Publications

Milk Glycoproteome

Dallas DC, Guerrero A, Parker EA, Garay LA, Bhandari A, Lebrilla CB, Barile D, German JB. Peptidomic Profile of Milk of Holstein Cows at Peak Lactation. J Agric Food Chem. 2013 Dec 23. [Epub ahead of print] PubMed PMID: 24344900.
Hong Q, Lebrilla CB, Miyamoto S, Ruhaak LR. Absolute quantitation of immunoglobulin G and its glycoforms using multiple reaction monitoring. Anal Chem. 2013 Sep 17;85(18):8585-93. doi: 10.1021/ac4009995. Epub 2013 Aug 30. PubMed PMID: 23944609; PubMed Central PMCID: MC3857154.
Hua S, Hu CY, Kim BJ, Totten SM, Oh MJ, Yun N, Nwosu CC, Yoo JS, Lebrilla CB, An HJ. Glyco-analytical multispecific proteolysis (Glyco-AMP): a simple method for detailed and quantitative Glycoproteomic characterization. J Proteome Res. 2013 Oct 4;12(10):4414-23. doi: 10.1021/pr400442y. Epub 2013 Sep 20. PubMed PMID: 24016182.
Ozcan, S. B. J. Kim, G. Ro, J.-H. Kim, L. T. Bereuter, C. Reiter, L. Dimapasoc, D. Garrido, D. A. Mills, R. Grimm, C. B. Lebrilla and H. J. An. Glycosylated proteins preserved over millennia: N-glycan analysis of Tyrolean Iceman, Scythian Princess and Warrior. Nature Scientific Reports (16 May 2014).
Smilowitz JT, Totten SM, Huang J, Grapov D, Durham HA, Lammi-Keefe CJ, Lebrilla C, German JB. Human milk secretory immunoglobulin a and lactoferrin N-glycans are altered in women with gestational diabetes mellitus. J Nutr. 2013 Dec;143(12):1906-12. doi: 10.3945/jn.113.180695. Epub 2013 Sep 18. PubMed PMID: 24047700; PubMed Central PMCID: PMC3827637.
Dallas DC, Guerrero A, Khaldi N, Castillo PA, Martin WF, Smilowitz JT, Bevins CL, Barile D, German JB, Lebrilla CB. Extensive in vivo human milk peptidomics reveals specific proteolysis yielding protective antimicrobial peptides. J Proteome Res. 2013 May 3;12(5):2295-304. doi: 10.1021/pr400212z. Epub 2013 Apr 24. PubMed PMID: 23586814; PubMed Central PMCID: PMC3662810.
Vijayakumar V, Guerrero AN, Davey N, Lebrilla CB, Shields DC, Khaldi N. Enzyme Predictor: a tool for predicting and visualizing enzymatic cleavages of digested proteins. J Proteome Res. 2012 Dec 7; 11(12):6056-65. doi: 10.1021/pr300721f. Epub 2012 Nov 9. PubMed PMID: 23098558.
Garrido D, Nwosu C, Ruiz-Moyano S, Aldredge D, German JB, Lebrilla CB, Mills DA. Endo-β-N-acetylglucosaminidases from Infant Gut-associated Bifidobacteria Release Complex N-glycans from Human Milk Glycoproteins. Mol Cell Proteomics. 2012 Sep;11(9):775-85.
Dallas DC, Martin WF, Hua S, German JB. Automated glycopeptide analysis--review of current state and future directions. Brief Bioinform. 2012 Jul 27. [Epub ahead of print]
Barboza M, Pinzon J, Wickramasinghe S, Froehlich JW, Moeller I, Smilowitz JT, Ruhaak LR, Huang J, Lönnerdal B, German JB, Medrano JF, Weimer BC, Lebrilla CB. Glycosylation of human milk lactoferrin exhibits dynamic changes during early lactation enhancing its role in pathogenic bacteria-host interactions. Mol Cell Proteomics. 2012 Jun;11(6):M111.015248.
Hua S, Nwosu CC, Strum JS, Seipert RR, An HJ, Zivkovic AM, German JB, Lebrilla CB. Site-specific protein glycosylation analysis with glycan isomer differentiation. Anal Bioanal Chem. 2012 May;403(5):1291-302.
Nwosu CC, Aldredge DL, Lee H, Lerno LA, Zivkovic AM, German JB, Lebrilla CB. Comparison of the human and bovine milk N-glycome via high-performance microfluidic chip liquid chromatography and tandem mass spectrometry. J Proteome Res. 2012 May 4;11(5):2912-24.
Froehlich JW, Barboza M, Chu C, Lerno LA Jr, Clowers BH, Zivkovic AM, German JB, Lebrilla CB. Nano-LC-MS/MS of glycopeptides produced by nonspecific proteolysis enables rapid and extensive site-specific glycosylation determination. Anal Chem. 2011 Jul 15;83(14):5541-7.
Nwosu CC, Seipert R, Strum JS, Hua SS, An HJ, Zivkovic AM, German JB, Lebrilla CB. Simultaneous and Extensive Site-specific N- and O-Glycosylation Analysis in Protein Mixtures.J Proteome Res. 2011 May 6; 10(5):2612-24.
Dallas DC, Martin WF, Strum JS, Zivkovic AM, Smilowitz JT, Underwood MA, Affolter M, Lebrilla CB, German JB. N-linked glycan profiling of mature human milk by high-performance microfluidic chip liquid chromatography time-of-flight tandem mass spectrometry. J Agric Food Chem. 2011 Apr 27;59(8):4255-63.
An HJ, Lebrilla CB. Structure elucidation of native N- and O-linked glycans by tandem mass spectrometry (tutorial). Mass Spectrom Rev. 2011 Jul-Aug;30(4):560-78.
Nwosu CC, Strum JS, An HJ, Lebrilla CB. Enhanced detection and identification of glycopeptides in negative ion mode mass spectrometry. Anal Chem. 2010 Dec 1;82(23):9654-62.
Froehlich JW, Chu CS, Tang N, Waddell K, Grimm R, Lebrilla CB. Label-free liquid chromatography-tandem mass spectrometry analysis with automated phosphopeptide enrichment reveals dynamic human milk protein phosphorylation during lactation. Anal Biochem. 2011 Jan 1;408(1):136-46.
Froehlich JW, Dodds ED, Barboza M, et al. Glycoprotein Expression in Human Milk during Lactation. J Agric Food Chem 2010; 58(10): 6440-8.
Dodds, E. D., R. R. Seipert, et al. (2009). "Analytical performance of immobilized pronase for glycopeptide footprinting and implications for surpassing reductionist glycoproteomics." J Proteome Res 8(2): 502-12.
An HJ, Froehlich JW, Lebrilla CB. Determination of glycosylation sites and site-specific heterogeneity in glycoproteins. Curr Opin Chem Biol. 2009 Oct;13(4):421-6.
Tao N, DePeters EJ, Freeman S, German JB, Grimm R, Lebrilla CB. Bovine milk glycome. J Dairy Sci 2008;91:3768-78.
Seipert, R. R., E. D. Dodds, et al. (2008). "Factors that influence fragmentation behavior of N-linked glycopeptide ions." Anal Chem 80(10): 3684-92.
Dodds, E. D., J. B. German, et al. (2007). "Enabling MALDI-FTICR-MS/MS for high-performance proteomics through combination of infrared and collisional activation." Anal Chem 79(24): 9547-56.

Milk Oligosaccharides

Sela, D. A. and D. A. Mills. 2014. The marriage of nutrigenomics with the microbiome: the case of infant-associated bifidobacteria and milk. The American Journal of Clinical Nutrition (March 2014) 99:697S-703S.
Smilowitz, J. T., C. B. Lebrilla, D. A. Mills, J. B. German and S. L. Freeman. Breast milk oligosaccharides: Structure function relationships in the neonate. Annual Review of Nutrition 2014;34:143-69. doi: 10.1146/annurev-nutr-071813-105721. Epub 2014 May 15.

Hong Q, Ruhaak LR, Totten SM, Smilowitz JT, German JB, Lebrilla CB. Label-free absolute quantitation of oligosaccharides using multiple reaction monitoring. Anal Chem. 2014 Mar 4;86(5):2640-7. doi: 10.1021/ac404006z. Epub 2014 Feb 20. PubMed PMID: 24502421; PubMed Central PMCID: PMC3983013.
Lee H., D. Garrido D., D. A. Mills, D. Barile. 2014. Hydrolysis of milk gangliosides by infant-gut associated bifidobacteria determined by microfluidic chips and high-resolution mass spectrometry. Electrophoresis 2014 Jun;35(11):1742-50. doi: 10.1002/elps.201300653. Epub 2014 Mar 20.
Lewis, Z. and D. A. Mills. 2014. Oligosaccharides as functional foods. In: D. R. Heldman, D. Hoover, M. B. Wheeler and A. B. Damania Eds. Encyclopedia of Biotechnology in Agriculture and Food (In Press).
Smilowitz JT, Lebrilla CB, Mills DA, German JB, Freeman SL. Breast Milk Oligosaccharides: Structure-Function Relationships in the Neonate. Annu Rev Nutr. 2013 Jul 22. [Epub ahead of print] PubMed PMID: 24850388.
Kailemia MJ, Ruhaak LR, Lebrilla CB, Amster IJ. Oligosaccharide analysis by mass spectrometry: a review of recent developments. Anal Chem. 2014 Jan 7; 86(1):196-212. doi: 10.1021/ac403969n. Epub 2013 Dec 16. PubMed PMID: 24313268; PubMed Central PMCID: PMC3924431.
Guerrero A, Lebrilla CB. New strategies for resolving oligosaccharide isomers by exploiting mechanistic and thermochemical aspects of fragment ion formation. Int J Mass Spectrom. 2013 Nov 15;354-355. doi: 10.1016/j.ijms.2013.05.002. PubMed PMID: 24273436; PubMed Central PMCID: PMC3835204.
Barile D, Rastall RA. Human milk and related oligosaccharides as prebiotics. Curr Opin Biotechnol. 2013 Apr; 24(2):214-9. doi: 10.1016/j.copbio.2013.01.008. Epub 2013 Feb 19. Review. PubMed PMID: 23434179.
De Leoz, M. L., S. Wu, J. S. Strum, M. R. Niñonuevo, S. C. Gaerlan, M. Mirmiran, J. B. German, D. A. Mills, C. B. Lebrilla, M. A. Underwood. A quantitative and comprehensive structural method to analyze human milk oligosaccharides in the urine and feces of infants. Analytical and Bioanalytical Chemistry (May 2013) 405:4089-4105.
Ruiz-Moyano, S., S. M. Totten, D. A. Garrido, J. T. Smilowitz, J. B. German, C. B. Lebrilla and D. A. Mills. 2013. Variation in consumption of human milk oligosaccharides by infant-gut associated strains of Bifidobacterium breve. Applied and Environmental Microbiology 79:6040-6049.
Zivkovic, A. M., Z. T. Lewis, J. B. German and D. A. Mills. 2013. Establishment of a milk-oriented microbiota (MOM) in early life: How babies meet their MOMs. Functional Food Reviews 5:3-12.
Totten SM, Zivkovic AM, Wu S, Ngyuen U, Freeman SL, Ruhaak LR, Darboe MK, German JB, Prentice AM, Lebrilla CB. Comprehensive profiles of human milk oligosaccharides yield highly sensitive and specific markers for determining secretor status in lactating mothers. J Proteome Res. 2012 Dec 7;11(12):6124-33. doi: 10.1021/pr300769g. Epub 2012 Nov 19. PubMed PMID: 23140396.
Underwood MA. Human milk for the premature infant. Pediatr Clin North Am. 2013 Feb;60(1):189-207. doi: 10.1016/j.pcl.2012.09.008. Epub 2012 Oct 18. Review. PubMed PMID: 23178065; PubMed Central PMCID: PMC3508468.
De Leoz ML, Gaerlan SC, Strum JS, Dimapasoc LM, Mirmiran M, Tancredi DJ, Smilowitz JT, Kalanetra KM, Mills DA, German JB, Lebrilla CB, Underwood MA. Lacto-N-tetraose, fucosylation, and secretor status are highly variable in human milk oligosaccharides from women delivering preterm. J Proteome Res. 2012 Sep 7;11(9):4662-72.
Chichlowski M, De Lartigue G, German JB, Raybould HE, Mills DA. Bifidobacteria isolated from infants and cultured on human milk oligosaccharides affect intestinal epithelial function. J Pediatr Gastroenterol Nutr. 2012 Sep;55(3):321-7.
Wu S, Salcedo J, Tang N, Waddell K, Grimm R, German JB, Lebrilla CB. Employment of tandem mass spectrometry for the accurate and specific identification of oligosaccharide structures. Anal Chem. 2012 Sep 4;84(17):7456-62.
Ruhaak LR, Lebrilla CB. Analysis and role of oligosaccharides in milk. BMB Rep. 2012 Aug;45(8):442-51.
Garrido D, Ruiz-Moyano S, Mills DA. Release and utilization of N-acetyl-d-glucosamine from human milk oligosaccharides by Bifidobacterium longum subsp. infantis. Anaerobe. 2012 Aug;18(4):430-5.
Strum JS, Kim J, Wu S, De Leoz ML, Peacock K, Grimm R, German JB, Mills DA, Lebrilla CB. Identification and Accurate Quantitation of Biological Oligosaccharide Mixtures. Anal Chem. 2012 Aug 29. [Epub ahead of print]
Strum JS, Aldredge D, Barile D, Lebrilla CB. Coupling flash liquid chromatography with mass spectrometry for enrichment and isolation of milk oligosaccharides for functional studies. Anal Biochem. 2012 May 15;424(2):87-96.
Garrido D, Barile D, Mills DA. A molecular basis for bifidobacterial enrichment in the infant gastrointestinal tract. Adv Nutr. 2012 May 1;3(3):415S-21S.
Ruhaak LR, Lebrilla CB. Advances in analysis of human milk oligosaccharides. Adv Nutr. 2012 May 1;3(3):406S-14S.
Sela DA, Garrido D, Lerno L, Wu S, Tan K, Eom HJ, Joachimiak A, Lebrilla CB, Mills DA. Bifidobacterium longum subsp. infantis ATCC 15697 α-fucosidases are active on fucosylated human milk oligosaccharides. Appl Environ Microbiol. 2012 Feb;78(3):795-803.
Marcobal A, Barboza M, Sonnenburg ED, Pudlo N, Martens EC, Desai P, Lebrilla CB, Weimer BC, Mills DA, German JB, Sonnenburg JL. Bacteroides in the infant gut consume milk oligosaccharides via mucus-utilization pathways. Cell Host Microbe. 2011 Nov 17;10(5):507-14.
Sela DA, Li Y, Lerno L, Wu S, Marcobal AM, German JB, Chen X, Lebrilla CB, Mills DA. An infant-associated bacterial commensal utilizes breast milk sialyloligosaccharides. J Biol Chem. 2011 Apr 8; 286(14):11909-18. Erratum in: J Biol Chem. 2011 Jul 1; 286(26):23620.
Garrido D, Kim JH, German JB, Raybould HE, Mills DA. Oligosaccharide binding proteins from Bifidobacterium longum subsp. infantis reveal a preference for host glycans. PLoS One. 2011 Mar 15;6(3):e17315.
Zivkovic AM, German JB, Lebrilla CB, Mills DA. Human milk glycobiome and its impact on the infant gastrointestinal microbiota. Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4653-8.
Wu S, Grimm R, German JB, Lebrilla CB. Annotation and structural analysis of sialylated human milk oligosaccharides. J Proteome Res. 2011 Feb 4;10(2):856-68.
Tao N, Wu S, Kim J, An HJ, Hinde K, Power ML, Gagneux P, German JB, Lebrilla CB. Evolutionary Glycomics: Characterization of Milk Oligosaccharides in Primates. J Proteome Res. 2011 Apr 1;10(4):1548-57.
Chichlowski M, German JB, Lebrilla CB, Mills DA. The influence of milk oligosaccharides on microbiota of infants: opportunities for formulas. Annu Rev Food Sci Technol. 2011;2:331-51. Review.
Barile D, Marotta M, Chu C, Mehra R, Grimm R, Lebrilla CB, German JB. Neutral and acidic oligosaccharides in Holstein-Friesian colostrum during the first 3 days of lactation measured by high performance liquid chromatography on a microfluidic chip and time-of-flight mass spectrometry. J. Dairy Sci. 2010; 93: 3940-3949.
Sela DA, Mills DA. Nursing our microbiota: molecular linkages between bifidobacteria and milk oligosaccharides. Trends Microbiol. 2010 Jul;18(7):298-307.
Wu S, Tao N, German JB, Grimm R, Lebrilla CB. The development of an annotated library of neutral human milk oligosaccharides. J Proteome Res. 2010 Aug 6;9(8):4138-51.
Tao N, Ochonicky KL, German JB, Donovan SM, Lebrilla CB. Structural determination and daily variations of porcine milk oligosaccharides. J Agric Food Chem 2010;58:4653-9.
Marcobal A, Barboza M, Froehlich JW, Block, D., German, J.B., Lebrilla, C.B., Mills, D.A. Consumption of Human Milk Oligosaccharides by Gut-Related Microbes. J Agric Food Chem 2010; 58(9): 5334-40.
Niñonuevo MR, Lebrilla CB. Mass spectrometric methods for analysis of oligosaccharides in human milk. Nutr Rev. 2009 Nov;67 Suppl 2:S216-26.
Tao N, DePeters EJ, German JB, Grimm R, Lebrilla CB. Variations in bovine milk oligosaccharides during early and middle lactation stages analyzed by high-performance liquid chromatography-chip/mass spectrometry. J Dairy Sci 2009; 92:2991-3001.
Barboza M, Sela DA, Pirim C, et al. Glycoprofiling bifidobacterial consumption of galacto-oligosaccharides by mass spectrometry reveals strain-specific, preferential consumption of glycans. Appl Environ Microbiol 2009;75:7319-25.
Barile D, Tao N, Lebrilla CB, Coisson JD, Arlorio M, German JB. Permeate from cheese whey ultrafiltration is a source of milk oligosaccharides. Int Dairy J 2009;19:524-530.
Sela, D. A., J. Chapman, et al. (2008). "The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome." Proc Natl Acad Sci U S A 105(48): 18964-9.
German, J. B., S. L. Freeman, et al. (2008). "Human milk oligosaccharides: evolution, structures and bioselectivity as substrates for intestinal bacteria."Nestle Nutr Workshop Ser Pediatr Program 62: 205-18; discussion 218-22.
Ninonuevo, M. R., P. D. Perkins, et al. (2008). "Daily variations in oligosaccharides of human milk determined by microfluidic chips and mass spectrometry." J Agric Food Chem 56(2): 618-26.
Seipert, R. R., M. Barboza, et al. (2008). "Analysis and quantitation of fructooligo-saccharides using matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry." Anal Chem 80(1): 159-65.
Ward, R. E., M. Ninonuevo, et al. (2007). "In vitro fermentability of human milk oligosaccharides by several strains of bifidobacteria." Mol Nutr Food Res 51(11): 1398-405.
LoCascio, R. G., M. R. Ninonuevo, et al. (2007). "Glycoprofiling of bifidobacterial consumption of human milk oligosaccharides demonstrates strain specific, preferential consumption of small chain glycans secreted in early human lactation." J Agric Food Chem 55(22): 8914-9.
Ninonuevo, M. R., R. E. Ward, et al. (2007). "Methods for the quantitation of human milk oligosaccharides in bacterial fermentation by mass spectrometry." Anal Biochem 361(1): 15-23.
Ninonuevo, M. R., Y. Park, et al. (2006). "A strategy for annotating the human milk glycome." J Agric Food Chem 54(20): 7471-80.
Ward, R. E., M. Ninonuevo, et al. (2006). "In vitro fermentation of breast milk oligosaccharides by Bifidobacterium infantis and Lactobacillus gasseri." Appl Environ Microbiol 72(6): 4497-9.

Bioactive Glycopeptides

Song T, Ozcan S, Becker A, Lebrilla CB. In-Depth Method for the Characterization of Glycosylation in Manufactured Recombinant Monoclonal Antibody Drugs. Anal Chem. 2014 May 27. [Epub ahead of print] PubMed PMID: 24828102.
Ozcan S, Kim BJ, Ro G, Kim JH, Bereuter TL, Reiter C, Dimapasoc L, Garrido D, Mills DA, Grimm R, Lebrilla CB, An HJ. Glycosylated proteins preserved over millennia: N-glycan analysis of Tyrolean Iceman, Scythian Princess and Warrior. Sci Rep. 2014 May 16;4:4963. doi: 10.1038/srep04963. PubMed PMID: 24831691.
Nwosu CC, Huang J, Aldredge DL, Strum JS, Hua S, Seipert RR, Lebrilla CB. In-gel nonspecific proteolysis for elucidating glycoproteins: a method for targeted protein-specific glycosylation analysis in complex protein mixtures. Anal Chem. 2013 Jan 15;85(2):956-63. doi: 10.1021/ac302574f. Epub 2012 Dec 28. PubMed PMID: 23215446; PubMed Central PMCID: PMC3547527.
Strum JS, Nwosu CC, Hua S, Kronewitter SR, Seipert RR, Bachelor RJ, An HJ, Lebrilla CB. Automated assignments of N- and O-site specific glycosylation with extensive glycan heterogeneity of glycoprotein mixtures. Anal Chem. 2013 Jun 18;85(12):5666-75. doi: 10.1021/ac4006556. Epub 2013 May 24. PubMed PMID: 23662732; PubMed Central PMCID: PMC3692395.
Garrido D, Nwosu C, Ruiz-Moyano S, Aldredge D, German JB, Lebrilla CB, Mills DA. Endo-β-N-acetylglucosaminidases from infant gut-associated bifidobacteria release complex N-glycans from human milk glycoproteins. Mol Cell Proteomics. 2012 Sep;11(9):775-85. doi: 0.1074/mcp.M112.018119. Epub 2012 Jun 27. PubMed PMID: 22745059; PubMed Central PMCID: PMC3434770.
Garrido, D. A., D. C. Dallas and D. A. Mills. 2013. Consumption of human milk glycoconjugates by infant-associated bifidobacteria: Mechanisms and implications. Microbiology 159:649-664.
Froehlich JW, Dodds ED, Barboza M, et al. Glycoprotein Expression in Human Milk during Lactation. J Agric Food Chem 2010; 58(10): 6440-8.
An HJ, Froehlich JW, Lebrilla CB. Determination of glycosylation sites and site-specific heterogeneity in glycoproteins. Curr Opin Chem Biol. 2009 Oct;13(4):421-6.
Dodds, E. D., R. R. Seipert, et al. (2009). "Analytical performance of immobilized pronase for glycopeptide footprinting and implications for surpassing reductionist glycoproteomics." J Proteome Res 8(2): 502-12.
Seipert, R. R., E. D. Dodds, et al. (2008). "Factors that influence fragmentation behavior of N-linked glycopeptide ions." Anal Chem 80(10): 3684-92.
Dodds, E. D., J. B. German, et al. (2007). "Enabling MALDI-FTICR-MS/MS for high-performance proteomics through combination of infrared and collisional activation." Anal Chem 79(24): 9547-56.

Glycolipids

Lee H, Lerno LA Jr, Choe Y, Chu CS, Gillies LA, Grimm R, Lebrilla CB, German JB. Multiple Precursor Ion Scanning of Gangliosides and Sulfatides with a Reversed-Phase Microfluidic Chip and Quadrupole Time-of-Flight Mass Spectrometry. Anal Chem. 2012 Jul 17;84(14):5905-12.
Lee H, An HJ, Lerno LA Jr, German JB, Lebrilla CB. Rapid Profiling of Bovine and Human Milk Gangliosides by Matrix-Assisted Laser Desorption/Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Int J Mass Spectrom. 2011 Aug 15;305(2-3):138-150.
Lerno LA, German JB, Lebrilla CB. Method for the Identification of Lipid Classes Based on Referenced Kendrick Mass Analysis. Anal Chem 2010; 82(10): 4236-45.
Schombs M, Park FE, Du W, Kulkarni SS, Gervay-Hague J. One-Pot Syntheses of Immunostimulatory Glycolipids. J Org Chem. 2010 Apr 13.

Synthesis of Novel Glycans

Hwang J, Yu H, Malekan H, Sugiarto G, Li Y, Qu J, Nguyen V, Wu D, Chen X. Highly efficient one-pot multienzyme (OPME) synthesis of glycans with fluorous-tag assisted purification. Chem Commun (Camb). 2014 Mar 25; 50(24):3159-62. doi: 10.1039/c4cc00070f. Epub 2014 Jan 29. PubMed PMID: 24473465.
Chen Y, Li Y, Yu H, Sugiarto G, Thon V, Hwang J, Ding L, Hie L, Chen X. Tailored design and synthesis of heparan sulfate oligosaccharide analogues using sequential one-pot multienzyme systems. Angew Chem Int Ed Engl. 2013 Nov 4; 52(45):11852-6. doi: 10.1002/anie.201305667. Epub 2013 Sep 13. PubMed PMID: 24038939; PubMed Central PMCID: PMC3943747.
Li L, Liu Y, Wan Y, Li Y, Chen X, Zhao W, Wang PG. Efficient enzymatic synthesis of guanosine 5'-diphosphate-sugars and derivatives. Org Lett. 2013 Nov 1; 15(21):5528-30. doi: 10.1021/ol402585c. Epub 2013 Oct 11. PubMed PMID: 24117142; PubMed Central PMCID: PMC3915774.
Khedri Z, Li Y, Muthana S, Muthana MM, Hsiao CW, Yu H, Chen X. Chemoenzymatic synthesis of sialosides containing C7-modified sialic acids and their application in sialidase substrate specificity studies. Carbohydr Res. 2014 May 7; 389:100-11. doi: 10.1016/j.carres.2014.02.021. Epub 2014 Mar 6. PubMed PMID: 24680514.
Malekan H, Fung G, Thon V, Khedri Z, Yu H, Qu J, Li Y, Ding L, Lam KS, Chen X. One-pot multi-enzyme (OPME) chemoenzymatic synthesis of sialyl-Tn-MUC1 and sialyl-T-MUC1 glycopeptides containing natural or non-natural sialic acid. Bioorg Med Chem. 2013 Aug 15; 21(16):4778-85. doi: 10.1016/j.bmc.2013.02.040. Epub 2013 Mar 7. PubMed PMID: 23535562; PubMed Central PMCID: PMC3722252.
Lau K, Thon V, Yu H, Ding L, Chen Y, Muthana MM, Wong D, Huang R, Chen X. Highly efficient chemoenzymatic synthesis of beta1-4-linked galactosides with promiscuous bacterial beta1-4-galactosyltransferases. Chem Commun (Camb). 2010 Jul 12.
Schombs M, Park FE, Du W, Kulkarni SS, Gervay-Hague J. One-Pot Syntheses of Immunostimulatory Glycolipids. J Org Chem. 2010 Apr 13.
Horn EJ, Gervay-Hague J. Efficient method for the preparation of peracetylated Neu5Ac2en by flash vacuum pyrolysis. J Org Chem. 2009 Jun 5;74(11):4357-9.
Saludes JP, Ames JB, Gervay-Hague J. Synthesis and structural characterization of sialic acid-glutamic acid hybrid foldamers as conformational surrogates of alpha-2,8-linked polysialic acid. J Am Chem Soc. 2009 Apr 22;131(15):5495-505.
Cheng J, Yu H, Lau K, Huang S, Chokhawala HA, Li Y, Tiwari VK, Chen X: Multifunctionality of Campylobacter jejuni sialyltransferase CstII: characterization of GD3/GT3 oligosaccharide synthase, GD3 oligosaccharide sialidase, and trans-sialidase activities. Glycobiology 2008, 18:686-697.
Sun M, Li Y, Chokhawala HA, Henning R, Chen X: N-Terminal 112 amino acid residues are not required for the sialyltransferase activity of Photobacterium damsela alpha2,6-sialyltransferase. Biotechnol Lett 2008, 30:671-676.
Chokhawala HA, Huang S, Lau K, Yu H, Cheng J, Thon V, Hurtado-Ziola N, Guerrero JA, Varki A, Chen X: Combinatorial chemoenzymatic synthesis and high-throughput screening of sialosides. ACS Chem Biol 2008, 3:567-576.
Kulkarni SS, Gervay-Hague J. Two-step synthesis of the immunogenic bacterial glycolipid BbGL1. Org Lett. 2008 Nov 6;10(21):4739-42.
Li Y, Sun M, Huang S, Yu H, Chokhawala HA, Thon V, Chen X: The Hd0053 gene of Haemophilus ducreyi encodes an alpha2,3-sialyltransferase. Biochem Biophys Res Commun 2007, 361:555-560.
Du W, Kulkarni SS, Gervay-Hague J. Efficient, one-pot syntheses of biologically active alpha-linked glycolipids. Chem Commun (Camb). 2007 Jun 21;(23):2336-8.
Yu H, Chokhawala HA, Varki A, Chen X: Efficient chemoenzymatic synthesis of biotinylated human serum albumin-sialoglycoside conjugates containing O-acetylated sialic acids. Org Biomol Chem 2007, 5:2458-2463.
Yu H, Chokhawala HA, Huang S, Chen X: One-pot three-enzyme chemoenzymatic approach to the synthesis of sialosides containing natural and non-natural functionalities. Nat Protoc 2006, 1:2485-2492.
Yu H, Chen X: Aldolase catalyzed synthesis of beta-D-Gal p -(1-9)-D-KDN: A novel acceptor for sialyltransferases. Org Lett 2006, 8:2393-2396.
Yu H, Huang S, Chokhawala H, Sun M, Zheng H, Chen X: Highly efficient chemoenzymatic synthesis of naturally occurring and non-natural alpha-2,6-linked sialosides: A P. damsela alpha-2,6-sialyltransferase with extremely flexible donor-substrate specificity. Angew Chem Int Ed Engl 2006, 45:3938-3944.

Infant Microbiome

Sela, D. A. and D. A. Mills. 2014. The marriage of nutrigenomics with the microbiome: the case of infant-associated bifidobacteria and milk. The American Journal of Clinical Nutrition (March 2014) 99:697S-703S.
Underwood, M. A., K. M. Kalanetra, N. A. Bokulich, M. Mirmiran, D. Barile, D. J. Tancredi, J. B. German, C. B. Lebrilla and D. A. Mills. 2014. Prebiotic oligosaccharides in premature infants. Journal of Pediatric Gastroenterology & Nutrition 58:352-360.
Lee H., D. Garrido D., D. A. Mills, D. Barile. 2014. Hydrolysis of milk gangliosides by infant-gut associated bifidobacteria determined by microfluidic chips and high-resolution mass spectrometry. Electrophoresis 2014 Jun;35(11):1742-50. doi: 10.1002/elps.201300653. Epub 2014 Mar 20.
Garrido, D., S. Ruiz-Moyano, J. Jimenez-Espinoza, H-J. Eom, D. E. Block and D. A. Mills. 2013. Utilization of galactooligosaccharides by Bifidobacterium longum subsp. infantis isolates. Food Microbiology 33:262–270.
Kim JH, An HJ, Garrido D, German JB, Lebrilla CB, Mills DA. Proteomic analysis of Bifidobacterium longum subsp. infantis reveals the metabolic insight on consumption of prebiotics and host glycans. PLoS One. 2013;8(2):e57535. doi: 10.1371/journal.pone.0057535. Epub 2013 Feb 26. PubMed PMID: 23469017; PubMed Central PMCID: PMC3582569.
Dvorak K, Coursodon-Boyiddle CF, Snarrenberg CL, Kananurak A, Underwood MA, Dvorak B. Helicobacter hepaticus increases intestinal injury in a rat model of necrotizing enterocolitis. Am J Physiol Gastrointest Liver Physiol. 2013 Oct 15;305(8):G585-92. doi: 10.1152/ajpgi.00483.2012. Epub 2013 Aug 29. PubMed PMID: 23989006; PubMed Central PMCID: PMC3798735.
Bokulich, N. A., D. A. Mills and M. Underwood. 2013. Surface microbes in the neonatal intensive care unit: Changes with routine cleaning and over time. Journal of Clinical Microbiology 51:2617-2624.
Garrido, D. A., D. C. Dallas and D. A. Mills. 2013. Consumption of human milk glycoconjugates by infant-associated bifidobacteria: Mechanisms and implications. Microbiology 159:649-664.
Peacock, K., R. L. Ruhaak, M. K. Tsui, D. A. Mills, C. B. Lebrilla. Isomer-specific consumption of galactooligosaccharides by bifidobacterial species. 2013. Journal of Agricultural and Food Chemistry 61:12612-12619.
Ruiz-Moyano, S., S. M. Totten, D. A. Garrido, J. T. Smilowitz, J. B. German, C. B. Lebrilla and D. A. Mills. 2013. Variation in consumption of human milk oligosaccharides by infant-gut associated strains of Bifidobacterium breve. Applied and Environmental Microbiology 79:6040-6049.
Zivkovic, A. M., Z. T. Lewis, J. B. German and D. A. Mills. 2013. Establishment of a milk-oriented microbiota (MOM) in early life: How babies meet their MOMs. Functional Food Reviews 5:3-12.
Underwood MA. Human milk for the premature infant. Pediatr Clin North Am. 2013 Feb;60(1):189-207. doi: 10.1016/j.pcl.2012.09.008. Epub 2012 Oct 18. Review. PubMed PMID: 23178065; PubMed Central PMCID: PMC3508468.
Underwood, M., K. Kalanetra, N. Bokulich, Z. T. Lewis, M. Mirmiran, D. Tancredi and D. A. Mills. 2013. A comparison of two probiotic strains of bifidobacteria in premature infants. Journal of Pediatrics 163:1585-1591.
Underwood MA. Paneth cells and necrotizing enterocolitis. Gut Microbes. 2012 Nov-Dec; 3(6): 562-5. doi: 10.4161/gmic.21738. Epub 2012 Aug 16. Review. PubMed PMID: 22895084; PubMed Central PMCID: PMC3495794.
McElroy SJ, Underwood MA, Sherman MP. Paneth cells and necrotizing enterocolitis: a novel hypothesis for disease pathogenesis. Neonatology. 2013; 103(1):10-20. doi: 10.1159/000342340. Epub 2012 Sep 20. Review. PubMed PMID: 23006982; PubMed Central PMCID: PMC3609425.
Lewis ZT, Bokulich NA, Kalanetra KM, Ruiz-Moyano S, Underwood MA, Mills DA. Use of bifidobacterial specific terminal restriction fragment length polymorphisms to complement next generation sequence profiling of infant gut communities. Anaerobe. 2013 Feb; 19:62-9. doi: 10.1016/j.anaerobe.2012.12.005. Epub 2012 Dec 20. PubMed PMID: 23261904.
De Leoz ML, Gaerlan SC, Strum JS, Dimapasoc LM, Mirmiran M, Tancredi DJ, Smilowitz JT, Kalanetra KM, Mills DA, German JB, Lebrilla CB, Underwood MA. Lacto-N-tetraose, fucosylation, and secretor status are highly variable in human milk oligosaccharides from women delivering preterm. J Proteome Res. 2012 Sep 7;11(9):4662-72.
Chichlowski M, De Lartigue G, German JB, Raybould HE, Mills DA. Bifidobacteria isolated from infants and cultured on human milk oligosaccharides affect intestinal epithelial function. J Pediatr Gastroenterol Nutr. 2012 Sep;55(3):321-7.
Garrido D, Ruiz-Moyano S, Mills DA. Release and utilization of N-acetyl-d-glucosamine from human milk oligosaccharides by Bifidobacterium longum subsp. infantis. Anaerobe. 2012 Aug;18(4):430-5.
Garrido D, Barile D, Mills DA. A molecular basis for bifidobacterial enrichment in the infant gastrointestinal tract. Adv Nutr. 2012 May 1;3(3):415S-21S.
Sela DA, Garrido D, Lerno L, Wu S, Tan K, Eom HJ, Joachimiak A, Lebrilla CB, Mills DA. Bifidobacterium longum subsp. infantis ATCC 15697 α-fucosidases are active on fucosylated human milk oligosaccharides. Appl Environ Microbiol. 2012 Feb;78(3):795-803.
Marcobal A, Barboza M, Sonnenburg ED, Pudlo N, Martens EC, Desai P, Lebrilla CB, Weimer BC, Mills DA, German JB, Sonnenburg JL. Bacteroides in the infant gut consume milk oligosaccharides via mucus-utilization pathways. Cell Host Microbe. 2011 Nov 17;10(5):507-14.
Garrido D, Kim JH, German JB, Raybould HE, Mills DA. Oligosaccharide binding proteins from Bifidobacterium longum subsp. infantis reveal a preference for host glycans. PLoS One. 2011 Mar 15;6(3):e17315.
Zivkovic AM, German JB, Lebrilla CB, Mills DA. Human milk glycobiome and its impact on the infant gastrointestinal microbiota. Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4653-8.
Wu S, Grimm R, German JB, Lebrilla CB. Annotation and structural analysis of sialylated human milk oligosaccharides. J Proteome Res. 2011 Feb 4;10(2):856-68.
Chichlowski M, German JB, Lebrilla CB, Mills DA. The influence of milk oligosaccharides on microbiota of infants: opportunities for formulas. Annu Rev Food Sci Technol. 2011;2:331-51. Review.
Sela DA, Li Y, Lerno L, Wu S, Marcobal AM, German JB, Chen X, Lebrilla CB, Mills DA. An infant-associated bacterial commensal utilizes breast milk sialyloligosaccharides. J Biol Chem. 2011 Apr 8; 286(14):11909-18. Erratum in: J Biol Chem. 2011 Jul 1; 286(26):23620.
Zivkovic AM, German JB, Lebrilla CB, Mills DA. Microbes and Health Sackler Colloquium: Human milk glycobiome and its impact on the infant gastrointestinal microbiota. Proc Natl Acad Sci U S A. 2010 Aug 2.
Sela DA, Mills DA. Nursing our microbiota: molecular linkages between bifidobacteria and milk oligosaccharides. Trends Microbiol. 2010 Jul;18(7):298-307.
Wu S, Tao N, German JB, Grimm R, Lebrilla CB. The development of an annotated library of neutral human milk oligosaccharides. J Proteome Res. 2010 Aug 6;9(8):4138-51.
Marcobal A, Barboza M, Froehlich JW, Block, D., German, J.B., Lebrilla, C.B., Mills, D.A. Consumption of Human Milk Oligosaccharides by Gut-Related Microbes. J Agric Food Chem 2010; 58(9): 5334-40.
Barboza M, Sela DA, Pirim C, et al. Glycoprofiling bifidobacterial consumption of galacto-oligosaccharides by mass spectrometry reveals strain-specific, preferential consumption of glycans. Appl Environ Microbiol 2009;75:7319-25.
Sela, D. A., J. Chapman, et al. (2008). "The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome." Proc Natl Acad Sci U S A 105(48): 18964-9.
German, J. B., S. L. Freeman, et al. (2008). "Human milk oligosaccharides: evolution, structures and bioselectivity as substrates for intestinal bacteria."Nestle Nutr Workshop Ser Pediatr Program 62: 205-18; discussion 218-22.
Ward, R. E., M. Ninonuevo, et al. (2007). "In vitro fermentability of human milk oligosaccharides by several strains of bifidobacteria." Mol Nutr Food Res 51(11): 1398-405.
LoCascio, R. G., M. R. Ninonuevo, et al. (2007). "Glycoprofiling of bifidobacterial consumption of human milk oligosaccharides demonstrates strain specific, preferential consumption of small chain glycans secreted in early human lactation." J Agric Food Chem 55(22): 8914-9.
Ninonuevo, M. R., R. E. Ward, et al. (2007). "Methods for the quantitation of human milk oligosaccharides in bacterial fermentation by mass spectrometry."Anal Biochem 361(1): 15-23.
Ward, R. E., M. Ninonuevo, et al. (2006). "In vitro fermentation of breast milk oligosaccharides by Bifidobacterium infantis and Lactobacillus gasseri." Appl Environ Microbiol 72(6): 4497-9.

Host-Microbe Interactions

Underwood MA. Intestinal dysbiosis: Novel mechanisms by which gut microbes trigger and prevent disease. Prev Med. 2014 May 20;65C:133-137. doi: 10.1016/j.ypmed.2014.05.010. [Epub ahead of print] PubMed PMID: 24857830.
Halder S, Cotmore S, Heimburg-Molinaro J, Smith DF, Cummings RD, Chen X, Trollope AJ, North SJ, Haslam SM, Dell A, Tattersall P, McKenna R, Agbandje-McKenna M. Profiling of glycan receptors for minute virus of mice in permissive cell lines towards understanding the mechanism of cell recognition. PLoS One. 2014 Jan 27; 9(1):e86909. doi: 10.1371/journal.pone.0086909. eCollection 2014. PubMed PMID: 24475195; PubMed Central PMCID: PMC3903596.
Huda, M N., Z. Lewis, K. Kalanetra, M. Rashid, S. Ahmad, R. Raqib, F. Qadri, M. A. Underwood, D. A. Mills and C. Stephensen. Stool microbiota and vaccine responses of infants. Pediatrics 2014 Aug;134(2):e362-72. doi: 10.1542/peds.2013-3937. Epub 2014 Jul 7.
Tsuei, J., T. Chau, D. A. Mills and Y.-J. Y. Wan. Bile acid dysregulation, gut dysbiosis, and GI cancer. Experimental Biology and Medicine. 2014 Jun 20. pii: 1535370214538743.
Underwood, M., J. Arriola, C. Gerber, A. Kaveti, K. Kalanetra, A. Kananurak, C. Bevins, D. A. Mills, and B. Dvorak. Bifidobacterium longum subsp. infantis in experimental necrotizing enterocolitis: alterations in inflammation, innate immune response, and the microbiota. Pediatric Research. 2014 Jul 7. doi: 10.1038/pr.2014.102.
Ellis, C. L., N. A. Bokulich, K. M. Kalanetra, M. Mirmiran, J. Elumalai, L. Haapanen, T. Schegg, J. C. Rutledge, G. Raff, D. A. Mills, M. A. Underwood. 2013. Probiotic administration in congenital heart disease: A pilot study. Journal of Perinatology 33:691-697.
Gordon, J. I., K. Dewey, D. A. Mills and R M. Medzhitov. 2012. The human gut microbiota and undernutrition. Science Translational Medicine 4:137ps12.
Ma, B. W., N. A. Bokulich, P. A. Castillo, A. Kananurak, M. A. Underwood, D. A. Mills, C. L. Bevins. 2012. Routine habitat change: A source of unrecognized transient alteration of intestinal microbiota in laboratory mice. PLoS One 7(10): e47416.
Barboza M, Pinzon J, Wickramasinghe S, Froehlich JW, Moeller I, Smilowitz JT, Ruhaak LR, Huang J, Lönnerdal B, German JB, Medrano JF, Weimer BC, Lebrilla CB. Glycosylation of human milk lactoferrin exhibits dynamic changes during early lactation enhancing its role in pathogenic bacteria-host interactions. Mol Cell Proteomics. 2012 Jun;11(6):M111.015248.
Cooke CL, An HJ, Kim J, Canfield DR, Torres J, Lebrilla CB, Solnick JV. Modification of gastric mucin oligosaccharide expression in rhesus macaques after infection with Helicobacter pylori. Gastroenterology. 2009 Sep;137(3):1061-71, 1071.e1-8.
Sun YS, Landry JP, Fei YY, Zhu X, Luo JT, Wang XB, Lam KS: Macromolecular scaffolds for immobilizing small molecule microarrays in label-free detection of protein-ligand interactions on solid support. Anal Chem 2009, Jul 1;81(13):5373-80.
Landry JP, Sun YS, Guo XW, Zhu XD: Protein reactions with surface-bound molecular targets detected by oblique-incidence reflectivity difference microscopes. Appl Opt 2008, 47:3275-3288.
Sun YS, Landry JP, Fei YY, Zhu XD, Luo JT, Wang XB, Lam KS: Effect of fluorescently labeling protein probes on kinetics of protein-ligand reactions. Langmuir 2008, 24:13399-13405.
Fei YY, Landry JP, Sun YS, Zhu XD, Luo JT, Wang XB, Lam KS: A novel high-throughput scanning microscope for label-free detection of protein and small-molecule chemical microarrays. Rev Sci Instrum 2008, 79:013708.
Desai PT, Walsh MK, Weimer BC: Solid-phase capture of pathogenic bacteria by using gangliosides and detection with real-time PCR. Appl Environ Microbiol 2008, 74:2254-2258.
Zhu X, Landry JP, Sun YS, Gregg JP, Lam KS, Guo X: Oblique-incidence reflectivity difference microscope for label-free high-throughput detection of biochemical reactions in a microarray format. Appl Opt 2007, 46:1890-1895.
Landry JP, Zhu XD, Gregg JP: Label-free detection of microarrays of biomolecules by oblique-incidence reflectivity difference microscopy. Opt Lett 2004, 29:581-583.

Immune Senescence Project

Freeman SL, Fisher L, German JB, Leung PS, Prince H, Selmi C, Naguwa SM, Gershwin ME. Dairy proteins and the response to pneumovax in senior citizens: a randomized, double-blind, placebo-controlled pilot study. Ann NY Acad Sci 2010; 1190: 97-103.

Bovine Genomics Project

Wickramasinghe S, Hua S, Rincon G, Islas-Trejo A, German JB, Lebrilla CB, Medrano JF. Transcriptome Profiling of Bovine Milk Oligosaccharide Metabolism Genes Using RNA-Sequencing. PLoS One. 2011 Apr 25;6(4):e18895.
Lemay DG, Rijnkels M, German JB, Lessons from the bovine genome: implications for human nutrition and research, Nutr. 2009 Jul;139(7):1271-2.
Bovine Genome Sequencing and Analysis Consortium, Elsik CG, Tellam RL, et al, The genome sequence of taurine cattle: a window to ruminant biology and evolution, Science. 2009 Apr 24;324(5926):522-8.
Tellam RL, Lemay DG, Van Tassell CP, Lewin HA, Worley KC, Elsik CG. Unlocking the bovine genome. BMC Genomics. 2009 Apr 24;10:193.
Lemay DG, Lynn DJ, Martin W, et al, The bovine lactation genome: insights into the evolution of mammalian milk, Genome Biol. 2009;10(4):R43.

Bioactives from Whey Processing

Dallas DC, Lee H, Parc AL, de Moura Bell JM, Barile D. Coupling Mass Spectrometry-Based "Omic" Sciences with Bioguided Processing to Unravel Milk's Hidden Bioactivities. J Adv Dairy Res. 2013 Jul 24;1(2):104. PubMed PMID: 24818172; PubMed Central PMCID: PMC4012335.
Mehra R, Barile D, Marotta M, Lebrilla CB, Chu C, German JB. Novel high-molecular weight fucosylated milk oligosaccharides identified in dairy streams. PLoS One. 2014 May 8;9(5):e96040. doi: 10.1371/journal.pone.0096040. eCollection 2014. PubMed PMID: 24810963; PubMed Central PMCID: PMC4014476
Zivkovic AM, Barile D. Bovine milk as a source of functional oligosaccharides for improving human health. Adv Nutr. 2011 May;2(3):284-9.
Barile D, Marotta M, Chu C, Mehra R, Grimm R, Lebrilla CB, German JB. Neutral and acidic oligosaccharides in Holstein-Friesian colostrum during the first 3 days of lactation measured by high performance liquid chromatography on a microfluidic chip and time-of-flight mass spectrometry. J. Dairy Sci. 2010; 93: 3940-3949.
Barile D, Tao N, Lebrilla CB, Coisson JD, Arlorio M, German JB. Permeate from cheese whey ultrafiltration is a source of milk oligosaccharides. Int Dairy J 2009;19:524-530.

Milk Protein Phosphorylation Project

Froehlich JW, Chu CS, Tang N, Waddell K, Grimm R, Lebrilla CB. Label-free liquid chromatography-tandem mass spectrometry analysis with automated phosphopeptide enrichment reveals dynamic human milk protein phosphorylation during lactation. Anal Biochem. 2011 Jan 1;408(1):136-46.

Lactosome Biology Project

Argov-Argaman N, Smilowitz JT, Bricarello DB, Barboza M, Lerno L, Froehlich J, Lee H, Zivkovic AM, Lemay DG, Freeman S, Lebrilla CB, Parikh A, German JB, Lactosomes: structural and compositional classification of unique nanometer-sized protein lipid particles of human milk, J Agric Food Chem, 2010 Oct 6 [Epub ahead of print].
Argov N, Wachsmann-Hogiu S, Freeman SL, Huser T, Lebrilla CB, German JB. Size-dependent lipid content in human milk fat globules. J Agric Food Chem. 2008 Aug 27;56(16):7446-50.

Bovine Milk Oligosaccharides Project

Le Parc A, Dallas DC, Duaut S, Leonil J, Martin P, Barile D. Characterization of goat milk lactoferrin N-glycans and comparison with the N-glycomes of human and bovine milk. Electrophoresis. 2014 Feb 12. doi: 10.1002/elps.201300619. [Epub ahead of print] PubMed
Aldredge DL, Geronimo MR, Hua S, Nwosu CC, Lebrilla CB, Barile D. Annotation and structural elucidation of bovine milk oligosaccharides and determination of novel fucosylated structures. Glycobiology. 2013 Jun; 23(6):664-76. doi: 10.1093/glycob/cwt007. Epub 2013 Feb 22. PubMed PMID: 23436288; PubMed Central PMCID: PMC3641798.
Mehra R, Barile D, Marotta M, Lebrilla CB, Chu C, German JB. Novel high-molecular weight fucosylated milk oligosaccharides identified in dairy streams. PLoS One. 2014 May 8; 9(5):e96040. doi: 10.1371/journal.pone.0096040. eCollection 2014. PubMed PMID: 24810963; PubMed Central PMCID: PMC4014476.
Lee H, German JB, Kjelden R, Lebrilla CB, Barile D. Quantitative analysis of gangliosides in bovine milk and colostrum-based dairy products by ultrahigh performance liquid chromatography-tandem mass spectrometry. J Agric Food Chem. 2013 Oct 9;61(40):9689-96. doi: 10.1021/jf402255g. Epub 2013 Sep 30. PubMed PMID:24024650.
Meyrand M, Dallas DC, Caillat H, Bouvier F, Martin P, Barile D. Comparison of milk oligosaccharides between goats with and without the genetic ability to synthesize α(s1)-casein. Small Rumin Res. 2013 Jul 1;113(2-3):411-420. PubMed PMID: 24587592; PubMed Central PMCID: PMC3935728.
Sundekilde UK, Barile D, Meyrand M, Poulsen NA, Larsen LB, Lebrilla CB, German JB, Bertram HC. Natural variability in bovine milk oligosaccharides from Danish Jersey and Holstein-Friesian breeds. J Agric Food Chem. 2012 Jun 20;60(24):6188-96.
Zivkovic AM, Barile D. Bovine milk as a source of functional oligosaccharides for improving human health. Adv Nutr. 2011 May;2(3):284-9.
Wu S, Grimm R, German JB, Lebrilla CB. Annotation and structural analysis of sialylated human milk oligosaccharides. J Proteome Res. 2011 Feb 4;10(2):856-68.
Tao N, Wu S, Kim J, An HJ, Hinde K, Power ML, Gagneux P, German JB, Lebrilla CB. Evolutionary Glycomics: Characterization of Milk Oligosaccharides in Primates. J Proteome Res. J Proteome Res. 2011 Apr 1;10(4):1548-57.
Barile D, Marotta M, Chu C, Mehra R, Grimm R, Lebrilla CB, German JB. Neutral and acidic oligosaccharides in Holstein-Friesian colostrum during the first 3 days of lactation measured by high performance liquid chromatography on a microfluidic chip and time-of-flight mass spectrometry. J. Dairy Sci. 2010; 93: 3940-3949.
Zivkovic AM, German JB, Lebrilla CB, Mills DA. Microbes and Health Sackler Colloquium: Human milk glycobiome and its impact on the infant gastrointestinal microbiota. Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4653-8.
Sela DA, Mills DA. Nursing our microbiota: molecular linkages between bifidobacteria and milk oligosaccharides. Trends Microbiol. 2010 Jul;18(7):298-307.
Wu S, Tao N, German JB, Grimm R, Lebrilla CB. The development of an annotated library of neutral human milk oligosaccharides. J Proteome Res. 2010 Aug 6;9(8):4138-51.
Marcobal A, Barboza M, Froehlich JW, Block, D., German, J.B., Lebrilla, C.B., Mills, D.A. Consumption of Human Milk Oligosaccharides by Gut-Related Microbes. J Agric Food Chem 2010; 58(9): 5334-40.
Tao N, DePeters EJ, German JB, Grimm R, Lebrilla CB. Variations in bovine milk oligosaccharides during early and middle lactation stages analyzed by high-performance liquid chromatography-chip/mass spectrometry. J Dairy Sci 2009; 92:2991-3001.
Dodds, E. D., R. R. Seipert, et al. (2009). "Analytical performance of immobilized pronase for glycopeptide footprinting and implications for surpassing reductionist glycoproteomics." J Proteome Res 8(2): 502-12.
Niñonuevo MR, Lebrilla CB. Mass spectrometric methods for analysis of oligosaccharides in human milk. Nutr Rev. 2009 Nov;67 Suppl 2:S216-26.
Barile D, Tao N, Lebrilla CB, Coisson JD, Arlorio M, German JB. Permeate from cheese whey ultrafiltration is a source of milk oligosaccharides. Int Dairy J 2009;19:524-530.
Barboza M, Sela DA, Pirim C, et al. Glycoprofiling bifidobacterial consumption of galacto-oligosaccharides by mass spectrometry reveals strain-specific, preferential consumption of glycans. Appl Environ Microbiol 2009;75:7319-25.
Sela, D. A., J. Chapman, et al. (2008). "The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome." Proc Natl Acad Sci U S A 105(48): 18964-9.
Tao N, DePeters EJ, Freeman S, German JB, Grimm R, Lebrilla CB. Bovine milk glycome. J Dairy Sci 2008;91:3768-78.
Seipert, R. R., E. D. Dodds, et al. (2008). "Factors that influence fragmentation behavior of N-linked glycopeptide ions." Anal Chem 80(10): 3684-92.
Ninonuevo, M. R., P. D. Perkins, et al. (2008). "Daily variations in oligosaccharides of human milk determined by microfluidic chips and mass spectrometry." J Agric Food Chem 56(2): 618-26.
LoCascio, R. G., M. R. Ninonuevo, et al. (2007). "Glycoprofiling of bifidobacterial consumption of human milk oligosaccharides demonstrates strain specific, preferential consumption of small chain glycans secreted in early human lactation." J Agric Food Chem 55(22): 8914-9.
Dodds, E. D., J. B. German, et al. (2007). "Enabling MALDI-FTICR-MS/MS for high-performance proteomics through combination of infrared and collisional activation." Anal Chem 79(24): 9547-56.
Ward, R. E., M. Ninonuevo, et al. (2007). "In vitro fermentability of human milk oligosaccharides by several strains of bifidobacteria." Mol Nutr Food Res 51(11): 1398-405.

Comparative Lactation Project

Lemay DG, Ballard OA, Hughes MA, Morrow AL, Horseman ND, Nommsen-Rivers LA. RNA sequencing of the human milk fat layer transcriptome reveals distinct gene expression profiles at three stages of lactation. PLoS One. 2013 Jul 5;8(7):e67531. doi: 10.1371/journal.pone.0067531. Print 2013. PubMed PMID:23861770; PubMed Central PMCID: PMC3702532.
Rijnkels M, Freeman-Zadrowski C, Hernandez J, Potluri V, Wang L, Li W, Lemay DG. Epigenetic modifications unlock the milk protein gene loci during mouse mammary gland development and differentiation. PLoS One. 2013;8(1):e53270. doi: 10.1371/journal.pone. 0053270. Epub 2013 Jan 2. PubMed PMID: 23301053; PubMed Central PMCID: PMC3534698.
Smilowitz JT, Gho DS, Mirmiran M, German JB, Underwood MA. Rapid measurement of human milk macronutrients in the neonatal intensive care unit: accuracy and precision of fourier transform mid-infrared spectroscopy. J Hum Lact. 2014 May; 30(2):180-9. doi: 10.1177/0890334413517941. Epub 2014 Jan 14. PubMed PMID: 24423984.
Hinde K, German JB. Food in an evolutionary context: insights from mother's milk. J Sci Food Agric. 2012 Aug 30;92(11):2219-23.
Tao N, Wu S, Kim J, An HJ, Hinde K, Power ML, Gagneux P, German JB, Lebrilla CB. Evolutionary Glycomics: Characterization of Milk Oligosaccharides in Primates. J Proteome Res. J Proteome Res. 2011 Apr 1;10(4):1548-57.
Hinde, K., Capitanio, JP. (2010) Lactational programming? Mother's milk predicts infant temperament and behavior. Am J Primatol Jun;72(6):522-9.
Hinde, K. (2009) Richer milk for sons but more milk for daughters: sex biased investment during lactation varies with maternal life history in rhesus macaques. Am J Hum Biol 21:512-519.
Hinde, K., M. Power, and O. Oftedal, (2009) Rhesus macaque milk: Magnitude, sources, and consequences of individual variation over lactation. Am J Phys Anth. 138:148-57.
Hinde, K., (2007) Milk composition varies in relation to the presence and abundance of Balantidium coli in the mother in captive rhesus macaques (Macaca mulatta). Am J Primatol 69:625-634.
Hinde, K., (2007) First-time macaque mothers bias milk composition in favor of sons. Current Biology 17: R958-R959.

Gates Foundation Milk and Microbiome Project

Gordon JI, Dewey KG, Mills DA, Medzhitov RM. The human gut microbiota and undernutrition. Sci Transl Med. 2012 Jun 6;4(137):137ps12.

HDL Composition

Huang J, Lee H, Zivkovic AM, Smilowitz JT, Rivera N, German JB, Lebrilla CB. Glycomic analysis of high density lipoprotein shows a highly sialylated particle. J Proteome Res. 2014 Feb 7; 13(2): 681-91. doi: 10.1021/pr4012393. Epub 2014 Jan 21. PubMed PMID: 24417605; PubMed Central PMCID: PMC3975653.
Bricarello DA, Smilowitz JT, Zivkovic AM, German JB, Parikh AN. Reconstituted lipoprotein: a versatile class of biologically-inspired nanostructures. ACS Nano. 2011 Jan 25;5(1):42-57.
Smilowitz JT, Argov N, Wiest MM, Freeman SL, Newman JW, German JB, Effects of a saturated versus unsaturated dietary fat challenge on plasma HDL lipid moieties and lipoprotein subclass distribution in the postprandial state, EJCN, 2010 submitted
Bricarello DA, Mills EJ, Petrlova J, Voss JC, Parikh AN. Ganglioside embedded in reconstituted lipoprotein binds cholera toxin with elevated affinity. J Lipid Res. 2010 May 14.
Zivkovic AM, Wiest MM, Nguyen U, Nording ML, Watkins SM, German JB. Assessing individual metabolic responsiveness to a lipid challenge using a targeted metabolomic approach. Metabolomics. 2009;5(2):209-218.
Smilowitz JT, Wiest MM, Watkins SM, Teegarden D, Zemel MB, German JB, Van Loan MD. Lipid metabolism predicts changes in body composition during energy restriction in overweight humans. J Nutr. 2009 Feb;139(2):222-9.
Zivkovic AM, Wiest MM, Nguyen UT, Davis R, Watkins SM, German JB. Effects of sample handling and storage on quantitative lipid analysis in human serum. Metabolomics. 2009 Dec;5(4):507-516.
Argov N, Wachsmann-Hogiu S, Freeman SL, Huser T, Lebrilla CB, German JB. Size-dependent lipid content in human milk fat globules. J Agric Food Chem. 2008 Aug 27;56(16):7446-50.
Wang L, Sapuri-Butti AR, Aung HH, Parikh AN, Rutledge JC. Triglyceride-rich lipoprotein lipolysis increases aggregation of endothelial cell membrane microdomains and produces reactive oxygen species. Am J Physiol Heart Circ Physiol. 2008 Jul;295(1):H237-44.
Newman JW, Kaysen GA, Hammock BD, Shearer GC. Proteinuria increases oxylipid concentrations in VLDL and HDL but not LDL particles in the rat. J Lipid Res. 2007 Aug;48(8):1792-800.
German, J. Bruce, Jennifer T. Smilowitz, and Angela M. Zivkovic. Lipoproteins: When size really matters. Current Opinion in Colloid & Interface Science, 11(2-3):171-181, 2006.
Shearer GC, Newman JW, Hammock BD, Kaysen GA. Graded effects of proteinuria on HDL structure in nephrotic rats. J Am Soc Nephrol. 2005 May;16(5):1309-19.

HDL Clearance

Newman JW, Kaysen GA, Hammock BD, Shearer GC. Proteinuria increases oxylipid concentrations in VLDL and HDL but not LDL particles in the rat. J Lipid Res. 2007 Aug;48(8):1792-800.
Shearer GC, Newman JW, Hammock BD, Kaysen GA. Graded effects of proteinuria on HDL structure in nephrotic rats. J Am Soc Nephrol. 2005 May;16(5):1309-19.

Postprandial Response

German JB, Zivkovic AM, Dallas DC, Smilowitz JT. Nutrigenomics and Personalized Diets, What Will They Mean for Food, Annu Rev Food Sci Technol. 2011; 2:97-123. Review.
Smilowitz, J.T., German, J.B., Zivkovic, A.M., Food Intake and Obesity: The Case of Fat, in Fat Detection: Taste,Texture, and Post Ingestive Effects, Montmayeur, Jean-Pierre, and Johannes Le Coutre (Editors), Boca Raton: CRC Press/Taylor & Francis, 2010.
Zivkovic AM, German JB. Metabolomics for assessment of nutritional status. Curr Opin Clin Nutr Metab Care. 2009 Sep;12(5):501-7.
Zivkovic AM, Wiest MM, Nguyen U, Nording ML, Watkins SM, German JB. Assessing individual metabolic responsiveness to a lipid challenge using a targeted metabolomic approach. Metabolomics. 2009;5(2):209-218.

HDL Function

Bricarello DA, Smilowitz JT, Zivkovic AM, German JB, Parikh AN. Reconstituted lipoprotein: a versatile class of biologically-inspired nanostructures. ACS Nano. 2011 Jan 25;5(1):42-57.
Bricarello DA, Mills EJ, Petrlova J, Voss JC, Parikh AN. Ganglioside embedded in reconstituted lipoprotein binds cholera toxin with elevated affinity. J Lipid Res. 2010 May 14.
Zivkovic AM, Wiest MM, Nguyen UT, Davis R, Watkins SM, German JB. Effects of sample handling and storage on quantitative lipid analysis in human serum. Metabolomics. 2009 Dec;5(4):507-516.
Vinchurkar MS, Bricarello DA, Lagerstedt JO, Buban JP, Stahlberg H, Oda MN, Voss JC, Parikh AN. Bridging across length scales: multi-scale ordering of supported lipid bilayers via lipoprotein self-assembly and surface patterning. J Am Chem Soc. 2008 Aug 20;130(33):11164-9.
Newman JW, Kaysen GA, Hammock BD, Shearer GC. Proteinuria increases oxylipid concentrations in VLDL and HDL but not LDL particles in the rat. J Lipid Res. 2007 Aug;48(8):1792-800.
Shearer GC, Newman JW, Hammock BD, Kaysen GA. Graded effects of proteinuria on HDL structure in nephrotic rats. J Am Soc Nephrol. 2005 May;16(5):1309-19.

Oxylipid Signaling

Sitepu IR, Sestric R, Ignatia L, Levin D, German JB, Gillies LA, Almada LA, Boundy-Mills KL. Manipulation of culture conditions alters lipid content and fatty acid profiles of a wide variety of known and new oleaginous yeast species. Bioresour Technol. 2013 Sep; 144:360-9. doi: 10.1016/j.biortech.2013.06.047. Epub 2013 Jun 28. PubMed PMID: 23891835; PubMed Central PMCID: PMC3819430.
Garay LA, Boundy-Mills KL, German JB. Accumulation of high-value lipids in single-cell microorganisms: a mechanistic approach and future perspectives. J Agric Food Chem. 2014 Apr 2;62(13):2709-27. doi: 10.1021/jf4042134. Epub 2014 Mar 25. PubMed PMID: 24628496; PubMed Central PMCID: PMC3983371.
Nording ML, Yang J, Georgi K, Hegedus Karbowski C, German JB, Weiss RH, Hogg RJ, Trygg J, Hammock BD, Zivkovic AM. Individual variation in lipidomic profiles of healthy subjects in response to omega-3 Fatty acids. PLoS One. 2013 Oct 24;8(10):e76575. doi: 10.1371/journal.pone.0076575. eCollection 2013. PubMed PMID: 24204640; PubMed Central PMCID: PMC3811983
Lundström SL, Yang J, Källberg HJ, Thunberg S, Gafvelin G, Haeggström JZ, Grönneberg R, Grunewald J, van Hage M, Hammock BD, Eklund A, Wheelock ÅM, Wheelock CE. Allergic asthmatics show divergent lipid mediator profiles from healthy controls both at baseline and following birch pollen provocation. PLoS One. 2012;7(3):e33780.
Heinze CR, Hawkins MG, Gillies LA, Wu X, Walzem RL, German JB, Klasing KC. Effect of dietary omega-3 fatty acids on red blood cell lipid composition and plasma metabolites in the cockatiel, Nymphicus hollandicus. J Anim Sci. 2012 Sep;90(9):3068-79. doi: 10.2527/jas.2011-4450. Epub 2012 May 14. PubMed PMID: 22585819.
Lundström SL, Levänen B, Nording M, Klepczynska-Nyström A, Sköld M, Haeggström JZ, Grunewald J, Svartengren M, Hammock BD, Larsson BM, Eklund A, Wheelock ÅM, Wheelock CE. Asthmatics exhibit altered oxylipin profiles compared to healthy individuals after subway air exposure. PLoS One. 2011;6(8):e23864.
Yang J, Dong H, Hammock BD. Profiling the regulatory lipids: another systemic way to unveil the biological mystery. Curr Opin Lipidol. 2011 Jun;22(3):197-203. Review.
Nording, ML; Yang, J; Hegedus, CM; Bhushan, A; Kenyon, NJ; Davis, CE; Hammock, BD. 2010. Endogenous levels of five fatty acid metabolites in exhaled breath condensate to monitor asthma by high-performance liquid chromatography: electrospray tandem mass spectrometry. IEEE Sensors Journal, 10(1), 123- 130.
Liu JY, Yang J, Inceoglu B, Qiu H, Ulu A, Hwang SH, Chiamvimonvat N, Hammock BD. 2010. Inhibition of soluble epoxide hydrolase enhances the anti-inflammatory effects of aspirin and 5-lipoxygenase activation protein inhibitor in a murine model. Biochemical Pharmacology 79, 880–887.
Yang J, Schmelzer K, Georgi K, Hammock BD. 2009. Quantitative Profiling Method for Oxylipin Metabolome by Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometry. Anal. Chem. 81, 8085-93.
Inceoglu, B; Jinks, SL; Ulu, A; Hegedus, CM; Georgi, K; Schmelzer, KR; Wagner, K; Jones, PD; Morisseau, C; Hammock, BD, 2008. Soluble epoxide hydrolase and epoxyeicosatrienoic acids modulate two distinct analgesic pathways. PNAS , 105(48), 18901-18906.
Inceoglu B., Schmelzer K.R., Morisseau C., Jinks S.L., Hammock B.D. 2007. Soluble epoxide hydrolase inhibition reveals novel biological functions of epoxyeicosatrienoic acids (EETs). Prostaglandins Other Lipid Mediat. 82(1-4):42-49.
Newman, J.W., T. Watanabe, B.D. Hammock. 2002. The simultaneous quantification of cytochrome P450 dependent linoleate and arachidonate metabolites in urine by high-performance liquid chromatography - tandem mass spectroscopy. J Lipid Res. 43:1563-1578.

Postprandial Metabolism

Kilpatrick LA, Coveleskie K, Connolly L, Labus JS, Ebrat B, Stains J, Jiang Z, Suyenobu BY, Raybould HE, Tillisch K, Mayer EA. Influence of sucrose ingestion on brainstem and hypothalamic intrinsic oscillations in lean and obese women. Gastroenterology. 2014 May;146(5):1212-21. doi: 10.1053/j.gastro.2014.01.023. Epub 2014 Jan 28. PubMed PMID: 24480616.
Eisner F, Martin EM, Küper MA, Raybould HE, Glatzle J. CCK1-receptor stimulation protects against gut mediator-induced lung damage during endotoxemia. Cell Physiol Biochem. 2013;32(6):1878-90. doi: 10.1159/000356644. Epub 2013 Dec 20. PubMed PMID: 24356325; PubMed Central PMCID: PMC3959982.
Connolly L, Coveleskie K, Kilpatrick LA, Labus JS, Ebrat B, Stains J, Jiang Z, Tillisch K, Raybould HE, Mayer EA. Differences in brain responses between lean and obese women to a sweetened drink. Neurogastroenterol Motil. 2013 Jul;25(7):579-e460. doi: 10.1111/nmo.12125. Epub 2013 Apr 9. PubMed PMID: 23566308.
Raybould HE. The heat is on: does direct application of capsaicin to autonomic nerves produce a specific deafferentation? J Physiol. 2013 Mar 15; 591(Pt 6):1405. doi: 10.1113/jphysiol. 2013.251868. PubMed PMID: 23504233; PubMed Central PMCID:PMC3607161.
Smilowitz JT, Zivkovic AM, Wan YJ, Watkins SM, Nording ML, Hammock BD, German JB. Nutritional lipidomics: molecular metabolism, analytics, and diagnostics. Mol Nutr Food Res. 2013 Aug;57(8):1319-35. doi: 10.1002/mnfr.201200808. Epub 2013 Jul 1. Review. PubMed PMID: 23818328; PubMed Central PMCID: PMC3806310.
Zivkovic AM, Yang J, Georgi K, Hegedus C, Nording ML, O'Sullivan A, German JB, Hogg RJ, Weiss RH, Bay C, Hammock BD. Serum oxylipin profiles in IgA nephropathy patients reflect kidney functional alterations. Metabolomics. 2012 Dec;8(6):1102-1113. PubMed PMID: 23833568; PubMed Central PMCID: PMC3700377.
Zivkovic AM, Wiest MM, Nguyen U, Nording ML, Watkins SM, German JB. Assessing individual metabolic responsiveness to a lipid challenge using a targeted metabolomic approach. Metabolomics. 2009;5(2):209-218.
Stanhope KL, Schwarz JM, Keim NL, Griffen SC, Bremer AA, Graham JL, Hatcher B, Cox CL, Dyachenko A, Zhang W, McGahan JP, Seibert A, Krauss RM, Chiu S, Schaefer EJ, Ai M, Otokozawa S, Nakajima K, Nakano T, Beysen C, Hellerstein MK, Berglund L, Havel PJ. Consuming fructose-sweetened, not glucose-sweetened, beverages increases visceral adiposity and lipids and decreases insulin sensitivity in overweight/obese humans. J Clin Invest. 2009: 119(5):1322-34.
Nakajima K, Nakano T, Moon HD, Nagamine T, Stanhope KL, Havel PJ, Warnick GR. The correlation between TG vs remnant lipoproteins in the fasting and postprandial plasma of 23 volunteers. Clin Chim Acta. 2009 Jun 27;404(2):124-7.
Teff KL, Grudziak J, Townsend RR, Dunn TN, Grant RW, Adams SH, Keim NL, Cummings BP, Stanhope KL, Havel PJ. Endocrine and metabolic effects of consuming fructose- and glucose-sweetened beverages with meals in obese men and women: influence of insulin resistance on plasma triglyceride responses. J Clin Endocrinol Metab. 2009 May;94(5):1562-9.
Stanhope KL, Havel PJ. Endocrine and metabolic effects of consuming beverages sweetened with fructose, glucose, sucrose, or high-fructose corn syrup. Am J Clin Nutr. 2008 Dec;88(6):1733S-1737S.
Stanhope KL, Griffen SC, Bair BR, Swarbrick MM, Keim NL, Havel PJ. Twenty-four-hour endocrine and metabolic profiles following consumption of high-fructose corn syrup-, sucrose-, fructose-, and glucose-sweetened beverages with meals. Am J Clin Nutr. 2008 May;87(5):1194-203.
Swarbrick MM, Stanhope KL, Elliott SS, Graham JL, Krauss RM, Christiansen MP, Griffen SC, Keim NL, Havel PJ. Consumption of fructose-sweetened beverages for 10 weeks increases postprandial triacylglycerol and apolipoprotein-B concentrations in overweight and obese women. Br J Nutr. 2008 Nov;100(5):947-52.
Stanhope KL, Havel PJ. Fructose consumption: potential mechanisms for its effects to increase visceral adiposity and induce dyslipidemia and insulin resistance. Curr Opin Lipidol. 2008 Feb;19(1):16-24.
Teff KL, Elliott SS, Tschöp M, Kieffer TJ, Rader D, Heiman M, Townsend RR, Keim NL, D'Alessio D, Havel PJ. Dietary fructose reduces circulating insulin and leptin, attenuates postprandial suppression of ghrelin, and increases triglycerides in women. J Clin Endocrinol Metab. 2004 Jun;89(6):2963-72.

Metabolomics

Lemay DG, Hovey RC, Hartono SR, Hinde K, Smilowitz JT, Ventimiglia F, Schmidt KA, Lee JW, Islas-Trejo A, Silva PI, Korf I, Medrano JF, Barry PA, German JB. Sequencing the transcriptome of milk production: milk trumps mammary tissue. BMC Genomics. 2013 Dec 12;14:872. doi: 10.1186/1471-2164-14-872. PubMed PMID: 24330573; PubMed Central PMCID: PMC3871720.
Lemay DG, Pollard KS, Martin WF, Freeman Zadrowski C, Hernandez J, Korf I, German JB, Rijnkels M. From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome. PLoS One. 2013 Sep 26;8(9):e75030. doi: 10.1371/journal.pone.0075030. eCollection 2013. PubMed PMID: 24086428; PubMed Central PMCID: PMC3784412.
De Leoz, M. L., S. Wu, J. S. Strum, M. R. Niñonuevo, S. C. Gaerlan, M. Mirmiran, J. B. German, D. A. Mills, C. B. Lebrilla, M. A. Underwood. A quantitative and comprehensive structural method to analyze human milk oligosaccharides in the urine and feces of infants. Analytical and Bioanalytical Chemistry 405:4089-4105.
Khaldi N, Vijayakumar V, Dallas DC, Guerrero A, Wickramasinghe S, Smilowitz JT, Medrano JF, Lebrilla CB, Shields DC, German JB. Predicting the important enzyme players in human breast milk digestion. J Agric Food Chem. 2014 Mar 12. PubMed PMID: 24620897.
Dallas DC, Guerrero A, Khaldi N, Borghese R, Bhandari A, Underwood MA, Lebrilla CB, German JB, Barile D. A peptidomic analysis of human milk digestion in the infant stomach reveals protein-specific degradation patterns. J Nutr. 2014 Jun; 144(6):815-20. doi: 10.3945/jn.113.185793. Epub 2014 Apr 3. PubMed PMID: 24699806; PubMed Central PMCID: PMC4018946.
Smilowitz JT, O'Sullivan A, Barile D, German JB, Lönnerdal B, Slupsky CM. The human milk metabolome reveals diverse oligosaccharide profiles. J Nutr. 2013 Nov; 143(11):1709-18. doi: 10.3945/jn.113.178772. Epub 2013 Sep 11. PubMed PMID: 24027187.
Vijayakumar V, Guerrero AN, Davey N, Lebrilla CB, Shields DC, Khaldi N. Enzyme Predictor: a tool for predicting and visualizing enzymatic cleavages of digested proteins. J Proteome Res. 2012 Dec 7; 11(12):6056-65. doi: 10.1021/pr300721f. Epub 2012 Nov 9. PubMed PMID: 23098558.
Stephens NS, Siffledeen J, Su X, Murdoch TB, Fedorak RN, Slupsky CM. Urinary NMR metabolomic profiles discriminate inflammatory bowel disease from healthy. J Crohns Colitis. 2012 May 22. [Epub ahead of print]
McNiven EM, German JB, Slupsky CM. Analytical metabolomics: nutritional opportunities for personalized health. J Nutr Biochem. 2011 Nov;22(11):995-1002.
O'Sullivan A, Gibney MJ, Brennan L. Dietary intake patterns are reflected in metabolomic profiles: potential role in dietary assessment studies. Am J Clin Nutr. 2011 Feb;93(2):314-21.
Slupsky CM. NMR-based analysis of metabolites in urine provides rapid diagnosis and etiology of pneumonia. Biomark Med. 2010 Apr;4(2):195-7.
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. Pneumococcal pneumonia: potential for diagnosis through a urinary metabolic profile. J Proteome Res. 2009 Dec;8(12):5550-8.
Zivkovic AM, Wiest MM, Nguyen UT, Davis R, Watkins SM, German JB. Effects of sample handling and storage on quantitative lipid analysis in human serum. Metabolomics. 2009 Dec;5(4):507-516.
Zivkovic AM, German JB. Metabolomics for assessment of nutritional status. Curr Opin Clin Nutr Metab Care. 2009 Sep;12(5):501-7.
Slupsky CM, Cheypesh A, Chao DV, Fu H, Rankin KN, Marrie TJ, Lacy P. Streptococcus pneumoniae and Staphylococcus aureus pneumonia induce distinct metabolic responses. J Proteome Res. 2009 Jun;8(6):3029-36.
Smilowitz JT, Wiest MM, Watkins SM, Teegarden D, Zemel MB, German JB, Van Loan MD. Lipid metabolism predicts changes in body composition during energy restriction in overweight humans. J Nutr. 2009 Feb;139(2):222-9.
Zivkovic AM, Wiest MM, Nguyen U, Nording ML, Watkins SM, German JB. Assessing individual metabolic responsiveness to a lipid challenge using a targeted metabolomic approach. Metabolomics. 2009;5(2):209-218.
Mahadevan S, Shah SL, Marrie TJ, Slupsky CM. Analysis of metabolomic data using support vector machines. Anal Chem. 2008 Oct 1;80(19):7562-70.
Murdoch TB, Fu H, MacFarlane S, Sydora BC, Fedorak RN, Slupsky CM. Urinary metabolic profiles of inflammatory bowel disease in interleukin-10 gene-deficient mice. Anal Chem. 2008 Jul 15;80(14):5524-31.
Slupsky CM, Rankin KN, Wagner J, Fu H, Chang D, Weljie AM, Saude EJ, Lix B, Adamko DJ, Shah S, Greiner R, Sykes BD, Marrie TJ. Investigations of the effects of gender, diurnal variation, and age in human urinary metabolomic profiles. Anal Chem. 2007 Sep 15;79(18):6995-7004.
Lemay DG, Zivkovic AM, German JB. Building the bridges to bioinformatics in nutrition research. Am J Clin Nutr. 2007 Nov;86(5):1261-9.
German JB, Gillies LA, Smilowitz JT, Zivkovic AM, Watkins SM. Lipidomics and lipid profiling in metabolomics. Curr Opin Lipidol. 2007 Feb;18(1):66-71.
Dettmer K, Aronov PA, Hammock BD. Mass spectrometry-based metabolomics. Mass Spectrom Rev. 2007 Jan-Feb;26(1):51-78.
Weljie AM, Newton J, Mercier P, Carlson E, Slupsky CM. Targeted profiling: quantitative analysis of 1H NMR metabolomics data. Anal Chem. 2006 Jul 1;78(13):4430-42.
Dixon RA, Gang DR, Charlton AJ, Fiehn O, Kuiper HA, Reynolds TL, Tjeerdema RS, Jeffery EH, German JB, Ridley WP, Seiber JN. Applications of metabolomics in agriculture. J Agric Food Chem. 2006 Nov 29;54(24):8984-94.
German, J. Bruce, Jennifer T. Smilowitz, and Angela M. Zivkovic. Lipoproteins: When size really matters. Current Opinion in Colloid & Interface Science, 11(2-3):171-181, 2006.
German JB, Hammock BD, Watkins SM. Metabolomics: building on a century of biochemistry to guide human health. Metabolomics. 2005 Mar;1(1):3-9.
German JB, Watkins SM, Fay LB. Metabolomics in practice: emerging knowledge to guide future dietetic advice toward individualized health. J Am Diet Assoc. 2005 Sep;105(9):1425-32.
Zeisel SH, Freake HC, Bauman DE, Bier DM, Burrin DG, German JB, Klein S, Marquis GS, Milner JA, Pelto GH, Rasmussen KM. The nutritional phenotype in the age of metabolomics. J Nutr. 2005 Jul;135(7):1613-6.
Dettmer K, Hammock BD. Metabolomics--a new exciting field within the "omics" sciences. Environ Health Perspect. 2004 May;112(7):A396-7.
German JB, Bauman DE, Burrin DG, Failla ML, Freake HC, King JC, Klein S, Milner JA, Pelto GH, Rasmussen KM, Zeisel SH. Metabolomics in the opening decade of the 21st century: building the roads to individualized health. J Nutr. 2004 Oct;134(10):2729-32.
German JB, Roberts MA, Watkins SM. Personal metabolomics as a next generation nutritional assessment. J Nutr. 2003 Dec;133(12):4260-6.
German JB, Roberts MA, Watkins SM. Genomics and metabolomics as markers for the interaction of diet and health: lessons from lipids. J Nutr. 2003 Jun;133(6 Suppl 1):2078S-2083S.
Watkins SM, German JB. Toward the implementation of metabolomic assessments of human health and nutrition. Curr Opin Biotechnol. 2002 Oct;13(5):512-6.
Watkins SM, Reifsnyder PR, Pan HJ, German JB, Leiter EH. Lipid metabolome-wide effects of the PPARgamma agonist rosiglitazone. J Lipid Res. 2002 Nov;43(11):1809-17.
German JB, Roberts MA, Fay L, Watkins SM. Metabolomics and individual metabolic assessment: the next great challenge for nutrition. J Nutr. 2002 Sep;132(9):2486-7.

Endocrine Signaling

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Vitamin D Assessment

O'Sullivan A, Balducci D, Paradisi F, Cashman KD, Gibney MJ, Brennan L. Effect of supplementation with vitamin D(3) on glucose production pathways in human subjects. Mol Nutr Food Res. 2011 Jul;55(7):1018-25.
O'Sullivan A, Gibney MJ, Connor AO, Mion B, Kaluskar S, Cashman KD, Flynn A, Shanahan F, Brennan L. Biochemical and metabolomic phenotyping in the identification of a vitamin D responsive metabotype for markers of the metabolic syndrome. Mol Nutr Food Res. 2011 May;55(5):679-90.
Hall LM; Kimlin MG; Aronov PA; Hammock BD; Slusser JR; Woodhouse LR; Stephensen CB. 2010. Vitamin D intake needed to maintain target serum 25-hydroxyvitamin D concentrations in participants with low sun exposure and dark skin pigmentation is substantially higher than current recommendations. The Journal of Nutrition 140(3), 542-50.
Aronov PA, Hall LM, Dettmer K, Stephensen CB, Hammock BD. Metabolic profiling of major vitamin D metabolites using Diels-Alder derivatization and ultra-performance liquid chromatography-tandem mass spectrometry. Anal Bioanal Chem. 2008 Jul;391(5):1917-30.

Lactation Study

Wu S, Grimm R, German JB, Lebrilla CB. Annotation and structural analysis of sialylated human milk oligosaccharides. J Proteome Res. 2011 Feb 4;10(2):856-68.
Sela DA, Li Y, Lerno L, Wu S, Marcobal AM, German JB, Chen X, Lebrilla CB, Mills DA. An infant-associated bacterial commensal utilizes breast milk sialyloligosaccharides.J Biol Chem. 2011 Apr 8;286(14):11909-18.
Wu S, Tao N, German JB, Grimm R, Lebrilla CB. The development of an annotated library of neutral human milk oligosaccharides. J Proteome Res. 2010 Aug 6;9(8):4138-51.
Marcobal A, Barboza M, Froehlich JW, Block, D., German, J.B., Lebrilla, C.B., Mills, D.A. Consumption of Human Milk Oligosaccharides by Gut-Related Microbes. J Agric Food Chem 2010; 58(9): 5334-40.
Froehlich JW, Dodds ED, Barboza M, et al. Glycoprotein Expression in Human Milk during Lactation. J Agric Food Chem 2010; 58(10): 6440-8.
Barboza M, Sela DA, Pirim C, et al. Glycoprofiling bifidobacterial consumption of galacto-oligosaccharides by mass spectrometry reveals strain-specific, preferential consumption of glycans. Appl Environ Microbiol 2009;75:7319-25.
German, J. B., S. L. Freeman, et al. (2008). "Human milk oligosaccharides: evolution, structures and bioselectivity as substrates for intestinal bacteria." Nestle Nutr Workshop Ser Pediatr Program 62: 205-18; discussion 218-22.
Ninonuevo, M. R., P. D. Perkins, et al. (2008). "Daily variations in oligosaccharides of human milk determined by microfluidic chips and mass spectrometry." J Agric Food Chem 56(2): 618-26.
Ward, R. E., M. Ninonuevo, et al. (2007). "In vitro fermentability of human milk oligosaccharides by several strains of bifidobacteria." Mol Nutr Food Res 51(11): 1398-405.
LoCascio, R. G., M. R. Ninonuevo, et al. (2007). "Glycoprofiling of bifidobacterial consumption of human milk oligosaccharides demonstrates strain specific, preferential consumption of small chain glycans secreted in early human lactation." J Agric Food Chem 55(22): 8914-9.
Ninonuevo, M. R., R. E. Ward, et al. (2007). "Methods for the quantitation of human milk oligosaccharides in bacterial fermentation by mass spectrometry."Anal Biochem 361(1): 15-23.
Ninonuevo, M. R., Y. Park, et al. (2006). "A strategy for annotating the human milk glycome." J Agric Food Chem 54(20): 7471-80.
Ward, R. E., M. Ninonuevo, et al. (2006). "In vitro fermentation of breast milk oligosaccharides by Bifidobacterium infantis and Lactobacillus gasseri." Appl Environ Microbiol 72(6): 4497-9.

Children's Health and Education

Schaefer SE, Ching CC, Breen HL, German JB. Wearing, thinking & moving: assessment of health tracking in diverse, urban youth. Amer J Health Educ. In Press 2015.
Schaefer SE, Gomez-Camacho R, Sadeghi B, Kaiser L, German JB, de la Torre A. Assessing child obesity and physical activity in a hard to reach population in California’s Central Valley. Prev Chronic Dis In Press 2015
Schaefer SE, Van Loan M, German JB. Feasibility study of wearable activity monitors in pre-adolescent school age children. Prev Chronic Dis 2014;11:130262
Ching CC & Schaefer S. Identities in motion, identities at rest: Addressing the mind-body split in gaming research and design. To appear in V Lee (ed), Learning technologies and the body: Integration and implementation. New York, NY: Routledge. Publication 2014
De la Torre A, Sadeghi B, Green R, Kaiser LL, Flores YG, Jackson CF, Shaikh U, Whent LS, Schaefer SE. Niños Sanos, Familia Sana: Mexican immigrant study protocol for a multifaceted CBPR intervention to combat childhood obesity in two rural California towns. BMC Public Health 2013;13:1033
Schaefer SE, Erber E, Trzaskos JP, Roache C, Osborne G, Sharma S. Sources of food affect dietary adequacy of Inuit women of childbearing age in Arctic Canada. J Health Popul Nutr 2011;29(5):454-64
Fleige LE, Moore WR, Garlick PJ, Murphy SP, Lynch SR, Turner EH, Dunn ML, van Lengerich B, Orthoefer FT, Schaefer SE. Recommendations for product optimization of U.S. Public Law 480 fortified blended foods. Nutr Rev 2010; 68(5):290-315
Schaefer SE, Van Loan MD, Salazar M, Bruhn CE, Saviano D, Boushey C. Influence of race, acculturation, and socioeconomic status on tendency toward overweight in Asian-American and Mexican-American early adolescent females. J Immigrant Minority Health 2009; 11:188-97.
O’Sullivan A, German JB, Smilowitz JT, Zivkovic AM, Martin W, Dixon BE, Schaefer SE. Toolkit for the 21st Century: Maximizing Personal Health and Nutrition. J Food Ag Chem Forthcoming 2015.
Schaefer SE, Whent LS, de la Torre A. Use of worn accelerometers to measure physical activity in Mexican-heritage children in California’s Central Valley. J Nutr Educ Behav 2013;45(4):S89-S89.
Schaefer SE, Van Loan M, Allen L, JB German JB. Feasibility of accelerometers for measuring children's daily physical activity. FASEB 2012;26.
Schaefer SE, Salazar ML, Bruhn CM, Van Loan MD. Relationship between acculturation and body fat in Asian and Hispanic adolescent girls. FASEB 2004 18(5):A902-A902
Moher T, Ching CC, Schaefer S, Lee VR, Enyedy N, Danish J, Guerra P, et al. Becoming reflective: designing for reflection on physical performances. ICLS 2014 Proceedings, 1273
Sadeghi B, Martinez LC, Gomez-Camacho R, Schaefer SE. A significant dissociation between parental perception and actual obesity status in Mexican-American children in Central Valley California: Impact and Implications. J Nutr Educ Behav 2014;46(4), S200-S200.

Yakes EA, Arsenault JE, Islam MM, Ahmed T, German JB, Drake C, Hossain MB, Lewis BL, Rahman AS, Jamil KM, Brown KH. Dietary Intake of Polyunsaturated Fatty Acids Among Breast-feeding and Non-breast-feeding 24- to 48-month-old Children in Bangladesh. J Pediatr Gastroenterol Nutr. 2011 Mar;52(3):351-9.

Premie NEC

Wu S, Grimm R, German JB, Lebrilla CB. Annotation and structural analysis of sialylated human milk oligosaccharides. J Proteome Res. 2011 Feb 4;10(2):856-68.
Sela DA, Li Y, Lerno L, Wu S, Marcobal AM, German JB, Chen X, Lebrilla CB, Mills DA. An infant-associated bacterial commensal utilizes breast milk sialyloligosaccharides.J Biol Chem. 2011 Apr 8;286(14):11909-18.
Zivkovic AM, German JB, Lebrilla CB, Mills DA. Microbes and Health Sackler Colloquium: Human milk glycobiome and its impact on the infant gastrointestinal microbiota.Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4653-8.
Wu S, Tao N, German JB, Grimm R, Lebrilla CB. The development of an annotated library of neutral human milk oligosaccharides. J Proteome Res. 2010 Aug 6;9(8):4138-51.
German, J. B., S. L. Freeman, et al. (2008). "Human milk oligosaccharides: evolution, structures and bioselectivity as substrates for intestinal bacteria."Nestle Nutr Workshop Ser Pediatr Program 62: 205-18; discussion 218-22.