Publications

Publications

Feature-based molecular networking in the GNPS analysis environment

Nothias LF, Petras D, Schmid R, Dührkop K, Rainer J, Sarvepalli A, Protsyuk I, Ernst M,Tsugawa H, Fleischauer M, Aicheler F, Aksenov AA, Alka O, Allard PM, BarschA,Cachet X, Caraballo-Rodriguez AM, Da Silva RR, Dang T, Garg N, Gauglitz JM,Gurevich A, Isaac G, Jarmusch AK, Kameník Z, Kang KB, Kessler N, Koester I, KorfA, Le Gouellec A, Ludwig M, Martin H C, McCall LI, McSayles J, Meyer SW,Mohimani H, Morsy M,Moyne O, Neumann S, Neuweger H, Nguyen NH,Nothias-Esposito M, Paolini J, Phelan VV, Pluskal T, Quinn RA, Rogers S, ShresthaB, Tripathi A, van der Hooft JJJ, Vargas F, Weldon KC, Witting M, Yang H, Zhang Z,Zubeil F, Kohlbacher O, Böcker S, Alexandrov T,Bandeira N, Wang M, DorresteinPC. Nature methods. 2020 September;17(9):905-908. PubMed PMID: 32839597;PubMed Central PMCID: PMC7885687; DOI: 10.1038/s41592-020-0933-6.

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.

Depression in Individuals Coinfected with HIV and HCV Is Associated with Systematic Differences in the Gut Microbiome and Metabolome

Taylor BC, Weldon KC, Ellis RJ, Franklin D, Groth T, Gentry EC, Tripathi A, McDonald D, Humphrey G, Bryant M, Toronczak J, Schwartz T, Oliveira MF, Heaton R, Grant I, Gianella S, Letendre S, Swafford A, Dorrestein PC, Knight R. Depression in Individuals Coinfected with HIV and HCV Is Associated with Systematic Differences in the Gut Microbiome and Metabolome. mSystems. 2020 Sep 29;5(5):e00465-20. doi: 10.1128/mSystems.00465-20. PMID: 32994287; PMCID: PMC7527136..

Reduced Independence in Daily Living Is Associated with the Gut Microbiome in People with HIV and HCV

Taylor BC, Weldon KC, Ellis RJ, Franklin D, McDonald D, Humphrey G, Bryant M, Toronczak J, Schwartz T, Iudicello J, Heaton R, Grant I, Gianella S, Letendre S, Swafford A, Dorrestein PC, Knight R. Reduced Independence in Daily Living Is Associated with the Gut Microbiome in People with HIV and HCV. mSystems. 2020 Oct 13;5(5):e00528-20. doi: 10.1128/mSystems.00528-20. PMID: 33051377; PMCID: PMC7567581.

Plasma and serum oxylipin, endocannabinoid, bile acid, steroid, fatty acid and nonsteroidal anti-inflammatory drug quantification in a 96-well plate format

Pedersen TL, Gray IJ, Newman JW. Plasma and serum oxylipin, endocannabinoid, bile acid, steroid, fatty acid and nonsteroidal anti-inflammatory drug quantification in a 96-well plate format. Anal Chim Acta. 2021 Jan 25;1143:189-200. doi: 10.1016/j.aca.2020.11.019. Epub 2020 Nov 23. PMID: 33384117.

Genetic architecture of host proteins involved in SARS-CoV-2 infection

Pietzner M, Wheeler E, Carrasco-Zanini J, Raffler J, Kerrison ND, Oerton E, Auyeung VPW, Luan J, Finan C, Casas JP, Ostroff R, Williams SA, Kastenmüller G, Ralser M, Gamazon ER, Wareham NJ, Hingorani AD, Langenberg C. Genetic architecture of host proteins involved in SARS-CoV-2 infection. Nat Commun. 2020 Dec 16;11(1):6397. doi: 10.1038/s41467-020-19996-z. Erratum in: Nat Commun. 2021 Feb 2;12(1):845. PMID: 33328453; PMCID: PMC7744536.

Assigning confidence to structural annotations from mass spectra with COSMIC

Hoffmann MA, Nothias L-F, Ludwig M, Fleischauer M, Gentry EC, Witting M, Dorrestein PC, Dührkop K, Böcker S.bioRxiv 2021.03.18.435634; doi: https://doi.org/10.1101/2021.03.18.435634

Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis

Heinken A, Hertel J, Thiele I. Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis. NPJ Syst Biol Appl. 2021 May 6;7(1):19. doi: 10.1038/s41540-021-00178-6. PMID: 33958598; PMCID: PMC8102608.

Multi-omics driven predictions of response to acute phase combination antidepressant therapy: a machine learning approach with cross-trial replication

Joyce JB, Grant CW, Liu D, MahmoudianDehkordi S, Kaddurah-Daouk R, Skime M, Biernacka J, Frye MA, Mayes T, Carmody T, Croarkin PE, Wang L, Weinshilboum R, Bobo WV, Trivedi MH, Athreya AP. Multi-omics driven predictions of response to acute phase combination antidepressant therapy: a machine learning approach with cross-trial replication. Transl Psychiatry. 2021 Oct 7;11(1):513. doi: 10.1038/s41398-021-01632-z. PMID: 34620827; PMCID: PMC8497535.

Multi-omics of human plasma reveals molecular features of dysregulated inflammation and accelerated aging in schizophrenia

Campeau A, Mills RH, Stevens T, Rossitto LA, Meehan M, Dorrestein P, Daly R, Nguyen TT, Gonzalez DJ, Jeste DV, Hook V. Multi-omics of human plasma reveals molecular features of dysregulated inflammation and accelerated aging in schizophrenia. Mol Psychiatry. 2022 Feb;27(2):1217-1225. doi: 10.1038/s41380-021-01339-z. Epub 2021 Nov 5. PMID: 34741130; PMCID: PMC9054664.

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.

EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-Omic Data

Cantrell K, Fedarko MW, Rahman G, McDonald D, Yang Y, Zaw T, Gonzalez A, Janssen S, Estaki M, Haiminen N, Beck KL, Zhu Q, Sayyari E, Morton JT, Armstrong G, Tripathi A, Gauglitz JM, Marotz C, Matteson NL, Martino C, Sanders JG, Carrieri AP, Song SJ, Swafford AD, Dorrestein PC, Andersen KG, Parida L, Kim HC, Vázquez-Baeza Y, Knight R. EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets. mSystems. 2021 Mar 16;6(2):e01216-20. doi: 10.1128/mSystems.01216-20. PMID: 33727399; PMCID: PMC8546999.

Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis

Heinken A, Hertel J, Thiele I. npj Syst Biol Appl. 2021 May 6;7(19). doi: https://doi.org/10.1038/s41540-021-00178-6.

XomicsToModel: Omics data integration and generation of thermodynamically consistent metabolic models

Preciat G, Wegrzyn AB, Thiele I, Hankemeier T, Fleming RMT bioRxiv 2021.11.08.467803; doi: https://doi.org/10.1101/2021.11.08.467803

Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities

Heinken A, Thiele I. Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities. Bioinformatics. 2022 Apr 12;38(8):2367-2368. doi: 10.1093/bioinformatics/btac082. PMID: 35157025; PMCID: PMC9004645.

Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data

Armstrong G, Rahman G, Martino C, McDonald D, Gonzalez A, Mishne G, Knight R. Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data. Front Bioinform. 2022 Feb 24;2:821861. doi: 10.3389/fbinf.2022.821861. PMID: 36304280; PMCID: PMC9580878.

Multi-Omics Characterization of Early- and Adult-Onset Major Depressive Disorder

Grant CW, Barreto EF, Kumar R, Kaddurah-Daouk R, Skime M, Mayes T, Carmody T, Biernacka J, Wang L, Weinshilboum R, Trivedi MH, Bobo WV, Croarkin PE, Athreya AP. Multi-Omics Characterization of Early- and Adult-Onset Major Depressive Disorder. J Pers Med. 2022 Mar 6;12(3):412. doi: 10.3390/jpm12030412. PMID: 35330412; PMCID: PMC8949112.

Conserved cell-type specific signature of resilience to Alzheimer’s disease nominates role for excitatory intratelencephalic cortical neurons

Telpoukhovskaia MA, Hadad N, Gurdon B, Dai Y, Ouellette AR, Neuner SM, Dunn AR, Willcox JAL, Wu Y, Dumitrescu L, Bellur O, Zhang J-G, O’Connell KMS, Dammer EB, Seyfried NT, Muzumdar S, Gillis J, Robson P, Arnold M, Hohman MP, Philip VW, Menon V, Kaczorowski CC. bioRxiv 2022.04.12.487877; doi: https://doi.org/10.1101/2022.04.12.487877

Gut microbiome-mediated regulation of neuroinflammation

Bostick JW, Schonhoff AM, Mazmanian SK. Gut microbiome-mediated regulation of neuroinflammation. Curr Opin Immunol. 2022 Jun;76:102177. doi: 10.1016/j.coi.2022.102177. Epub 2022 Apr 21. PMID: 35462279; PMCID: PMC9167715.

Open Access Repository-Scale Propagated Nearest Neighbor Suspect Spectral Library for Untargeted Metabolomics

Bittremieux W, Avalon NE, Thomas SP, Kakhkhorov SA, Aksenov AA, Gomes PWP, Aceves CM, Caraballo-Rodríguez AM, Gauglitz JM, Gerwick WH, Huan T, Jarmusch AK, Kaddurah-Daouk RF, Kang KB, Kim HW, Kondić T, Mannochio-Russo H, Meehan MJ, Melnik AV, Nothias LF, O’Donovan C, Panitchpakdi M, Petras D, Schmid R, Schymanski EL, van der Hooft JJJ, Weldon KC, Yang H, Xing S, Zemlin J, Wang M, Dorrestein PC. Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics. Nat Commun. 2023 Dec 20;14(1):8488. doi: 10.1038/s41467-023-44035-y. PMID: 38123557; PMCID: PMC10733301.

Genomics-based identification of a potential causal role for acylcarnitine metabolism in depression

Milaneschi Y, Arnold M, Kastenmüller G, Dehkordi SM, Krishnan RR, Dunlop BW, Rush AJ, Penninx BWJH, Kaddurah-Daouk R; Mood Disorders Precision Medicine Consortium (MDPMC). Genomics-based identification of a potential causal role for acylcarnitine metabolism in depression. J Affect Disord. 2022 Jun 15;307:254-263. doi: 10.1016/j.jad.2022.03.070. Epub 2022 Apr 2. PMID: 35381295.

Integrative metabolomic and proteomic signatures define clinical outcomes in severe COVID-19

Buyukozkan M, Alvarez-Mulett S, Racanelli AC, Schmidt F, Batra R, Hoffman KL, Sarwath H, Engelke R, Gomez-Escobar L, Simmons W, Benedetti E, Chetnik K, Zhang G, Schenck E, Suhre K, Choi JJ, Zhao Z, Racine-Brzostek S, Yang HS, Choi ME, Choi AMK, Cho SJ, Krumsiek J. Integrative metabolomic and proteomic signatures define clinical outcomes in severe COVID-19. iScience. 2022 Jul 15;25(7):104612. doi: 10.1016/j.isci.2022.104612. Epub 2022 Jun 17. PMID: 35756895; PMCID: PMC9212983.

Multi-omics profiling of Earth’s biomes reveals patterns of diversity and co-occurrence in microbial and metabolite composition

Shaffer JP, Nothias L-F, Thompson LR, Sanders JG, Salido RA, Couvillion SP, Brejnrod AD, Lejzerowicz F, Haiminen N, Huang S, Lutz HL, Zhu Q, Martino C, Morton JT, Karthikeyan S, Nothias-Esposito M, Dührkop K, Böcker S, Kim HW, Aksenov AA, Bittremieux W, Minich JJ, Marotz C, Bryant MM, Sanders K, Schwartz T, Humphrey G, Vásquez-Baeza Y, Tripathi A, Parida L, Carrieri AP, Beck KL, Das P, González A, McDonald D, Karst SM, Albertsen M, Ackermann G, DeReus J, Thomas T, Petras D, Shade A, Stegen J, Song SJ, Metz TO, Swafford AD, Dorrestein PC, Jansson JK, Gilbert JA, Knight R, the Earth Microbiome Project 500 (EMP500) Consortium

bioRxiv 2021.06.04.446988; doi: https://doi.org/10.1101/2021.06.04.446988

The hidden link between circadian entropy and mental health disorders

Alachkar A, Lee J, Asthana K, Vakil Monfared R, Chen J, Alhassen S, Samad M, Wood M, Mayer EA, Baldi P. The hidden link between circadian entropy and mental health disorders. Transl Psychiatry. 2022 Jul 14;12(1):281. doi: 10.1038/s41398-022-02028-3. PMID: 35835742; PMCID: PMC9283542.

Comparison of Cosine, Modified Cosine, and Neutral Loss Based Spectrum Alignment For Discovery of Structurally Related Molecules

Bittremieux W, Schmid R, Huber F, van der Hooft JJJ, Wang M, Dorrestein PC. Comparison of Cosine, Modified Cosine, and Neutral Loss Based Spectrum Alignment For Discovery of Structurally Related Molecules. J Am Soc Mass Spectrom. 2022 Sep 7;33(9):1733-1744. doi: 10.1021/jasms.2c00153. Epub 2022 Aug 12. PMID: 35960544.

Dynamic patterns of postprandial metabolic responses to three dietary challenges

Weinisch P, Fiamoncini J, Schranner D, Raffler J, Skurk T, Rist MJ, Römisch-Margl W, Prehn C, Adamski J, Hauner H, Daniel H, Suhre K, Kastenmüller G. Dynamic patterns of postprandial metabolic responses to three dietary challenges. Front Nutr. 2022 Sep 22;9:933526. doi: 10.3389/fnut.2022.933526. PMID: 36211489; PMCID: PMC9540193.

Network science approach elucidates integrative genomic-metabolomic signature of antidepressant response and lifetime history of attempted suicide in adults with major depressive disorder

Grant CW, Wilton AR, Kaddurah-Daouk R, Skime M, Biernacka J, Mayes T, Carmody T, Wang L, Lazaridis K, Weinshilboum R, Bobo WV, Trivedi MH, Croarkin PE, Athreya AP. Network science approach elucidates integrative genomic-metabolomic signature of antidepressant response and lifetime history of attempted suicide in adults with major depressive disorder. Front Pharmacol. 2022 Oct 3;13:984383. doi: 10.3389/fphar.2022.984383. PMID: 36263124; PMCID: PMC9573988.

Rare and common genetic determinants of metabolic individuality and their effects on human health

Surendran P, Stewart ID, Au Yeung VPW, Pietzner M, Raffler J, Wörheide MA, Li C, Smith RF, Wittemans LBL, Bomba L, Menni C, Zierer J, Rossi N, Sheridan PA, Watkins NA, Mangino M, Hysi PG, Di Angelantonio E, Falchi M, Spector TD, Soranzo N, Michelotti GA, Arlt W, Lotta LA, Denaxas S, Hemingway H, Gamazon ER, Howson JMM, Wood AM, Danesh J, Wareham NJ, Kastenmüller G, Fauman EB, Suhre K, Butterworth AS, Langenberg C. Rare and common genetic determinants of metabolic individuality and their effects on human health. Nat Med. 2022 Nov;28(11):2321-2332. doi: 10.1038/s41591-022-02046-0. Epub 2022 Nov 10. PMID: 36357675; PMCID: PMC9671801..

Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity

Shaffer JP, Nothias LF, Thompson LR, Sanders JG, Salido RA, Couvillion SP, Brejnrod AD, Lejzerowicz F, Haiminen N, Huang S, Lutz HL, Zhu Q, Martino C, Morton JT, Karthikeyan S, Nothias-Esposito M, Dührkop K, Böcker S, Kim HW, Aksenov AA, Bittremieux W, Minich JJ, Marotz C, Bryant MM, Sanders K, Schwartz T, Humphrey G, Vásquez-Baeza Y, Tripathi A, Parida L, Carrieri AP, Beck KL, Das P, González A, McDonald D, Ladau J, Karst SM, Albertsen M, Ackermann G, DeReus J, Thomas T, Petras D, Shade A, Stegen J, Song SJ, Metz TO, Swafford AD, Dorrestein PC, Jansson JK, Gilbert JA, Knight R; Earth Microbiome Project 500 (EMP500) Consortium. Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity. Nat Microbiol. 2022 Dec;7(12):2128-2150. doi: 10.1038/s41564-022-01266-x. Epub 2022 Nov 28. PMID: 36443458; PMCID: PMC9712116.

foodMASST: A Mass Spectrometry Search Tool for Foods and Beverages.

West KA, Schmid R, Gauglitz JM, Wang M, Dorrestein PC. foodMASST a mass spectrometry search tool for foods and beverages. NPJ Sci Food. 2022 Apr 20;6(1):22. doi: 10.1038/s41538-022-00137-3. PMID: 35444218; PMCID: PMC9021190.

maplet: An extensible R toolbox for modular and reproducible omics pipelines

Chetnik K, Benedetti E, Gomari DP, Schweickart A, Batra R, Buyukozkan M, Wang Z, Arnold M, Zierer J, Suhre K, Krumsiek J. maplet: an extensible R toolbox for modular and reproducible metabolomics pipelines. Bioinformatics. 2022 Jan 27;38(4):1168-1170. doi: 10.1093/bioinformatics/btab741. PMID: 34694386; PMCID: PMC8796365.

Towards Standards for Human Fecal Sample Preparation in Targeted and Untargeted LC-HRMS Studies

Hosseinkhani F, Dubbelman A-C, Karu N, Harms AC, Hankemeier T. Metabolites. 2021 Jun 7; 11(6):364. doi: 10.3390/metabo11060364.

Longitudinal analysis of UK Biobank participants suggests sex and APOE-dependent alterations in energy metabolism in development of dementia

Liu J, Amin N, Sproviero W, Arnold M, Batra R, Bonnechere B, Chiou Y-J, Fernandes M, Krumsiek J, Newby D, Nho K, Kim JP, Saykin AJ, Shi L, Winchester L, Yang Y, Nevado-Holgado AJ, Kastenmüller, Kaddurah-Daouk R, van Duijn CM. medRxiv. 2022 doi: https://doi.org/10.1101/2022.02.25.22271530.

Integration of proteomics and metabolomics – insights into inflammation, metabolic dysregulation, and vascular aspects in AD

Borkowski K, Seyfried NT, Arnold M, Lah JJ, Levey AI, Hales CM, Dammer EB, Blach C, Louie G, Kaddurah-Daouk R, Newman J, Alzheimers Disease Metabolomics Consortiums. 2022 doi: https://doi.org/10.1101/2022.02.18.22271208.

A comparison of six DNA extraction protocols for 16S, ITS, and shotgun metagenomic sequencing of microbial communities

Shaffer JP, Carpenter CS, Martino C, Salido RA, Minich JJ, Bryant M, Sanders K, Schwartz T, Humphrey G, Swafford AD, Knight R. A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities. Biotechniques. 2022 Jun;73(1):34-46. doi: 10.2144/btn-2022-0032. Epub 2022 Jun 17. PMID: 35713407; PMCID: PMC9361692.

GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser

Petras D, Phelan VV, Acharya D, Allen AE, Aron AT, Bandeira N, Bowen BP, Belle-Oudry D, Boecker S, Cummings DA, Deutsch JM, Fahy E, Garg N, Gregor R, Handelsman J, Navarro-Hoyos M, Jarmusch AK, Jarmusch SA, Louie, K, Maloney KN, Marty MT, Meijler MM, Mizrahi I, Neve RL, Northen TR, Molina-Santiago C, Panitchpakdi M, Pullman B, Puri AW, Schmid R, Subramaniam S, Thukral M, Vasquez-Castro F, Dorrestein PC, Wang, M. 2022. Nature Methods, 19(2), 134-136. https://doi.org/10.1038/s41592-021-01339-5.

A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities

Shaffer JP, Marotz C, Belda-Ferre P, Martino C, Wandro S, Estaki M, Salido RA, Carpenter CS, Zaramela LS, Minich JJ, Bryant M, Sanders K, Fraraccio S, Ackermann G, Humphrey G, Swafford AD, Miller-Montgomery S, Knight R. BioTechniques. 2021, 70(3). doi: https://doi.org/10.2144/btn-2020-0153.

Dietary Regulation of Gut-Brain Axis in Alzheimer’s Disease: Importance of Microbiota Metabolites

Frausto DM, Forsyth CB, Keshavarzain A, Voight RM. 2021. Front. Neurosci. doi: https://doi.org/10.3389/fnins.2021.736814.

Quick-start infrastructure for untargeted metabolomics analysis in GNPS

Leao TF, Bauermeister A, Elijah EO, Gentry EC, Husband M, Oliverira MF, Banderia N, Wang M, Dorrestein PC. Nature Metabolism, 3(7): 880-882. doi: 10.1038/s42255-021-00429-0 .

Serum metabolomic biomarkers of perceptual speed in cognitively normal and mildly impaired subjects with fasting state stratification

Borkowski K, Taha AY, Pedersen TL, De Jager PH, Bennett DA, Arnold M, Kaddurdah-Daouk R, Newman JW. 2021. Scientific Reports, 11:18964. doi: https://doi.org/10.1038/s41598-021-98640-2.

Association of plasma and CSF cytochrome P450, soluble epoxide hydrolase, and ethanolamide metabolism with Alzheimer’s disease

Borkowski K, Pedersen TL, Seyfried NT, Lah JL, Level AI, Hales CM, Dammer EB, Blach C, Louie G, Kaddurdah-Daouk R, Newman, JW, Alzheimers Disease Metabolomics Consortium. Nature Alzheimer’s Research & Therapy, 13(149). doi: 10.1186/s13195-021-00893-6 .

GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser

Petra D, Phelan VV, Acharya D, Allen AE, Aron AT, Bandeira N, Bowen BP, Belle-Oudry D, Boecker S, Cummings DA, Deutsch JM, Fahy E, Garg N, Gregor R, Handelsman, Navarro-Hoyos, M, Jaarmusch AK, Jarmusch SA, Louie K, Maloney KN, Mart MT, Meijler MM, Mizrahi I, Neve RL, Northen TR, Molina-Santiago C, Panitchpakdi M, Pullman B, Puri AW, Schmid R, Subramaniam S, Thukral M, Vasquez-Castro F, Dorrestein PC, Wang M. 2022. Nature Methods, 19, 134-136. doi: https://doi.org/10.1038/s41592-021-01339-5.

Reduced Independence in Daily Living Is Associated with the Gut Microbiome in People with HIV and HCV

Taylor BC, Weldon KC, Ellis RJ, Franklin RJ, McDonald D, Humphrey D, Humphrey G, Bryant M, Toronczak J, Schwartz T, Iudicello J, Heaton R, Grant I, Gianella S, Letendre S, Swafford A, Dorrestein PC, Knight R. 2020. American Society for Microbiology, 5(5). doi: https://doi.org/10.1128/mSystems.00528-20

Angiopoietin 2 Is Associated with Vascular Necroptosis Induction in Coronavirus Disease 2019 Acute Respiratory Distress Syndrome

Price DR , Benedetti E, Hoffman KL, Gomez-Escobar L, Alvarez-Mulett S, Capili A, Sarwath H, Parkhurst CN, Lafond E, Weidman K, Ravishankar A, Cheong JG, Batra R, Büyüközkan M, Chetnik K, Easthausen I, Schenck EJ, Racanelli AC, Reed HO, Laurence J, Josefowicz SZ, Lief L, Choi ME, Schmidt F, Borczuk AC, Choi AMK, Krumsiek J, Rafii S,. 2022. Am J Patho, 192, 7 1001-1015. doi:10.1016/j.ajpath.2022.04.002..

The landscape of metabolic brain alterations in Alzheimer's disease

Batra R, Arnold M, Wörheide MA, Allen M, Wang X, Blach C, Levey AI, Seyfried NT, Erktekin-Taner N, Bennet DA, Kastenmüller G, Kaddurah-Daouk RF. 2022. Alzheimer’s Dement, 1-19. doi:10.1002/alz.12714.

Metabolomic and inflammatory signatures of symptom dimensions in major depression

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Infection and inflammation: New perspectives on Alzheimer's disease

Whitson HE, Colton C, El Khoury J, Gate D, Goate A, Heneka MT, Kaddurah-Daouk R, Klein RS, Shinohara ML, Sisodia S, Spudich SS, Stevens B, Tanzi R, Ting JP, Garden G, Aiello A, Chiba-Falek O, Heitman J, Johnson KG, Luftig M, Moseman A, Rawls J, Shinohara ML, Swanstrom R, Terrando N. 2022. Brain, Behavior, & Immunity, 22, 100462. doi:10.1016/j.bbih.2022.100462.

MiMeDB: the Human Microbial Metabolome Database.

Wishart DS, Oler E, Peters H, Guo A, Girod S, Han S, Saha S, Lui VW, LeVatte M, Gautam V, Kaddurah-Daouk R, Karu N. Nucleic Acids Research. 2023 Jan;51(D1):D611-D620. DOI: 10.1093/nar/gkac868. PMID: 36215042; PMCID: PMC9825614.

DEMETER: Efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations

Heinken A, Magnúsdóttir S, Fleming RMT, Thiele I. 2021. Bioinformatics, 2;37(21):3974-5, doi:10.1093/bioinformatics/btab622. Epub ahead of print. PMID: 34473240; PMCID: PMC8570805.

MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions.

Thiele I, Preciat G, Fleming RMT. MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions. Bioinformatics. 2022 Oct 14;38(20):4831-4832. doi: 10.1093/bioinformatics/btac596. PMID: 36047841; PMCID: PMC9563688.

Comprehensive genetic analysis of the human lipidome identifies loci associated with lipid homeostasis with links to coronary artery disease

Cadby G, Giles C, Melton PE, Huynh K, Mellett NA, Duong T, Nguyen A, Cinel M, Smith A, Olshansky G, Wang T, Brozynska M, Inouye M, McCarthy NS, Ariff A, Hung J, Hui J, Beilby J, Dubé MP, Watts GF, Shah S, Wray NR, Lim WLF, Chatterjee P, Martins I, Laws SM, Porter T, Vacher M, Bush AI, Rowe CC, Villemagne VL, Ames D, Masters CL, Taddei K, Arnold M, Kastenmüller G, Nho K, Saykin AJ, Han X, Kaddurah-Daouk R, Martins RN, Blangero J, Meikle PJ, Moses EK. 2022. Nat Commun. 2022 Jun 6;13(1):3124. doi: 10.1038/s41467-022-30875-7. PMID: 35668104; PMCID: PMC9170690.

Effects of a ketogenic and low-fat diet on the human metabolome, microbiome, and foodome in adults at risk for Alzheimer's disease

Dilmore, AH, Martino, C, Neth, BJ, West KA, Zemln J, Rahman G, Panitchpakdi M, Meehan MJ, Weldon KC, Blach C, Schimmel L, Kaddurdah-Daouk R, Dorrestein PC, Knight R, Craft, S, Alzheimer Gut Microbiome Project. Alzheimer’s Dement. 2023; 1-12. doi: 10.1002/alz.1300710.1093/bioinformatics/btac596.

Large-scale tandem mass spectrum clustering using fast nearest neighbor searching

Bittremieux W, Laukens K, Noble WS, Dorrestein PC. Large-scale tandem mass spectrum clustering using fast nearest neighbor searching. Rapid Commun Mass Spectrom. 2021 Jun 25:e9153. doi: 10.1002/rcm.9153. Epub ahead of print. PMID: 34169593; PMCID: PMC8709870.

The critical role that spectral libraries play in capturing the metabolomics community knowledge

Bittremieux W, Wang M, Dorrestein PC. The critical role that spectral libraries play in capturing the metabolomics community knowledge. Metabolomics. 2022 Nov 19;18(12):94. doi: 10.1007/s11306-022-01947-y. PMID: 36409434.

Integrative metabolomics-genomics approach reveals key metabolic pathways and regulators of Alzheimer's disease

Horgusluoglu E, Neff R, Song WM, Wang M, Wang Q, Arnold M, Krumsiek J, Galindo-Prieto B, Ming C, Nho K, Kastenmüller G, Han X, Baillie R, Zeng Q, Andrews S, Cheng H, Hao K, Goate A, Bennett DA, Saykin AJ, Kaddurah-Daouk R, Zhang B; Alzheimer’s Disease Neuroimaging Initiative (ADNI); Alzheimer Disease Metabolomics Consortium. Integrative metabolomics-genomics approach reveals key metabolic pathways and regulators of Alzheimer’s disease. Alzheimers Dement. 2022 Jun;18(6):1260-1278. doi: 10.1002/alz.12468. Epub 2021 Nov 10. PMID: 34757660; PMCID: PMC9085975.

SGI: automatic clinical subgroup identification in omics datasets

Buyukozkan M, Suhre K, Krumsiek J. SGI: automatic clinical subgroup identification in omics datasets. Bioinformatics. 2022 Jan 3;38(2):573-576. doi: 10.1093/bioinformatics/btab656. PMID: 34529048; PMCID: PMC8723155.

A gut-derived metabolite alters brain activity and anxiety behaviour in mice

Needham BD, Funabashi M, Adame MD, Wang Z, Boktor JC, Haney J, Wu WL, Rabut C, Ladinsky MS, Hwang SJ, Guo Y, Zhu Q, Griffiths JA, Knight R, Bjorkman PJ, Shapiro MG, Geschwind DH, Holschneider DP, Fischbach MA, Mazmanian SK. A gut-derived metabolite alters brain activity and anxiety behaviour in mice. Nature. 2022 Feb;602(7898):647-653. doi: 10.1038/s41586-022-04396-8. Epub 2022 Feb 14. PMID: 35165440; PMCID: PMC9170029.

Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy

Zhu Q, Huang S, Gonzalez A, McGrath I, McDonald D, Haiminen N, Armstrong G, Vázquez-Baeza Y, Yu J, Kuczynski J, Sepich-Poore GD, Swafford AD, Das P, Shaffer JP, Lejzerowicz F, Belda-Ferre P, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Kim HC, Jain M, Inouye M, Gilbert JA, Knight R. Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy. mSystems. 2022 Apr 26;7(2):e0016722. doi: 10.1128/msystems.00167-22. Epub 2022 Apr 4. PMID: 35369727; PMCID: PMC9040630.

Variational autoencoders learn transferrable representations of metabolomics data

Gomari DP, Schweickart A, Cerchietti L, Paietta E, Fernandez H, Al-Amin H, Suhre K, Krumsiek J. Variational autoencoders learn transferrable representations of metabolomics data. Commun Biol. 2022 Jun 30;5(1):645. doi: 10.1038/s42003-022-03579-3. PMID: 35773471; PMCID: PMC9246987.

Mass spectrometry-based metabolomics in microbiome investigations

Bauermeister A, Mannochio-Russo H, Costa-Lotufo LV, Jarmusch AK, Dorrestein PC. Mass spectrometry-based metabolomics in microbiome investigations. Nat Rev Microbiol. 2022 Mar;20(3):143-160. doi: 10.1038/s41579-021-00621-9. Epub 2021 Sep 22. PMID: 34552265; PMCID: PMC9578303.

High-confidence structural annotation of metabolites absent from spectral libraries

Hoffmann MA, Nothias LF, Ludwig M, Fleischauer M, Gentry EC, Witting M, Dorrestein PC, Dührkop K, Böcker S. High-confidence structural annotation of metabolites absent from spectral libraries. Nat Biotechnol. 2022 Mar;40(3):411-421. doi: 10.1038/s41587-021-01045-9. Epub 2021 Oct 14. PMID: 34650271; PMCID: PMC8926923.

Optimizing UniFrac with OpenACC Yields Greater Than One Thousand Times Speed Increase

Sfiligoi I, Armstrong G, Gonzalez A, McDonald D, Knight R. Optimizing UniFrac with OpenACC Yields Greater Than One Thousand Times Speed Increase. mSystems. 2022 Jun 28;7(3):e0002822. doi: 10.1128/msystems.00028-22. Epub 2022 May 31. PMID: 35638356; PMCID: PMC9239203.

Microbiota succession throughout life from the cradle to the grave

Martino C, Dilmore AH, Burcham ZM, Metcalf JL, Jeste D, Knight R. Microbiota succession throughout life from the cradle to the grave. Nat Rev Microbiol. 2022 Dec;20(12):707-720. doi: 10.1038/s41579-022-00768-z. Epub 2022 Jul 29. PMID: 35906422.

EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

Cantrell K, Fedarko MW, Rahman G, McDonald D, Yang Y, Zaw T, Gonzalez A, Janssen S, Estaki M, Haiminen N, Beck KL, Zhu Q, Sayyari E, Morton JT, Armstrong G, Tripathi A, Gauglitz JM, Marotz C, Matteson NL, Martino C, Sanders JG, Carrieri AP, Song SJ, Swafford AD, Dorrestein PC, Andersen KG, Parida L, Kim HC, Vázquez-Baeza Y, Knight R. EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets. mSystems. 2021 Mar 16;6(2):e01216-20. doi: 10.1128/mSystems.01216-20. PMID: 33727399; PMCID: PMC8546999.

Indoxyl sulfate, a gut microbiome-derived uremic toxin, is associated with psychic anxiety and its functional magnetic resonance imaging-based neurologic signature

Brydges CR, Fiehn O, Mayberg HS, Schreiber H, Dehkordi SM, Bhattacharyya S, Cha J, Choi KS, Craighead WE, Krishnan RR, Rush AJ, Dunlop BW, Kaddurah-Daouk R; Mood Disorders Precision Medicine Consortium. Indoxyl sulfate, a gut microbiome-derived uremic toxin, is associated with psychic anxiety and its functional magnetic resonance imaging-based neurologic signature. Sci Rep. 2021 Oct 25;11(1):21011. doi: 10.1038/s41598-021-99845-1. PMID: 34697401; PMCID: PMC8546034.

Interplay of Metabolome and Gut Microbiome in Individuals With Major Depressive Disorder vs Control Individuals

Amin A, Liu J, Bonnechere B, MahmoudianDehkordi S, Arnold M, Batra R, Chiou Y-J, Fernandes M, Ikram MA, Kraaij R, Krumsiek J, Newby D, Nho K, Radjabzadeh D, Saykin AJ, Shi L, Sproviero S, Winchester W, Yang Y, Nevado-Holgado AJ, Kastenmüller G, Kaddurah-Daouk R, van Duijn CM. JAMA Psychiatry. 2023 Published online April 19, 2023. doi:10.1001/jamapsychiatry.2023.0685

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine

Heinken A, Hertel J, Acharya G, Ravcheev DA, Nyga M, Okpala OE, Hogan M, Magnúsdóttir S, Martinelli F, Nap B, Preciat G, Edirisinghe JN, Henry CS, Fleming RMT, Thiele I. Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine. Nat Biotechnol. 2023 Jan 19. doi: 10.1038/s41587-022-01628-0. Epub ahead of print. PMID: 36658342.

Circulating metabolites modulated by diet are associated with depression

van der Spek A, Stewart ID, Kühnel B, Pietzner M, Alshehri T, Gauß F, Hysi PG, MahmoudianDehkordi S, Heinken A, Luik AI, Ladwig K-H, Kastenmüller G, Menni C, Hertel J, Ikram MA, Mutsert R, Suhre K, Gieger C, Strauch K, Völzke H, Meitinger T, Mangino M, Flaquer A, Waldenberger M, Peters A, Thiele I, Kaddurah-Daouk R, Dunlop BW, Rosendaal FR, Wareham NJ, Spector TD, Junze S, Grabe HJ, Mook-Kanamori DO, Langenberg C, van Duin CM, & Amin N. Molecular Psychiatry. 2023
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Gut Microbiome-Linked Metabolites in the Pathobiology of Major Depression With or Without Anxiety-A Role for Bile Acids

MahmoudianDehkordi S, Bhattacharyya S, Brydges CR, Jia W, Fiehn O, Rush AJ, Dunlop BW, Kaddurah-Daouk R. Gut Microbiome-Linked Metabolites in the Pathobiology of Major Depression With or Without Anxiety-A Role for Bile Acids. Front Neurosci. 2022 Jul 20;16:937906. doi: 10.3389/fnins.2022.937906. PMID: 35937867; PMCID: PMC9350527.

Comparative metabolomics and microbiome analysis of Ethanol vs. OMNImet/gene®•GUT fecal stabilization

Isokääntä H, Pinto da Silva L, Karu N, Kallonen T, Aatsinki A, Hankemeier T, Schimmel L , Diaz E, Hyötyläinen T, Dorrestein P, Knight R, Oresic M, Kaddurah-Daouk R, Dickens A, Lamichhane S, Alzheimer Gut Microbiome Project. bioRxiv 2023.08.29.555241; doi: https://doi.org/10.1101/2023.08.29.555241

BIRDMAn: A Bayesian differential abundance framework that enables robust inference of host-microbe associations

Rahman G, Morton JT, Martino C, Sepich-Poore GD, Allaband C, Guccione C, Chen Y, Hakim D, Estaki M, Knight R. BIRDMAn: A Bayesian differential abundance framework that enables robust inference of host-microbe associations. bioRxiv [Preprint]. 2023 Feb 2:2023.01.30.526328. doi: 10.1101/2023.01.30.526328. PMID: 36778470; PMCID: PMC9915500.

Urine-based multi-omic comparative analysis of COVID-19 and bacterial sepsis-induced ARDS

Batra R, Uni R, Akchurin OM, Alvarez-Mulett S, Gómez-Escobar LG, Patino E, Hoffman KL, Simmons W, Whalen W, Chetnik K, Buyukozkan M, Benedetti E, Suhre K, Schenck E, Cho SJ, Choi AMK, Schmidt F, Choi ME, Krumsiek J. Urine-based multi-omic comparative analysis of COVID-19 and bacterial sepsis-induced ARDS. Mol Med. 2023 Jan 26;29(1):13. doi: 10.1186/s10020-023-00609-6. PMID: 36703108; PMCID: PMC9879238.

Predictive metabolic networks reveal sex- and APOE genotype-specific metabolic signatures and drivers for precision medicine in Alzheimer's disease

Chang R, Trushina E, Zhu K, Zaidi SSA, Lau BM, Kueider-Paisley A, Moein S, He Q, Alamprese ML, Vagnerova B, Tang A, Vijayan R, Liu Y, Saykin AJ, Brinton RD, Kaddurah-Daouk R; Alzheimer’s Disease Neuroimaging Initiative† and the Alzheimer’s Disease Metabolomics Consortium. Predictive metabolic networks reveal sex- and APOE genotype-specific metabolic signatures and drivers for precision medicine in Alzheimer’s disease. Alzheimers Dement. 2023 Feb;19(2):518-531. doi: 10.1002/alz.12675. Epub 2022 Apr 28. PMID: 35481667; PMCID: PMC10402890.

The Gut Microbial Bile Acid Modulation and Its Relevance to Digestive Health and Diseases

Fogelson KA, Dorrestein PC, Zarrinpar A, Knight R. The Gut Microbial Bile Acid Modulation and Its Relevance to Digestive Health and Diseases. Gastroenterology. 2023 Jun;164(7):1069-1085. doi: 10.1053/j.gastro.2023.02.022. Epub 2023 Feb 24. Erratum in: Gastroenterology. 2024 Jan;166(1):228. PMID: 36841488; PMCID: PMC10205675.

Differences and commonalities in the genetic architecture of protein quantitative trait loci in European and Arab populations

Thareja G, Belkadi A, Arnold M, Albagha OME, Graumann J, Schmidt F, Grallert H, Peters A, Gieger C, Consortium TQGPR, Suhre K. Differences and commonalities in the genetic architecture of protein quantitative trait loci in European and Arab populations. Hum Mol Genet. 2023 Mar 6;32(6):907-916. doi: 10.1093/hmg/ddac243. PMID: 36168886; PMCID: PMC9990988.

Signatures of HIV and Major Depressive Disorder in the Plasma Microbiome

Taylor BC, Sheikh Andalibi M, Wandro S, Weldon KC, Sepich-Poore GD, Carpenter CS, Fraraccio S, Franklin D, Iudicello JE, Letendre S, Gianella S, Grant I, Ellis RJ, Heaton RK, Knight R, Swafford AD. Signatures of HIV and Major Depressive Disorder in the Plasma Microbiome. Microorganisms. 2023 Apr 14;11(4):1022. doi: 10.3390/microorganisms11041022. PMID: 37110445; PMCID: PMC10146336.

Testing GitHub projects on custom resources using unprivileged Kubernetes runners

Sfiligoi I, McDonald D, Knight R, & Würthwein F. 2023. Testing GitHub projects on custom resources using unprivileged Kubernetes runners. In Practice and Experience in Advanced Research Computing (PEARC ’23). Association for Computing Machinery, New York, NY, USA, 332–335. https://doi.org/10.1145/3569951.3597586

Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta

Noecker C, Sanchez J, Bisanz JE, Escalante V, Alexander M, Trepka K, Heinken A, Liu Y, Dodd D, Thiele I, DeFelice BC, Turnbaugh PJ. Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta. PLoS Biol. 2023 May 19;21(5):e3002125. doi: 10.1371/journal.pbio.3002125. PMID: 37205710; PMCID: PMC10234575.

Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution

Brennan C, Salido RA, Belda-Ferre P, Bryant M, Cowart C, Tiu MD, González A, McDonald D, Tribelhorn C, Zarrinpar A, Knight R. Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution. mSystems. 2023 Aug 31;8(4):e0000623. doi: 10.1128/msystems.00006-23. Epub 2023 Jun 23. PMID: 37350611; PMCID: PMC10469589.

Determination of Effect Sizes for Power Analysis for Microbiome Studies Using Large Microbiome Databases

Rahman G, McDonald D, Gonzalez A, Vázquez-Baeza Y, Jiang L, Casals-Pascual C, Hakim D, Dilmore AH, Nowinski B, Peddada S, Knight R. Determination of Effect Sizes for Power Analysis for Microbiome Studies Using Large Microbiome Databases. Genes (Basel). 2023 Jun 9;14(6):1239. doi: 10.3390/genes14061239. PMID: 37372419; PMCID: PMC10297957.

Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics

Basile A, Heinken A, Hertel J, Smarr L, Li W, Treu L, Valle G, Campanaro S, Thiele I. Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics. Gut Microbes. 2023 Jan-Dec;15(1):2226921. doi: 10.1080/19490976.2023.2226921. PMID: 37438876; PMCID: PMC10339767.

A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data

Zuffa S, Schmid R, Bauermeister A, Gomes PWP, Caraballo-Rodriguez AM, Abiead YE, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, de Cassia Pessotti R, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, Dos Santos MS, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, de León AVP, Pope PB, Rosa SL, Barbera G, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O’Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, Dorrestein PC. A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data. Res Sq [Preprint]. 2023 Aug 3:rs.3.rs-3189768. doi: 10.21203/rs.3.rs-3189768/v1. Update in: Nat Microbiol. 2024 Feb;9(2):336-345. PMID: 37577622; PMCID: PMC10418563.

Trajectory of plasma lipidomes associated with the risk of late-onset Alzheimer’s disease pathogenesis: a longitudinal study in the ADNI cohort

Wang T, Arnold M, Huynh K, Weinisch P, Giles C, Mellett NA, Duong T, Marella B, Nho K, De Livera A, Han X, Blach C, Saykin AJ, Kastenmüller G, Meikle PJ, Kaddurah-Daouk R, the Alzheimer’s Disease Neuroimaging Initiative. medRxiv 2023.06.07.23291081; doi: https://doi.org/10.1101/2023.06.07.23291081

Circulating lipid profiles are associated with cross-sectional and longitudinal changes of central biomarkers for Alzheimer's disease

Kim JP, Nho K, Wang T, Huynh K, Arnold M, Risacher SL, Bice PJ, Han X, Kristal BS, Blach C, Baillie R, Kastenmüller G, Meikle PJ, Saykin AJ, Kaddurah-Daouk R; Alzheimer’s Disease Neuroimaging Initiative; Alzheimer’s Disease Metabolomics Consortium. Circulating lipid profiles are associated with cross-sectional and longitudinal changes of central biomarkers for Alzheimer’s disease. medRxiv [Preprint]. 2023 Jun 21:2023.06.12.23291054. doi: 10.1101/2023.06.12.23291054. PMID: 37398438; PMCID: PMC10312871.

Therapeutic potential of a modified Mediterranean ketogenic diet in reversing the peripheral lipid signature of Alzheimer’s disease

Neth BJ, Huynh K, Giles C, Wang T, Mellett NA, Duong T, Blach C, Schimmel L, Register TC, Blennow K, Zetterberg H, Batra R, Schweickart A, Dilmore AH, Martino C, Arnold M, Krumsiek J, Han X, Dorrestein PC, Knight R, Meikle PJ, Craft S, Kaddurah-Daouk R medRxiv 2023.06.13.23291049; doi: https://doi.org/10.1101/2023.06.13.23291049

Greengenes2 unifies microbial data in a single reference tree

McDonald D, Jiang Y, Balaban M, Cantrell K, Zhu Q, Gonzalez A, Morton JT, Nicolaou G, Parks DH, Karst SM, Albertsen M, Hugenholtz P, DeSantis T, Song SJ, Bartko A, Havulinna AS, Jousilahti P, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Lahti L, Mirarab S, Knight R. Greengenes2 unifies microbial data in a single reference tree. Nat Biotechnol. 2023 Jul 27:10.1038/s41587-023-01845-1. doi: 10.1038/s41587-023-01845-1. Epub ahead of print. Erratum in: Nat Biotechnol. 2023 Oct 18;: PMID: 37500913; PMCID: PMC10818020.

Generation of accurate, expandable phylogenomic trees with uDance

Balaban M, Jiang Y, Zhu Q, McDonald D, Knight R, Mirarab S. Generation of accurate, expandable phylogenomic trees with uDance. Nat Biotechnol. 2023 Jul 27:10.1038/s41587-023-01868-8. doi: 10.1038/s41587-023-01868-8. Epub ahead of print. Erratum in: Nat Biotechnol. 2023 Oct 18;: PMID: 37500914; PMCID: PMC10818028.

Comparative brain metabolomics reveals shared and distinct metabolic alterations in Alzheimer’s disease and progressive supranuclear palsy

Batra R, Krumsiek J, Wang X, Allen M, Blach C, Kastenmüller G, Arnold M, Ertekin-Taner N, Kaddurah-Daouk RF; Alzheimer’s Disease Metabolomics Consortium (ADMC). Comparative brain metabolomics reveals shared and distinct metabolic alterations in Alzheimer’s disease and progressive supranuclear palsy. medRxiv [Preprint]. 2023 Jul 27:2023.07.25.23293055. doi: 10.1101/2023.07.25.23293055. PMID: 37546878; PMCID: PMC10402214.

The HuMet Repository: Watching human metabolism at work

Weinisch P, Raffler J, Römisch-Margl W, Arnold M, Mohney RP, Rist MJ, Prehn C, Skurk T, Hauner H, Daniel H, Suhre K, Kastenmüller G. The HuMet Repository: Watching human metabolism at work. bioRxiv [Preprint]. 2023 Aug 9:2023.08.08.550079. doi: 10.1101/2023.08.08.550079. PMID: 37609175; PMCID: PMC10441358.

Integration of plasma and CSF metabolomics with CSF proteomic reveals novel associations between lipid mediators and central nervous system vascular and energy metabolism

Borkowski K, Seyfried NT, Arnold M, Lah JJ, Levey AI, Hales CM, Dammer EB, Blach C, Louie G, Kaddurah-Daouk R, Newman JW. Integration of plasma and CSF metabolomics with CSF proteomic reveals novel associations between lipid mediators and central nervous system vascular and energy metabolism. Sci Rep. 2023 Aug 23;13(1):13752. doi: 10.1038/s41598-023-39737-8. PMID: 37612324; PMCID: PMC10447532.

Cardinality optimization in constraint-based modelling: application to human metabolism.

Fleming RMT, Haraldsdottir HS, Minh LH, Vuong PT, Hankemeier T, Thiele I. Cardinality optimization in constraint-based modelling: application to human metabolism. Bioinformatics. 2023 Sep 2;39(9):btad450. doi: 10.1093/bioinformatics/btad450. PMID: 37697651; PMCID: PMC10495685.

Whole-body modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer’s disease

Martinelli F, Heinken A, Henning AK, Wörheide MA, Hensen T, González A, Arnold M, Asthana S, Budde K, Engelman CD, Estaki M, Grabe HJ, Heston M, Johnson S, Kastenmüller G, Martino C, McDonald D, Rey F, Kilimann I, Peters O, Wang X, Spruth EJ, Schneider A, Fliessbach K, Wiltfang J, Hansen N, Glanz W, Buerger K, Janowitz D, Laske C, Munk MH, Spottke A, Roy N, Nauck M, Teipel S, Knight R, Kaddurah-Daouk R, Bendlin BB, Hertel J, Thiele I. Whole-body modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer’s disease. Res Sq [Preprint]. 2023 Sep 6:rs.3.rs-3306891. doi: 10.21203/rs.3.rs-3306891/v1. PMID: 37720019; PMCID: PMC10503865.

AutoFocus: A hierarchical framework to explore multi-omic disease associations spanning multiple scales of biomolecular interaction

Schweickart A, Chetnik K, Batra R, Kaddurah-Daouk R, Suhre K, Halama A, Krumsiek A

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Brain cross-omics integration in Alzheimer’s disease

Eteleeb AM, Novotny BC, Tarraga CS, Sohn C, Dhungel E, Brase L, Nallapu A, Buss J, Farias F, Bergmann K, Bradley J, Norton J, Gentsch J, Wang F, Davis AA, Morris JC, Karch CM, Perrin RJ, Benitez BA, Harari O

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The Metabolome-Wide Signature of Major Depressive Disorder

Jansen R, Milaneschi Y, Schranner D, Kastenmuller G, Arnold M, Han X, Dunlop BW; Mood Disorder Precision Medicine Consortium; Rush AJ, Kaddurah-Daouk R, Penninx BW. The Metabolome-Wide Signature of Major Depressive Disorder. Res Sq [Preprint]. 2023 Sep 21:rs.3.rs-3127544. doi: 10.21203/rs.3.rs-3127544/v1. PMID: 37790319; PMCID: PMC10543022.

Associations of circulating saturated long-chain fatty acids with risk of mild cognitive impairment and Alzheimer’s disease in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort

Fan L, Borenstein AR, Wang S, Nho K, Zhu X, Wen W, Huang X, Mortimer JA, Shrubsole MJ, Dai Q; Alzheimer’s Disease Neuroimaging Initiative. Associations of circulating saturated long-chain fatty acids with risk of mild cognitive impairment and Alzheimer’s disease in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort. EBioMedicine. 2023 Nov;97:104818. doi: 10.1016/j.ebiom.2023.104818. Epub 2023 Oct 2. PMID: 37793213; PMCID: PMC10562835.

APOLLO: A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites

Heinken A, Hulshof TO, Nap B, Martinelli F, Basile A, O’Brolchain A, O’Sullivan NF, Gallagher C, Magee E, McDonagh F, Lalor I, Bergin M, Evans P, Daly R, Farrell R, Delaney RM, Hill S, McAuliffe SR, Kilgannon T, Fleming RMT, Thinnes CC, Thiele I. APOLLO: A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites. bioRxiv [Preprint]. 2023 Oct 3:2023.10.02.560573. doi: 10.1101/2023.10.02.560573. PMID: 37873072; PMCID: PMC10592896.

Circular-SWAT for deep learning based diagnostic classification of Alzheimer's disease: application to metabolome data

Jo T, Kim J, Bice P, Huynh K, Wang T, Arnold M, Meikle PJ, Giles C, Kaddurah-Daouk R, Saykin AJ, Nho K; Alzheimer’s Disease Metabolomics Consortium (ADMC); Alzheimer’s Disease Neuroimaging Initiative (ADNI). Circular-SWAT for deep learning based diagnostic classification of Alzheimer’s disease: application to metabolome data. EBioMedicine. 2023 Nov;97:104820. doi: 10.1016/j.ebiom.2023.104820. Epub 2023 Oct 7. PMID: 37806288; PMCID: PMC10579282.

Causal inference on microbiome-metabolome relations in observational host-microbiome data via in silico in vivo association pattern analyses

Hertel J, Heinken A, Fässler D, Thiele I. Causal inference on microbiome-metabolome relations in observational host-microbiome data via in silico in vivo association pattern analyses. Cell Rep Methods. 2023 Oct 23;3(10):100615. doi: 10.1016/j.crmeth.2023.100615. Epub 2023 Oct 16. PMID: 37848031; PMCID: PMC10626217.

Oxylipin transport by lipoprotein particles and its functional implications for cardiometabolic and neurological disorders

Liang N, Harsch BA, Zhou S, Borkowska A, Shearer GC, Kaddurah-Daouk R, Newman JW, Borkowski K. Oxylipin transport by lipoprotein particles and its functional implications for cardiometabolic and neurological disorders. Prog Lipid Res. 2024 Jan;93:101265. doi: 10.1016/j.plipres.2023.101265. Epub 2023 Nov 17. PMID: 37979798.

A Modified Mediterranean Ketogenic Diet mitigates modifiable risk factors of Alzheimer's Disease: a serum and CSF-based metabolic analysis

Schweickart A, Batra R, Neth BJ, Martino C, Shenhav L, Zhang AR, Shi P, Karu N, Huynh K, Meikle PJ, Schimmel L, Dilmore AH, Blennow K, Zetterberg H, Blach C, Dorrestein PC, Knight R; Alzheimer’s Gut Microbiome Project Consortium; Craft S, Kaddurah-Daouk R, Krumsiek J. A Modified Mediterranean Ketogenic Diet mitigates modifiable risk factors of Alzheimer’s Disease: a serum and CSF-based metabolic analysis. medRxiv [Preprint]. 2023 Nov 27:2023.11.27.23298990. doi: 10.1101/2023.11.27.23298990. PMID: 38076824; PMCID: PMC10705656.

Oxylipin transport by lipoprotein particles and its functional implications for cardiometabolic and neurological disorders

Liang N, Nho K, Newman JW, Arnold M, Huynh K, Meikle PJ, Borkowski K, Kaddurah-Daouk R, Consortium AsDM, Initiative AsDN. Peripheral inflammation is associated with structural brain atrophy and cognitive decline linked to mild cognitive impairment and Alzheimer’s disease. medRxiv. 2023:2023.12.08.23299734. doi: 10.1101/2023.12.08.23299734. PubMed PMID: pub.1166896419.

Serum Bile Acids Improve Prediction of Alzheimer's Progression in a Sex‐Dependent Manner

Chen T, Wang L, Xie G, Kristal BS, Zheng X, Sun T, Arnold M, Louie G, Li M, Wu L, Mahmoudiandehkordi S, Sniatynski MJ, Borkowski K, Guo Q, Kuang J, Wang J, Nho K, Ren Z, Kueider-Paisley A, Blach C, Kaddurah-Daouk R, Jia W; Alzheimer’s Disease Neuroimaging Initiative (ADNI) and the Alzheimer Disease Metabolomics Consortium (ADMC). Serum Bile Acids Improve Prediction of Alzheimer’s Progression in a Sex-Dependent Manner. Adv Sci (Weinh). 2024 Mar;11(9):e2306576. doi: 10.1002/advs.202306576. Epub 2023 Dec 13. PMID: 38093507; PMCID: PMC10916590.

Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics

Bittremieux W, Avalon NE, Thomas SP, Kakhkhorov SA, Aksenov AA, Gomes PWP, Aceves CM, Caraballo-Rodríguez AM, Gauglitz JM, Gerwick WH, Huan T, Jarmusch AK, Kaddurah-Daouk RF, Kang KB, Kim HW, Kondić T, Mannochio-Russo H, Meehan MJ, Melnik AV, Nothias LF, O’Donovan C, Panitchpakdi M, Petras D, Schmid R, Schymanski EL, van der Hooft JJJ, Weldon KC, Yang H, Xing S, Zemlin J, Wang M, Dorrestein PC. Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics. Nat Commun. 2023 Dec 20;14(1):8488. doi: 10.1038/s41467-023-44035-y. PMID: 38123557; PMCID: PMC10733301.

Can the gut microbiome inform the effects of omega-3 fatty acid supplementation trials on cognition?

Kerman BE, Self W, Yassine HN. Can the gut microbiome inform the effects of omega-3 fatty acid supplementation trials on cognition? Curr Opin Clin Nutr Metab Care. 2024 Mar 1;27(2):116-124. doi: 10.1097/MCO.0000000000001007. Epub 2023 Dec 22. PMID: 38170690; PMCID: PMC10872319.

Metabolomics profiling reveals distinct, sex-specific signatures in the serum and brain metabolomes in the mouse models of Alzheimer’s disease

Pandey, R.S., Hoffmann, B., Arnold, M., Greene, A.S., Kaddurah-Daouk, R.F. and Carter, G.W. (2022), Metabolomics profiling reveals distinct signatures in the serum and brain metabolomes in mouse models of Alzheimer’s Disease. Alzheimer’s Dement., 18: e064137. https://doi.org/10.1002/alz.064137

longmixr: a tool for robust clustering of high-dimensional cross-sectional and longitudinal variables of mixed data types

Hagenberg J, Budde M, Pandeva T, Kondofersky I, Schaupp SK, Theis FJ, Schulze TG, Müller NS, Heilbronner U, Batra R, Knauer-Arloth J. longmixr: a tool for robust clustering of high-dimensional cross-sectional and longitudinal variables of mixed data types. Bioinformatics. 2024 Mar 29;40(4):btae137. doi: 10.1093/bioinformatics/btae137. PMID: 38485697; PMCID: PMC10994717.

Individual bioenergetic capacity as a potential source of resilience to Alzheimer’s disease

Arnold M, Buyukozkan M, Doraiswamy PM, Nho K, Wu T, Gudnason V, Launer LJ, Wang-Sattler R, Adamski J; Alzheimer’s Disease Neuroimaging Initiative; Alzheimer’s Disease Metabolomics Consortium; De Jager PL, Ertekin-Taner N, Bennett DA, Saykin AJ, Peters A, Suhre K, Kaddurah-Daouk R, Kastenmüller G, Krumsiek J. Individual bioenergetic capacity as a potential source of resilience to Alzheimer’s disease. medRxiv [Preprint]. 2024 Jan 24:2024.01.23.23297820. doi: 10.1101/2024.01.23.23297820. PMID: 38313266; PMCID: PMC10836119.

microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data

Zuffa S, Schmid R, Bauermeister A, P Gomes PW, Caraballo-Rodriguez AM, El Abiead Y, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, Pessotti RC, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, Silva Dos Santos M, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, Vera Ponce de León A, Pope PB, La Rosa SL, La Barbera G, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O’Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, Dorrestein PC. microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data. Nat Microbiol. 2024 Feb;9(2):336-345. doi: 10.1038/s41564-023-01575-9. Epub 2024 Feb 5. PMID: 38316926; PMCID: PMC10847041.

Acylcarnitines metabolism in depression: association with diagnostic status, depression severity and symptom profile in the NESDA cohort

Montanari S, Jansen R, Schranner D, Kastenmüller G, Arnold M, Janiri D, Sani G, Bhattacharyya S, Dehkordi SM, Dunlop BW, Rush AJ, Penninx BWHJ, Kaddurah-Daouk R, Milaneschi Y. Acylcarnitines metabolism in depression: association with diagnostic status, depression severity and symptom profile in the NESDA cohort. medRxiv [Preprint]. 2024 Feb 15:2024.02.14.24302813. doi: 10.1101/2024.02.14.24302813. PMID: 38405847; PMCID: PMC10889013.

New directions for Alzheimer's disease research from the Jackson Laboratory Center for Alzheimer's and Dementia Research 2022 workshop

Telpoukhovskaia MA, Murdy TJ, Marola OJ, Charland K, MacLean M, Luquez T, Lish AM, Neuner S, Dunn A, Onos KD, Wiley J, Archer D, Huentelman MJ, Arnold M, Menon V, Goate A, Van Eldik LJ, Territo PR, Howell GR, Carter GW, O’Connell KMS, Kaczorowski CC; 2022 JAX CADR Workshop. New directions for Alzheimer’s disease research from the Jackson Laboratory Center for Alzheimer’s and Dementia Research 2022 workshop. Alzheimers Dement (N Y). 2024 Mar 10;10(1):e12458. doi: 10.1002/trc2.12458. PMID: 38469553; PMCID: PMC10925728.

The underappreciated diversity of bile acid modifications

Mohanty I, Mannochio-Russo H, Schweer JV, El Abiead Y, Bittremieux W, Xing S, Schmid R, Zuffa S, Vasquez F, Muti VB, Zemlin J, Tovar-Herrera OE, Moraïs S, Desai D, Amin S, Koo I, Turck CW, Mizrahi I, Kris-Etherton PM, Petersen KS, Fleming JA, Huan T, Patterson AD, Siegel D, Hagey LR, Wang M, Aron AT, Dorrestein PC. The underappreciated diversity of bile acid modifications. Cell. 2024 Mar 28;187(7):1801-1818.e20. doi: 10.1016/j.cell.2024.02.019. Epub 2024 Mar 11. PMID: 38471500.

Whole-body metabolic modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer's disease

Martinelli F, Heinken A, Henning AK, Ulmer MA, Hensen T, González A, Arnold M, Asthana S, Budde K, Engelman CD, Estaki M, Grabe HJ, Heston MB, Johnson S, Kastenmüller G, Martino C, McDonald D, Rey FE, Kilimann I, Peters O, Wang X, Spruth EJ, Schneider A, Fliessbach K, Wiltfang J, Hansen N, Glanz W, Buerger K, Janowitz D, Laske C, Munk MH, Spottke A, Roy N, Nauck M, Teipel S, Knight R, Kaddurah-Daouk RF, Bendlin BB, Hertel J, Thiele I. Whole-body metabolic modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer’s disease. Sci Rep. 2024 Mar 13;14(1):6095. doi: 10.1038/s41598-024-55960-3. PMID: 38480804; PMCID: PMC10937638..

Medication Use is Associated with Distinct Microbial Features in Anxiety and Depression

Dilmore AH, Kuplicki R, McDonald D, Kumar M, Estaki M, Youngblut N, Tyakht A, Ackermann G, Blach C, MahmoudianDehkordi S, Dunlop BW, Bhattacharyya S, Guinjoan S, Mandaviya P, Ley RE, Kaddaruh-Dauok R, Paulus MP, Knight R; Alzheimer Gut Microbiome Project Consortium. Medication Use is Associated with Distinct Microbial Features in Anxiety and Depression. bioRxiv [Preprint]. 2024 Mar 19:2024.03.19.585820. doi: 10.1101/2024.03.19.585820. PMID: 38562901; PMCID: PMC10983923.

The changing metabolic landscape of bile acids - keys to metabolism and immune regulation

Mohanty I, Allaband C, Mannochio-Russo H, El Abiead Y, Hagey LR, Knight R, Dorrestein PC. The changing metabolic landscape of bile acids – keys to metabolism and immune regulation. Nat Rev Gastroenterol Hepatol. 2024 Apr 4. doi: 10.1038/s41575-024-00914-3. Epub ahead of print. PMID: 38575682.

Comparative Metabolomics and Microbiome Analysis of Ethanol versus OMNImet/gene•GUT Fecal Stabilization

Isokääntä H, Pinto da Silva L, Karu N, Kallonen T, Aatsinki AK, Hankemeier T, Schimmel L, Diaz E, Hyötyläinen T, Dorrestein PC, Knight R, Orešič M, Kaddurah-Daouk R, Dickens AM, Lamichhane S. Comparative Metabolomics and Microbiome Analysis of Ethanol versus OMNImet/gene•GUT Fecal Stabilization. Anal Chem. 2024 Jun 4;96(22):8893-8904. doi: 10.1021/acs.analchem.3c04436. Epub 2024 May 23. PMID: 38782403; PMCID: PMC11154662.

α-Synuclein Overexpression and the Microbiome Shape the Gut and Brain Metabolome in Mice

Morais LH, Boktor JC, MahmoudianDehkordi S, Kaddurah-Daouk R, Mazmanian SK. α-synuclein overexpression and the microbiome shape the gut and brain metabolome in mice. NPJ Parkinsons Dis. 2024 Oct 30;10(1):208. doi: 10.1038/s41531-024-00816-w. PMID: 39477976; PMCID: PMC11525669.

Serum and CSF metabolomics analysis shows Mediterranean Ketogenic Diet mitigates risk factors of Alzheimer’s disease

Schweickart A, Batra R, Neth BJ, Martino C, Shenhav L, Zhang AR, Shi P, Karu N, Huynh K, Meikle PJ, Schimmel L, Dilmore AH, Blennow K, Zetterberg H, Blach C, Dorrestein PC, Knight R; Alzheimer’s Gut Microbiome Project Consortium; Craft S, Kaddurah-Daouk R, Krumsiek J. Serum and CSF metabolomics analysis shows Mediterranean Ketogenic Diet mitigates risk factors of Alzheimer’s disease. NPJ Metab Health Dis. 2024;2(1):15. doi: 10.1038/s44324-024-00016-3. Epub 2024 Jul 1. PMID: 38962750; PMCID: PMC11216994.

The metabolome-wide signature of major depressive disorder

Jansen R, Milaneschi Y, Schranner D, Kastenmuller G, Arnold M, Han X, Dunlop BW; Mood Disorder Precision Medicine Consortium; Rush AJ, Kaddurah-Daouk R, Penninx BW. The Metabolome-Wide Signature of Major Depressive Disorder. Res Sq [Preprint]. 2023 Sep 21:rs.3.rs-3127544. doi: 10.21203/rs.3.rs-3127544/v1. Update in: Mol Psychiatry. 2024 Jun 7. doi: 10.1038/s41380-024-02613-6. PMID: 37790319; PMCID: PMC10543022.

Effects of intensive lifestyle changes on the progression of mild cognitive impairment or early dementia due to Alzheimer's disease: a randomized, controlled clinical trial.

Ornish D, Madison C, Kivipelto M, Kemp C, McCulloch CE, Galasko D, Artz J, Rentz D, Lin J, Norman K, Ornish A, Tranter S, DeLamarter N, Wingers N, Richling C, Kaddurah-Daouk R, Knight R, McDonald D, Patel L, Verdin E, E Tanzi R, Arnold SE. Effects of intensive lifestyle changes on the progression of mild cognitive impairment or early dementia due to Alzheimer’s disease: a randomized, controlled clinical trial. Alzheimers Res Ther. 2024 Jun 7;16(1):122. doi: 10.1186/s13195-024-01482-z. PMID: 38849944; PMCID: PMC11157928.

The HuMet Repository: Watching human metabolism at work

Weinisch P, Raffler J, Römisch-Margl W, Arnold M, Mohney RP, Rist MJ, Prehn C, Skurk T, Hauner H, Daniel H, Suhre K, Kastenmüller G. The HuMet Repository: Watching human metabolism at work. bioRxiv [Preprint]. 2023 Aug 9:2023.08.08.550079. doi: 10.1101/2023.08.08.550079. Update in: Cell Rep. 2024 Jul 20;43(8):114416. doi: 10.1016/j.celrep.2024.114416. PMID: 37609175; PMCID: PMC10441358.

Peripheral inflammation is associated with brain atrophy and cognitive decline linked to mild cognitive impairment and Alzheimer’s disease

Liang N, Nho K, Newman JW, Arnold M, Huynh K, Meikle PJ, Borkowski K, Kaddurah-Daouk R; Alzheimer’s Disease Metabolomics Consortium. Peripheral inflammation is associated with brain atrophy and cognitive decline linked to mild cognitive impairment and Alzheimer’s disease. Sci Rep. 2024 Jul 29;14(1):17423. doi: 10.1038/s41598-024-67177-5. PMID: 39075118; PMCID: PMC11286782.

Microbial metabolism marvels: a comprehensive review of microbial drug transformation capabilities

Martinelli F, Thiele I. Microbial metabolism marvels: a comprehensive review of microbial drug transformation capabilities. Gut Microbes. 2024 Jan-Dec;16(1):2387400. doi: 10.1080/19490976.2024.2387400. Epub 2024 Aug 16. PMID: 39150897; PMCID: PMC11332652.

Interlaboratory comparison of standardised metabolomics and lipidomics analyses in human and rodent blood using the MxP® Quant 500 kit

Zararsiz GE, Lintelmann J, Cecil A, Kirwan J, Poschet G, Gegner HM, Schuchardt S, Guan XL, Saigusa D, Wishart D, Zheng J, Mandal R, Adams K, Thompson JW, Snyder MP, Contrepois K, Chen S, Ashrafi N, Akyol S, Yilmaz A, Graham SF, O’Connell TM, Kalecký K, Bottiglieri T, Limonciel A, Pham HT, Koal T, Adamski J, Kastenmüller G. Interlaboratory comparison of standardised metabolomics and lipidomics analyses in human and rodent blood using the MxP® Quant 500 kit. bioRxiv [Preprint]. 2024 Nov 14:2024.11.13.619447. doi: 10.1101/2024.11.13.619447. PMID: 39605511; PMCID: PMC11601468.

Multiplatform metabolomic interlaboratory study of a whole human stool candidate reference material from omnivore and vegan donors

Cruz AK, Alves MA, Andresson T, Bayless AL, Bloodsworth KJ, Bowden JA, Bullock K, Burnet MC, Neto FC, Choy A, Clish CB, Couvillion SP, Cumeras R, Dailey L, Dallmann G, Davis WC, Deik AA, Dickens AM, Djukovic D, Dorrestein PC, Eder JG, Fiehn O, Flores R, Gika H, Hagiwara KA, Pham TH, Harynuk JJ, Aristizabal-Henao JJ, Hoyt DW, Jean-François F, Kråkström M, Kumar A, Kyle JE, Lamichhane S, Li Y, Nam SL, Mandal R, de la Mata AP, Meehan MJ, Meikopoulos T, Metz TO, Mouskeftara T, Munoz N, Gowda GAN, Orešic M, Panitchpakdi M, Pierre-Hugues S, Raftery D, Rushing B, Schock T, Seifried H, Servetas S, Shen T, Sumner S, Carrillo KST, Thibaut D, Trejo JB, Van Meulebroek L, Vanhaecke L, Virgiliou C, Weldon KC, Wishart DS, Zhang L, Zheng J, Da Silva S. Multiplatform metabolomic interlaboratory study of a whole human stool candidate reference material from omnivore and vegan donors. Metabolomics. 2024 Nov 4;20(6):125. doi: 10.1007/s11306-024-02185-0. PMID: 39495321.

Comparative brain metabolomics reveals shared and distinct metabolic alterations in Alzheimer's disease and progressive supranuclear palsy

Batra R, Krumsiek J, Wang X, Allen M, Blach C, Kastenmüller G, Arnold M, Ertekin-Taner N, Kaddurah-Daouk R; Alzheimer’s Disease Metabolomics Consortium (ADMC). Comparative brain metabolomics reveals shared and distinct metabolic alterations in Alzheimer’s disease and progressive supranuclear palsy. Alzheimers Dement. 2024 Oct 22. doi: 10.1002/alz.14249. Epub ahead of print. PMID: 39439201.

Empirically establishing drug exposure records directly from untargeted metabolomics data.

Zhao HN, Kvitne KE, Brungs C, Mohan S, Charron-Lamoureux V, Bittremieux W, Tang R, Schmid R, Lamichhane S, El Abiead Y, Andalibi MS, Mannochio-Russo H, Ambre M, Avalon NE, Bryant M, Caraballo-Rodríguez AM, Maya MC, Chin L, Ellis RJ, Franklin D, Girod S, Gomes PWP, Hansen L, Heaton R, Iudicello JE, Jarmusch AK, Khatib L, Letendre S, Magyari S, McDonald D, Mohanty I, Cumsille A, Moore DJ, Rajkumar P, Ross DH, Sapre H, Shahneh MRZ, Thomas SP, Tribelhorn C, Tubb HM, Walker C, Wang CX, Xing S, Zemlin J, Zuffa S, Wishart DS, Kaddurah-Daouk R, Wang M, Raffatellu M, Zengler K, Pluskal T, Xu L, Knight R, Tsunoda SM, Dorrestein PC. Empirically establishing drug exposure records directly from untargeted metabolomics data. bioRxiv [Preprint]. 2024 Oct 26:2024.10.07.617109. doi: 10.1101/2024.10.07.617109. PMID: 39416075; PMCID: PMC11482764.

Mitigating memory latency in FM Index search

I. Sfiligoi, D. McDonald and R. Knight, “Mitigating memory latency in FM Index search,” 2024 IEEE 20th International Conference on e-Science (e-Science), Osaka, Japan, 2024, pp. 1-2, doi: 10.1109/e-Science62913.2024.10678707.

Gut Microbiome Compositional and Functional Features Associate with Alzheimer's Disease Pathology

Kang JW, Khatib LA, Heston MB, Dilmore AH, Labus JS, Deming Y, Schimmel L, Blach C, McDonald D, Gonzalez A, Bryant M, Sanders K, Schwartz A, Ulland TK, Johnson SC, Asthana S, Carlsson CM, Chin NA, Blennow K, Zetterberg H, Rey FE; Alzheimer Gut Microbiome Project Consortium; Kaddurah-Daouk R, Knight R, Bendlin BB. Gut Microbiome Compositional and Functional Features Associate with Alzheimer’s Disease Pathology. medRxiv [Preprint]. 2024 Sep 5:2024.09.04.24313004. doi: 10.1101/2024.09.04.24313004. PMID: 39281749; PMCID: PMC11398448.

AutoFocus: a hierarchical framework to explore multi-omic disease associations spanning multiple scales of biomolecular interaction

Schweickart A, Chetnik K, Batra R, Kaddurah-Daouk R, Suhre K, Halama A, Krumsiek J. AutoFocus: a hierarchical framework to explore multi-omic disease associations spanning multiple scales of biomolecular interaction. Commun Biol. 2024 Sep 6;7(1):1094. doi: 10.1038/s42003-024-06724-2. PMID: 39237774; PMCID: PMC11377741.

Gut Microbiome Compositional and Functional Features Associate with Alzheimer's Disease Pathology

Kang JW, Khatib LA, Heston MB, Dilmore AH, Labus JS, Deming Y, Schimmel L, Blach C, McDonald D, Gonzalez A, Bryant M, Sanders K, Schwartz A, Ulland TK, Johnson SC, Asthana S, Carlsson CM, Chin NA, Blennow K, Zetterberg H, Rey FE; Alzheimer Gut Microbiome Project Consortium; Kaddurah-Daouk R, Knight R, Bendlin BB. Gut Microbiome Compositional and Functional Features Associate with Alzheimer’s Disease Pathology. medRxiv [Preprint]. 2024 Sep 5:2024.09.04.24313004. doi: 10.1101/2024.09.04.24313004. PMID: 39281749; PMCID: PMC11398448.

Effects of intensive lifestyle changes on the progression of mild cognitive impairment or early dementia due to Alzheimer's disease: a randomized, controlled clinical trial

Ornish D, Madison C, Kivipelto M, Kemp C, McCulloch CE, Galasko D, Artz J, Rentz D, Lin J, Norman K, Ornish A, Tranter S, DeLamarter N, Wingers N, Richling C, Kaddurah-Daouk R, Knight R, McDonald D, Patel L, Verdin E, E Tanzi R, Arnold SE. Effects of intensive lifestyle changes on the progression of mild cognitive impairment or early dementia due to Alzheimer’s disease: a randomized, controlled clinical trial. Alzheimers Res Ther. 2024 Jun 7;16(1):122. doi: 10.1186/s13195-024-01482-z. PMID: 38849944; PMCID: PMC11157928.

The metabolome-wide signature of major depressive disorder

Jansen R, Milaneschi Y, Schranner D, Kastenmuller G, Arnold M, Han X, Dunlop BW; Mood Disorder Precision Medicine Consortium; Rush AJ, Kaddurah-Daouk R, Penninx BWJH. The metabolome-wide signature of major depressive disorder. Mol Psychiatry. 2024 Dec;29(12):3722-3733. doi: 10.1038/s41380-024-02613-6. Epub 2024 Jun 7. PMID: 38849517.

Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies

Brennan C, Belda-Ferre P, Zuffa S, Charron-Lamoureux V, Mohanty I, Ackermann G, Allaband C, Ambre M, Boyer T, Bryant M, Cantrell K, Gonzalez A, McDonald D, Salido RA, Song SJ, Wright G, Dorrestein PC, Knight R. Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies. mSystems. 2024 Oct 22;9(10):e0098524. doi: 10.1128/msystems.00985-24. Epub 2024 Sep 16. PMID: 39283083; PMCID: PMC11494942.

Last updated December 2024