Publications

Publications Acknowledging the Emory Comprehensive Glycomics Core

  1. Agravat, S. B., Song, X., Rojsajjakul, T., Cummings, R. D., and Smith, D. F. (2016) Computational approaches to define a human milk metaglycome. Bioinformatics 32, 1471-1478.
  2. Wu, Z., Liu, Y., Ma, C., Li, L., Bai, J., Byrd-Leotis, L., Lasanajak, Y., Guo, Y., Wen, L., Zhu, H., Song, J., Li, Y., Steinhauer, D. A., Smith, D. F., Zhao, B., Chen, X., Guan, W., and Wang, P. G. (2016) Identification of the binding roles of terminal and internal glycan epitopes using enzymatically synthesized N-glycans containing tandem epitopes. Org Biomol Chem Oct 18. [Epub ahead of print].


Publications in Glycomics from ECGC Personnel

  1. Song, X., Ju, H., Lasanajak, Y., Kudelka, M. R., Smith, D. F., and Cummings, R. D. (2016) Oxidative release of natural glycans for functional glycomics. Nat Methods 13, 528-534
  2. Noll, A. J., Yu, Y., Lasanajak, Y., Duska-McEwen, G., Buck, R., Smith, D. F., and Cummings, R. D. (2016) Human DC-SIGN Binds Specific Human Milk Glycans. Biochem J
  3. Mickum, M. L., Prasanphanich, N. S., Song, X., Dorabawila, N., Mandalasi, M., Lasanajak, Y., Luyai, A., Secor, W. E., Wilkins, P. P., Van Die, I., Smith, D. F., Nyame, A. K., Cummings, R. D., and Rivera-Marrero, C. A. (2016) Identification of Antigenic Glycans from Schistosoma mansoni by Using a Shotgun Egg Glycan Microarray. Infection and immunity 84, 1371-1386
  4. Noll, A. J., Gourdine, J. P., Yu, Y., Lasanajak, Y., Smith, D. F., and Cummings, R. D. (2016) Galectins are human milk glycan receptors. Glycobiology
  5. Agravat, S. B., Song, X., Rojsajjakul, T., Cummings, R. D., and Smith, D. F. (2016) Computational approaches to define a human milk metaglycome. Bioinformatics 32, 1471-1478.
  6. Song X, Ju H, Quan Y, Smith DF, and Cummings RD (submitted) “Mapping the Glycome with a Chemical Approach.” Nature Methods, in Review.
  7. Noll AJ, Yu Y, Lasanajak Y, Duska-McEwen G, Buck RH, Smith DF, and Cummings RD (submitted) Human DC-SIGN Binds Specific Human Milk Glycans. Biochemical Journal, in review.
  8. Mickum ML, Prasanphanich NS, Song X, Dorabawila N, Mandalasi M, Lasanajak Y, Luyai A, Secor WE, Wilkins PP, IVan Die I, Smith DF, Nyame AK, Cummings RD, and Rivera-Marrero CA (submitted) Identification of Antigenic Glycans from Schistosoma mansoni Using a Shotgun Egg Glycan Microarray. Infection and Immunity, in review.
  9. Noll AJ, Gourdine J-P, Yu Y, Lasanajak Y, Smith DF, and Cummings RD (2015) Galectins are Human Milk Receptors. Glycobiology, in revision.
  10. Agravat SB, Song X, Rojsajjakul T, Cummings RD, and Smith DF (2015) Computational Approaches to Define a Human Milk Metaglycome. Bioinformatics, in revision.
  11. Ryan J. Blackler RJ, Evans DW, Smith DF, Cummings RD, Brooks CL, Braulke T, Liu X, Evans SV, Müller-Loennies S (2015) Single-chain antibody-fragment M6P-1 possesses a mannose 6-phosphate monosaccharide specific binding pocket that distinguishes A and C-branch phosphorylation in N-glycans. 2015 Oct 26. pii: cwv093. [Epub ahead of print]. PMID: 26503547 [PubMed - as supplied by publisher]
  12. Kudelka, M.R., Antonopoulos, A., Wang, Y-C, Duong, D.M., Song, X-Z, Seyfried, D.T., Haslam, S., Dell, A., Cummings, R.D. and Ju, T.: (2015) Cellular O-Glycome Reporter/Amplification to Explore O-Glycans of Living Cells. Nature Methods, doi:10.1038/nmeth.3675 [Epub ahead of print].
  13. Zhang, W., James, P.M., Ng, B.G., Li, X., Xia, B., Jiang, R., Asif, G., Raymond, K., Jones, M.A., Hegde, M., Ju, T., Cummings, R.D., Clarkson, K., Wood, T., Boerkoel, C.F., Freeze, H.H., and He, M.: (2015) A Novel N-Tetrasaccharide in Patients with Congenital Disorders of Glycosylation Including Asparagine-Linked Glycosylation Protein 1, Phosphomannomutase 2, and Phosphomannose Isomerase Deficiencies. Clin Chem. pii: clinchem.2015.243279. [Epub ahead of print].
  14. Zeng, J-W, MI, R-J, Wang, Y-C, Li, Y-J, Lin, L., Yao, B., Song, L-N, van Die I., Chapman, A., Jin, P., Cummings, R.D. and Ju, T.: (2015) Promoters of Human Cosmc and T-synthase Are Similar in Structure, Yet Different in Epigenetic Regulation. J. Biol. Chem., 290, 19018-19033 PMCID:PMC4521027.
  15. Stowell, S.R., Ju T, Cummings, R.D.: (2015) Protein Glycosylation in Cancer. Annual Review of Pathology: Mechanisms of Disease, 10:473-510.
  16. Wesener DA, Wangkanont K, McBride R, Song X, Kraft MB, Zarling LC, Splain RS, Smith DF, Cummings RD, Paulson JC, Forest KT, Kiessling LL (2015) Recognition of Microbial Glycans by Human Intelectin-1. Nature Structural & Molecular Biology, 22(8):603-10. PMID: 26148048 [PubMed - in process] PMCID: PMC4526365.
  17. Schneider C, Smith DF, Cummings RD, Boligan KF, Hamilton RG, Bochner BS, Miescher S, Simon H-U, Pashov A, Vassilev T, and von Gunten, S (2015) The Human IgG Anti-carbohydrate Repertoire Exhibits a Universal Architecture and Contains Specificity for Microbial Attachment Sites. Science Transl. Med. Jan 7;7(269):269ra1. doi: 10.1126/scitranslmed.3010524. PMID: 25568069 [PubMed - in process]
  18. Olson LJ, Castonguay AC, Lasanajak Y, Peterson FC, Cummings RD, Smith DF, and Nancy M. Dahms NM (2015) Identification of a Fourth Mannose 6-Phosphate Binding Site in the Cation-Independent Mannose 6-Phosphate Receptor. Biochemistry Glycobiology, 25(6):591-606. PMID: 25573276 [PubMed - in process] PMCID: PMC4410830
  19. * Song X, Heimburg-Molinaro J., Smith DF, Cummings RD, Glycan microarrays of fluorescently-tagged natural glycans. Glycoconjugate J., Ahead of Print (2015); *Corresponding author.
  20. Prasanphanich NS, Song X, Heimburg-Molinaro J, Luyai AE, Lasanajak Y, Cutler CE, Smith DF, Cummings RD, Intact Reducing Glycan Promotes the Specific Immune Response to Lacto-N-neotetraose-BSA Neoglycoconjugates. Bioconjugate Chem. 26, 559-571 (2015).
  21. Krishnamurthy VR, Sardar MYR, Yu Y, Song X, Haller C, Dai E, Wang X, Hanjaya-Putra D, Sun L, Morikis V, Simon SI, Woods RJ, Cummings RD, Chaikof EL, Glycopeptide analogues of PSGL-1 inhibit P-selectin in vitro and in vivo. Nat Commun 6, 6387 (2015).
  22. Javed MA, van Alphen LB, Sacher J, Ding W, Kelly J, Nargang C, Smith DF, Cummings RD, Szymanski CM (2014) A receptor binding protein of Campylobacter jejuni bacteriophage NCTC 12673 recognizes flagellin glycosylated with acetamidino-modified pseudaminic acid. Mol. Microbiol. 95(1):101-15. PMID: 25354466
  23. Ju, T, Aryal, R.P., Kudelka, M.R., Wang Y., Cummings, R.D.: (2014) The Cosmc connection to the Tn antigen in cancer. Cancer Biomarkers, 14:63-81
  24. Lehoux, SD, Mi, R, Aryal, RP, Wang, Y, Schjoldager, KT, Clausen, H, van Die I, Han Y, Chapman, AB, Cummings, RD and *Ju, T (2014) Identification of Distinct Glycoforms of IgA1 in Plasma from Patients with IgA Nephropathy and Healthy Individuals. Molecular Cellular Proteomics, 13(11):3097-113 PMCID: PMC4223494. *Corresponding author
  25. Agravat SB, Saltz JH, Cummings RD, Smith DF (2014) GlycoPattern: A Web Platform for Glycan Array Mining. Bioinformatics, 30(23):3417-8. PMID: 25143288 [PubMed - indexed for MEDLINE] PMCID: PMC4296152 [Available on 2015-12-01]
  26. Yu Y, Song X, Smith DF, Cummings RD. Applications of glycan microarrays to functional glycomics (Elsevier B.V., 2014), vol. 63, pp. 281-303.
  27. Yu Y, Lasanajak Y, Song X, Hu L, Ramani S, Mickum ML, Ashline DJ, Venkataram Prasad VB, Estes MK, Reinhold VN, Cummings RD, Smith DF. (2014) Human Milk Contains Novel Glycans That Are Potential Decoy Receptors for Neonatal Rotaviruses. Mol. Cell. Proteomics 13, 2944-2960.
  28. *Song X, Ju H, Zhao C, Lasanajak Y, Novel Strategy to Release and Tag N-Glycans for Functional Glycomics. Bioconjugate Chem. 25, 1881-1887 (2014). *Corresponding author.
  29. *Song X, Heimburg-Molinaro J, Cummings RD, Smith DF (2014), Chemistry of natural glycan microarrays. Curr. Opin. Chem. Biol. 18, 70-77 (2014). *Corresponding author.
  30. Prasanphanich NS, Luyai AE, Song X, Heimburg-Molinaro J., Mandalasi M, Mickum ML, Smith DF, Nyame AK, Cummings RD (2014) Immunization with recombinantly expressed glycan antigens from Schistosoma mansoni induces glycan-specific antibodies against the parasite. Glycobiology 24, 619-637.
  31. Stowell, SR, Arthur CM, McBride R, Berger O, Razi N, Heimburg-Molinaro J, Rodrigues LC, Gourdine J-P, Noll AJ, von Gunten S, Smith DF, Knirel YA, Paulson JC & Cummings RD (2014) Microbial glycan microarrays define key features of host-microbial interactions. Nature, Chem. Biol., 10(6):470-6. PMID: 24814672
  32. Luyai AE, Heimburg-Molinaro J, Prasanphanich NS, Mickum ML, Lasanajak Y, Song X, Nyame AK, Wilkins P, Rivera-Marrero CA, Smith DF, Van Die I, Secor E, Cummings RD (2014) Differential expression of anti-glycan antibodies in schistosome-infected humans, rhesus monkeys and mice. Glycobiology 24, 602-618.
  33. Byrd-Leotis L, Liu R, Bradley KC, Lasanajak Y, Cummings SF, Song X, Heimburg-Molinaro J, Galloway SE, Culhane MR, Smith DF, Steinhauer DA, Cummings RD (2014) Shotgun glycomics of pig lung identifies natural endogenous receptors for influenza viruses. Proc. Natl. Acad. Sci. U. S. A. 111, E2241-E2250.
  34. Ashline DJ, Yu Y, Lasanajak Y, Song X, Hu L, Ramani S, Prasad V, Estes MK, Cummings RD, Smith DF, Reinhold VN (2014) Structural Characterization by Multistage Mass Spectrometry (MSn) of Human Milk Glycans Recognized by Human Rotaviruses. Mol. Cell. Proteomics 13, 2961-2974.
  35. Song X, Smith DF, Cummings RD (2013). Glycan-based arrays for determining specificity of carbohydrate-binding proteins. CRC Press, pp. 163-173.
  36. Smith DF and Cummings RD (2014) Investigating Virus-Glycan Interactions Using Glycan Microarrays. Current Opinion in Virology, 7:79-87. PMID: 24995558
  37. Wang L, Cummings RD, Smith DF, Huflejt M, Campbell CT, Gildersleeve JC, Gerlach JQ, Kilcoyne M, Joshi L, Serna S, Reichardt N-C, Pera NP, Pieters R, Eng W, Mahal LK (2014) Cross-platform comparison of glycan microarray formats. Glycobiology, 24(6):507-17. PMCID: PMC4001710
  38. York WS, Agravat S, Aoki-Kinoshita KF, McBride R, Campbell MP, Costello CE, Dell A, Feizi T, Haslam SM, Karlsson N, Khoo KH, Kolarich D, Liu Y, Novotny M, Packer NH, Paulson JC, Rapp E, Ranzinger R, Rudd PM, Smith DF, Struwe WB, Tiemeyer M, Wells L, Zaia J, Kettner C. (2014) MIRAGE: the Minimum Information Required for a Glycomics Experiment, Glycobiology, 24(5):402-408. PMID: 24653214 PMCID: PMC3976285
  39. 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. (2014) 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. PMID: 24475195 PMCID: PMC3903596
  40. Gulati S, Lasanajak Y, Smith DF, Cummings RD and Air GM (2014) Glycan Array Analysis of Influenza H1N1 Binding and Release. Cancer Biomark., 14(1):43-53. PMID: 24643041
  41. Mandalasi M. Nelum D, Smith DF, Heimburg-Molinaro J., Cummings RD, Nyame K (2013) Development and characterization of a specific IgGmonoclonal antibody toward the Lewis x antigen using splenocytes of Schistosoma mansoni-infected mice. Glycobiology, 23(7): 877-892. PMID: 23542315 PMCID: PMC3671776
  42. Smith DF and Cummings RD (2013) Application of Microarrays to Deciphering the Structure and Function of the Human Glycome. Mol. and Cell. Proteomics, 12(4):902-912. PMID: 23412570 PMCID: PMC3617337
  43. *Song X, Johns BA, H. H, Lasanajak Y, Zhao C, Smith DF, Cummings RD (2013) Novel Cleavage of Reductively Aminated Glycan-Tags by N-Bromosuccinimide to Regenerate Free, Reducing Glycans. ACS Chem. Biol. 8, 2478-2483. *Corresponding author
  44. Heimburg-Molinaro J, Priest JW, Live D, Boons G-J, Song X, Cummings RD, Mead JR (2013) Microarray analysis of the human antibody response to synthetic Cryptosporidium glycopeptides. Int. J. Parasitol. 43, 901-907.
  45. Ghasemi F, Eftekahr AA, Gottfried DS, Song X, Cummings RD, Adibi A (2013) Self-referenced silicon nitride array microring biosensor for toxin detection using glycans at visible wavelength. Proc. SPIE 8594, 85940A/85941-85940A/85949.
  46. Yu Y, Mishra S, Song X, Lasanajak Y, Bradley KC, Tappert MM, Air GM, Steinhauer DA, Halder S, Cotmore S, Tattersall P, Agbandje-McKenna M, Cummings RD and Smith DF (2012) Functional Glycomic Analysis of Human Milk Glycans Reveals Presence of Virus Receptors and Embryonic Stem Cell Biomarkers. J Biol Chem. 287(53):44784-99. PMCID: PMC3531791.
  47. *Song X, Smith DF, and Cummings RD. (2012) Non-enzymatic Release of Free Reducing Glycans from Glycosphingolipids. Anal. Biochem., 429(1):82-7. PMID: 22776091 *Corresponding author
  48. Song X, Heimburg-Molinaro J, Smith DF, Cummings RD, Glycan microarrays. Methods Mol. Biol. (N. Y., NY, U. S.) 800, 163-171 (2012).
  49. Song X, Heimburg-Molinaro J, Dahms NM, Smith DF, Cummings RD (2012) Preparation of a mannose-6-phosphate glycan microarray through fluorescent derivatization, phosphorylation, and immobilization of natural high-mannose N-glycans and application in ligand identification of P-type lectins. Methods Mol. Biol. (N. Y., NY, U. S.) 808, 137-148.
  50. Padler-Karavani V, Song X, Yu H, Hurtado-Ziola N, Huang S, Muthana S, Chokhawala HA, Cheng J, Verhagen A, Langereis MA, Kleene R, Schachner M, de Groot RJ, Lasanajak Y, Matsuda H, Schwab R, Chen X, Smith DF, Cummings RD, Varki A (2012) Cross-comparison of protein recognition of sialic acid diversity on two novel sialoglycan microarrays. J Biol. Chem., 287(27):22593-608. PMCID: PMC3391140
  51. Heimburg-Molinaro J, Tappert M, Song X, Lasanajak Y, Air G, Smith DF, Cummings RD (2012) Probing virus-glycan interactions using glycan microarrays. Methods Mol. Biol. 808:251-67. PMID: 22057531.
  52. Cholleti S, Sanjay Agravat S, Morris T, Saltz JH, Song X, Cummings RD, and Smith DF. (2012) Automated Motif Discovery from Glycan Array Data. OMICS: A Journal of Integrative Biology, 6(10): 497-512. PMCID: PMC3459425.
  53. Castonguay AC, Lasanajak Y, Song X, Olson LJ, Cummings RD, Smith DF, and Dahms NM. (2012) The Carbohydrate Binding Properties of the Cation-Independent Mannose 6-Phosphate Receptor are Evolutionary Conserved in Vertebrates. Glycobiology 22(7):983-96. PMCID: PMC3355666
  54. Borgert A, Heimburg-Molinaro J, Song X, Lasanajak, Y, Ju T, Liu, M, Thompson P, Rafupathi G, Barany G, Smith DF, Cummings RD, Live D. (2012) Deciphering structural elements of mucin glycoprotein recognition. ACS Chem. Biol. 7(6):1031-9. PMID: 22444368.
  55. Song X, Yu H, Chen X, Lasanajak Y, Tappert MM, Air GM, Tiwari VK, Cao H, Chokhawala HA, Zheng H, Cummings RD and Smith DF. (2011) A Sialylated Glycan Microarray Reveals Novel Interactions of Modified Sialic Acid with Proteins and Viruses. J. Biol. Chem. 286(36):31610-22. PMCID: PMC3173124.
  56. Song X, Lasanajak Y, Xia B, Heimburg-Molinaro J, Rhea JN, Ju H, Zhao C, Molinaro RJ, Cummings RD, and Smith DF (2011) Shotgun Glycomics: A Microarray Strategy for Functional Glycomics. Nature Methods 8(1), 85–90. PMCID: PMC3074519.
  57. Heimburg-Molinaro J, Song X, Smith DF, Cummings RD. (2011) Preparation and analysis of glycan microarrays. Curr Protoc Protein Sci. ;Chapter 12:Unit12 0. PMCID: 3097418.
  58. Bradley KC, Galloway SE, Lasanajak Y, Song X, Heimburg-Molinaro J, Chen X, Russell RJ, Talekar GR, Smith DF, Cummings RD, and Steinhauer DA. (2011) Characterization of Influenza HA Binding Site Mutants with Limited Receptor Recognition Properties and Species-dependent Replication Characteristics. J. Virol. 85(23):12387-12398. PMCID: PMC3209400.
  59. Smith DF, Song X, and Cummings RD (2010) Use of Glycan Microarrays to Explore Specificity of Glycan-Binding Proteins. Methods in Enzymology, 480, 417-444. PMID: 20816220
  60. Krishnamurthy VR, Wilson JT, Cui W, Song X, Lasanajak Y, Cummings RD, Chaikof EL (2010) Chemoselective immobilization of peptides on abiotic and cell surfaces at controlled densities. Langmuir 26, 7675-7678.
  61. Krishnamurthy VR, Dougherty A, Kamat M, Song X, Cummings RD, Chaikof EL (2010) Synthesis of an Fmoc-threonine bearing core-2 glycan: a building block for PSGL-1 via Fmoc-assisted solid-phase peptide synthesis. Carbohydr Res 345, 1541-1547.
  62. N. Hotaling N, P. M. Kou PM, Song X, Smith DF, Cummings RD, Babensee JE (2010) Dendritic cell responses to surfaces presenting defined glycans. Trans. Annu. Meet. Soc. Biomater. 32, 621.
  63. Dong H, Song X, Lasanajak Y, Cummings RD, Chaikof EL (2010) Facile construction of fluorescent peptide microarrays: One-step fluorescent derivatization of sub-microscale peptide aldehydes for selective terminal immobilization. Anal. Biochem. 398, 132-134.
  64. S. R. Stowell SR, M. Cho M, C. L. Feasley CL, C. M. Arthur CM, X. Song X, J. K. Colucci JK, S. Karmakar S, P. Mehta P, M. Dias-Baruffi M, R. P. McEver RP, R. D. Cummings RD (2009) Ligand Reduces Galectin-1 Sensitivity to Oxidative Inactivation by Enhancing Dimer Formation. J. Biol. Chem. 284, 4989-4999.
  65. Song X, Xia B, Stowell SR, Lasanajak Y, Smith DF and Cummings RD. (2009) Fluorescent Glycan Microarray Strategy Reveals Ligands for Galectin. Chem. Biol., 16(1):36-47. PMCID: PMC2662446
  66. Song X, Lasanajak Y, Xia B, Smith DF, and Cummings, RD (2009). Fluorescent Glycosylamides Produced by Microscale Derivatization of Free Glycans for Natural Glycan Microarrays. ACS Chemical Biology, 4(9):741-50. PMCID: PMC2746876.
  67. Song X, Lasanajak Y, Rivera-Marrero C, Luyai A, Willard M, Smith DF, Cummings RD (2009). Generation of a Natural Glycan Microarray Using 9-Fluorenylmethyl Chloroformate (FmocCl) as a Cleavable Fluorescent Tag. Analytical Biochemistry, 395(2):151-60. PMCID: PMC2761097.
  68. Song X, Lasanajak Y, Olson LJ, Boonen M, Dahms NM, Kornfeld S, Cummings RD and Smith DF (2009). Glycan Microarray Analysis of P-Type Lectins Reveals Distinct Phospho-Mannose Glycan Recognition. J. Biol. Chem., 284: 35201-35214. PMCID: PMC2787380.
  69. Luyai A, Lasanajak Y, Smith DF, Cummings RD and *Song X (2009) Facile preparation of fluorescent neoglycoproteins using p-nitrophenyl anthranilate as a heterobifunctional linker. Bioconjugate Chem. 20 (8): 1618–1624. PMCID: PMC2729569 *Corresponding author.
  70. Bohnsack RN, Song X, Olson LJ, Boonen M, Kudo M, Gotschall RR, Canfield WM, Kornfeld S, Cummings RD, Smith DF, and Dahms NM (2009). Cation-Independent Mannose 6-Phosphate Receptor: A Composite of Distinct Phosphomannosyl Binding Sites. J. Biol. Chem., 284: 35215-35226. PMCID: PMC2787381.
  71. Song X, Xia B, Lasanajak Y, Smith DF, Cummings RD. (2008) Quantifiable Fluorescent Glycan Microarrays. Glycoconjugate Journal 25(1):15-25. PMID: 17763939.