Search Results - "Alexandrov, Theodore"

Spatial Metabolomics and Imaging Mass Spectrometry in the Age of Artificial Intelligence by Alexandrov, Theodore

“…Spatial metabolomics is an emerging field of omics research that has enabled localizing metabolites, lipids, and drugs in tissue sections, a feat considered…”
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MALDI imaging mass spectrometry: statistical data analysis and current computational challenges by Alexandrov, Theodore

“…Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) imaging mass spectrometry, also called MALDI-imaging, is a label-free bioanalytical…”
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Critical Role of Type III Interferon in Controlling SARS-CoV-2 Infection in Human Intestinal Epithelial Cells by Stanifer, Megan L., Kee, Carmon, Cortese, Mirko, Zumaran, Camila Metz, Triana, Sergio, Mukenhirn, Markus, Kraeusslich, Hans-Georg, Alexandrov, Theodore, Bartenschlager, Ralf, Boulant, Steeve

“…Severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) is an unprecedented worldwide health problem that requires concerted and global approaches…”
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OffsampleAI: artificial intelligence approach to recognize off-sample mass spectrometry images by Ovchinnikova, Katja, Kovalev, Vitaly, Stuart, Lachlan, Alexandrov, Theodore

“…Imaging mass spectrometry (imaging MS) is an enabling technology for spatial metabolomics of tissue sections with rapidly growing areas of applications in…”
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FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry by Palmer, Andrew, Phapale, Prasad, Chernyavsky, Ilya, Lavigne, Regis, Fay, Dominik, Tarasov, Artem, Kovalev, Vitaly, Fuchser, Jens, Nikolenko, Sergey, Pineau, Charles, Becker, Michael, Alexandrov, Theodore

“…The authors present a computational framework for false-discovery-rate-controlled metabolite annotation from high-resolution imaging mass spectrometry data…”
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Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation by Nothias, Louis-Félix, Nothias-Esposito, Mélissa, da Silva, Ricardo, Wang, Mingxun, Protsyuk, Ivan, Zhang, Zheng, Sarvepalli, Abi, Leyssen, Pieter, Touboul, David, Costa, Jean, Paolini, Julien, Alexandrov, Theodore, Litaudon, Marc, Dorrestein, Pieter C

“…It is a common problem in natural product therapeutic lead discovery programs that despite good bioassay results in the initial extract, the active compound(s)…”
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Enablers and challenges of spatial omics, a melting pot of technologies by Alexandrov, Theodore, Saez-Rodriguez, Julio, Saka, Sinem K

“…Spatial omics has emerged as a rapidly growing and fruitful field with hundreds of publications presenting novel methods for obtaining spatially resolved…”
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Interspecies interactions stimulate diversification of the Streptomyces coelicolor secreted metabolome by Traxler, Matthew F, Watrous, Jeramie D, Alexandrov, Theodore, Dorrestein, Pieter C, Kolter, Roberto

“…Soils host diverse microbial communities that include filamentous actinobacteria (actinomycetes). These bacteria have been a rich source of useful metabolites,…”
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Molecular cartography of the human skin surface in 3D by 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.

“…Significance The paper describes the implementation of an approach to study the chemical makeup of human skin surface and correlate it to the microbes that…”
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DeepCycle reconstructs a cyclic cell cycle trajectory from unsegmented cell images using convolutional neural networks by Rappez, Luca, Rakhlin, Alexander, Rigopoulos, Angelos, Nikolenko, Sergey, Alexandrov, Theodore

“…The advent of single‐cell methods is paving the way for an in‐depth understanding of the cell cycle with unprecedented detail. Due to its ramifications in…”
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Single‐cell analyses reveal SARS‐CoV‐2 interference with intrinsic immune response in the human gut by 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

“…Exacerbated pro‐inflammatory immune response contributes to COVID‐19 pathology. However, despite the mounting evidence about SARS‐CoV‐2 infecting the human…”
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Mass spectral molecular networking of living microbial colonies by 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

“…Integrating the governing chemistry with the genomics and phenotypes of microbial colonies has been a “holy grail” in microbiology. This work describes a…”
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A pathogen-specific isotope tracing approach reveals metabolic activities and fluxes of intracellular Salmonella by Mitosch, Karin, Beyß, Martin, Phapale, Prasad, Drotleff, Bernhard, Nöh, Katharina, Alexandrov, Theodore, Patil, Kiran R, Typas, Athanasios

“…Pathogenic bacteria proliferating inside mammalian host cells need to rapidly adapt to the intracellular environment. How they achieve this and scavenge…”
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A Method of Trend Extraction Using Singular Spectrum Analysis by Theodore Alexandrov

“…The paper presents a new method of trend extraction in the framework of the Singular Spectrum Analysis (SSA) approach. This method is easy to use, does not…”
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3D molecular cartography using LC–MS facilitated by Optimus and 'ili software by Protsyuk, Ivan, Melnik, Alexey V, Nothias, Louis-Felix, Rappez, Luca, Phapale, Prasad, Aksenov, Alexander A, Bouslimani, Amina, Ryazanov, Sergey, Dorrestein, Pieter C, Alexandrov, Theodore

“…3D molecular cartography is used for mapping of metabolites in our environment. This protocol describes the procedures for sample collection and processing,…”
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METASPACE-ML: Context-specific metabolite annotation for imaging mass spectrometry using machine learning by Wadie, Bishoy, Stuart, Lachlan, Rath, Christopher M., Drotleff, Bernhard, Mamedov, Sergii, Alexandrov, Theodore

“…Imaging mass spectrometry is a powerful technology enabling spatial metabolomics, yet metabolites can be assigned only to a fraction of the data generated…”
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Rapid response of fly populations to gene dosage across development and generations by Li, Xueying C., Gandara, Lautaro, Ekelöf, Måns, Richter, Kerstin, Alexandrov, Theodore, Crocker, Justin

“…Although the effects of genetic and environmental perturbations on multicellular organisms are rarely restricted to single phenotypic layers, our current…”
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Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal Samples by Melnik, Alexey V, da Silva, Ricardo R, Hyde, Embriette R, Aksenov, Alexander A, Vargas, Fernando, Bouslimani, Amina, Protsyuk, Ivan, Jarmusch, Alan K, Tripathi, Anupriya, Alexandrov, Theodore, Knight, Rob, Dorrestein, Pieter C

“…Increasing appreciation of the gut microbiome’s role in health motivates understanding the molecular composition of human feces. To analyze such complex…”
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Lifestyle chemistries from phones for individual profiling by Bouslimani, Amina, Melnik, Alexey V., Xu, Zhenjiang, Amir, Amnon, da Silva, Ricardo R., Wang, Mingxun, Bandeira, Nuno, Alexandrov, Theodore, Knight, Rob, Dorrestein, Pieter C.

“…Imagine a scenario where personal belongings such as pens, keys, phones, or handbags are found at an investigative site. It is often valuable to the…”
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evolving field of imaging mass spectrometry and its impact on future biological research by Watrous, Jeramie D, Alexandrov, Theodore, Dorrestein, Pieter C

“…Within the past decade, imaging mass spectrometry (IMS) has been increasingly recognized as an indispensable technique for studying biological systems. Its…”
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