Publications
Publications
Feature-based molecular networking in the GNPS analysis environment
Auto-deconvolution and molecular networking of gas chromatography - mass spectrometry data.
Aksenov AA, Laponogov I, Zhang Z, Doran SLF, Belluomo I, Veselkov D, Bittremieux W, Nothias LF, Nothias-Esposito M, Maloney KN, Misra BB, Melnik AV, Smirnov A, Du X, Jones KL 2nd, Dorrestein K, Panitchpakdi M, Ernst M, van der Hooft JJJ, Gonzalez M, Carazzone C, Amézquita A, Callewaert C, Morton JT, Quinn RA, Bouslimani A, Orio AA, Petras D, Smania AM, Couvillion SP, Burnet MC, Nicora CD, Zink E, Metz TO, Artaev V, Humston-Fulmer E, Gregor R, Meijler MM, Mizrahi I, Eyal S, Anderson B, Dutton R, Lugan R, Boulch PL, Guitton Y, Prevost S, Poirier A, Dervilly G, Le Bizec B, Fait A, Persi NS, Song C, Gashu K, Coras R, Guma M, Manasson J, Scher JU, Barupal DK, Alseekh S, Fernie AR, Mirnezami R, Vasiliou V, Schmid R, Borisov RS, Kulikova LN, Knight R, Wang M, Hanna GB, Dorrestein PC, Veselkov K.. Nat Biotechnol. 2021 Feb;39(2):169-173. doi: 10.1038/s41587-020-0700-3. Epub 2020 Nov 9. PMID: 33169034; PMCID: PMC7971188.
Chemically informed analyses of metabolomics mass spectrometry data with Qemistree.
Tripathi A, Vázquez-Baeza Y, Gauglitz JM, Wang M, Dührkop K, Nothias-Esposito M, Acharya DD, Ernst M, van der Hooft JJJ, Zhu Q, McDonald D, Brejnrod AD, Gonzalez A, Handelsman J, Fleischauer M, Ludwig M, Böcker S, Nothias LF, Knight R, Dorrestein PC.. Nat Chem Biol. 2021 Feb;17(2):146-151. doi: 10.1038/s41589-020-00677-3. Epub 2020 Nov 16. PMID: 33199911; PMCID: PMC8189545.
Plasma metabolites to profile pathways in noncommunicable disease multimorbidity
Pietzner M, Stewart ID, Raffler J, Khaw KT, Michelotti GA, Kastenmüller G, Wareham NJ, Langenberg C.. Nat Med. 2021 Mar;27(3):471-479. doi: 10.1038/s41591-021-01266-0. Epub 2021 Mar 11. PMID: 33707775; PMCID: PMC8127079.
Genome-Scale Metabolic Modeling of the Human Microbiome in the Era of Personalized Medicine
Heinken A, Basile A, Hertel J, Thinnes C, Thiele I. Annu Rev Microbiol. 2021 Jul;27:146-151.doi: 10.1146/annurev-micro-060221-012134. Epub ahead of print. PMID: 34314593.
An Integrated Molecular Atlas of Alzheimer's Disease
Wörheide MA, Krumsiek J, Nataf S, Nho K, Greenwood AK, Wu T, Huynh K, Weinisch P, Römisch-Margl W, Lehner N, The AMP-AD Consortium, The Alzheimer’s Disease Neuroimaging Initiative, The Alzheimer’s Disease Metabolomics Consortium, Baumbach J, Meikle PJ, Saykin AJ, Doraiswamy PM, van Duijn C, Suhre K, Kaddurdah-Daouk R, Kastenmüller G, Arnold M. medRxiv. 2021 Sep 22. doi: https://doi.org/10.1101/2021.09.14.21263565.
Integration of constraint-based modeling with fecal metabolomics reveals large deleterious effects of Fusobacterium spp. on community butyrate production
Hertel J, Heinken A, Martinelli F, Thiele I. Gut Microbes. 2021 Jan-Dec; 13(1):1-23.doi: 10.1080/19490976.2021.1915673. PMID: 34057024.
SGI: Automatic clinical subgroup identification in omics datasets
Buyukozkan M, Suhre K, Krumsiek J. Bioinfomatics. 2021 Sep 16;btab656. doi: 10.1093/bioinformatics/btab656. PMID: 34529048.
Identification of plasma proteins relating to brain neurodegeneration and vascular pathology in cognitively normal individuals
Shi L, Buchanan CR, Cox SR, Hillary RF, Marioni RE, Campbell A, Hayward C, Stolicyn A, Whalley HC, Harris MA, Waymont J, Waiter G, Backhouse E, Wardlaw JM, Steele D, Mcintoch A, Lovestone S, Buckley NJ, Nevado-Holgado AJ. Alzheimers Dement (Amst). 2021 Sep 27; 13(1)e12240. doi: 10.1002/dad2.12240. PMID: 34604499.
Advances in constraint-based modelling of microbial communities
Heinken A, Basile A, Thiele I. Curr Opi Sys Biol. 2021 Sep 27;100346. doi: https://doi.org/10.1016/j.coisb.2021.05.007.
Causal inference on microbiome-metabolome relations via in silico in vivo association pattern analyses
Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis
foodMASST: A Mass Spectrometry Search Tool for Foods and Beverages.
maplet: An extensible R toolbox for modular and reproducible omics pipelines
Towards Standards for Human Fecal Sample Preparation in Targeted and Untargeted LC-HRMS Studies
Longitudinal analysis of UK Biobank participants suggests sex and APOE-dependent alterations in energy metabolism in development of dementia
Integration of proteomics and metabolomics – insights into inflammation, metabolic dysregulation, and vascular aspects in AD
A comparison of six DNA extraction protocols for 16S, ITS, and shotgun metagenomic sequencing of microbial communities
GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser
A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities
Dietary Regulation of Gut-Brain Axis in Alzheimer’s Disease: Importance of Microbiota Metabolites
Quick-start infrastructure for untargeted metabolomics analysis in GNPS
Serum metabolomic biomarkers of perceptual speed in cognitively normal and mildly impaired subjects with fasting state stratification
Association of plasma and CSF cytochrome P450, soluble epoxide hydrolase, and ethanolamide metabolism with Alzheimer’s disease
GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser
Reduced Independence in Daily Living Is Associated with the Gut Microbiome in People with HIV and HCV
Angiopoietin 2 Is Associated with Vascular Necroptosis Induction in Coronavirus Disease 2019 Acute Respiratory Distress Syndrome
The landscape of metabolic brain alterations in Alzheimer's disease
Metabolomic and inflammatory signatures of symptom dimensions in major depression
Infection and inflammation: New perspectives on Alzheimer's disease
MiMeDB: the Human Microbial Metabolome Database.
DEMETER: Efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations
MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions.
Comprehensive genetic analysis of the human lipidome identifies loci associated with lipid homeostasis with links to coronary artery disease
Effects of a ketogenic and low-fat diet on the human metabolome, microbiome, and foodome in adults at risk for Alzheimer's disease
Large-scale tandem mass spectrum clustering using fast nearest neighbor searching
The critical role that spectral libraries play in capturing the metabolomics community knowledge
Integrative metabolomics-genomics approach reveals key metabolic pathways and regulators of Alzheimer's disease
SGI: automatic clinical subgroup identification in omics datasets
A gut-derived metabolite alters brain activity and anxiety behaviour in mice
Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy
Variational autoencoders learn transferrable representations of metabolomics data
Mass spectrometry-based metabolomics in microbiome investigations
High-confidence structural annotation of metabolites absent from spectral libraries
Optimizing UniFrac with OpenACC Yields Greater Than One Thousand Times Speed Increase
Microbiota succession throughout life from the cradle to the grave
EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets
Indoxyl sulfate, a gut microbiome-derived uremic toxin, is associated with psychic anxiety and its functional magnetic resonance imaging-based neurologic signature
Interplay of Metabolome and Gut Microbiome in Individuals With Major Depressive Disorder vs Control Individuals
Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine
Circulating metabolites modulated by diet are associated with depression
JAMA Psychiatry. 2023 Published online JUly 26, 2023. doi.org/10.1038/s41380-023-02180-2