Madeleine Ernst

Madeleine Ernst


Madeleine Ernst , Congenital Disorders
T. +45 32688498 @.

Research area

I am heading the Metabolomics Research Group at the Section for Clinical Mass Spectrometry, Danish Center for Neonatal Screening, Department of Congenital Disorders. Our group’s research aims at developing population size mass spectrometry-based metabolomics approaches for predictive, personalized and preventive diagnostics in early life using the massive sample resource at the Danish National Biobank. Using metabolomics approaches mainly on neonatal dried blood spots we aim at unravelling metabolic signatures of neonatal health and disease, as well as studying impacts of pre- and postnatal exposure on future health outcomes. Our group works in close collaboration with national and international research groups, universities and centers of excellence at the interphase of personalized medicine, metabolomics, microbiome and register-based research and epidemiology. Our collaboration partners include PREDICT, iPSYCH, COPSAC, Rigshospitalet and many more.


Before starting my position as a research scientist at Statens Serum Institut, I held a postdoctoral position at The Dorrestein Laboratory at the University of California in San Diego. Here, I participated in diverse research projects within computational metabolomics. Among other things, I investigated how the integration of diverse metabolome mining tools, such as mass spectral molecular networking through GNPS and MS2LDA can enhance chemical structural information retrieved in metabolomics experiments. I obtained my PhD in plant chemical diversity and evolution through the Marie Curie Initial Training Network MedPlant at the University of Copenhagen in Denmark. My fascination for the vast chemical space of small molecules started in the field of natural products chemistry. During my MSc in professor Norberto Peporine Lopes’ group at the University of São Paulo in Ribeirão Preto, Brazil, I investigated metabolomics approaches based on matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) for the taxonomic classification of diverse plant families in a biodiversity hotspot in the Brazilian savanna.

Google Scholar


My responsibilities as a group leader encompass guiding the development of novel computational metabolomics approaches for the analysis of large population-based LC-MS/MS metabolomics cohorts as well as supervision of the analytical method development. I review and ensure data quality, high throughput metabolite annotation and biological interpretation.

Selected publications

  • Madeleine Ernst, Simon Rogers, Ulrik Lausten-Thomsen, Anders Björkbom, Susan Svane Laursen, Julie Courraud, Anders Børglum, Merete Nordentoft, Thomas Werge, Preben Bo Mortensen, David M. Hougaard & Arieh S. Cohen. Gestational age-dependent development of the neonatal metabolome. Pediatric Research 89/2020, 1396-1404.
  • Madeleine Ernst, Kyo Bin Kang, Andrés Mauricio Caraballo-Rodríguez, Louis-Félix Nothias, Joe Wandy, Christopher Chen, Ming Wang, Simon Rogers, Marnix H. Medema, Pieter C. Dorrestein, Justin J.J. van der Hooft. MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools. Metabolites 9/2019, 144.
  • Louis-Félix Nothias, Daniel Petras, Robin Schmid, Kai Dührkop, Johannes Rainer, Abinesh Sarvepalli, Ivan Protsyuk, Madeleine Ernst, Hiroshi Tsugawa, et al. Feature-based molecular networking in the GNPS analysis environment. Nature Methods 17/2020:905-908.
  • Anupriya Tripathi, Yoshiki Vázquez-Baeza, Julia M. Gauglitz, Mingxun Wang, Kai Dührkop, Mélissa Nothias-Esposito, Deepa D. Acharya, Madeleine Ernst, Justin J. J. van der Hooft, Qiyun Zhu, Daniel McDonald, Asker D. Brejnrod, Antonio Gonzalez, Jo Handelsman, Markus Fleischauer, Marcus Ludwig, Sebastian Böcker, Louis-Félix Nothias, Rob Knight & Pieter C. Dorrestein. Chemically informed analyses of metabolomics mass spectrometry data with Qemistree. Nature Chemical Biology 17/2021:146-151.
  • Mingxun Wang, Alan K. Jarmusch, Fernando Vargas, Alexander A. Aksenov, Julia M. Gauglitz, Kelly Weldon, Daniel Petras, Ricardo da Silva, Robert Quinn, Alexey V. Melnik, Justin J. J. van der Hooft, Andrés Mauricio Caraballo-Rodríguez, Louis Felix Nothias, Christine M. Aceves, Morgan Panitchpakdi, Elizabeth Brown, Francesca Di Ottavio, Nicole Sikora, Emmanuel O. Elijah, Lara Labarta-Bajo, Emily C. Gentry, Shabnam Shalapour, Kathleen E. Kyle, Sara P. Puckett, Jeramie D. Watrous, Carolina S. Carpenter, Amina Bouslimani, Madeleine Ernst, Austin D. Swafford, Elina I. Zúñiga, Marcy J. Balunas, Jonathan L. Klassen, Rohit Loomba, Rob Knight, Nuno Bandeira & Pieter C. Dorrestein. Mass spectrometry searches using MASST. Nature Biotechnology 38/2020: 23-26.
  • Alan K. Jarmusch, Mingxun Wang, Christine M. Aceves, Rohit S. Advani, Shaden Aguirre, Alexander A. Aksenov, Gajender Aleti, Allegra T. Aron, Anelize Bauermeister, Sanjana Bolleddu, Amina Bouslimani, Andres Mauricio Caraballo Rodriguez, Rama Chaar, Roxana Coras, Emmanuel O. Elijah, Madeleine Ernst, Julia M. Gauglitz, Emily C. Gentry, Makhai Husband, Scott A. Jarmusch, Kenneth L. Jones II, Zdenek Kamenik, Audrey Le Gouellec, Aileen Lu, Laura-Isobel McCall, Kerry L. McPhail, Michael J. Meehan, Alexey V. Melnik, Riya C. Menezes, Yessica Alejandra Montoya Giraldo, Ngoc Hung Nguyen, Louis Felix Nothias, Mélissa Nothias-Esposito, Morgan Panitchpakdi, Daniel Petras, Robert A. Quinn, Nicole Sikora, Justin J. J. van der Hooft, Fernando Vargas, Alison Vrbanac, Kelly C. Weldon, Rob Knight, Nuno Bandeira & Pieter C. Dorrestein. ReDU: a framework to find and reanalyze public mass spectrometry data. Nature Methods 17/2020: 901–904.
  • Simon Rogers, Cher Wei Ong, Joe Wandy, Madeleine Ernst, Lars Ridder and Justin J. J. van der Hooft. Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra. Faraday Discussions 218/2019: 284-302.
  • Laura-Isobel McCall, Chris Callewaert, Qiyun Zhu, Se Jin Song, Amina Bouslimani, Jeremiah J. Minich, Madeleine Ernst, Jean F. Ruiz-Calderon, Humberto Cavallin, Henrique S. Pereira, Atila Novoselac, Jean Hernandez, Rafael Rios, OraLee H. Branch, Martin J. Blaser, Luciana C. Paulino, Pieter C. Dorrestein, Rob Knight & Maria G. Dominguez-Bello. Home chemical and microbial transitions across urbanization. Nature Microbiology 5/2020: 108-115.