Publications

See also my Google scholar profile and publications in PubMed.

Research articles

Naake T., D’Auria J.C., Fernie A.R., Scossa F. Phylogenomic and synteny analysis of BAHD and SCP/SCPL gene families reveal their evolutionary histories in plant specialized metabolism. Philosophical Transactions B, 2024; https://doi.org/10.1098/rstb.2023.0349.

Gegner H.M., Naake T., Aljakouch K., Dugourd A., Kliewer G., Müller T., Schilling D., Schneider M.A., Kunze-Rohrbach N., Grünewald T.G.P., Hell R., Saez-Rodriguez J., Huber W., Poschet G., Krijgsveld J. A single-sample workflow for joint metabolomic and proteomic analysis of clinical specimens. Clinical Proteomics, 2024; https://doi.org/10.1186/s12014-024-09501-9; preprint.

Roessner P.M., Seufert I., Chapaprieta V., Jayabalan R., Briesch H., Massoni-Badosa R., Boskovic P., Beckendorff J., Roider T., Arseni L., Coelho M., Chakraborty S., Vaca A., Sivina M., Muckenhuber M., Rodriguez-Rodriguez S., Bonato A., Herbst S.A., Zapatka M., Sun C., Kretzmer H., Naake T., Bruch P.-M., Czernilofsky F., ten Hacken E., Schneider M., Helm D., Yosifov D.Y., Kauer J., Danilov A.V., Bewarder M., Heyne K., Schneider C., Stilgenbauer S., Wiestner A., Mallm J.-P., Burger J.A., Efremov D.G., Lichter P., Dietrich S., Martin-Subero J.I., Rippe K., Seiffert M. T-bet suppresses proliferation of malignant B cells in chronic lymphocytic leukemia. Blood, 2024; https://doi.org/10.1182/blood.2023021990.

Naake T., Rainer J., Huber W. MsQuality - an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data. Bioinformatics, 2023; https://doi.org/10.1093/bioinformatics/btad618; preprint.

Naake T., Zhu F., Alseekh S., Scossa F., Perez de Souza L., Borghi M., Brotman Y., Mori T., Nakabayashi R., Tohge T., Fernie A.R. Genome-wide association studies of seed metabolites identify loci controlling specialized seed metabolites in Arabidopsis. Plant Physiology, 2023; https://doi.org/10.1093/plphys/kiad511; preprint.

Gegner H.M., Naake T., Dugourd A., Müller T., Czernilofsky F., Kliewer G., Jaeger E., Helm B., Kunze-Rohrbach N., Klingmüller U., Hopf C., Müller-Tidow C., Dietrich S., Saez-Rodriguez J., Huber W., Hell R., Poschet G., Krijgsveld J. Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis. Frontiers Molecular Biosciences, 2022; https://doi.org/10.3389/fmolb.2022.961448; preprint.

Perez de Souza L., Naake T., Fernie A.R. Computational approaches that aid annotation in metabolomics. Trends in Plant Science, 2022; https://doi.org/10.1016/j.tplants.2022.06.010.

Amara A., Frainay C., Jourdan F., Naake T., Neumann S., Novoa-del-Toro E.M., Salek R., Salzer L., Scharfenberg S., Witting M.A. Networks and graphs discovery in metabolomics data analysis and interpretation. Frontiers in Molecular Biosciences, 2022. https://doi.org/10.3389/fmolb.2022.841373.

Naake T., Huber W. MatrixQCvis: shiny-based interactive data quality exploration for omics data. Bioinformatics, 2022; https://doi.org/10.1093/bioinformatics/btab748; preprint.

Zhu F., Alseekh S., Koper K., Tong H., Nikoloski Z., Naake T., Liu H., Yan J., Brotman Y., Wen W., Maeda H., Cheng Y., Fernie A.R. Genome-wide association of the metabolic shifts underpinning dark-induced senescence in Arabidopsis. The Plant Cell, 2022; https://doi.org/10.1093/plcell/koab251.

Aneklaphakij C., Saigo T., Watanabe M., Naake T., Fernie A.R., Bunsupa S., Satitpatipan V., Tohge T. Diversity of chemical structures and biosynthesis of polyphenols in nut bearing species. Frontiers in Plant Science, 2021; https://doi.org/10.3389/fpls.2021.642581.

Naake T., Maeda H.A., Proost S., Tohge T., Fernie A.R. Kingdom-wide analysis of the evolution of the plant type III polyketide synthase superfamily. Plant Physiology, 2020; https://doi.org/10.1093/plphys/kiaa086; preprint.

Yan S., Liu Q., Naake T., Huang W., Chen M., Kong Q., Zhang S., Li W., Li X., Liu Q., Yang J., Fernie A.R., Liu B. OsGF14b modulates defense signaling pathways in rice panicle blast response. The Crop Journal, 2020; https://doi.org/10.1016/j.cj.2020.10.007.

Aarabi F., Naake T., Fernie A.R., Hoefgen R. Coordinating Sulfur Pools under Sulfate Deprivation. Trends in Plant Science, 2020; https://doi.org/10.1016/j.tplants.2020.07.007.

Toleco M.R., Naake T., Zhang Y., Heazlewood J.L., Fernie A.R. Plant Mitochondrial Carriers: Molecular Gatekeepers that Help to Regulate Plant Central Carbon Metabolism. Plants 9, 2020; https://doi.org/10.3390/plants9010117.

Perez de Souza L., Alseekh S., Naake T., Fernie A.R. Mass spectrometry based untargeted plant metabolomics. Current Protocols in Plant Biology 4, 2019; https://doi.org/10.1002/cppb.20100.

Stanstrup J., Broeckling C.D., Helmus R., Hofmann N., Mathe E., Naake T., Nicolotti L., Peters K., Rainer J., Salek R.M., Schulze T., Schymanski E.L., Stravs M.A., Thevenot E., Treutler H., Weber R.J.M., Willighagen E., Witting M., Neumann S. The metaRbolomics toolbox in Bioconductor and beyond. Metabolites 9, 2019; https://doi.org/10.3390/metabo9100200.

Naake T., Fernie A.R. MetNet: Metabolite Network Prediction from High-Resolution Mass Spectrometry Data in R Aiding Metabolite Annotation. Analytical Chemistry 91, 2019; https://doi.org/10.1021/acs.analchem.8b04096.

Gallage N., Jørgensen K., Janfelt C., Nielsen A., Naake, T., Dalsten L., Grisoni M., Møller B.L. The Intracellular Localization of the Vanillin Biosynthetic Machinery in Pods of Vanilla planifolia. Plant Cell Physiology 59, 2018; https://doi.org/10.1093/pcp/pcx185.

Perez de Souza L., Naake T., Tohge T., Fernie A.R. From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics. Gigascience 6, 2017; https://doi.org/10.1093/gigascience/gix037.

Naake T., Gaquerel E. MetCirc: Navigating mass spectral similarity in high-resolution MS/MS metabolomics data. Bioinformatics 33, 2017; https://doi.org/10.1093/bioinformatics/btx159.

Christoforou A., Mulvey C.M., Breckels L.M., Geladaki A., Hurrell T., Hayward P.C., Naake T., Gatto L., Viner R., Arias A.M., Lilley K.S. A draft map of the mouse pluripotent stem cell spatial proteome. Nature Communications 7, 2016; https://doi.org/10.1038/ncomms9992.

Gatto L., Breckels L.M., Naake T., Gibb S. Visualisation of proteomics data using R and Bioconductor. PROTEOMICS 15, 2015; https://doi.org/10.1002/pmic.201400392.

Books/book chapters

Stanstrup J., Broeckling C.D., Helmus R., Hoffmann N., Mathe E., Naake T., Nicolotti L., Peters K., Rainer J., Salek R.M., Schulze T., Schymanski E.L., Stravs M.A., Thevenot E.A., Treutler H., Weber R.J.M., Willighagen E., Witting M., Neumann S. The MetaRbolomics book. Available at https://rformassspectrometry.github.io/metaRbolomics-book/.

Naake T., Gaquerel E., Fernie A.R. Annotation of specialized metabolites from high-throughput and high-resolution mass spectrometry metabolomics. Springer Protocols, Methods in Molecular Biology, Computational methods and Data Analysis for Metabolomics, 2020; https://doi.org/10.1007/978-1-0716-0239-3.

Recent talks

Naake T., Rainer J., Huber W. MsQuality - an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data. 27/11/2023 - 01/12/2023, Novo Nordisk Foundation Science Cluster Hillerød, Protein Signaling - in space and time (selected talk).

Neumann S., Burgess K., da Silva R.R., Schirra H., Naake T.. Hitchhikers’ guide to networks in metabolomics. 20/06/2022, Valencia, Metabolomics 2022 (selected talk).

Naake T. MsQuality: quality metrics for mass spectrometry data. 23/11/2021, Wittenberg, de.NBI CompMS metaRbolomics.

Hoffmann N., Gatto L., Gibb S., Rainer J., Stanstrup J., Broeckling C.D., Helmus R., Mathe E., Naake T., Nicolotti L., Peters K., Salek R., Schulze T., Schymanski E.L., Stravs M.A., Thevenot E., Treutler H., Weber R., Willighagen E., Witting M., Neumann S (presented by Hoffmann N.). The metaRbolomics Toolbox in Bioconductor and beyond. 13/07/2020–16/07/2020, virtual, ISMB 2020 28th Conference on Intelligent Systems for Molecular Biology.

Naake T. MetCirc: Navigating mass spectral similarity in high-resolution MS/MS metabolomics data - Recent updates. 25/07/2019, Brixen, CSAMA: Statistical Data Analysis for Genome-Scale Biology.

Naake T., Tohge T., Fernie A.R. Plant kingdom-wide analysis to study the evolution of the type III polyketide synthase superfamily. 24/06/2019, Pamplona, 1st PhD meeting in Plant Science (invited talk).

Naake T. MetNet: Metabolite Network Prediction from High-Resolution Mass Spectrometry Data in R Aiding Metabolite Annotation. 02/04/2019, Wittenberg, de.NBI CompMS metaRbolomics.

Posters

Ali S.A., Naake T., Henneman P. Aljakouch K. Huber W., Krijgsveld J. Multi-omics analysis of RAS mutant and isoform cell lines delineates RAS-dependent signalling networks. 18-22/11/2024, Novo Nordisk Foundation Science Cluster Hillerød, Metabolism in Action - Time, Space and Treatment.

Aljakouch K., Liao Q.-W., Schneider M., Helm B., Frey D., Schmidt C., Naake T., Zhou Q., Poschet G., Hell R., Winter H., Saez-Rodriguez J., Huber W., Hopf C., Klingmüller U., Krijgsveld U., Lu J. Identifying mass spectrometry-based biomarkers for predicting tumor recurrence in lung cancer. 20-24/10/2024, Dresden, HUPO 2024.

Rainer J., Louail P., Vicini A., Gine R., Badia J.M., Stravs M., Garcia-Aloy M., Huber C., Salzer L., Stanstrup J., Shahaf N., Panse C., Naake T., Kumler W., Vangeenderhuysen P., Brunius C., Hecht H., Neumann S., Witting M., Gibb S., Gatto L. An Open Software Development-based Ecosystem of R Packages for Metabolomics Data Analysis. 16-20/06/2024, Osaka, Metabolomics 2024.

Vicini A., Gine R., Stravs M., Badia J.M., Huber C., Salzer L., Stanstrup J., Shahaf N., Naake T., Hecht H., Neumann S., Witting M., Gibb S., Gatto L., Rainer J. An Open Software Development-based Ecosystem of R Packages for Metabolomics Data Analysis. 18-22/06/2023, Niagara Falls, Metabolomics 2023.

Naake T., Rainer J., Huber W. MsQuality - an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data. 19-23/06/2022, Valencia, Metabolomics 2022.

Naake T., Huber W. MatrixQCvis - shiny-based interactive data quality exploration for omics data. 27-30/09/2021, Bad Dürkheim, MsCoreSys Summer School: Mass spectrometry meets system medicine.

Naake T., Tohge T., Fernie A.R. Plant kingdom-wide analysis to study the evolution of the polyketide synthase superfamily. 16–23/09/2018, Greifswald, Greifolution: 1st Greifswald Summer school on Mathematics of Evolution.

Naake T., Tohge T., Fernie A.R. Exploring the natural variation of specialized seed metabolites of Arabidopsis thaliana to detect biosynthetic and regulatory genes using GWAS. 18–21/06/2018, Copenhagen, Plant Biology Europe 2018.

Gatto L., Breckels L.M., Naake T., Wieczorek S., Burger T., Lilley K.S. A state-of-the-art machine learning pipeline for the analysis of spatial proteomics data. 05–08/10/2014, Madrid, HUPO meeting.