Simone Zuffa

Photo of Simone Zuffa
Title(s)Postdoctoral Scholar, School of Pharmacy and Pharmaceutical Science
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
ORCID ORCID Icon0000-0001-7237-3402 Additional info
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Bridging complexity and accessibility in metabolomics with MetaboApps. Nat Methods. 2026 Jul 24. Mannochio-Russo H, Gonçalves Nunes WD, Zhao HN, Kvitne KE, Xing S, Gouda H, Agongo J, Mohanty I, Charron-Lamoureux V, Rajkumar P, Pakkir Shah AK, Walter A, Krishnaraj R, El Abiead Y, Ferreira PC, Zuffa S, Patan A, Caraballo-Rodríguez AM, Bittremieux W, Petras D, Wang M, Dorrestein PC. PMID: 42498881.
      View in: PubMed   Mentions:    Fields:    
    2. Effect of perinatal ampicillin or amoxicillin/clavulanate exposure on maternal and infant gut microbiome, metabolome, and infant responses to the 20-valent pneumococcal conjugate vaccine. Gut Microbes Rep. 2026; 3(1):2705707. Suzuki E, Deleray V, Zemlin J, Kousha A, Nonoguchi H, Sun D, Tsai CM, Zuffa S, Kvitne KE, Dorrestein PC, Tsunoda SM, Nizet V, Liu GY, Askarian F. PMID: 42482833; PMCID: PMC13387116.
      View in: PubMed   Mentions:
    3. Comparative genomic analysis of Bacteroides fragilis from intestinal and extra-intestinal sites. Microbiol Spectr. 2026 Jul 14; e0030626. Oles RE, Carrillo Terrrazas M, Loomis LR, Zuffa S, Neal MJ, Hsu C-Y, Vasquez Ayala A, Tribelhorn C, Belda-Ferre P, Zhao J, Bryant M, Zemlin J, Young J, Dulai PS, Sandborn WJ, Sivagnanam M, Pride D, Zengler K, Dorrestein PC, Knight R, Chu H. PMID: 42446195.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    4. Perinatal ampicillin exposure alters murine maternal fecal bile acid and acylcarnitine profiles. Gut Microbes. 2026 Dec 31; 18(1):2690698. Zuffa S, Thomas SP, Patan A, Mohanty I, El Abiead Y, Deleray V, Kvitne KE, Kousha A, Suzuki E, Tsai CM, Nguyen G, Ho B, Y Liu G, Nizet V, Dorrestein PC, Askarian F, Tsunoda SM. PMID: 42374604; PMCID: PMC13321893.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    5. A multi-organ metabolomics atlas reveals molecular dysregulations in Alzheimer's disease mouse models. Cell Rep. 2026 Jun 23; 45(6):117499. Zuffa S, Allaband C, Charron-Lamoureux V, Caraballo-Rodriguez AM, Patan A, Mohanty I, Agongo J, Bostick JW, Connerly TJ, Thron T, Needam BD, de Castro Fonseca M, Benitez RS, Hansen L, Tubb H, Cao J, Kalecký K, Bottiglieri T, MahmoudianDehkordi S, Schimmel L, Kueider-Paisley A, Graham SF, Siegel D, Wang M, Knight R, Kaddurah-Daouk R, Dorrestein PC, Mazmanian SK, Alzheimer Gut Microbiome Project Consortium. PMID: 42308105.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    6. Structure-centric searching enables global mapping of the public metabolome. Nat Biotechnol. 2026 Apr 15. El Abiead Y, Seo JI, Charron-Lamoureux V, Strobel M, Gonçalves Nunes WD, Zhao HN, Kvitne KE, Zuffa S, Mannochio-Russo H, Gouda H, Bez C, Patan A, Xing S, Zemlin J, Mohany I, Agongo J, Caraballo Rodriguez AM, Burnett LA, Deleray V, Pakkir Shah AK, Kalinski JC, Petras D, Alygizakis N, Carver J, Yurekten O, Payne T, Fahy E, Subramaniam S, Vizcaíno JA, Wang M, Dorrestein PC. PMID: 41986697.
      View in: PubMed   Mentions:    Fields:    
    7. Antibiotic Exposure Through Human Milk Influences the Infant Gut Microbiome. bioRxiv. 2026 Apr 01. Kvitne KE, Zuffa S, Charron-Lamoureux V, Patan A, Agongo J, Cai J, Deleray V, El Abiead Y, Xing S, Zemlin J, Thomas S, Nelson MR, Gant A, Ghadishah A, Lam A, Ho B, Momper JD, Suhandynata RT, Bertrand K, Knight R, Chambers C, Dorrestein PC, Tsunoda SM. PMID: 41959458; PMCID: PMC13060235.
      View in: PubMed   Mentions:
    8. Farnesoid X receptor-dependent microbiome-bile acid signaling mediates obstructive sleep apnea-induced atherosclerosis. bioRxiv. 2026 Apr 01. Xue J, Allaband C, Zuffa S, Zhou D, Poulsen O, Meadows J, McDonald D, Ambre M, Ackermann G, Birmingham A, Cao J, Mohanty I, Dorrestein PC, Knight R, Haddad GG. PMID: 41959535; PMCID: PMC13060084.
      View in: PubMed   Mentions:
    9. A searchable metadata network graph for microbiome metabolomics. bioRxiv. 2026 Feb 05. Charron-Lamoureux V, Xing S, Patan A, Walker C, Monter RA, Abiead YE, Zhao HN, Patel L, Weng Y, Gonzalez A, Ackermann G, Deleray V, Gandhi V, Mohanty I, Caraballo-Rodriguez AM, Kvitne KE, Zuffa S, Norman A, Martin A, Chin L, Paz-Gonzalez R, Sala-Climent M, Suryawinata N, Zemlin J, Gouda H, Hu Z, Norton G, Rajkumar P, Molina AJ, Bergstrom J, Pinner M, Giddings S, Aron AT, Liang L, Dahesh S, Lamichhane S, Reilly ER, Nizet V, Skrip A, Lukowski AL, Shore SFH, Ghoshal S, Engevik MA, Horvath TD, Renwick S, Agongo J, Marco ML, Mazmanian SK, Wang M, Yang H, McDonald D, Guma M, Stegmann E, Hernandez Perez N, Stincone P, Kemen E, Pakkir Shah AK, Bode L, Petras D, Siegel D, Raffatellu M, Patterson AD, Devkota S, Jinich A, Knight R, Zengler K, Dorrestein PC. PMID: 41676651; PMCID: PMC12889665.
      View in: PubMed   Mentions:
    10. Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data. bioRxiv. 2026 Jan 26. Mannochio-Russo H, Gonçalves Nunes WD, Xing S, de Oliveira F, Caraballo-Rodríguez AM, Gomes PWP, Charron-Lamoureux V, Agongo J, Avalon NE, Bui T, Cancelada L, Chevrette MG, Cumsille A, de Araújo MB, De Graeve M, Deleray V, Donia MS, Dzveta MB, El Abiead Y, Ellis RJ, Franklin D, Garg N, Gouda H, Djande CYH, Hiskia A, Ho BN, Hughes CC, Hwang S, Iliakopoulou S, Iudicello JE, Jarmusch AK, Kaloudis T, Koester I, Konkel R, Koolen HHF, Kvitne KE, La Rosa SL, Lam A, Lamichhane S, Lephatsi M, Letendre S, Magyari S, Mazur-Marzec H, McDonald D, Mohanty I, Monge-Loría M, Moore DJ, Veiga TAM, Mulaudzi MS, Nephali L, Nguyen G, Orságh M, Patan A, Pluskal T, Pope PB, de Medeiros LS, Stincone P, Tekel A, Thomas S, Torres RR, Tsunoda SM, Tugizimana F, van Faassen M, Vasquez-Castro F, Vitale GA, Wagner BC, Wang CX, Zervou SK, Zhao HN, Zuffa S, Petras D, McCall LI, Knight R, Wang M, Dorrestein PC. PMID: 41659575; PMCID: PMC12874021.
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    11. Fecal microbial and metabolic signatures in children with very early onset inflammatory bowel disease. NPJ Biofilms Microbiomes. 2025 Dec 31; 12(1):33. Kvitne KE, Zuffa S, Charron-Lamoureux V, Mohanty I, Patan A, Mannochio-Russo H, Zemlin J, Burnett LA, Zhang LS, Cecala MC, Ersoz C, Connelly JA, Halasa N, Nicholson M, Dorrestein PC, Tsunoda SM, Markle J. PMID: 41476253; PMCID: PMC12864830.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    12. A resource to empirically establish drug exposure records directly from untargeted metabolomics data. Nat Commun. 2025 Dec 09; 16(1):10600. Zhao HN, Kvitne KE, Brungs C, Mohan S, Charron-Lamoureux V, Bittremieux W, Tang R, Schmid R, Lamichhane S, Xing S, El Abiead Y, Andalibi MS, Mannochio-Russo H, Ambre M, Avalon NE, Bryant M, Burnett LA, Caraballo-Rodríguez AM, Maya MC, Chin L, Corominas L, Ellis RJ, Franklin D, Girod S, Gomes PWP, Hansen L, Heaton RK, 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, Gil-Solsona R, Thomas SP, Tribelhorn C, Tubb HM, Walker C, Wang CX, Zemlin J, Zuffa S, Wishart DS, Gago-Ferrero P, Kaddurah-Daouk R, Wang M, Raffatellu M, Zengler K, Pluskal T, Xu L, Knight R, Tsunoda SM, Dorrestein PC. PMID: 41366203; PMCID: PMC12689629.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    13. Effect of Perinatal Ampicillin or Amoxicillin/Clavulanate Exposure on Maternal and Infant Gut Microbiome, Metabolome, and Infant Responses to the 20-valent Pneumococcal Conjugate Vaccine. bioRxiv. 2025 Dec 08. Suzuki E, Deleray V, Zemlin J, Kousha A, Nonoguchi H, Sun D, Tsai CM, Zuffa S, Kvitne KE, Dorrestein PC, Tsunoda SM, Nizet V, Liu GY, Askarian F. PMID: 41427374; PMCID: PMC12713748.
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    14. Microbiome-derived bile acid signatures in early life and their association with islet autoimmunity. Nat Commun. 2025 12 03; 17(1):38. Lamichhane S, Dickens AM, Buchacher T, Lou T, Charron-Lamoureux V, Kattelus R, Karmacharya P, da Silva LP, Kråkström M, Rasool O, Sen P, Walker C, Patan A, Gentry EC, Zuffa S, Arzoomand A, Lakshmikanth T, Mikeš J, Mebrahtu A, Vatanen T, Raffatellu M, Zengler K, Hyötyläinen T, Xavier RJ, Brodin P, Lahesmaa R, Dorrestein PC, Knip M, Orešic M. PMID: 41339624; PMCID: PMC12764907.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    15. The undiscovered natural product potential of Actinomycetes. J Antibiot (Tokyo). 2026 Feb; 79(2):80-92. Caraballo-Rodríguez AM, Cumsille A, Magyari S, Taboada-Alquerque M, Behsaz B, Leão TF, Broders K, El Abiead Y, Clement JA, Charron-Lamoureux V, Zuffa S, Nothias LF, Hu M, Leone C, Kakhkhorov SA, Cámara B, Mohimani H, Dorrestein PC. PMID: 41331045; PMCID: PMC12834688.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    16. Environmental and maternal imprints on infant gut metabolic development. Cell Host Microbe. 2025 Dec 10; 33(12):2130-2147.e7. Kvitne KE, Allaband C, Onuora JC, Perry D, Zuffa S, Patel L, Charron-Lamoureux V, Mohanty I, Sejane K, Patan A, Mahmud AA, Ahmed T, Bassani DG, González A, Hamer DH, Haque R, Ho B, Hossain MI, Islam MS, McDonald D, Pell LG, Qamar H, Roth DE, Saha S, Shah PS, Siddiqui MM, Sarker SA, Sultana S, Thomas S, Burnett LA, Tsunoda SM, Bode L, Dorrestein PC, Knight R. PMID: 41308639; PMCID: PMC12875530.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    17. Charting the Undiscovered Metabolome with Synthetic Multiplexing. bioRxiv. 2025 Nov 19. Patan A, Xing S, Charron-Lamoureux V, Hu Z, Deleray V, Agongo J, El Abiead Y, Mannochio-Russo H, Mohanty I, Gouda H, Zemlin J, Rajkumar P, Lee C, Leanos D, Weimann N, Tsuda W, Giddings S, Bui T, Kvitne KE, Zhao HN, Zuffa S, Nguyen V, Andrade A, Gonçalves Nunes WD, Caraballo-Rodríguez AM, Caetano David L, Carver J, Bandeira N, Wang M, Burnett LA, Siegel D, Dorrestein PC. PMID: 41332743; PMCID: PMC12667992.
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    18. Targeted Microbial Shifts and Metabolite Profiles Were Associated with Clinical Response to an Anti-Inflammatory Diet in Osteoarthritis. Nutrients. 2025 Aug 22; 17(17). Sala-Climent M, Bu K, Coras R, Cedeno M, Zuffa S, Murillo-Saich J, Mannochio-Russo H, Allaband C, Hose MK, Quan A, Choi SI, Nguyen K, Golshan S, Blank RB, Holt T, Lane NE, Knight R, Scher J, Dorrestein P, Clemente J, Guma M. PMID: 40944120; PMCID: PMC12430150.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCTClinical Trials
    19. Environmental and Maternal Imprints on Infant Gut Metabolic Programming. bioRxiv. 2025 Jul 24. Kvitne KE, Allaband C, Onuora JC, Perry D, Zuffa S, Patel L, Charron-Lamoureux V, Mohanty I, Sejane K, Patan A, Al Mahmud A, Ahmed T, Bassani DG, González A, Hamer DH, Haque R, Ho B, Hossain MI, Islam MS, McDonald D, Pell LG, Qamar H, Roth DE, Saha S, Shah PS, Siddiqui MM, Sarker SA, Sultana S, Thomas S, Burnett LA, Tsunoda SM, Bode L, Dorrestein PC, Knight R. PMID: 40777448; PMCID: PMC12330730.
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    20. Influence of perinatal ampicillin exposure on maternal fecal microbial and metabolic profiles. bioRxiv. 2025 Jun 30. Zuffa S, Thomas SP, Mohanty I, El Abiead Y, Deleray V, Kvitne KE, Kousha A, Suzuki E, Tsai CM, Nguyen G, Ho B, Liu GY, Nizet V, Dorrestein PC, Askarian F, Tsunoda SM. PMID: 40631287; PMCID: PMC12236745.
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    21. Enabling pan-repository reanalysis for big data science of public metabolomics data. Nat Commun. 2025 May 24; 16(1):4838. El Abiead Y, Strobel M, Payne T, Fahy E, O'Donovan C, Subramamiam S, Vizcaíno JA, Yurekten O, Deleray V, Zuffa S, Xing S, Mannochio-Russo H, Mohanty I, Zhao HN, Caraballo-Rodriguez AM, P Gomes PW, Avalon NE, Northen TR, Bowen BP, Louie KB, Dorrestein PC, Wang M. PMID: 40413169; PMCID: PMC12103507.
      View in: PubMed   Mentions: 16     Fields:    Translation:Humans
    22. Milk phospholipid-coated lipid droplets modulate the infant gut microbiota and metabolome influencing weight gain. Microbiome. 2025 05 14; 13(1):120. Zuffa S, Lay C, Wimborne EA, Rodriguez AH, Wu Y, Nobrega FL, Bartke N, Hokken-Koelega ACS, Knol J, Roeselers G, Swann JR. PMID: 40369689; PMCID: PMC12076826.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    23. MS/MS Mass Spectrometry Filtering Tree for Bile Acid Isomer Annotation. bioRxiv. 2025 Mar 09. Mohanty I, Xing S, Castillo V, Agongo J, Patan A, Abiead YE, Mannochio-Russo H, Zuffa S, Zemlin J, Tronel A, Gouellec AL, Soranzo T, Wang CX, Iudicello JE, Andalibi MS, Ellis RJ, Moore DJ, Franklin DR, Sala-Climent M, Guma M, Voigt RM, Kaddaruh-Dauok R, Siegel D, Wang M, Hagey LR, Dorrestein PC. PMID: 41659560; PMCID: PMC12874289.
      View in: PubMed   Mentions: 2  
    24. Gut microbiota and derived metabolites mediate obstructive sleep apnea induced atherosclerosis. Gut Microbes. 2025 Dec; 17(1):2474142. Xue J, Allaband C, Zuffa S, Poulsen O, Meadows J, Zhou D, Dorrestein PC, Knight R, Haddad GG. PMID: 40025767; PMCID: PMC11881840.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    25. Discovery of metabolites prevails amid in-source fragmentation. Nat Metab. 2025 Mar; 7(3):435-437. El Abiead Y, Rutz A, Zuffa S, Amer B, Xing S, Brungs C, Schmid R, Correia MSP, Caraballo-Rodriguez AM, Zarrinpar A, Mannochio-Russo H, Witting M, Mohanty I, Pluskal T, Bittremieux W, Knight R, Patterson AD, van der Hooft JJJ, Böcker S, Dunn WB, Linington RG, Wishart DS, Wolfender JL, Fiehn O, Zamboni N, Dorrestein PC. PMID: 40021935; PMCID: PMC13111153.
      View in: PubMed   Mentions: 11     Fields:    
    26. Human Untargeted Metabolomics in High-Throughput Gut Microbiome Research: Ethanol vs Methanol. Anal Chem. 2025 Mar 11; 97(9):4945-4953. Zuffa S, Charron-Lamoureux V, Brennan C, Ambre M, Knight R, Dorrestein PC. PMID: 40015251; PMCID: PMC11912123.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    27. The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns. Cell. 2025 Apr 03; 188(7):2022-2041.e23. Salido RA, Zhao HN, McDonald D, Mannochio-Russo H, Zuffa S, Oles RE, Aron AT, El Abiead Y, Farmer S, González A, Martino C, Mohanty I, Parker CW, Patel L, Portal Gomes PW, Schmid R, Schwartz T, Zhu J, Barratt MR, Rubins KH, Chu H, Karouia F, Venkateswaran K, Dorrestein PC, Knight R. PMID: 40020666; PMCID: PMC12068931.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    28. To Impute or Not To Impute in Untargeted Metabolomics─That is the Compositional Question. J Am Soc Mass Spectrom. 2025 Apr 02; 36(4):742-759. Krutkin DD, Thomas S, Zuffa S, Rajkumar P, Knight R, Dorrestein PC, Kelley ST. PMID: 40007142; PMCID: PMC11969646.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    29. Gut Microbiota and Derived Metabolites Mediate Obstructive Sleep Apnea Induced Atherosclerosis. bioRxiv. 2024 Nov 19. Xue J, Allaband C, Zuffa S, Poulsen O, Meadows J, Zhou D, Dorrestein PC, Knight R, Haddad GG. PMID: 39605650; PMCID: PMC11601605.
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    30. Empirically establishing drug exposure records directly from untargeted metabolomics data. bioRxiv. 2024 Oct 26. 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. PMID: 39416075; PMCID: PMC11482764.
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    31. Receptor and metabolic insights on the ability of caffeine to prevent alcohol-induced stimulation of mesolimbic dopamine transmission. Transl Psychiatry. 2024 09 28; 14(1):391. Bassareo V, Maccioni R, Talani G, Zuffa S, El Abiead Y, Lorrai I, Kawamura T, Pantis S, Puliga R, Vargiu R, Lecca D, Enrico P, Peana A, Dazzi L, Dorrestein PC, Sanna PP, Sanna E, Acquas E. PMID: 39341817; PMCID: PMC11438888.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    32. Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data. Nat Protoc. 2025 01; 20(1):92-162. Pakkir Shah AK, Walter A, Ottosson F, Russo F, Navarro-Diaz M, Boldt J, Kalinski JJ, Kontou EE, Elofson J, Polyzois A, González-Marín C, Farrell S, Aggerbeck MR, Pruksatrakul T, Chan N, Wang Y, Pöchhacker M, Brungs C, Cámara B, Caraballo-Rodríguez AM, Cumsille A, de Oliveira F, Dührkop K, El Abiead Y, Geibel C, Graves LG, Hansen M, Heuckeroth S, Knoblauch S, Kostenko A, Kuijpers MCM, Mildau K, Papadopoulos Lambidis S, Portal Gomes PW, Schramm T, Steuer-Lodd K, Stincone P, Tayyab S, Vitale GA, Wagner BC, Xing S, Yazzie MT, Zuffa S, de Kruijff M, Beemelmanns C, Link H, Mayer C, van der Hooft JJJ, Damiani T, Pluskal T, Dorrestein P, Stanstrup J, Schmid R, Wang M, Aron A, Ernst M, Petras D. PMID: 39304763.
      View in: PubMed   Mentions: 26     Fields:    
    33. Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies. mSystems. 2024 10 22; 9(10):e0098524. 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. PMID: 39283083; PMCID: PMC11494942.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    34. Dietary iron intake has long-term effects on the fecal metabolome and microbiome. Metallomics. 2024 07 01; 16(7). Kostenko A, Zuffa S, Zhi H, Mildau K, Raffatellu M, Dorrestein PC, Aron AT. PMID: 38992131; PMCID: PMC11272056.
      View in: PubMed   Mentions: 3     Fields:    Translation:Animals
    35. Pathogenic Bacteroides fragilis strains can emerge from gut-resident commensals. bioRxiv. 2024 Jun 19. Oles RE, Terrazas MC, Loomis LR, Neal MJ, Paulchakrabarti M, Zuffa S, Hsu CY, Vasquez Ayala A, Lee MH, Tribelhorn C, Belda-Ferre P, Bryant M, Zemlin J, Young J, Dulai P, Sandborn WJ, Sivagnanam M, Raffatellu M, Pride D, Dorrestein PC, Zengler K, Choudhury B, Knight R, Chu H. PMID: 38948766; PMCID: PMC11213024.
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    36. Receptor and metabolic insights on the ability of caffeine to prevent alcohol-induced stimulation of mesolimbic dopamine transmission. Res Sq. 2024 Jun 11. Maccioni R, Bassareo V, Talani G, Zuffa S, El Abiead Y, Lorrai I, Kawamura T, Pantis S, Puliga R, Vargiu R, Lecca D, Enrico P, Peana A, Dazzi L, Dorrestein PC, Sanna PP, Sanna E, Acquas E. PMID: 38946995; PMCID: PMC11213171.
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    37. plantMASST - Community-driven chemotaxonomic digitization of plants. bioRxiv. 2024 May 14. Gomes PWP, Mannochio-Russo H, Schmid R, Zuffa S, Damiani T, Quiros-Guerrero LM, Caraballo-Rodríguez AM, Zhao HN, Yang H, Xing S, Charron-Lamoureux V, Chigumba DN, Sedio BE, Myers JA, Allard PM, Harwood TV, Tamayo-Castillo G, Kang KB, Defossez E, Koolen HHF, da Silva MN, E Silva CYY, Rasmann S, Walker TWN, Glauser G, Chaves-Fallas JM, David B, Kim H, Lee KH, Kim MJ, Choi WJ, Keum YS, de Lima EJSP, de Medeiros LS, Bataglion GA, Costa EV, da Silva FMA, Carvalho ARV, Reis JDE, Pamplona S, Jeong E, Lee K, Kim GJ, Kil YS, Nam JW, Choi H, Han YK, Park SY, Lee KY, Hu C, Dong Y, Sang S, Morrison CR, Borges RM, Teixeira AM, Lee SY, Lee BS, Jeong SY, Kim KH, Rutz A, Gaudry A, Bruelhart E, Kappers IF, Karlova R, Meisenburg M, Berdaguer R, Tello JS, Henderson D, Cayola L, Wright SJ, Allen DN, Anderson-Teixeira KJ, Baltzer JL, Lutz JA, McMahon SM, Parker GG, Parker JD, Northen TR, Bowen BP, Pluskal T, van der Hooft JJJ, Carver JJ, Bandeira N, Pullman BS, Wolfender JL, Kersten RD, Wang M, Dorrestein PC. PMID: 38798440; PMCID: PMC11118438.
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    38. The underappreciated diversity of bile acid modifications. Cell. 2024 Mar 28; 187(7):1801-1818.e20. 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. PMID: 38471500; PMCID: PMC12248420.
      View in: PubMed   Mentions: 101     Fields:    Translation:HumansAnimals
    39. microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data. Nat Microbiol. 2024 02; 9(2):336-345. 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. PMID: 38316926; PMCID: PMC10847041.
      View in: PubMed   Mentions: 62     Fields:    Translation:Humans
    40. Reverse metabolomics for the discovery of chemical structures from humans. Nature. 2024 02; 626(7998):419-426. Gentry EC, Collins SL, Panitchpakdi M, Belda-Ferre P, Stewart AK, Carrillo Terrazas M, Lu HH, Zuffa S, Yan T, Avila-Pacheco J, Plichta DR, Aron AT, Wang M, Jarmusch AK, Hao F, Syrkin-Nikolau M, Vlamakis H, Ananthakrishnan AN, Boland BS, Hemperly A, Vande Casteele N, Gonzalez FJ, Clish CB, Xavier RJ, Chu H, Baker ES, Patterson AD, Knight R, Siegel D, Dorrestein PC. PMID: 38052229; PMCID: PMC10849969.
      View in: PubMed   Mentions: 86     Fields:    Translation:HumansAnimalsCells
    41. Ex vivo study of molecular changes of stained teeth following hydrogen peroxide and peroxymonosulfate treatments. Sci Rep. 2023 09 28; 13(1):16349. P Gomes PW, Zuffa S, Bauermeister A, Caraballo-Rodríguez AM, Zhao HN, Mannochio-Russo H, Dogo-Isonagie C, Patel O, Pimenta P, Gronlund J, Lavender S, Pilch S, Maloney V, North M, Dorrestein PC. PMID: 37770593; PMCID: PMC10539445.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    42. A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data. Res Sq. 2023 Aug 03. 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. PMID: 37577622; PMCID: PMC10418563.
      View in: PubMed   Mentions:
    43. Early-life differences in the gut microbiota composition and functionality of infants at elevated likelihood of developing autism spectrum disorder. Transl Psychiatry. 2023 07 13; 13(1):257. Zuffa S, Schimmel P, Gonzalez-Santana A, Belzer C, Knol J, Bölte S, Falck-Ytter T, Forssberg H, Swann J, Diaz Heijtz R. PMID: 37443359; PMCID: PMC10344877.
      View in: PubMed   Mentions: 35     Fields:    Translation:Humans
    44. A Complete Pipeline for Untargeted Urinary Volatolomic Profiling with Sorptive Extraction and Dual Polar and Nonpolar Column Methodologies Coupled with Gas Chromatography Time-of-Flight Mass Spectrometry. Anal Chem. 2023 01 17; 95(2):758-765. Wen Q, Myridakis A, Boshier PR, Zuffa S, Belluomo I, Parker AG, Chin ST, Hakim S, Markar SR, Hanna GB. PMID: 36602225; PMCID: PMC9850407.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    45. Transfer of antibiotics and their metabolites in human milk: Implications for infant health and microbiota. Pharmacotherapy. 2023 05; 43(5):442-451. Thomas SP, Denizer E, Zuffa S, Best BM, Bode L, Chambers CD, Dorrestein PC, Liu GY, Momper JD, Nizet V, Tsunoda SM, Tremoulet AH. PMID: 36181712; PMCID: PMC10763576.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    46. Variation of volatile organic compound levels within ambient room air and its impact upon the standardisation of breath sampling. Sci Rep. 2022 09 23; 12(1):15887. Hewitt MJ, Belluomo I, Zuffa S, Boshier PR, Myridakis A. PMID: 36151300; PMCID: PMC9508138.
      View in: PubMed   Mentions: 5     Fields:    
    47. Post-weaning A1/A2 β-casein milk intake modulates depressive-like behavior, brain μ-opioid receptors, and the metabolome of rats. iScience. 2021 Sep 24; 24(9):103048. Osman A, Zuffa S, Walton G, Fagbodun E, Zanos P, Georgiou P, Kitchen I, Swann J, Bailey A. PMID: 34585111; PMCID: PMC8450247.
      View in: PubMed   Mentions: 10  
    48. Author Correction: Obesity and ethnicity alter gene expression in skin. Sci Rep. 2021 Mar 31; 11(1):7524. Walker JM, Garcet S, Aleman JO, Mason CE, Danko D, Butler D, Zuffa S, Swann JR, Krueger J, Breslow JL, Holt PR. PMID: 33790371; PMCID: PMC8012637.
      View in: PubMed   Mentions:    Fields:    
    49. Obesity and ethnicity alter gene expression in skin. Sci Rep. 2020 08 21; 10(1):14079. Walker JM, Garcet S, Aleman JO, Mason CE, Danko D, Butler D, Zuffa S, Swann JR, Krueger J, Breslow JL, Holt PR. PMID: 32826922; PMCID: PMC7442822.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    50. Faecal virome transplantation decreases symptoms of type 2 diabetes and obesity in a murine model. Gut. 2020 12; 69(12):2122-2130. Rasmussen TS, Mentzel CMJ, Kot W, Castro-Mejía JL, Zuffa S, Swann JR, Hansen LH, Vogensen FK, Hansen AK, Nielsen DS. PMID: 32165408.
      View in: PubMed   Mentions: 133     Fields:    Translation:Animals
    51. Reclassification of Eubacterium hallii as Anaerobutyricum hallii gen. nov., comb. nov., and description of Anaerobutyricum soehngenii sp. nov., a butyrate and propionate-producing bacterium from infant faeces. Int J Syst Evol Microbiol. 2018 Dec; 68(12):3741-3746. Shetty SA, Zuffa S, Bui TPN, Aalvink S, Smidt H, De Vos WM. PMID: 30351260.
      View in: PubMed   Mentions: 69     Fields:    Translation:HumansCells
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