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ArticlesPeer ReviewedFull Text
MALDI imaging mass spectrometry: statistical data analysis and current computational challenges
Author / Creator:Alexandrov, Theodore
Publisher:England: BioMed Central
Journal title:BMC bioinformatics, 2012, Vol.13 (S16), p.S11-S11, Article S11
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ArticlesPeer ReviewedFull Text
OffsampleAI: artificial intelligence approach to recognize off-sample mass spectrometry images
Author / Creator:Ovchinnikova, Katja ; Kovalev, Vitaly ; Stuart, Lachlan ; Alexandrov, Theodore
Publisher:England: BioMed Central Ltd
Journal title:BMC bioinformatics, 2020-04, Vol.21 (1), p.129-129, Article 129
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FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry
Author / Creator:Palmer, Andrew ; Phapale, Prasad ; Chernyavsky, Ilya ; Lavigne, Regis ; Fay, Dominik ; Tarasov, Artem ; Kovalev, Vitaly ; Fuchser, Jens ; Nikolenko, Sergey ; Pineau, Charles ; Becker, Michael ; Alexandrov, Theodore
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2017-01, Vol.14 (1), p.57-60
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Enablers and challenges of spatial omics, a melting pot of technologies
Author / Creator:Alexandrov, Theodore ; Saez‐Rodriguez, Julio ; Saka, Sinem K
Publisher:Germany: EMBO Press
Journal title:Molecular systems biology, 2023-11, Vol.19 (11), p.e10571-n/a
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Molecular cartography of the human skin surface in 3D
Author / Creator:Bouslimani, Amina ; Porto, Carla ; Rath, Christopher M. ; Wang, Mingxun ; Guo, Yurong ; Gonzalez, Antonio ; Berg-Lyon, Donna ; Ackermann, Gail ; Christensen, Gitte Julie Moeller ; Nakatsuji, Teruaki ; Zhang, Lingjuan ; Borkowski, Andrew W. ; Meehan, Michael J. ; Dorrestein, Kathleen ; Gallo, Richard L. ; Bandeira, Nuno ; Knight, Rob ; Alexandrov, Theodore ; Dorrestein, Pieter C.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2015-04, Vol.112 (17), p.E2120-E2129
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A pathogen-specific isotope tracing approach reveals metabolic activities and fluxes of intracellular Salmonella
Author / Creator:Mitosch, Karin ; Beyß, Martin ; Phapale, Prasad ; Drotleff, Bernhard ; Nöh, Katharina ; Alexandrov, Theodore ; Patil, Kiran R. ; Typas, Athanasios
Publisher:San Francisco: Public Library of Science
Journal title:PLoS biology, 2023-08, Vol.21 (8), p.e3002198-e3002198
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Single‐cell analyses reveal SARS‐CoV‐2 interference with intrinsic immune response in the human gut
Author / Creator:Triana, Sergio ; Metz‐Zumaran, Camila ; Ramirez, Carlos ; Kee, Carmon ; Doldan, Patricio ; Shahraz, Mohammed ; Schraivogel, Daniel ; Gschwind, Andreas R ; Sharma, Ashwini K ; Steinmetz, Lars M ; Herrmann, Carl ; Alexandrov, Theodore ; Boulant, Steeve ; Stanifer, Megan L
Publisher:London: Nature Publishing Group UK
Journal title:Molecular systems biology, 2021-04, Vol.17 (4), p.e10232-n/a
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ArticlesPeer ReviewedFull Text
METASPACE-ML: Context-specific metabolite annotation for imaging mass spectrometry using machine learning
Author / Creator:Wadie, Bishoy ; Stuart, Lachlan ; Rath, Christopher M. ; Drotleff, Bernhard ; Mamedov, Sergii ; Alexandrov, Theodore
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2024-10, Vol.15 (1), p.9110-16, Article 9110
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DeepCycle reconstructs a cyclic cell cycle trajectory from unsegmented cell images using convolutional neural networks
Author / Creator:Rappez, Luca ; Rakhlin, Alexander ; Rigopoulos, Angelos ; Nikolenko, Sergey ; Alexandrov, Theodore
Publisher:London: Nature Publishing Group UK
Journal title:Molecular systems biology, 2020-10, Vol.16 (10), p.e9474-n/a
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Mass spectral molecular networking of living microbial colonies
Author / Creator:Watrous, Jeramie ; Roach, Patrick ; Alexandrov, Theodore ; Heath, Brandi S ; Yang, Jane Y ; Kersten, Roland D ; van der Voort, Menno ; Pogliano, Kit ; Gross, Harald ; Raaijmakers, Jos M ; Moore, Bradley S ; Laskin, Julia ; Bandeira, Nuno ; Dorrestein, Pieter C
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2012-06, Vol.109 (26), p.E1743-E1752
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ArticlesPeer ReviewedFull Text
Rapid response of fly populations to gene dosage across development and generations
Author / Creator:Li, Xueying C. ; Gandara, Lautaro ; Ekelöf, Måns ; Richter, Kerstin ; Alexandrov, Theodore ; Crocker, Justin
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2024-05, Vol.15 (1), p.4551-14, Article 4551
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ArticlesPeer ReviewedFull Text
3D molecular cartography using LC–MS facilitated by Optimus and 'ili software
Author / Creator:Protsyuk, Ivan ; Melnik, Alexey V ; Nothias, Louis-Felix ; Rappez, Luca ; Phapale, Prasad ; Aksenov, Alexander A ; Bouslimani, Amina ; Ryazanov, Sergey ; Dorrestein, Pieter C ; Alexandrov, Theodore
Publisher:London: Nature Publishing Group UK
Journal title:Nature protocols, 2018-01, Vol.13 (1), p.134-154
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Where imaging mass spectrometry stands: here are the numbers
Author / Creator:Palmer, Andrew ; Trede, Dennis ; Alexandrov, Theodore
Publisher:New York: Springer US
Journal title:Metabolomics, 2016-06, Vol.12 (6), p.1, Article 107
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ArticlesPeer ReviewedFull Text
Single‐cell transcriptomics reveals immune response of intestinal cell types to viral infection
Author / Creator:Triana, Sergio ; Stanifer, Megan L ; Metz‐Zumaran, Camila ; Shahraz, Mohammed ; Mukenhirn, Markus ; Kee, Carmon ; Serger, Clara ; Koschny, Ronald ; Ordoñez‐Rueda, Diana ; Paulsen, Malte ; Benes, Vladimir ; Boulant, Steeve ; Alexandrov, Theodore
Publisher:London: Nature Publishing Group UK
Journal title:Molecular systems biology, 2021-07, Vol.17 (7), p.e9833-n/a
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ArticlesPeer ReviewedFull Text
Lifestyle chemistries from phones for individual profiling
Author / Creator:Bouslimani, Amina ; Melnik, Alexey V. ; Xu, Zhenjiang ; Amir, Amnon ; da Silva, Ricardo R. ; Wang, Mingxun ; Bandeira, Nuno ; Alexandrov, Theodore ; Knight, Rob ; Dorrestein, Pieter C.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2016-11, Vol.113 (48), p.E7645-E7654
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ArticlesPeer ReviewedFull Text
Quantification reveals early dynamics in Drosophila maternal gradients
Author / Creator:Shlemov, Alex ; Alexandrov, Theodore ; Golyandina, Nina ; Holloway, David ; Baumgartner, Stefan ; Spirov, Alexander V.
Publisher:San Francisco, CA USA: Public Library of Science
Journal title:PloS one, 2021-08, Vol.16 (8), p.e0244701-e0244701
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Phenalenone-type phytoalexins mediate resistance of banana plants (Musa spp.) to the burrowing nematode Radopholus similis
Author / Creator:Hölscher, Dirk ; Dhakshinamoorthy, Suganthagunthalam ; Alexandrov, Theodore ; Becker, Michael ; Bretschneider, Tom ; Buerkert, Andreas ; Crecelius, Anna C. ; Waele, Dirk De ; Elsen, Annemie ; Heckel, David G. ; Heklau, Heike ; Hertweck, Christian ; Kai, Marco ; Knop, Katrin ; Krafft, Christoph ; Maddula, Ravi K. ; Matthäus, Christian ; Popp, Jürgen ; Schneider, Bernd ; Schubert, Ulrich S. ; Sikora, Richard A. ; Svatoš, Aleš ; Swennen, Rony L.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2014-01, Vol.111 (1), p.105-110
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ArticlesPeer ReviewedFull Text
Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae
Author / Creator:Luzzatto-Knaan, Tal ; Garg, Neha ; Wang, Mingxun ; Glukhov, Evgenia ; Peng, Yao ; Ackermann, Gail ; Amir, Amnon ; Duggan, Brendan M ; Ryazanov, Sergey ; Gerwick, Lena ; Knight, Rob ; Alexandrov, Theodore ; Bandeira, Nuno ; Gerwick, William H ; Dorrestein, Pieter C
Publisher:England: eLife Science Publications, Ltd
Journal title:eLife, 2017-05, Vol.6
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The Community Ecology of Microbial Molecules
Author / Creator:Quinn, Robert A. ; Alexandrov, Theodore
Publisher:Boston: Springer US
Journal title:Journal of chemical ecology, 2014-12, Vol.40 (11-12), p.1161-1162
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Facilitating Imaging Mass Spectrometry of Microbial Specialized Metabolites with METASPACE
Author / Creator:Nguyen, Don D. ; Saharuka, Veronika ; Kovalev, Vitaly ; Stuart, Lachlan ; Del Prete, Massimo ; Lubowiecka, Kinga ; De Mot, René ; Venturi, Vittorio ; Alexandrov, Theodore
Publisher:Basel: MDPI AG
Journal title:Metabolites, 2021-07, Vol.11 (8), p.477
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MALDI imaging mass spectrometry: statistical data analysis and current computational challenges

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

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

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

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Molecular cartography of the human skin surface in 3D

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

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

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METASPACE-ML: Context-specific metabolite annotation for imaging mass spectrometry using machine learning

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

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Mass spectral molecular networking of living microbial colonies

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Rapid response of fly populations to gene dosage across development and generations

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3D molecular cartography using LC–MS facilitated by Optimus and 'ili software

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Where imaging mass spectrometry stands: here are the numbers

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

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Lifestyle chemistries from phones for individual profiling

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Quantification reveals early dynamics in Drosophila maternal gradients

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Phenalenone-type phytoalexins mediate resistance of banana plants (Musa spp.) to the burrowing nematode Radopholus similis

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

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The Community Ecology of Microbial Molecules

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Facilitating Imaging Mass Spectrometry of Microbial Specialized Metabolites with METASPACE

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