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Thomas Naake

A draft map of the mouse pluripotent stem cell spatial proteome
2016 · Andy Christoforou, Claire M. Mulvey, et al. · Nature Communications · 218
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Mass Spectrometry‐Based Untargeted Plant Metabolomics
2019 · Leonardo Perez de Souza, Saleh Alseekh, et al. · Current Protocols in Plant Biology · 110
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Coordinating Sulfur Pools under Sulfate Deprivation
2020 · Fayezeh Aarabi, Thomas Naake, et al. · Trends in Plant Science · 109
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Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation
2022 · Adam Amara, Clément Frainay, et al. · Frontiers in Molecular Biosciences · 95
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The metaRbolomics Toolbox in Bioconductor and beyond
2019 · Jan Stanstrup, Corey Broeckling, et al. · Metabolites · 92
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From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics
2017 · Leonardo Perez de Souza, Thomas Naake, et al. · GigaScience · 81
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Genome-wide association of the metabolic shifts underpinning dark-induced senescence in Arabidopsis
2021 · Feng Zhu, Saleh Alseekh, et al. · The Plant Cell · 64
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The Intracellular Localization of the Vanillin Biosynthetic Machinery in Pods of Vanilla planifolia
2017 · Nethaji J Gallage, Kirsten Jørgensen, et al. · Plant and Cell Physiology · 60
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Visualization of proteomics data using R and Bioconductor
2015 · Laurent Gatto, Lisa M. Breckels, et al. · PROTEOMICS · 59
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Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis
2022 · Hagen M. Gegner, Thomas Naake, et al. · Frontiers in Molecular Biosciences · 51
Kingdom-wide analysis of the evolution of the plant type III polyketide synthase superfamily
2020 · Thomas Naake, Hiroshi A Maeda, et al. · PLANT PHYSIOLOGY · 42
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Diversity of Chemical Structures and Biosynthesis of Polyphenols in Nut-Bearing Species
2021 · Chaiwat Aneklaphakij, Tomoki Saigo, et al. · Frontiers in Plant Science · 39
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MetNet: Metabolite Network Prediction from High-Resolution Mass Spectrometry Data in R Aiding Metabolite Annotation
2018 · Thomas Naake, Alisdair R. Fernie · Analytical Chemistry · 36
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Plant Mitochondrial Carriers: Molecular Gatekeepers That Help to Regulate Plant Central Carbon Metabolism
2020 · M. Toleco, Thomas Naake, et al. · Plants · 32
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MetCirc: navigating mass spectral similarity in high-resolution MS/MS metabolomics data
2017 · Thomas Naake, Emmanuel Gaquerel · Bioinformatics · 24
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OsGF14b modulates defense signaling pathways in rice panicle blast response
2020 · Shijuan Yan, Qing Liu, et al. · The Crop Journal · 22
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MatrixQCvis: shiny-based interactive data quality exploration for omics data
2021 · Thomas Naake, Wolfgang Huber · Bioinformatics · 15
A single-sample workflow for joint metabolomic and proteomic analysis of clinical specimens
2024 · Hagen M. Gegner, Thomas Naake, et al. · Clinical Proteomics · 13
Genome-wide association studies identify loci controlling specialized seed metabolites in Arabidopsis
2023 · Thomas Naake, Feng Zhu, et al. · PLANT PHYSIOLOGY · 13
MsQuality: an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data
2023 · Thomas Naake, Johannes Rainer, et al. · Bioinformatics · 11
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Phylogenomic and synteny analysis of BAHD and SCP/SCPL gene families reveal their evolutionary histories in plant specialized metabolism
2024 · Thomas Naake, John C. D'Auria, et al. · Philosophical Transactions of the Royal Society B Biological Sciences · 6
T-bet suppresses proliferation of malignant B cells in chronic lymphocytic leukemia
2024 · Philipp M. Roessner, Isabelle Seufert, et al. · Blood · 6
Computational approaches that aid annotation in metabolomics
2022 · Leonardo Perez de Souza, Thomas Naake, et al. · Trends in Plant Science · 4
Annotation of Specialized Metabolites from High-Throughput and High-Resolution Mass Spectrometry Metabolomics
2020 · Thomas Naake, Emmanuel Gaquerel, et al. · Methods in molecular biology · 4
SpectriPy: Enhancing Cross-Language Mass Spectrometry Data Analysis with R and Python
2025 · Marilyn De Graeve, Wout Bittremieux, et al. · The Journal of Open Source Software · 3
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Works count: 55
Citation count: 1,220
H-index: 16
I10-index: 20
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