Publications – Slupsky Lab

Recent publications by categories

Infant health:

Shoff S, Thomas S, Ji P, Parenti M, Slupsky CM (2025) “Dual impact of iron deficiency and antibiotics on host metabolism: A tissue-level analysis.” Metabolites 15(8):549.
Shoff S, He X, Lee H, Zhang Z, Mishchuk DO, Ozturk G, Barile D, Hartvigsen ML, Kvistgaard AS, Slupsky CM. (2025) “The role of a-lactalbumin in modulating tryptophan metabolism and serotonin synthesis.” npj Sci Food 9(1):120. PMID: 40610456.
He X, Tinghäll Nilsson U, Mishchuk DO, Hernell O, Lönnerdal B, Hartvigsen ML, Jacobsen LN, Kvistgaard AS, Slupsky CM, Karlsland Åkeson P. (2025) “Impact of formula protein quantity and source on infant metabolism: serum, urine and fecal metabolomes of a randomized controlled study.” Am J Clin Nutr 121(4):853-864. PMID: 39921093.
Wang A, Diana A, Rhamannia S, Gibson RS, Houghton LA, Slupsky CM (2023) “Impact of milk secretor status on fecal metabolome and microbiota of breastfed infants.” Gut Microbes 15(2):2257273. PMID: 37741856.
McClorry SV, Ji P, Parenti MG, Slupsky CM. (2023). “Antibiotics augment the impact of iron deficiency on metabolism in a piglet model” J Nutr Biochem. 119:109405. PMID: 37311489.
Sotelo-Orozco J, Schmidt RJ, Slupsky CM, Hertz-Picciotto I (2023) “Investigating the urinary metabolome in the first year of life and its association with later diagnosis of autism spectrum disorder or non-typical neurodevelopment in the MARBLES study.” Int J Mol Sci 24(11):9454. PMID: 37298406.
Larke JA, Kuhn-Riordon K, Taft DH, Sohn K, Iqbal S, Underwood MA, Mills DA, Slupsky CM. (2022). “Preterm infant fecal microbiota and metabolite profiles are modulated in a probiotic specific manner.” J Pediatr Gastroenterol Nutr 75(4):535-542. PMID: 35881967.
Lee HN, Li Z, Christensen B, Peng Y, Li X, Hernell O, Lonnerdal B, Slupsky CM (2022). “Metabolic phenotype and microbiome of infants fed formula containing Lactobacillus paracasei strain F-19”. Front Pediatr . 2:7:576966. PMID: 33634158
McMillen S, Thomas S, Liang E, Nonnecke EB, Slupsky C, Lonnerdal, B. (2022) “Gut microbiome alterations following postnatal iron supplementation depend on iron form and persist into adulthood” Nutrients . 14(3):412. PMID: 35276770.
Lee H, Slupsky CM, Heckmann AB, Christensen B, Peng Y, Li X, Hernell O, Lonnerdal B, Li Z (2021). “Milk fat globule membrane as a modulator of infant metabolism and gut microbiota: a formula supplement narrowing the metabolic differences between breast-fed and formula-fed infants”. Mol Nutr Food Res . 65(3):2000603. PMID: 33285021
He X, Sotelo Orozco J, Rudolph C, Lonnerdal B, Slupsky CM (2020). “The role of protein and free amino acids on intake, metabolism and gut microbiome: a comparison between breast-fed and formula-fed rhesus monkey infants”. Front Pediatr . 7:563. PMID: 32039120
McClorry S, Slupsky CM, Lind T, Karlsland Åkeson P, Hernell O, Öhlund I (2019). “Effectiveness of vitamin D supplementation in Swedish children may be negatively impacted by BMI and serum fructose”. J Nut Biochem. 75:108251. PMID: 31707286
He X, Parenti M, Grip T, Lönnerdal B, Timby N, Domellöf M, Hernell O, Slupsky CM (2019). “Fecal microbiome and metabolome of infants fed bovine MFGM supplemented formula or standard formula with breast-fed infants as reference: a randomized controlled trial“. Sci Rep. 9(1):11589. PMID: 31406230
He X, Parenti M, Grip T, Domellöf M, Lönnerdal B, Hernell O, Timby N, Slupsky CM (2019). “Metabolic phenotype of breast-fed infants, and infants fed standard formula or bovine MFGM supplemented formula: a randomized controlled trial“. Sci Rep. 9(1):339. PMID: 30674917
McClorry S, Zavaleta N, Llanos A, Casapía M, Lönnerdal B, Slupsky CM (2018). “Anemia in infancy is associated with alterations in systemic metabolism and microbial structure and function in a sex-specific manner: an observational study“. Am J Cliln Nutr. 108(6):1-11. PMID: 30351381
Lee H, Zavaleta N, Chen S, Lönnerdal B, Slupsky CM (2018). “Effect of bovine milk fat globule membrane as a complementary food on the serum metabolize and immune markers of 6-11-month-old Peruvian infants“. NPJ Sci Food. 2(6). PMID: 31304256
Slupsky CM, He X, Hernell O, Andersson Y, Rudolph C, Lönnerdal B, West CE (2017). “Postprandial response of breast-fed infants and infants fed lactose-free vs regular infant formula – unexpected metabolic effects on amino acid metabolism. A randomized controlled trial” Sci Rep. 7(1):3640. PMID: 28623320
Alexeev E, He X, Slupsky C, Lönnerdal B (2017) “Effects of iron supplementation on growth, gut microbiota, metabolomics and cognitive development of rat pups” Plos One 12(6): e0179713. PMID: 28662197
Smilowitz JT, Lemay DG, Kalenetra KM, Chin EL, Zivkovic AM, Breck MA, German JB, Mills DA, Slupsky C, Barile D (2017) “Tolerability and safety of the intake of bovine milk oligosaccharides extracted from cheese whey in healthy human adults.” J Nutr Sci. 6: e6. PMID: 28620481
He X, Slupsky CM, Dekker JW, Haggarty NW, Lönnerdal B (2016). “Integrated Role of Bifidobacterium animalis subsp. lactis Supplementation in Gut Microbiota, Immunity, and Metabolism of Infant Rhesus Monkeys.” mSystems. 1(6). PMID: 27921083
O’Sullivan A, He X, McNiven EM, Haggarty NW, Lönnerdal B, Slupsky CM (2013). “Early diet impacts infant rhesus gut microbiome, immunity, and metabolism.” J Proteome Res. 12, 2833-2845. PMID: 23651394
O’Sullivan A, He X, McNiven EM, Hinde K, Haggarty NW, Lönnerdal B, Slupsky CM (2013). “Metabolomic phenotyping validates the infant rhesus monkey as a model of human infant metabolism.” J Pediatr Gastroenterol Nutr. 56, 355-363. PMID: 23201704

Human milk:

Donovan SM, Aghaeepour N, Andres A, Azad MB, Becker M, Carlson SE, Järvinen KM, Lin W, Lönnerdal B, Slupsky CM, Steiber AL, Raiten DJ (2023). “Evidence for human milk as a biological system and recommendations for study design – a report from ‘Breastmilk Ecology: Genesis of Infant Nutrition (BEGIN)’ Working Group 4”. Am J Clin Nutr 117(Suppl 1) S61-S86. PMID: 37173061.
de Weerth C, Aatsinki AK, Azad MB, Bartol FF, Bode L, Collado MC, Dettmer AM, Field CJ, Guifoyle M, Hinde K, Korosi A, Lustermans H, Mohd Shukri NH, Moore SE, Pundir S, Rodriguez JM, Slupsky CM, Turner S, van Goudoever JB, Ziomkiewicz A, Beijers R. (2023) “Human milk: From complex tailored nutrition to bioactive impact on child cognition and behavior.” Crit Rev Food Sci Nutr 63(26):7945-82. PMID: 35352583.
Kortesniemi M, Slupsky CM, Aatsinki AK, Sinkkonen J, Karlsson L, Linderborg KM, Yang B, Karlsson H, Uusitupa HM (2021). “Human milk metabolome is associated with symptoms of maternal phychological distress and milk cortisol”. Food Chem . 356:129628. PMID: 33836356
Parenti M, McClorry S, Maga E, Slupsky CM (2021) “Metabolomic changes in severe acute malnutrition suggest hepatic oxidative stress: a secondary analysis” Nutr Res. 91:44-56. PMID: 34134040.
Wang A, Koleva P, du Toit E, Geddes DT, Munblit D, Prescott SL, Eggesbo M, Johnson C, Wegienka G, Shimojo N, Campbell D, Kozyrskyj A, Slupsky CM (2021). “The milk metabolome of non-secretor and Lewis negative mothers”. Front Nutr . 7:576966. PMID: 33634158
He X, McClorry S, Hernell O, Lonnerdal B, Slupsky CM (2020). “Digestion of human milk fat in healthy infants”. Nutr Res. 83: 15-29. PMID: 32987285
Slupsky CM (2019). “Metabolomics in Human Milk Research”. In Nestle Nutr Inst Workshop Ser. 90:179-190. PMID: 30865986
Lee H, Padhi E, Hasegawa Y, Larke J, Parenti M, Wang A, Hernell O, Lonnerdal B, Slupsky C (2018).“Compositional dynamics of the milk fat globule and its role in infant development“. Front Pediatr. 6(313), 1-21. PMID: 30460213
Hasegawa Y, Curtis B, Yutuc V, Rulien M, Morrisroe K, Watkins K, Ferrier C, English C, Hewitson L, Slupsky CM (2018). “Microbial structure and function in infant and juvenile rhesus macaques are primarily affected by age, not vaccination status“. Sci Rep. 8(1):15867. PMID: 30367140
Gay MCL, Koleva PT, Slupsky CM, Toit ED, Eggesbo M, Johnson CC, Wegienka G, Shimojo N, Campbell DE, Prescott SL, Munblit D, Geddes DT, Kozyrskyj AL; InVIVO LactoActive Study Investigators (2018). “Worldwide Variation in Human Milk Metabolome: Indicators of Breast Physiology and Maternal Lifestyle?” Nutrients 10(9). pii: E1151. PMID: 30420587
Munblit D, Peroni DG, Boix-Amorós A, Hsu PS, Land BV, Gay MCL, Kolotilina A, Skevaki C, Boyle RJ, Collado MC, Garssen J, Geddes DT, Nanan R, Slupsky C, Wegienka G, Kozyrskyj AL, Warner JO. (2017) “Human milk and allergic diseases: An unsolved puzzle” Nutrients 9(8) E894. PMID: 28817095
Spevacek AR, Smilowitz JT, Chin EL, Underwood MA, German JB, Slupsky CM (2015). “Infant Maturity at Birth Reveals Minor Differences in the Maternal Milk Metabolome in the First Month of Lactation.” J Nutr. jn210252. PMID: 26041675
Smilowitz JT, O’Sullivan A, Barile D, German JB, Lönnerdal B, Slupsky CM (2013). “The human milk metabolome reveals diverse oligosaccharide profiles.” J Nutr. 143, 1709-1718. PMID: 24027187

Maternal health:

Choi JW, Parenti M, Slupsky CM, Tancredi DJ, Schmidt RJ, Shin HM. (2025) “Maternal serum and placental metabolomes in association with prenatal exposure to per- and polyfluoroalkyl substances and their relevance to child neurodevelopment in an ASD-enriched cohort.” Environ Pollut 383:126811. PMID: 40645267.
Parenti M, Schmidt RJ, Tancredi DJ, Miller M, Hertz-Picciotto I, Walker CK, Slupsky CM. (2025) “Placental metabolism is linked to prenatal vitamin supplement use in the first month of pregnancy in the MARBLES cohort.” J Nutr 2185-2194. PMID: 40414302.
Parenti M, Schmidt RJ, Tancredi DJ, Miller M, Hertz-Picciotto I, Walker CK, Slupsky CM. (2025) “Placental metabolism is linked to prenatal vitamin supplement use in the first month of pregnancy in the MARBLES cohort.” J Nutr 2185-2194. PMID: 40414302.
Parenti M, Shoff S, Sotelo-Orozco J, Hertz-Picciotto I, Slupsky CM (2024) “Metabolomics of mothers of children with autism, idiopathic developmental delay, and Down syndrome.” Sci Rep 14(1):31981. PMID: 39738617.
Parenti M, Slupsky CM (2024). “Disrupted prenatal metabolism may explain the etiology of suboptimal neurodevelopment: A focus on phthalates and micronutrients and their relationship to autism spectrum disorder.” Adv Nutr 15(9):100279. PMID: 39059765.
Parenti M, Schmidt RJ, Tancredi DJ, Hertz-Picciotto I, Walker CK, Slupsky CM (2024) “Neurodevelopment and metabolism in the maternal-placental-fetal unit.” JAMA Netw Open 7(5):e2413399. PMID: 38805224. doi: 10.1001/jamanetworkopen.2024.13399.
French CD, Arnold CD, Taha AY, Engle-Stone R, Schmidt RJ, Hertz-Picciotto I, Slupsky CM (2023) “Assessing repeated urinary proline betaine measures as a biomarker of usual citrus intake during pregnancy: sources of within-person variation and correlation with reported intake.” Metabolites 13:904. PMID: 37623848.
Hasegawa Y, Kim DHJ, Zhang Z, Taha AY, Capitanio JP, Hogrefe CE, Bauman MD, Golub MS, Van de Water J, VandeVoort CA, Walker CK, Slupsky CM. (2023) “Calorie restriction and pravastatin administration during pregnancy in obese rhesus macaques modulates maternal and infant metabolism and infant brain and behavioral development.” Front Nutr 10:1146804. PMID: 37255938.
Parenti M, Schmidt RJ, Ozonoff S, Shin HM, Tancredi DJ, Krakowiak P, Hertz-Picciotto I, Walker CK, Slupsky CM. (2022). “Maternal serum and placental metabolomes in association with prenatal phthalate exposure and neurodevelopmental outcomes in the MARBLES cohort.” Metabolites 12(9):829. PMID: 36144233.
Laufer BI, Hasegawa Y, Zhang Z, Hogrefe CE, Del Rosso LA, Haapanan L, Hwang H, Bauman MD, Van de Water JA, Taha AY, Slupsky CM, Golub MS, Capitanio JP, VandeVoort CA, Walker CK, LaSalle JM (2022). “Multi-omic brain and behavioral correlates of cell-free fetal DNA methylation in macaque maternal obesity models.” Nat Commun 13(1):5538. PMID: 36130949.
Hasegawa Y, Zhang Z, Taha AY, Capitanio JP, Bauman MD, Golub MS, Van de Water J, VandeVoort CA, Walker CK, Slupsky CM. (2022). “Impact of maternal obesity on the gestational metabolome and infant metabolome, brain, and behavioral development in rhesus macaques.” Metabolites 12(8):764. PMID: 36005637.

Gut microbiome and host-microbial interaction

Uttarwar RG, Mekonnen SA, van Beeck W, Wang A, Finnegan P, Roberts RF, Merenstein D, Slupsky CM, Marco ML. (2024). “Effects of Bifidobacterium animalis subsp. lactis BB-12 and yogurt on mice during oral antibiotic administration.” Microbiol Res 286:127794. PMID: 38852301.
Larke JA, Heiss BE, Ehrlich AM, Taft DH, Raybould HE, Mills DA, Slupsky CM (2023). “Milk oligosaccharide driven persistence of Bifidobacterium pseudocatenulatum modulates local and systemic microbial metabolites upon synbiotic treatment in conventionally colonized mice.” Microbiome 11(1):194. PMID: 37635250.
Barouei J, Martinic A, Bendiks Z, Mishchuk D, Heeney D, Slupsky CM, Marco ML (2023). “Type 2 resistant starch and Lactiplantibacillus plantarum NCIMB 8826 result in additive and interactive effects in diet-induced obese mice.” Nutr Res 118:12-28. PMID: 37536013.
Shani G, Hoeflinger J, Heiss B, Masarweh C, Larke J, Jensen N, Wickramasinghe S, Davis J, Goonatilleke E, El-Hawiet A, Nguyen L, Klassen J, Slupsky C, Lebrilla C, Mills, D*. (2022) “Fucosylated human milk oligosaccharide foraging within the species Bifidobacterium pseudocatenulatum is driven by glycosyl hydrolase content and specificity.” Appl Environ Microbiol. 88(2):e0170721 PMID: 34757822
Heiss BE, Ehrlich AM, Maldonado-Gomez MX, Taft DH, Larke JA, Goodson ML, Slupsky CM, Tancredi DJ, Raybould HE, Mills DA*. (2021) “Bifidobacterium catabolism of human milk oligosaccharides overrides endogenous competitive exclusion driving colonization and protection.” Gut Microbes . 13(1):1986666 PMID: 34705611
Ehrlich AM, Pacheco AR, Henrick BM, Taft D, Xe G, Huda NM, Mishchuk D, Goodson M, Slupsky C, Barile D, Lebrilla CB, Stephensen CB, Mills DA, Raybould HE (2020) “Indole-3-lactic acid associated with Bifidobacterium-dominated microbiota significantly decreases inflammation in intestinal epithelial cells.” BMC Microbiol . 20(1):357 PMID: 33225894
Sanctuary MR, Kain JN, Chen SY, Kalanetra K, Lemay DG, Rose DR, Yang HT, Tancredi DJ, German JB, Slupsky CM, Ashwood, Mills DA, Smilowitz JT, Angkustsiri K (2019). “Pilot study of probiotic/colostrum supplementation on gut function in children with autism and gastrointestinal symptoms“. Plos One. 14(1):e0210064. PMID: 30625189
Heeney DD, Zhai Z, Bendiks Z, Barouei J, Martinic A, Slupsky C, Martin R, Marco ML. (2019) “ plantarum bacteriocin is associated with intestinal and systemic improvements in diet-induced obese mice and maintains epithelial barrier integrity in vitro” Gut Microbes 10(3): 382-397. PMID: 30409105
Martinic A, Barouei J, Bendiks Z, Mishchuk D, Heeney DD, Martin R, Marco M, and Slupsky CM (2018). “Supplementation of Lactobacillus plantarum Improves Markers of Metabolic Dysfunction Induced by a High Fat Diet“. J Proteome Res. 17(8), 2790-2802
Yin X, Heeney D, Srisengfa Y, Chen SY, Slupsky C, Marco M. (2018) “Sucrose metabolism alters Lactobacillus plantarum survival and interactions with the microbiota in the digestive tract”. FEMS Microbiol Ecol. 94(7). PMID: 29771345
Barouei J, Bendiks Z, Martinic A, Mishchuk D, Heeney D, Hsieh Y-H, Kieffer D, Zaragoza J, Martin R, Slupsky C, Marco M (2017). “Microbiota, metabolome, and immune alterations in obese mice fed a high fat diet containing type 2 resistant starch“. Mol Nutr Food Res. 61(11). PMID: 28736992
Moran-Ramos S, He X, Chin EL, Tovar AR, Torres N, Slupsky CM, Raybould HE (2017) “Nopal feeding reduces adiposity, intestinal inflammation and shifts the cecal microbiota and metabolism in high-fat fed rats.“ Plos One. 12(2). PMID: 28196086
Reverri EJ, Slupsky CM, Mishchuk DO, Steinberg FM (2017) “Metabolomics reveals differences between three daidzein metabolizing phenotypes in adults with cardiometabolic risk factors.” Mol Nutr Food Res. 16(1). PMID: 27364093
He X, Slupsky CM (2014) “Metabolic fingerprint of dimethyl sulfone (DMSO2) in microbial-mammalian co-metabolism.” J Proteome Res. 13(12), 5281-91. PMID: 25245235
He X, Mishchuk DO, Shah J, Weimer BC, Slupsky CM (2013) “Cross-talk between E. coli strains and a human colorectal adenocarcinoma-derived cell line.” Sci Rep. 3:3416. PMID: 24301462
He X, Marco ML, Slupsky CM (2013) “Emerging aspects of food and nutrition on gut microbiota.” J Agric Food Chem. 61(40):9559-74. PMID: 24028159

Food, plant health and agricultural practice:

Lombardi RL, Ramsey JS, Mahoney JE, MacCoss MJ, Heck ML, Slupsky CM (2024) “Longitudinal transcriptomic, proteomic, and metabolomic response of Citrus sinensis to Diaphorina citri inoculation of Candidatus Liberibacter asiaticus.” J Proteome Res 23(8):2857-2869. PMID: 38373055.
McNeil CJ, Araujo K, Godfrey K, Slupsky CM. (2023). “Metabolite signature and differential expression of genes in Washington navel oranges (Citrus sinensis) infected by Spiroplasma citri.” Phytopathology 113(2):299-308. PMID: 35984373. doi: 10.1094/PHYTO-05-22-0177-R.
Rumbaugh AC, Durbin-Johnson B, Padhi E, Lerno L, Cauduro Girardello R, Britton M, Slupsky C, Sudarshana MR, Oberholster A (2022). “Investigating grapevine red blotch virus infection in Vitis vinifera L. cv. Cabernet Sauvignon grapes: a multi-omics approach.” Int J Mol Sci 23(21):13248. PMID: 36362035.
Padhi EMT, Araujo KJ, Mitrovic E, Polek ML, Godfrey KE, Slupsky CM (2022) “The impact of Diaphorina citri vectored Candidatus Liberibacter asiaticus on citrus metabolism.” Phytopathol . 112(1):197-204. PMID: 34698540
McNeil CJ, Araujo K, Godfrey K, Slupsky CM (2021) “Effects of two citrus tristeza virus isolates on sweet orange (Citrus sinesis) propagated on citrus tristeza virus-tolerant rootstock: A metabolomics and transcriptomics approach.” ACS Agric Sci Tech . 1(4): 407-416.
Chin EL, Ramsey JS, Saha S, Mishchuk DO, Chavez JD, Howe K, Zhong X, Flores-Gonzalez M, Mitrovic E, Polek M, Godfrey K, Mueller LA, Bruce JE, Heck M, Slupsky CM (2021) “Multi-omics comparison reveals landscape of Citrus limon and Citrus sinesis (L.) Osbeck response to Candidatus Liberibacter asiaticus.” Phytofrontiers . 1(2):76-84.
Pereira GE, Padhi EMT, Sudarshana MY, Fialho FB, Plaza CM, Girardello RC, Tseng D, Bruce RC, Erdmann JN, Slupsky CM, Oberholster A (2020) “Impact of grapevine red blotch disease on primary and secondary metabolites in ‘Cabernet Sauvignon’ grape tissues.” Food Chem . 342:128312 PMID: 33268164
Coates LC, Mahoney J, Ramsey JS, Warwick E, Johnson R, MacCoss MJ, Krasnoff SB, Howe KJ, Moulton K, Saha S, Mueller LA, Hall DG, Shatters RG, Heck ML, Slupsky CM (2020) “Development on Citrus medica infected with ‘Candidatus Liberibacter asiaticus’ has sex-specific and -nonspecific impacts on adult Diaphorina citri and its endosymbionts’.” PLoS One . 15(10):e0239771. PMID: 33022020
Pereira GE, Padhi EMT, Girardello RC, Plaza CM, Tseng D, Bruce RC, Erdmann JN, Kurtural SK, Slupsky C, Oberholster A (2020) “Trunk Girdling Increased Stomatal Conductance in Cabernet Sauvignon Grapevines, Reduced Glutamine, and Increased Malvidin-3-Glucoside and Quercetin-3-Glucoside Concentrations in Skins and Pulp at Harvest.” Front Plant Sci. 11, 707. PMID: 32595661
Ramsey JS, Chin EL, Chavez JD, Saha S, Mishchuk DO, Mahoney J, Mohr J, Robinson FM, Foster E, Xu Y, Strickler S, Fernandez N, Zhong X, Polek M, Godfrey KE, Giovannoni JG, Mueller L, Slupsky CM, Bruce JE, Heck M. (2020) “Longitudinal transcriptomic, proteomic, and metabolomics analysis of Citrus Limon response to graft inoculation by ‘Candidatus Liberibacter asiaticus’.” J Proteome Res. 19(6), 2247-2263. PMID: 32338516
Chin EL, Ramsey JS, Mishchuk DO, Saha S, Foster E, Chavez JD, Howe K, Zhong X, Polek M, Godfrey KE, Mueller L, Bruce JE, Heck M, Slupsky CM (2020) “Longitudinal transcriptomic, proteomic, and metabolomics analyses of Citrus sinesis (L.) Osbeck graft-inoculated with ‘Candidatus Liberibacter asiaticus’.” J Proteome Res. 19(2): 719-732. PMID: 31885275
Lin SY, Slupsky CM, Mishchuk DO, Mau JL (2019) “Composition of Mycelia and Basidiomata of the Culinary-Medicinal Golden Oyster Mushroom, Pleurotus citrinopileatus (Agaricomycetes) by Nuclear Magnetic Resonance Spectroscopy” Int J Med Mushrooms 21 (10): 965-977.
Simons T, McNeil C, Pham VD, Wang S, Wang Y, Slupsky C, Guinard JX (2019). “Chemical and sensory analysis of commercial Navel oranges in California” npj Science of Food 3:22. PMID: 31701017
Simons TJ, McNeil CJ, Pham VD, Suh JH, Wang Y, Slupsky CM, Guinard JX (2019). “Evaluation of California-Grown Blood and Cara Cara Oranges Through Consumer Testing, Descriptive Analysis, and Targeted Chemical Profiling“. J Food Sci. 84(11):3246-3263. PMID: 31609472
Simons T, McNeil C, Pham V, Slupsky C, Guinard JX (2019). “Comparison of preference clustering outcomes from replicated consumer tests- A case study with mandarins” J Sens Studies. e12537
Padhi E, Maharaj N, Lin S-Y, Mishchuk D, Chin E, Godfrey K, Foster E, Polek M, Leveau J, Slupsky CM (2019). “Metabolome and microbiome signatures in the roots of citrus affected by Huanglongbing“.
Simons TJ, McNeil CJ, Pham VD, Slupsky CM, Roose ML, Guinard JX (2019). “Chemical, Sensory, and Consumer Evaluations of ‘DaisySL’ Mandarins Grafted onto Three Different Rootstocks“ Hort Sci. 54(7):1217-1222
Metrulas L, McNeil C, Slupsky CM, Bamforth C (2019). “The application of metabolomics to ascertain the significance of prolonged maturation in the production of lager‐style beers“. J I Brewing. 125(2), 242-249
Chin E, Godfrey K, Polek ML, Slupsky C (2017) “Metabolomic analysis of Citrus macrophylla subjected to Asian Citrus Psyllid (Diaphorina citri Kuwayama) feeding” Arthropod Plant Interact. 11(6):901–909
Lo YC, Chien SC, Mishchuk DO, Slupsky CM, Mau JL (2016) “Quantification of Water-Soluble Metabolites in Medicinal Mushrooms Using Proton NMR Spectroscopy.” Int J Med Mushrooms. 18 (5):413-24. PMID: 27649603
Spevacek AR, Benson KH, Bamforth CW, Slupsky CM (2016) “Beer metabolomics: Molecular details of the brewing process and the differential effects of late and dry hopping on yeast purine metabolism” J Inst Brew. 122 (1)
Kortesniemi M, Slupsky CM, Ollikka T, Kauko L, Spevacek AR, Sjövall O, Yang B, Kallio H (2016) “NMR profiling clarifies the characterization of Finnish honeys of different botanical origins” Food Res Int 86, 83-92.
Chin EL, Mishchuk DO, Breksa AP, Slupsky CM (2014) “Metabolite signature of Candidatus Liberibacter asiaticus infection in two citrus varieties.” J Agric Food Chem. 62:6585-91. PMID: 24959841
Chin E, Slupsky CM (2013) “Applications of metabolomics in food science: Food composition, quality, sensory and nutritional attributes.” In Metabolomics in Food and Nutrition. Weimer B, and Slupsky CM, eds. Woodhead, Cambridge, U.K.
Slisz A, Breksa AP, Mishchuk DO, McCollum G, Slupsky CM (2012) “Infection of citrus by Candidatus Liberibacter reveals insight into pathogenicity.” J Proteome Res 11: 4223-4230. PMID: 22698301
Zhang X, Breksa AP, Mishchuk DO, Fake C, O’Mahony MA, Slupsky CM (2012) “Fertilization and pesticides affect mandarin orange nutrient composition.” Food Chem 134: 1020 – 1024. PMID: 23107722
Zhang X, Breksa A, Mishchuk DO, Slupsky CM (2011) “Elevation, root stock, and soil depth affect nutritional quality of mandarin oranges.” J Agric Food Chem 59: 2672 – 2679. PMID: 21332232

Health and disease:

Chakraborty H, Sun Q, Bhupathiraju SN, Schenk JM, Mishchuk DO, Bain JR, He X, Sun J, Harnly J, Simmons W, Raftery D, Liang L, Newman JW, Fiehn O, Clish CB, Lampe JW, Bennett BJ, Navarro SL, Wang Y, Zhang C, Mossavar-Rahmani Y, McCullogh M, Huang Y, Shojaie A, Zhu W, Djukovic D, Sacks F, Williams J, Steinberg FM, Adams SH, Hu FB, Neuhouser ML, Slupsky CM, Maruvada P. (2025) “The Dietary Biomarkers Development Consortium: An initiative for discovery and validation of dietary biomarkers for precision nutrition.” Curr Dev Nutr 9(5):107435. PMID: 40641655.
Roslund KJ, Ramsey JJ, Rutkowsky JM, Zhou Z, Slupsky CM (2025) “Two-month ketogenic diet alters systemic and brain metabolism in middle-aged female mice.” GeroScience 47(1):935-952. PMID: 39180613.
Ko J, Yoo C, Xing D, Chun J, Gonzalez DE, Dickerson BL, Leonard M, Jenkins V, Van der Merwe M, Slupsky CM, Sowinski RJ, Rasmussen CJ, Kreider RB (2024) “Effects of human milk oligosaccharide 2’-Fucosyllactose ingestion on weight loss and markers of health” Nutrients 16(19):3387. PMID: 39408354.
Sukmak M, Kyaw TS, Nahok K, Sharma A, Silsirivanit A, Lert-itthiporn W, Japrung D, Pinlaor S, Anutrakulchai S, Selmi C, Slupsky CM, Hammock BD, Cha’on U (2024). “Urinary metabolic profile and its predictive indexes after MSG consumption in rat.” PLoS One 19(9):e0309728. PMID: 39226266.
Slupsky CM, Sykes BD, Lakey JRT (2024). “High-resolution magic angle spinning nuclear magnetic resonance of donor pancreatic tissue may predict islet viability prior to isolation.” NMR Biomed 37(11):e5207. PMID: 38979683.
Chien RC, Chen SY, Mishchuk DO, Slupsky CM (2023) “Hydrophilic metabolite composition of fruiting bodies and mycelia of edible mushroom species (Agaricomycetes).” Int J Med Mushrooms 25(11):27-40. PMID: 3783150
Yang G, Jena PK, Hu Y, Sheng L, Chen SY, Slupsky CM, Davis R, Tepper CG, Wan YY (2023). “The essential roles of FXR in diet and age influenced metabolic changes and liver disease development: a multi-omics study.” Biomark Res 11(1):20. PMID: 36803569. doi: 10.1186/s40364-023-00458-9.
Taren D, Akseer N, Davis CD, Miller JW, Moustaid-Moussa N, Novotny R, Slupsky CM, Saroja Voruganti V, Cameron JM. (2021) “Eighty years of nutritional sciences, and counting” Nutr Rev . 80(1): 1-5. PMID: 34891168.
Moon JM, Finnegan P, Stecker RA, Lee H, Ratliff KM, Jäger R, Purpura M, Slupsky CM, Marco ML, Wissent CJ, Theodosakis J, Kerksick CM. (2021) “Impact of glucosamine supplementation on gut health” Nutrients . 13: 2180. PMID: 34202877.
Price CA, Medici V, Nunez MV, Lee V, Sigala DM, Benyam Y, Keim NL, Mason AE, Chen SY, Parenti M, Slupsky C, Epel ES, Havel PJ, Stanhope KL (2021) “A pilot study comparing the effects of consuming 100% orange juice or sucrose-sweetened beverage on risk factors for cardiometabolic disease in women” Nutrients . 13(3):760. PMID: 33652807.
Zhang Z, Emami S, Hennebelle M, Morgan RK, Lerno L, Slupsky CM, Lein PJ, Taha AY (2021) “Linoleic acid-derived 13-hydroxyoctadecadieonic acid is absorbed and rapidly incorporated into rat tissues” BBA Mol Cell Biol Lipids . 1866(3):158870. PMID: 33340768.
Sotelo-Orozco J, Abbeduto L, Hertz-Picciotto I*, Slupsky CM (2020) “Association between plasma metabolites and psychometric scores among children with developmental disabilities: investigating sex-differences” Front Psychiatry . 11:579538. PMID: 33414730.
Hasegawa Y, Chen SY, Sheng L, Jena PK, Kalanetra KM, Mills DA, Wan YJY, Slupsky CM (2020) “Long-term effects of western diet consumption in male and female mice” Sci Rep . 10(1):14686. PMID: 32895402.
Tanguay LMH, Slupsky CM, Tsujimura T, Lix B, Sykes BD, Lakey JRT (2020) “1H MAS NMR of donor pancreatic tissue is a useful predictor of islet viability prior to islet isolation” bioRxiv. 2020.05.04.059998.
Sylvestre DA, Slupsky CM, Aviv R, Swardfager W, Taha A (2020) “Untargeted metabolomic analysis of plasma from relapsing-remitting multiple sclerosis patients reveals changes in metabolites associated with neurocognitive and structural changes in the brain” Brain Res. 1732:146589. PMID: 31816317.
Orozco JS, Hertz-Picciotto I, Abbeduto L, Slupsky CM (2019). “Metabolomics analysis of children with autism, idiopathic-developmental delays, and Down syndrome“. Transl Psychiratry. 9(1):243. PMID:31582732
French CD, Willoughby RE, Pan A, Wong SJ, Foley JF, Wheat LJ, Fernandez J, Encarnacion R, Ondrush JM, Fatteh N, Paez A, David D, Javaid W, Amzuta IG, Neilan AM, Robbins GK, Brunner AM, Hu WT, Mishchuk DO, Slupsky CM (2018). “NMR metabolomics of cerebrospinal fluid differentiates inflammatory diseases of the central nervous system“. PLos Negl Trop Dis. 12(12): e0007045. PMID: 30557317
Chen SY, Yu HT, Kao JP, Yang CC, Chiang SS, Mishchuk DO, Mau JL, Slupsky CM (2015) “Consumption of vitamin D2 enhanced mushrooms is associated with improved bone health” J Nutr Biochem. 26(7):696-703. PMID: 25792284
Chen SY, Yu HT, Kao JP, Yang CC, Chiang SS, Mishchuk DO, Mau JL, Sluspky CM (2014) “An NMR metabolomic study on the effect of alendronate in ovariectomized mice.” Plos One. 9, e106559. PMID: 25184758
Warden CH, Slupsky CM, Min E, Le A, Fisler JS, Hansen S, Haj F, Stern J (2014) “Brown Norway chromosome 1 congenic reduces symptoms of renal disease including distal tubular damage in fatty Zucker rats.” Plos One. 9, e87770. PMID: 24498189
Harris C, Chowanadisai W, Mishchuk DO, Satre M, Slupsky CM, Rucker RB (2013) “Dietary pyrroloquinoline quinone (PQQ) alters indicators of plasma antioxidant potential, inflammation, and mitochondrial-related metabolism in human subjects.” J Nutr Biochem. 24, 2076-84. PMID: 24231099
Tso V, Sydora BC, Foshaug RR, Churchill TA, Doyle J, Slupsky CM, Fedorak RN. (2013) “Metabolomic profiles are gender, disease, and time specific in the interleukin-10 gene-deficient mouse model of inflammatory bowel disease.” Plos One. 8, e67654. PMID: 23874435
O’Sullivan A, Willoughby RE, Mishchuk D, Alcarraz B, Cabezas-Sanchez C, Condori RE, David D, Encarnacion R, Fatteh N, Fernandez J, Franka R, Hedderwick S, McCaughey C, Ondrush J, Paez-Martinez A, Rupprecht C, Velasco-Villa A, Slupsky CM (2013) “Metabolomics of cerebrospinal fluid from humans treated for rabies.” J Proteome Res. 12, 481-490. PMID: 23163834
Stephens NS, Siffeldeen J, Su X, Murdoch TB, Fedorak RN, Slupsky CM (2013) “Urinary NMR metabolomics profiles discriminate inflammatory bowel disease from healthy.” J Crohns Colitis. 7: e42- e48. PMID: 22626506.
Reinke SN, Resch L, Maingat F, Branton W, Jackson A, Saxinger L, Holt R, Slupsky C, Marrie T, Sykes BD, Power C (2013) “Metagenomic and metabolomic characterization of rabies encephalitis – new insights into the treatment of an ancient disease.” J Infect Dis. 207, 1451-1456. PMID: 22927447
McNiven EM, German JB, Slupsky CM (2011) “Analytical metabolomics: Nutritional opportunities for personalized health.” J Nutr Biochem. 22: 995 – 1002. PMID: 21999844
Moroz J, Turner J, Slupsky C, Fallone G, Syme A (2011) “Tumor xenograft detection through quantitative analysis of the metabolic profile of urine in mice.” Phys Med Biol. 56: 535 – 556. PMID: 21212470
Slupsky CM (2011) “Nuclear magnetic resonance-based analysis of urine for the rapid etiological diagnosis of pneumonia.” Expert Opin Med Diagn. 5: 63 – 73. PMID: 23484477
Davis VW, Bathe OF, Schiller DE, Slupsky CM, Sawyer MB (2011) “Metabolomics and surgical oncology: Potential role for small molecule biomarkers.” J Surg Oncol. 103: 451 – 459. PMID: 21400531
Slupsky CM, Steed H, Wells TH, Dabbs K, Schepansky A, Capstick V, Faught W, Sawyer MB (2010) “Urine metabolite analysis offers potential early diagnosis of ovarian and breast cancers.” Clin Cancer Res. 16: 5835 – 5841. PMID: 20956617
Wang H, Tso V, Slupsky CM, Fedorak R (2010) “Metabolomics and detection of colorectal cancer in humans – A systematic review.” Future Oncol. 6: 1395 – 1406. PMID: 20919825
Slupsky CM (2010) “NMR-based analysis of metabolites in urine provides a rapid diagnosis and etiology of pneumonia.” Biomark Med. 4: 195 – 197. PMID: 20406062
Slupsky CM, Rankin KN, Fu H, Chang D, Rowe BH, Charles PG, McGeer A, Low D, Long R, Kunimoto D, Sawyer MB, Fedorak RN, Adamko DJ, Saude EJ, Shah SL, Marrie TJ (2009) “Pneumococcal pneumonia: potential for diagnosis through a urinary metabolic profile.” J Proteome Res. 8, 5550 – 5558. PMID: 19817432
Murdoch TB, Fu H, Martin S, Sydora B, Fedorak RN, Slupsky CM (2008) “Urinary metabolic profiles of inflammatory bowel disease in interleukin-10 gene deficient mice” Anal Chem. 80, 5524 – 5531. PMID: 18558774
McGrath BM, McKay R, Dave S, Seres P, Weljie AM, Slupsky CM, Hanstock CC, Greenshaw AJ, Silverstone PH (2008) “Acute dextro-amphetamine administration does not alter brain myo-inositol levels in humans and animals: MRS investigations at 3T and 18.8T” Neurosci Res. 61, 351 – 359. PMID: 18508145
McGrath BM, Greenshaw AJ, McKay R, Slupsky CM, Silverstone PH (2007) “Unlike lithium, anticonvulsants and antidepressants do not alter rat brain myo-inositol” Neuroreport. 18, 1595 – 1598. PMID: 17885608

Analytical and bioinformatics methods:

Zhang Z, Siddiqi H, Huang Y-P, McClorry S, Ji P, Barile D, Slupsky CM* (2024) “An LC-MS/MS method for the simultaneous quantification of insulin, cortisol, glucagon-like peptide 1, ghrelin, and osteocalcin.” Separations 11(2):41.
Sylvestre DA, Otoki Y, Metherel AH, Bazinet RP, Slupsky CM, Taha AY (2022) “Effects of hypercapnia / ischemia and dissection on the rat brain metabolome” Neurochem Int . 156:105294. PMID: 35104537.
Sotelo-Orozco J, Chen S-Y, Hertz-Picciotto I, Slupsky CM (2020) “A comparison of serum and plasma blood collection tubes for the integration of epidemiological and metabolomics data” Front Mol Biosci . 8:682134. PMID: 34307452.
Hasegawa Y, Otoki Y, McClorry S, Coates LC, Lombardi RL, Taha AY, Slupsky CM (2020) “Optimization of a method for the simultaneous extraction of polar and non-polar oxylipin metabolites, DNA, RNA, small RNA, and protein from a single small tissue sample” Meth Protocols . 3(3) E61. PMID: 32859006.
French CD, Arsenault JE, Arnold CD, Haile D, Luo H, Dodd KW, Vosti SA, Slupsky CM, Engle-Stone R (2021) “Within-person variation in nutrient intakes across populations and settings: Implications for the use of external estimates in modeling usual nutrient intake distributions” Adv Nutr . 12(2):429-451. PMID: 33063105.
Sotelo J, Slupsky CM (2013) “Metabolomics using nuclear magnetic resonance (NMR).” In Metabolomics in Food and Nutrition. Weimer B, and Slupsky CM, eds. Woodhead, Cambridge, U.K.
O’Sullivan A, Avizonis D, German JB, Slupsky CM (2011) “Software Tools for NMR Metabolomics.” In Encyclopedia of nuclear magnetic resonance. Harris RK, and Wasylishen R, eds. Wiley Interscience, Chichester, U.K. DOI: 10.1002/9780470034590.emrstm1232. Published 15th December 2011
Takeda I, Stretch C, Barnaby P, Bhatnager K, Rankin K, Fu H, Weljie A, Jha N, Slupsky C (2009) “Understanding the human salivary metabolome.” NMR Biomed. 22: 577 – 584. PMID: 19259987
Mahadevan S, Shah SL, Marrie TJ, Slupsky CM (2008) “Analysis of metabolomic data using support vector machines.” Anal Chem. 80, 7562 – 7570. PMID: 18767870
Slupsky CM, Rankin KN, Wagner J, Fu H, Chang D, Weljie AM, Saude EJ, Lix B, Adamko DJ, Shah S, Greiner R, Sykes BD, and Marrie TJ (2007) “Investigations of the effects of gender, diurnal variation, and age in human urinary metabolomic profiles.” Anal Chem. 79, 6995 – 7004. PMID: 17702530
Saude EJ, Slupsky CM, and Sykes BD (2006) “Optimization of NMR analysis of biological fluids for quantitative accuracy.” Metabolomics. 2, 113 – 123.
Weljie AM, Newton J, Mercier P, Carlson E and Slupsky CM (2006) “Targeted profiling: Quantitative analysis of 1H-NMR metabolomics data.” Anal Chem. 78, 4430 – 4442. PMID: 16808451

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