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. Empirically establishing drug exposure records directly from untargeted metabolomics data. bioRxiv. 2024 Oct 10. 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.
      View in: PubMed   Mentions:
    2. Receptor and metabolic insights on the ability of caffeine to prevent alcohol-induced stimulation of mesolimbic dopamine transmission. Transl Psychiatry. 2024 Sep 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:    Fields:    Translation:AnimalsCells
    3. Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data. Nat Protoc. 2024 Sep 20. 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: 1     Fields:    
    4. Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies. mSystems. 2024 Sep 16; 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.
      View in: PubMed   Mentions:    Fields:    
    5. 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:    Fields:    Translation:Animals
    6. 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.
      View in: PubMed   Mentions:
    7. 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.
      View in: PubMed   Mentions:
    8. 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.
      View in: PubMed   Mentions:
    9. 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.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimals
    10. microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data. Nat Microbiol. 2024 Feb; 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: 12     Fields:    Translation:Humans
    11. Reverse metabolomics for the discovery of chemical structures from humans. Nature. 2024 Feb; 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: 15     Fields:    Translation:HumansAnimalsCells
    12. 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
    13. 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:
    14. Early-life differences in the gut microbiota composition and functionality of infants at elevated likelihood of developing autism spectrum disorder. Transl Psychiatry. 2023 Jul 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: 7     Fields:    Translation:Humans
    15. 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: 3     Fields:    Translation:Humans
    16. 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: 3     Fields:    Translation:HumansCells
    17. 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: 4     Fields:    
    18. 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: 7  
    19. 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:    
    20. 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: 3     Fields:    Translation:HumansCells
    21. 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: 87     Fields:    Translation:Animals
    22. 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: 44     Fields:    Translation:HumansCells