguez, and Sinem K Saka
Published in: Mol Syst Biol, Issue 19: e10571, 2023, ISSN 1744-4292
Publisher: Nature Publishing Group

Facilitating imaging mass spectrometry of microbial specialized metabolites with METASPACE.

Author(s): Nguyen DD, Saharuka V, Kovalev V, Stuart L, Del Prete M, Lubowiecka K, De Mot R, Venturi V, Alexandrov T
Published in: Metabolites, 2021, ISSN 2218-1989
Publisher: MDPI
DOI: 10.3390/metabo11080477

PySpacell: A Python Package for Spatial Analysis of Cell Images

Author(s): France Rose, Luca Rappez, Sergio H. Triana, Theodore Alexandrov, Auguste Genovesio
Published in: Cytometry Part A, Issue 97/3, 2020, Page(s) 288-295, ISSN 1552-4922
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/cyto.a.23955

DeepCycle reconstructs a cyclic cell cycle trajectory from unsegmented cell images using convolutional neural networks

Author(s): Luca Rappez, Alexander Rakhlin, Angelos Rigopoulos, Sergey Nikolenko, Theodore Alexandrov
Published in: Molecular Systems Biology, Issue 16/10, 2020, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.20209474

Single‐cell transcriptomics reveals immune response of intestinal cell types to viral infection

Author(s): Sergio Triana, Megan L Stanifer, Camila Metz‐Zumaran, Mohammed Shahraz, Markus Mukenhirn, Carmon Kee, Clara Serger, Ronald Koschny, Diana Ordoñez‐Rueda, Malte Paulsen, Vladimir Benes, Steeve Boulant, Theodore Alexandrov
Published in: Molecular Systems Biology, Issue 17/7, 2021, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.20209833

Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis.

Author(s): Alexey V. Melnik; Yoshiki Vázquez-Baeza; Alexander A. Aksenov; Embriette R. Hyde; Andrew C. McAvoy; Mingxun Wang; Ricardo Silva; Ivan Protsyuk; Jason V. Wu; Amina Bouslimani; Yan Wei Lim; Tal Luzzatto-Knaan; William Comstock; Robert A. Quinn; Richard J. Wong; Greg Humphrey; Gail Ackermann; Timothy Spivey; Sharon S. Brouha; Nuno Bandeira; Grace Y. Lin; Forest Rohwer; Douglas Conrad; Theodore Alexa
Published in: mSystems, Vol 4, Iss 5 (2019), Issue 1, 2019, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1128/msystems.00375-19

Developmental phenomics suggests that H3K4 monomethylation confers multi-level phenotypic robustness

Author(s): Lautaro Gandara, Albert Tsai, Måns Ekelöf, Rafael Galupa, Ella Preger-Ben Noon, Theodore Alexandrov, Justin Crocker
Published in: Cell Reports, Issue 41, 11, 2022, ISSN 2211-1247
Publisher: Cell Press

Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states.

Author(s): Triana S, Vonficht D, Jopp-Saile L, Raffel S, Lutz R, Leonce D, Antes M, Hernández-Malmierca P, Ordoñez-Rueda D, Ramasz B, Boch T, Jann JC, Nowak D, Hofmann WK, Müller-Tidow C, Hübschmann D, Alexandrov T, Benes V, Trumpp A, Paulsen M, Velten L, Haas S
Published in: Nature Immunology, Issue 22, 2021, ISSN 1529-2908
Publisher: Nature Publishing Group
DOI: 10.1038/s41590-021-01059-0

A pathogen-specific isotope tracing approach reveals metabolic activities and fluxes of intracellular Salmonella

Author(s): Karin Mitosch, Martin Beyß, Prasad Phapale, Bernhard Drotleff, Katharina Nöh, Theodore Alexandrov, Kiran R. Patil , Athanasios Typas
Published in: PLoS Biology, Issue 21, 8, 2023, ISSN 1544-9173
Publisher: Public Library of Science

OffsampleAI: artificial intelligence approach to recognize off-sample mass spectrometry images

Author(s): Katja Ovchinnikova, Vitaly Kovalev, Lachlan Stuart, Theodore Alexandrov
Published in: BMC Bioinformatics, Issue 21/1, 2020, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-020-3425-x

A Model for Network-Based Identification and Pharmacological Targeting of Aberrant, Replication-Permissive Transcriptional Programs Induced by Viral Infection

Author(s): Laise, Pasquale; Stanifer, Megan L; Bosker, Gideon; Sun, Xiaoyun; Triana, Sergio; Doldan, Patricio; La Manna, Federico; De Menna, Marta; Realubit, Ronald B; Pampou, Sergey; Karan, Charles; Alexandrov, Theodore; Kruithof-de Julio, Marianna; Califano, Andrea; Boulant, Steeve; Alvarez, Mariano J
Published in: Communications Biology, Issue 5, 2022, ISSN 2399-3642
Publisher: Nature

ColocML: Machine learning quantifies co-localization between mass spectrometry images

Author(s): Katja Ovchinnikova, Lachlan Stuart, Alexander Rakhlin, Sergey Nikolenko, Theodore Alexandrov
Published in: Bioinformatics, 2020, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa085

SpaceM reveals metabolic states of single cells

Author(s): Luca Rappez, Mira Stadler, Sergio Triana, Rose Muthoni Gathungu, Katja Ovchinnikova, Prasad Phapale, Mathias Heikenwalder, Theodore Alexandrov
Published in: Nature Methods, Issue 18/7, 2021, Page(s) 799-805, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-021-01198-0

Mapping the epithelial–immune cell interactome upon infection in the gut and the upper airways

Author(s): Martina Poletti, Agatha Treveil, Luca Csabai, Leila Gul, Dezso Modos, Matthew Madgwick, Marton Olbei, Balazs Bohar, Alberto Valdeolivas, Denes Turei, Bram Verstockt, Sergio Triana, Theodore Alexandrov, Julio Saez-Rodriguez, Megan L. Stanifer, Steeve Boulant & Tamas Korcsmaros
Published in: npj Systems Biology and Applications, Issue 8, 15, 2022, ISSN 2056-7189
Publisher: Nature

FOXO1-mediated lipid metabolism maintains mammalian embryos in dormancy

Author(s): Vera A. van der Weijden, Maximilian Stötzel, Dhanur P. Iyer, Beatrix Fauler, Elzbieta Gralinska, Mohammed Shahraz, David Meierhofer, Martin Vingron, Steffen Rulands, Theodore Alexandrov, Thorsten Mielke & Aydan Bulut-Karslioglu
Published in: Nature Cell Biology, Issue 26, pages 181–193, 2024, ISSN 1476-4679
Publisher: Nature

Feature-based molecular networking in the GNPS analysis environment

Author(s): Louis-Félix Nothias, Daniel Petras, Robin Schmid, Kai Dührkop, Johannes Rainer, Abinesh Sarvepalli, Ivan Protsyuk, Madeleine Ernst, Hiroshi Tsugawa, Markus Fleischauer, Fabian Aicheler, Alexander A. Aksenov, Oliver Alka, Pierre-Marie Allard, Aiko Barsch, Xavier Cachet, Andres Mauricio Caraballo-Rodriguez, Ricardo R. Da Silva, Tam Dang, Neha Garg, Julia M. Gauglitz, Alexey Gurevich, Giorgis Isaac
Published in: Nature Methods, Issue 17/9, 2020, Page(s) 905-908, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-020-0933-6

Adaptive Pixel Mass Recalibration for Mass Spectrometry Imaging Based on Locally Endogenous Biological Signals

Author(s): Raphaël La Rocca, Christopher Kune, Mathieu Tiquet, Lachlan Stuart, Gauthier Eppe, Theodore Alexandrov, Edwin De Pauw, Loïc Quinton
Published in: Analytical Chemistry, Issue 93, 8, 2021, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.0c05071

Critical Role of Type III Interferon in Controlling SARS-CoV-2 Infection in Human Intestinal Epithelial Cells.

Author(s): Megan L. Stanifer; Megan L. Stanifer; Carmon Kee; Mirko Cortese; Camila Metz Zumaran; Sergio Triana; Markus Mukenhirn; Hans-Georg Kraeusslich; Theodore Alexandrov; Ralf Bartenschlager; Steeve Boulant; Steeve Boulant
Published in: Cell Reports, Issue 1, 2020, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2020.107863

Response Surface Methodology As a New Approach for Finding Optimal MALDI Matrix Spraying Parameters for Mass Spectrometry Imaging

Author(s): Dušan Veličković, Guanshi Zhang, Dejan Bezbradica, Arunima Bhattacharjee, Ljiljana Paša-Tolić, Kumar Sharma, Theodore Alexandrov, Christopher R. Anderton
Published in: Journal of the American Society for Mass Spectrometry, Issue 31/3, 2020, Page(s) 508-516, ISSN 1044-0305
Publisher: Elsevier BV
DOI: 10.1021/jasms.9b00074

Other (1)

Using Biological Signals for Mass Recalibration of Mass Spectrometry Imaging Data

Author(s): La Rocca, Raphaël; Kune, Christopher; Tiquet, Mathieu; Stuart, Lachlan; Alexandrov, Theodore; De Pauw, Edwin; Quinton, Loïc
Published in: Chemrxiv, Issue 1, 2020
Publisher: Chemrxiv
DOI: 10.26434/chemrxiv.12901679.v1

Non-peer reviewed articles (1)

Enhancing metabolite coverage in MALDI-MSI using laser post-ionisation (MALDI-2)

Author(s): J. C. McKinnon; H. H. Milioli; C. A. Purcell; C. L. Chaffer; B. Wadie; T. Alexandrov; T. W. Mitchell; S. R. Ellis
Published in: Chemrxiv, Issue 1, 2023, ISSN 2573-2293
Publisher: Chemrxiv
DOI: 10.1039/d3ay01046e

Intellectual Property Rights

Patent (1)

SINGLE-CELL IMAGING MASS SPECTROMETRY

Application/Publication number: 20 18059515
Date: 2018-04-13
Applicant(s): EUROPEAN MOLECULAR BIOLOGY LABORATORY