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.
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 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
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.
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.
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.
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.
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
Gut Microbiome-Linked Metabolites in the Pathobiology of Major Depression With or Without Anxiety-A Role for Bile Acids
Comparative metabolomics and microbiome analysis of Ethanol vs. OMNImet/gene®•GUT fecal stabilization
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.
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.
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.
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.
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.
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.
Last updated December 2024