Metabolism of a cell pictured by single-cell approach

Informazioni relative al progetto

METACELL

ID dell’accordo di sovvenzione: 773089

DOI

10.3030/773089

Progetto chiuso

Data della firma CE 12 Febbraio 2018

Data di avvio 1 Luglio 2018

Data di completamento 30 Aprile 2024

Finanziato da

• EXCELLENT SCIENCE - European Research Council (ERC)

Costo totale

€ 2 330 628,00

Contributo UE

€ 2 330 628,00

Coordinato da

EUROPEAN MOLECULAR BIOLOGY LABORATORY
Germany

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Pubblicazioni

Peer reviewed articles (22)

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

Autori: 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
Pubblicato in: Molecular Systems Biology, Vol 17, Iss 4, Pp n/a-n/a (2021), Numero 1, 2021, ISSN 1744-4292
Editore: Nature Publishing Group
DOI: 10.15252/msb.202110232

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

Autori: Martijn R Molenaar, Mohammed Shahraz, Jeany Delafiori, Andreas Eisenbarth, Måns Ekelöf, Luca Rappez, Theodore Alexandrov
Pubblicato in: Front Mol Biosci, Numero 9, 2022, ISSN 2296-889X
Editore: Frontiers

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

Autori: Theodore Alexandrov
Pubblicato in: Annual Review of Biomedical Data Science, Numero 3:61-87, 2020
Editore: 2574-3414

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

Autori: Theodore Alexandrov, Julio Saez‐Rodriguez, and Sinem K Saka
Pubblicato in: Mol Syst Biol, Numero 19: e10571, 2023, ISSN 1744-4292
Editore: Nature Publishing Group

Facilitating imaging mass spectrometry of microbial specialized metabolites with METASPACE.

Autori: Nguyen DD, Saharuka V, Kovalev V, Stuart L, Del Prete M, Lubowiecka K, De Mot R, Venturi V, Alexandrov T
Pubblicato in: Metabolites, 2021, ISSN 2218-1989
Editore: MDPI
DOI: 10.3390/metabo11080477

PySpacell: A Python Package for Spatial Analysis of Cell Images

Autori: France Rose, Luca Rappez, Sergio H. Triana, Theodore Alexandrov, Auguste Genovesio
Pubblicato in: Cytometry Part A, Numero 97/3, 2020, Pagina/e 288-295, ISSN 1552-4922
Editore: 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

Autori: Luca Rappez, Alexander Rakhlin, Angelos Rigopoulos, Sergey Nikolenko, Theodore Alexandrov
Pubblicato in: Molecular Systems Biology, Numero 16/10, 2020, ISSN 1744-4292
Editore: Nature Publishing Group
DOI: 10.15252/msb.20209474

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

Autori: 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
Pubblicato in: Molecular Systems Biology, Numero 17/7, 2021, ISSN 1744-4292
Editore: Nature Publishing Group
DOI: 10.15252/msb.20209833

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

Autori: 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
Pubblicato in: mSystems, Vol 4, Iss 5 (2019), Numero 1, 2019, ISSN 2211-1247
Editore: Cell Press
DOI: 10.1128/msystems.00375-19

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

Autori: Lautaro Gandara, Albert Tsai, Måns Ekelöf, Rafael Galupa, Ella Preger-Ben Noon, Theodore Alexandrov, Justin Crocker
Pubblicato in: Cell Reports, Numero 41, 11, 2022, ISSN 2211-1247
Editore: Cell Press

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

Autori: 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
Pubblicato in: Nature Immunology, Numero 22, 2021, ISSN 1529-2908
Editore: Nature Publishing Group
DOI: 10.1038/s41590-021-01059-0

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

Autori: Karin Mitosch, Martin Beyß, Prasad Phapale, Bernhard Drotleff, Katharina Nöh, Theodore Alexandrov, Kiran R. Patil , Athanasios Typas
Pubblicato in: PLoS Biology, Numero 21, 8, 2023, ISSN 1544-9173
Editore: Public Library of Science

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

Autori: Katja Ovchinnikova, Vitaly Kovalev, Lachlan Stuart, Theodore Alexandrov
Pubblicato in: BMC Bioinformatics, Numero 21/1, 2020, ISSN 1471-2105
Editore: 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

Autori: 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
Pubblicato in: Communications Biology, Numero 5, 2022, ISSN 2399-3642
Editore: Nature

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

Autori: Katja Ovchinnikova, Lachlan Stuart, Alexander Rakhlin, Sergey Nikolenko, Theodore Alexandrov
Pubblicato in: Bioinformatics, 2020, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btaa085

SpaceM reveals metabolic states of single cells

Autori: Luca Rappez, Mira Stadler, Sergio Triana, Rose Muthoni Gathungu, Katja Ovchinnikova, Prasad Phapale, Mathias Heikenwalder, Theodore Alexandrov
Pubblicato in: Nature Methods, Numero 18/7, 2021, Pagina/e 799-805, ISSN 1548-7091
Editore: 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

Autori: 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
Pubblicato in: npj Systems Biology and Applications, Numero 8, 15, 2022, ISSN 2056-7189
Editore: Nature

FOXO1-mediated lipid metabolism maintains mammalian embryos in dormancy

Autori: 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
Pubblicato in: Nature Cell Biology, Numero 26, pages 181–193, 2024, ISSN 1476-4679
Editore: Nature

Feature-based molecular networking in the GNPS analysis environment

Autori: 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
Pubblicato in: Nature Methods, Numero 17/9, 2020, Pagina/e 905-908, ISSN 1548-7091
Editore: Nature Publishing Group
DOI: 10.1038/s41592-020-0933-6

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

Autori: Raphaël La Rocca, Christopher Kune, Mathieu Tiquet, Lachlan Stuart, Gauthier Eppe, Theodore Alexandrov, Edwin De Pauw, Loïc Quinton
Pubblicato in: Analytical Chemistry, Numero 93, 8, 2021, ISSN 0003-2700
Editore: 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.

Autori: 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
Pubblicato in: Cell Reports, Numero 1, 2020, ISSN 2211-1247
Editore: 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

Autori: Dušan Veličković, Guanshi Zhang, Dejan Bezbradica, Arunima Bhattacharjee, Ljiljana Paša-Tolić, Kumar Sharma, Theodore Alexandrov, Christopher R. Anderton
Pubblicato in: Journal of the American Society for Mass Spectrometry, Numero 31/3, 2020, Pagina/e 508-516, ISSN 1044-0305
Editore: Elsevier BV
DOI: 10.1021/jasms.9b00074

Other (1)

Using Biological Signals for Mass Recalibration of Mass Spectrometry Imaging Data

Autori: La Rocca, Raphaël; Kune, Christopher; Tiquet, Mathieu; Stuart, Lachlan; Alexandrov, Theodore; De Pauw, Edwin; Quinton, Loïc
Pubblicato in: Chemrxiv, Numero 1, 2020
Editore: Chemrxiv
DOI: 10.26434/chemrxiv.12901679.v1

Non-peer reviewed articles (1)

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

Autori: J. C. McKinnon; H. H. Milioli; C. A. Purcell; C. L. Chaffer; B. Wadie; T. Alexandrov; T. W. Mitchell; S. R. Ellis
Pubblicato in: Chemrxiv, Numero 1, 2023, ISSN 2573-2293
Editore: Chemrxiv
DOI: 10.1039/d3ay01046e

Diritti di proprietà intellettuale

Patent (1)

SINGLE-CELL IMAGING MASS SPECTROMETRY

Numero candidatura/pubblicazione: 20 18059515
Data: 2018-04-13
Candidato/i: EUROPEAN MOLECULAR BIOLOGY LABORATORY