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

Publications

Peer reviewed articles (15)

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

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

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, 2021, ISSN 1529-2908
Publisher: Nature Publishing Group
DOI: 10.1038/s41590-021-01059-0

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

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

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: Crossref, Issue 1, 2022, ISSN 1664-3224
Publisher: Frontiers
DOI: 10.3389/fmolb.2022.1021889

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, 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)

Recognizing off-sample mass spectrometry images with machine and deep learning.

Author(s): Katja Ovchinnikova, Vitaly Kovalev, Lachlan Stuart, Theodore Alexandrov
Published in: biorxiv, 2019
Publisher: CSHL
DOI: 10.1101/518977