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List of works by Theodore Alexandrov

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

scientific article published on 21 December 2017

A Multimodal and Integrated Approach to Interrogate Human Kidney Biopsies with Rigor and Reproducibility: Guidelines from the Kidney Precision Medicine Project

scientific article published on 16 November 2020

AMASS: algorithm for MSI analysis by semi-supervised segmentation

scientific article

An approach to optimize sample preparation for MALDI imaging MS of FFPE sections using fractional factorial design of experiments.

scientific article

An atlas of healthy and injured cell states and niches in the human kidney ⬇️

Analysis and interpretation of imaging mass spectrometry data by clustering mass-to-charge images according to their spatial similarity.

scientific article

Application of Matrix-Assisted Laser Desorption/Ionization Mass Spectrometric Imaging for Photolithographic Structuring

scientific article published on 30 July 2012

Application of matrix-assisted laser desorption/ionization mass spectrometric imaging to monitor surface changes of UV-irradiated poly(styrene) films

scientific article

Benchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry

scientific article published on 4 May 2015

Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation.

scientific article published on 2 March 2018

Biomarker discovery in MALDI-TOF serum protein profiles using discrete wavelet transformation.

scientific article published on March 2009

Cadherin-11, Sparc-related modular calcium binding protein-2, and Pigment epithelium-derived factor are promising non-invasive biomarkers of kidney fibrosis

scientific article published in 2021

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

scientific article published on 12 February 2020

Computational Metabolomics: Identification, Interpretation, Imaging (Dagstuhl Seminar 17491)

proceedings

Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal Samples

scientific article published on 19 June 2017

Creating a 3D microbial and chemical snapshot of a human habitat

scientific article published on 27 February 2018

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

scientific article published on 19 June 2020

Critical role of type III interferon in controlling SARS-CoV-2 infection, replication and spread in primary human intestinal epithelial cells

scientific article published on 25 April 2020

Curatr: a web application for creating, curating, and sharing a mass spectral library

scientific article

DESI-MSI and METASPACE indicates lipid abnormalities and altered mitochondrial membrane components in diabetic renal proximal tubules

scientific article published on 10 January 2020

Data for spatial analysis of growth anomaly lesions on Montipora capitata coral colonies using 3D reconstruction techniques

scientific article

Data-Driven Rescoring of Metabolite Annotations Significantly Improves Sensitivity

scholarly article by Ana S. C. Silva et al published 2 October 2018 in Analytical Chemistry

Data-independent microbial metabolomics with ambient ionization mass spectrometry.

scientific article

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

scientific article published on 01 October 2020

Dependence of accuracy of ESPRIT estimates on signal eigenvalues: the case of a noisy sum of two real exponentials

scientific article published on February 2009

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

scientific article

Efficient spatial segmentation of large imaging mass spectrometry datasets with spatially aware clustering. ⬇️

scientific article published on July 2011

Exploring three-dimensional matrix-assisted laser desorption/ionization imaging mass spectrometry data: three-dimensional spatial segmentation of mouse kidney

scientific article

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

scientific article

Facilitating Imaging Mass Spectrometry of Microbial Specialized Metabolites with METASPACE

scientific article published in 2021

Feature-based molecular networking in the GNPS analysis environment

scientific article published on 24 August 2020

HERMES: a molecular-formula-oriented method to target the metabolome

scientific article published on 01 November 2021

Histomolecular interpretation of pleomorphic adenomas of the salivary gland by matrix-assisted laser desorption ionization imaging and spatial segmentation

scientific article

Imaging mass spectrometry reveals modified forms of histone H4 as new biomarkers of microvascular invasion in hepatocellular carcinomas

scientific article

Integration of 3D multimodal imaging data of a head and neck cancer and advanced feature recognition

scientific article

Interspecies interactions stimulate diversification of the Streptomyces coelicolor secreted metabolome ⬇️

scientific article

Investigating the spatial distribution of growth anomalies affecting Montipora capitata corals in a 3-dimensional framework

scientific article published on 20 August 2016

Learning how to run a lab: interviews with principal investigators

scientific article published on 7 November 2013

Lifestyle chemistries from phones for individual profiling

scientific article (publication date: 29 November 2016)

MALDI imaging mass spectrometry: discrimination of pathophysiological regions in traumatized skeletal muscle by characteristic peptide signatures

scientific article

MALDI imaging mass spectrometry: statistical data analysis and current computational challenges ⬇️

scientific article published on November 5, 2012

MALDI-imaging segmentation is a powerful tool for spatial functional proteomic analysis of human larynx carcinoma

scientific article

MRI-compatible pipeline for three-dimensional MALDI imaging mass spectrometry using PAXgene fixation.

scientific article

Magnification of label maps with a topology-preserving level-set method.

scientific article published on 15 May 2012

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

scientific article published on 02 May 2022

Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats.

scientific article published on 12 October 2016

Mass spectral molecular networking of living microbial colonies

scientific article

Measuring Gene Expression Noise in Early Drosophila Embryos: The Highly Dynamic Compartmentalized Micro-environment of the Blastoderm Is One of the Main Sources of Noise

article

Meta-mass shift chemical profiling of metabolomes from coral reefs.

scientific article published on 12 October 2017

Metabolic decisions in development and disease—a Keystone Symposia report

scientific article published in 2021

Metabolic profiling directly from the Petri dish using nanospray desorption electrospray ionization imaging mass spectrometry

scientific article published on 14 October 2013

Microbial metabolic exchange in 3D.

scientific article

Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project

scientific article published on 16 September 2020

Molecular analysis of model gut microbiotas by imaging mass spectrometry and nanodesorption electrospray ionization reveals dietary metabolite transformations

scientific article

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

scientific article published on 24 September 2019

Molecular and chemical dialogues in bacteria-protozoa interactions.

scientific article published on 6 August 2015

Molecular cartography of the human skin surface in 3D

scientific article published on 30 March 2015

N-acyl Taurines and Acylcarnitines Cause an Imbalance in Insulin Synthesis and Secretion Provoking β Cell Dysfunction in Type 2 Diabetes

scientific article published on June 2017

New analysis workflow for MALDI imaging mass spectrometry: application to the discovery and identification of potential markers of childhood absence epilepsy

scientific article

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

scientific article published on 03 April 2020

On the Importance of Mathematical Methods for Analysis of MALDI-Imaging Mass Spectrometry Data

scientific article published in March 2012

On the importance of mathematical methods for analysis of MALDI-imaging mass spectrometry data

scientific article

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

scientific article

Probing metabolism in time and space

scientific article published on 01 April 2020

Progression from cirrhosis to cancer is associated with early ubiquitin post-translational modifications: identification of new biomarkers of cirrhosis at risk of malignancy

scientific article

Proteomic pattern analysis discriminates among multiple sclerosis-related disorders

scientific article

Public LC-Orbitrap Tandem Mass Spectral Library for Metabolite Identification

scientific article published in 2021

PySpacell: A Python Package for Spatial Analysis of Cell Images

scientific article published on 24 December 2019

Rationale and design of the Kidney Precision Medicine Project

scientific article published on 23 February 2021

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

scholarly article published 14 January 2019

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

scientific article published on 06 February 2020

SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids

scientific article

Segmentation of confocal Raman microspectroscopic imaging data using edge-preserving denoising and clustering

scientific article

Serial 3D imaging mass spectrometry at its tipping point

scientific article published on 7 April 2015

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

scientific article (publication date: 9 August 2016)

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

scientific article published on 19 March 2021

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

scientific article published on 22 November 2021

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

scientific article

Singular Spectrum Analysis of Gene Expression Profiles of Early Drosophila embryo: Exponential-in-Distance Patterns

scientific article published on January 2008

SpaceM reveals metabolic states of single cells

scientific article published on 05 July 2021

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

scientific article published on 13 April 2020

Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen

scientific article (publication date: 20 December 2016)

Spatial segmentation of MALDI FT-ICR MSI data: a powerful tool to explore the head and neck tumor in situ lipidome.

scientific article

Spatial segmentation of imaging mass spectrometry data with edge-preserving image denoising and clustering

scientific article

Spatial single-cell profiling of intracellular metabolomes in situ: Supplementary Data S1

Storage conditions of human kidney tissue sections affect spatial lipidomics analysis reproducibility

scientific article published on 08 September 2020

Super-resolution segmentation of imaging mass spectrometry data: Solving the issue of low lateral resolution ⬇️

scientific article published on August 11, 2011

Testing for presence of known and unknown molecules in imaging mass spectrometry

scientific article

The community ecology of microbial molecules

scientific article

The evolving field of imaging mass spectrometry and its impact on future biological research.

scientific article published on 24 January 2011

The feasibility of MS and advanced data processing for monitoring Schistosoma mansoni infection

scientific article

The young PI buzz: learning from the organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013.

scientific article published on 7 November 2013

Three Dimensional Cartography of Microbiome and Metabolome Data onto Radiological Images of the Human Lung

scientific article published in 2018

Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung

scientific article published on 17 October 2017

Tumoral heterogeneity of hepatic cholangiocarcinomas revealed by MALDI imaging mass spectrometry

scientific article

Two-Exponential Models of Gene Expression Patterns for Noisy Experimental Data

scientific article published on 17 August 2018

Using collective expert judgements to evaluate quality measures of mass spectrometry images

scientific article published on 15 June 2015

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