Publications

Publications

Feature-based molecular networking in the GNPS analysis environment

NothiasLF, 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.

Chemically informed analyses of metabolomics mass spectrometry data with Qemistree.

Tripathi A, Vázquez-Baeza Y, Gauglitz JM, Wang M, Dührkop K, Nothias-Esposito M, Acharya DD, Ernst M, van der Hooft JJJ, Zhu Q, McDonald D, Brejnrod AD, Gonzalez A, Handelsman J, Fleischauer M, Ludwig M, Böcker S, Nothias LF, Knight R, Dorrestein PC.. Nat Chem Biol. 2021 Feb;17(2):146-151. doi: 10.1038/s41589-020-00677-3. Epub 2020 Nov 16. PMID: 33199911; PMCID: PMC8189545.

Plasma metabolites to profile pathways in noncommunicable disease multimorbidity

Pietzner M, Stewart ID, Raffler J, Khaw KT, Michelotti GA, Kastenmüller G, Wareham NJ, Langenberg C.. Nat Med. 2021 Mar;27(3):471-479. doi: 10.1038/s41591-021-01266-0. Epub 2021 Mar 11. PMID: 33707775; PMCID: PMC8127079.

Genome-Scale Metabolic Modeling of the Human Microbiome in the Era of Personalized Medicine

Heinken A, Basile A, Hertel J, Thinnes C, Thiele I. Annu Rev Microbiol. 2021 Jul;27:146-151.doi: 10.1146/annurev-micro-060221-012134. Epub ahead of print. PMID: 34314593.

An Integrated Molecular Atlas of Alzheimer's Disease

Wörheide MA, Krumsiek J, Nataf S, Nho K, Greenwood AK, Wu T, Huynh K, Weinisch P, Römisch-Margl W, Lehner N, The AMP-AD Consortium, The Alzheimer’s Disease Neuroimaging Initiative, The Alzheimer’s Disease Metabolomics Consortium, Baumbach J, Meikle PJ, Saykin AJ, Doraiswamy PM, van Duijn C, Suhre K, Kaddurdah-Daouk R, Kastenmüller G, Arnold M. medRxiv. 2021 Sep 22. doi: https://doi.org/10.1101/2021.09.14.21263565.

Integration of constraint-based modeling with fecal metabolomics reveals large deleterious effects of Fusobacterium spp. on community butyrate production

Hertel J, Heinken A, Martinelli F, Thiele I. Gut Microbes. 2021 Jan-Dec; 13(1):1-23.doi: 10.1080/19490976.2021.1915673. PMID: 34057024.

SGI: Automatic clinical subgroup identification in omics datasets

Buyukozkan M, Suhre K, Krumsiek J. Bioinfomatics. 2021 Sep 16;btab656. doi: 10.1093/bioinformatics/btab656. PMID: 34529048.

Identification of plasma proteins relating to brain neurodegeneration and vascular pathology in cognitively normal individuals

Shi L, Buchanan CR, Cox SR, Hillary RF, Marioni RE, Campbell A, Hayward C, Stolicyn A, Whalley HC, Harris MA, Waymont J, Waiter G, Backhouse E, Wardlaw JM, Steele D, Mcintoch A, Lovestone S, Buckley NJ, Nevado-Holgado AJ. Alzheimers Dement (Amst). 2021 Sep 27; 13(1)e12240. doi: 10.1002/dad2.12240. PMID: 34604499.

Advances in constraint-based modelling of microbial communities

Heinken A, Basile A, Thiele I. Curr Opi Sys Biol. 2021 Sep 27;100346. doi: https://doi.org/10.1016/j.coisb.2021.05.007.

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

Hertel J, Heinken A, Thiele I. bioRxiv. 2021 Mar 16. doi: https://doi.org/10.1101/2021.03.15.435397.

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.

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

Dorrestein P, West K, Schmid R, Gauglitz J, Wang Mingxun. Research Square. 2021 Sep 23. doi: https://doi.org/10.21203/rs.3.rs-778710/v1.

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

Chetnik K, Benedetti E, Gomari DP, Schweickart A, Barta R, Buyukozkan M, Wang Z, Arnold M, Zierer J, Suhre K, Krumsiek K. arXiv. 2021 May 6: 2105:04305v1.

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. bioRxiv. 2022. doi: https://doi.org/10.1101/2022.03.07.483343.

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

Brydges CR, Bhattacharyya S, Mahmoudian Dehkordi S, Milaneschi Y, Penninx B, Jansen R, Kristal BS, Han X, Arnold M, Kastenmüller G, Bekhbat M, Mayberg HS, Craighead WE, Rush AJ, Fiehn O, Dunlop BW, Kaddurah-Daouk RF. 2022. Brain, Behavior, and Immunity, 102, 42-52. doi: 10.1016/j.bbi.2022.02.003

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. Nucleic Acids Research. 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.