PUBLISHED WORK
Full list of publications here
** Indicates corresponding author ǂ Denotes equal contribution
(37) BUMP-AND-HOLE ENGINEERING OF HUMAN POLYPEPTIDE N-ACETYLGALACTOSAMINE TRANSFERASES TO DISSECT THEIR PROTEIN SUBSTRATES AND GLYCOSYLATION SITES IN CELLS
2023
Beatriz Calle, Edgar Gonzalez-Rodriguez, Keira E. Mahoney, Anna Cioce, Ganka Bineva-Todd, Omur Y. Tastan, Chloe Roustan, Helen Flynn, Stacy A. Malaker, and Benjamin Schumann. Bump-and-hole engineering of human polypeptide N-acetylgalactosamine transferases to dissect their protein substrates and glycosylation sites in cells. STAR Protocols. 2023, 4 (1): 101974. link
(36) COMPREHENSIVE ANALYSIS OF PLATELET GLYCOPROTEIN IBΑ ECTODOMAIN GLYCOSYLATION
2023
Marie A. Hollenhorst, Katherine H. Tiemeyer, Keira E. Mahoney, Kazuhiro Aoki, Mayumi Ishihara, Sarah C. Lowery, Valentina Rangel-Angarita, Carolyn R.Bertozzi, and Stacy A. Malaker**. Comprehensive analysis of platelet glycoprotein Ibα ectodomain glycosylation. Journal of Thrombosis and Haemostasis. 2023, In Press. link
(35) CELL-SPECIFIC BIOORTHOGONAL TAGGING OF GLYCOPROTEINS
2022
Anna Cioce, Beatriz Calle, Tatiana Rizou, Sarah C. Lowery, Victoria Bridgeman, Keira E. Mahoney, Andrea Marchesi, Ganka Bineva-Todd, Helen Flynn, Zhen Li, Omur Y. Tastan, Chloe Roustan, Thomas M. Wood, Tessa Keenan, Peter Both, Kun Huang, Fabio Parmeggiani, Ambrosius P. Snijders, Mark Skehel, Svend Kjaer, Martin A. Fascione, Carolyn R. Bertozzi, Sabine Flitsch, Stacy A. Malaker, Ilaria Malanchi, and Benjamin Schumann. Cell-specific Bioorthogonal Tagging of Glycoproteins. Nature Communications. 2022, 13 (1): 1-18. link
(34) A METZINCIN-LIKE O-GLYCOPEPTIDASE FROM AKKERMANSIA MUCINIPHILA REQUIRES THE TN ANTIGEN FOR CLEAVAGE OF THE PEPTIDE BOND
2022
Brendon J. Medley, Leif Leclaire, Nicole Thompson, Keira E. Mahoney, Benjamin Pluvinage, Matthew A. Parsons, John E. Burke, Stacy A. Malaker, Warren Wakarchuk, and Alisdair B. Boraston. A metzincin-like O-glycopeptidase from Akkermansia muciniphila requires the Tn antigen for cleavage of the peptide bond. Journal of Biological Chemistry. 2022, 298 (10): 102439 link
(33) GLYCOPROTEOMICS
2022
I. Bagdonaiteǂ, S.A. Malakerǂ, D.A. Polaskyǂ, N.M. Rileyǂ, K. Schjoldager, S.Y. Vakhrushev, A. Halim, K.F. Aoki-Kinoshita, A.I. Nesvizhskii, C.R. Bertozzi, H. Wandall, B.L. Parker, M. Thaysen-Andersen, and N.E. Scott. Glycoproteomics. Nature Reviews Methods Primers. 2022, 2: 48. link
(32) CURRENT STRATEGIES FOR CHARACTERIZATION OF MUCIN-DOMAIN GLYCOPROTEINS
2022
D. Ince, T.M. Lucas, and S.A. Malaker**. Current strategies for characterization of mucin-domain glycoproteins. Current Opinion in Chemical Biology. 2022, 69: 102174. link
(31) REVEALING THE HUMAN MUCINOME
2022
S.A. Malaker**ǂ, N.M. Rileyǂ, D.J. Shon, K. Pedram, V. Krishnan, O. Dorigo, and C.R. Bertozzi**. Revealing the human mucinome. Nature Communications, 2022, 13: 3542. link
(30) A SYSTEMATIC COMPARISON OF CURRENT BIOINFORMATIC TOOLS FOR GLYCOPROTEOMICS DATA
2022
V. Rangel-Angarita, K.E. Mahoney, D. Ince, and S.A. Malaker*. A systematic comparison of current bioinformatic tools for glycoproteomics data. 2022, Under Review. bioRXiv
(29) INHERITED DEFECT IN ST6GALNAC1 REVEALS ROLES OF SIALYLATION IN INTESTINAL HOMEOSTASIS
2022
Y. Yao, G. Kim, S. Shafer, Z. Chen, S. Kubo, Y. Ji, J. Luo, W. Yang, S. Perner, C. Kanellopoulou, A. Park, P. Jiang, S. Baris, E. Karakoc Aydiner, D. Ertem, D.J. Mulde, N. Warner, A.M. Griffiths, C. Topf-Olivestone, M. Kori, L. Werner, J. Ouahed, M. Field, C. Liu, B. Schwarz, S. Ganesan, J. Song, H. Urlaub, T. Oellerich, S.A. Malaker, L. Zheng, C.R. Bertozzi, Y. Zhang, H. Matthews, W. Montgomery, H. Shih, J. Jiang, S. Snapper, A.M. Muise, D. Shouval, A. Ozen , K. Pan, C. Wu, and M.J. Lenardo. Inherited defect in ST6GalNAc1 reveals roles of sialylation in intestinal homeostasis. Cell. 2022, 185 (7): 1172-1188.e28. link
(28) INTERLEUKIN-22 REGULATES B3GNT7 EXPRESSION TO INDUCE FUCOSYLATION OF GLYCOPROTEINS IN INTESTINAL EPITHELIAL CELLS
2022
D.J. Carroll, M.W.N. Burns, L. Mottram, D.C. Propheter, A. Boucher, G.M. Lessen, A. Kumar, S.A. Malaker, C. Xing, L.V. Hooper, U. Yrlid, J.J. Kohler. Interleukin-22 regulates B3GNT7 expression to induce fucosylation of glycoproteins in intestinal epithelial cells. Journal of Biological Chemistry. 2022, 298 (2): 101463. link
(27) ON-TISSUE SPATIALLY-RESOLVED GLYCOPROTEOMICS GUIDED BY N-GLYCAN IMAGING REVEAL GLOBAL DYSREGULATION OF CANINE GLIOMA GLYCOPROTEOMIC LANDSCAPE
2022
S. A. Malakerǂ, J.Quanicoǂ, A. Raffo Romero, F. Kobeissy, S. Aboulouard, D. Tierny, C. R. Bertozzi, I. Fournier, M. Salzet. On-tissue spatially-resolved glycoproteomics guided by N-glycan imaging reveal global dysregulation of canine glioma glycoproteomic landscape. Cell Chemical Biology. 2022, 29 (1): 30-42 e4. link
(26) NOVEL ANTIBODIES FOR THE SIMPLE AND EFFICIENT ENRICHMENT OF NATIVE O-GLCNAC MODIFIED PEPTIDES
2021
R.A. Burt, B. Dejanovic, H.J. Peckham, K.A. Lee, X.Li, J.R. Ounadjela, A. Rao, S.A. Malaker, S.A. Carr, and S.A. Myers. Novel antibodies for the simple and efficient enrichment of native O-GlcNAc modified peptides. Molecular and Cellular Proteomics. 2021, 20: 100167. link
(25) TUMOR INFILTRATING LYMPHOCYTES TARGET HLA-I PHOSPHOPEPTIDES DERIVED FROM CANCER SIGNALING IN COLORECTAL CANCER
2021
S.A. Penny, J.G. Abelin, S.A. Malaker, P.T. Myers, A.Z. Saeed, L.G. Steadman, D.L. Bai, S.T. Ward, J. Shabanowitz, D.F. Hunt, and M. Cobbold. Tumor infiltrating lymphocytes target HLA-I phosphopeptides derived from cancer signaling in colorectal cancer. Frontiers Immunology. 2021,12:723566. link
(24) MUCINOMICS AS THE NEXT FRONTIER OF MASS SPECTROMETRY
2021
Invited Review for Chemical Glycobiology Special Issue: V. Rangel-Angarita and S. A. Malaker**. Mucinomics as the next frontier of mass spectrometry. ACS Chemical Biology. 2021, 16(10): 1866-1883. link
(23) SMALL RNAS ARE MODIFIED WITH N-GLYCANS AND ARE PRIMARILY DISPLAYED ON THE SURFACE OF LIVING CELLS
2021
R.A. Flynn, K. Pedram, S.A. Malaker, P.J. Batista, B.A.H. Smith, A.G. Johnson, B.M. George, K. Majzoub, P.W. Villalta, J.E. Carette, and C.R. Bertozzi. Small RNAs are modified with N-glycans and are primarily displayed on the surface of living cells. Cell. 2021, 184(12): 3109-3124.e22 link
(22) CLASSIFICATION, STRUCTURAL BIOLOGY, AND APPLICATIONS OF MUCIN DOMAIN-TARGETING PROTEASES
2021
Invited review article: D.. Shon, A. Kuo, M.J. Ferracane, and S.A. Malaker**. Classification, structural biology, and applications of mucin domain-targeting proteases. Biochemical Journal. 2021. 478 (8): 1585-1603. link
(21) BENEFITS OF CHEMICAL SUGAR MODIFICATIONS INTRODUCED BY CLICK CHEMISTRY FOR GLYCOPROTEOMIC ANALYSES
2021
Invited article for “Emerging Talent” Special Issue: B. Calle‡, G. Bineva-Todd‡, A. Marchesi‡, H. Flynn, M. Ghirardello, O.Y. Tastan, C. Roustan, J. Choi, M.C. Galan, B. Schumann**, and S.A. Malaker**. Benefits of chemical sugar modifications introduced by click chemistry for glycoproteomic analyses. Journal of the American Society for Mass Spectrometry. 2021, 32(9): 2366-2375. link
(20) VECTORMOD: METHOD FOR BOTTOM-UP PROTEOMICS CHARACTERIZATION OF RAAV CAPSID PTMS AND VECTOR IMPURITIES
2021
Invited article: N.G. Rumachik, S.A. Malaker**, and N.K. Paulk**. VectorMOD: method for bottom-up proteomics characterization of rAAV capsid PTMs and vector impurities. Frontiers in Immunology. 2021. 12, 830. link
(19) GENOME-WIDE CRISPR SCREENS REVEAL A SPECIFIC LIGAND FOR GLYCAN-BINDING IMMUNE CHECKPOINT RECEPTOR SIGLEC-7
2021
S.P. Wisnovsky, L. Mockl, S.A. Malaker, K. Pedram, G. Hess, N.M. Riley, M.A. Gray, B.A.H. Smith, M.C. Bassik, W.E. Moerner, and C.R. Bertozzi. Genome-wide CRISPR screens reveal a specific ligand for glycan-binding immune checkpoint receptor Siglec-7. Proceedings of the National Academy of Sciences USA. 2021, 118(5): e2015024118. link
(18) GENERATING ORTHOGONAL GLYCOSYLTRANSFERASE-NUCLEOTIDE SUGAR PAIRS AS NEXT GENERATION GLYCOBIOLOGY TOOLS
2021
A. Coice, S.A. Malaker**, and B. Schumann**. Generating Orthogonal Glycosyltransferase-Nucleotide Sugar Pairs as Next Generation Glycobiology Tools. Current Opinion in Chemical Biology. 2021, 60: 66-78. link
(17) ELECTRON-BASED DISSOCIATION IS NEEDED FOR O-GLYCOPEPTIDES DERIVED FROM OPERATOR PROTEOLYSIS
2020
N.M. Riley, S.A. Malaker, and C.R. Bertozzi. Electron-Based Dissociation Is Needed for O-Glycopeptides Derived from OpeRATOR Proteolysis. Analytical Chemistry. 2020, 92(22): 14878-14884. link
(16) METABOLIC PRECISION LABELING ENABLES SELECTIVE PROBING OF O-LINKED N-ACETYLGALACTOSAMINE GLYCOSYLATION
2020
M.F. Debets, O.Y. Tastan, S.P. Wisnovsky, S.A. Malaker, N. Angelis, L.K.R. Moeckl, J. Choi, H. Flynn, L.J.S. Wagner, G. Bineva-Todd, A. Antononopoulos, A. Cioce, W.M. Browne, Z. Li, D.C. Briggs, H.L. Douglas, G.T. Hess, A.J. Agbay, C. Roustan, S. Kjaer, S.M. Haslam, A.P. Snijders, M.C. Bassik, W.E. Moerner, V.S.W. Li, C.R. Bertozzi, and B. Schumann. Metabolic precision labeling enables selective probing of O-linked N-acetylgalactosamine glycosylation. Proceedings of the National Academy of Sciences USA. 2020, 117(41); 25293-25301. link
(15) AN ENZYMATIC TOOLKIT FOR SELECTIVE PROTEOLYSIS, DETECTION, AND VISUALIZATION OF MUCIN-DOMAIN GLYCOPROTEINS
2020
D.J. Shon, S.A. Malaker, K. Pedram, E. Yang, V. Krishnan, O. Dorigo, and C.R. Bertozzi. An Enzymatic Toolkit for Selective Proteolysis, Detection, and Visualization of Mucin-Domain Glycoproteins. Proceedings of the National Academy of Sciences USA. 2020, 117(5); 21299-21307. link
(14) TARGETED GLYCAN DEGRADATION POTENTIATES THE ANTICANCER IMMUNE RESPONSE IN VIVO
2020
M.A. Gray, M.A. Stanczak, N.R. Mantuano, H. Xiao, J.F.A. Pijnenborg, S.A. Malaker, C.L. Miller, P.A. Weidenbacher, J. T. Tanzo, G. Ahn, E.C. Woods, H. Läubli, and C.R. Bertozzi. Targeted desialylation overcomes glyco-immune checkpoints and potentiates the anticancer immune response in vivo. Nature Chemical Biology. 2020, link
(13) OPTIMAL DISSOCIATION METHODS DIFFER FOR N- AND O-GLYCOPEPTIDES
2020
N.M. Riley, S.A. Malaker, M.D. Driessen, and C.R. Bertozzi. Optimal dissociation methods differ for N- and O-glycopeptides. Journal of Proteome Research. 2020; 19(8): 3286-3301. link
(12) BUMP-AND-HOLE ENGINEERING IDENTIFIES SPECIFIC SUBSTRATES OF GLYCOSYLTRANSFERASES IN LIVING CELLS
2020
B. Schumann, S.A. Malaker ǂ, S.P. Wisnovsky ǂ, M.F. Debets, A.J. Agbay, L.J.S. Wagner, L. Lin, Z. Li, J. Choi, D.M. Fox, J.M. Peh, M.A. Gray, K. Pedram, J.J. Kohler, M. Mrksich, and C.R. Bertozzi. Bump-and-Hole Engineering Identifies Specific Substrates of Glycosyltransferases in Living Cells. Molecular Cell, 2020. 78(5): 824-834.e15. link
(11) METHODS MATTER -- STANDARD PRODUCTION PLATFORMS FOR RECOMBINANT AAV PRODUCE CHEMICALLY AND FUNCTIONALLY DISTINCT VECTORS
2020
N.G. Rumachik, S.A. Malaker, N. Poweleit, L. Maynard, C.M. Adams, R. Leib, G. Cirolia, D. Thomas, S. Stamnes, K. Holt, P. Sinn, A.P. May, and N.K. Paulk. Methods Matter -- Standard Production Platforms for Recombinant AAV Produce Chemically and Functionally Distinct Vectors. Molecular Therapy: Methods & Clinical Development. 2020, 18: 98-118. link
(10) ENGINEERING ORTHOGONAL POLYPEPTIDE GALNAC-TRANSFERASE AND UDP-SUGAR PAIRS
2019
J. Choi, L.J.S. Wagner, S.B.P.E. Timmermans, S.A. Malaker, B. Schumann, M.A. Gray, M.F. Debets, M.Takashima, J.Gehring, and C.R. Bertozzi. Engineering Orthogonal Polypeptide GalNAc-Transferase and UDP-Sugar Pairs. Journal of the American Chemical Society. 2019; 141(34): 13442-13453. link
(9) THE MUCIN-SELECTIVE PROTEASE STCE ENABLES MOLECULAR AND FUNCTIONAL ANALYSIS OF HUMAN CANCER-ASSOCIATED MUCINS
2019
S.A. Malaker ǂ, K. Pedram ǂ, M.J. Ferracane, B.A. Bensing, V. Krishnan, C. Pett, J. Yu, E.C. Woods, J.R. Kramer, U. Westerlind, O. Dorigo, and C.R. Bertozzi. The mucin-selective protease StcE enables molecular and functional analysis of human cancer-associated mucins. Proceedings of the National Academy of Sciences USA. 2019, 116(15): 7278-7287. link
(8) ISOLATION OF MAJOR HISTOCOMPATIBILITY COMPLEX (MHC)-ASSOCIATED PEPTIDES BY IMMUNOAFFINITY PURIFICATION
2019
S.A. Penny and S.A. Malaker**. Isolation of Major Histocompatibility Complex (MHC)-Associated Peptides by Immunoaffinity Purification. In: Fulton K., Twine S. (eds) Immunoproteomics. Methods in Molecular Biology, 2019, vol 2024. Humana, New York, NY. link
(7) MASS SPECTROMETRIC IDENTIFICATION AND MOLECULAR MODELING OF GLYCOPEPTIDES PRESENTED BY MHC CLASS I AND II PROCESSING PATHWAYS
2019
S.A. Malaker**, Michael J. Ferracane. Mass Spectrometric Identification and Molecular Modeling of Glycopeptides Presented by MHC Class I and II Processing Pathways. In: Fulton K., Twine S. (eds) Immunoproteomics. Methods in Molecular Biology, 2019, vol 2024. Humana, New York, NY. link
(6) SHARED BINDING SPECIFICITIES OF HLA CLASS I AND CLASS II ALLELES ASSOCIATE WITH CUTANEOUS NEVIRAPINE HYPERSENSITIVITY AND IDENTIFY NOVEL RISK ALLELES
2017
R. Pavlos, E.J. McKinnon, D.A. Ostrov, B. Peters , S. Buus, D. Koelle, A. Chopra, R. Schutte, C. Rive, A. Redwood, S. Restrepo, A. Bracey, T. Kaever, P.T. Myers, E.H. Spears, S.A. Malaker, J. Shabanowitz, J. Yuan, S. Gaudieri, D.F. Hunt, M. Carrington, D.W. Haas, S. Mallal, and E.J. Phillips. Shared binding specificities of HLA Class I and Class II Alleles Associate with Cutaneous Nevirapine Hypersensitivity and Identify Novel Risk Alleles. Scientific Reports. 2017 Aug 17;7(1):8653. link
(5) IDENTIFICATION OF GLYCOPEPTIDES AS POSTTRANSLATIONALLY MODIFIED NEOANTIGENS IN LEUKEMIA
2017
S.A. Malaker ǂ, S.A. Penny ǂ, L. Steadman, P.T. Myers, J.C. Loke, M. Raghavan, D. L. Bai, J. Shabanowitz, D.F. Hunt, M. Cobbold. Identification of glycopeptides as post-translationally modified neoantigens in leukemia. Cancer Immunology Research. 2017, 5(5): 376-384. link
(4) PEPTIDE BINDING MOTIFS OF TWO COMMON EQUINE CLASS I MHC MOLECULES IN THOROUGHBRED HORSES
2017
T. Bergmann, M. Lindvall, E. Moore, E. Moore, J. Sidney, D. Miller, R. Tallmadge, P.T. Myers, S.A. Malaker, J. Shabanowitz, N. Osterrieder, B. Peters, D.F. Hunt, D.F. Antczak, and A. Sette. Peptide binding motifs of two common equine class I MHC molecules in thoroughbred horses. Immunogenetics. 2017; 69(5): 351-358. link
(3) CANONICAL AND CROSS-REACTIVE BINDING OF NK CELL INHIBITORY RECEPTORS TO HLA-C ALLOTYPES IS DICTATED BY PEPTIDES BOUND TO HLA-C
2017
M.J.W.Sim, S.A. Malaker, A. Khan, J.M. Stowell, J. Shabanowitz, M.E. Peterson, S. Rajagopalan, D.F. Hunt, D.M. Altmann, E.O. Long, and R.J. Boyton. Canonical and Cross-reactive Binding of NK Cell Inhibitory Receptors to HLA-C Allotypes Is Dictated by Peptides Bound to HLA-C. Frontiers Immunology. 2017, 8(193). link
(2) IDENTIFICATION AND CHARACTERIZATION OF COMPLEX GLYCOSYLATED PEPTIDES PRESENTED BY THE MHC CLASS II PROCESSING PATHWAY IN MELANOMA
2017
S.A. Malaker, M.J. Ferracane, F.R. Depontieu, A.L. Zarling, J. Shabanowitz, D.L. Bai, S. Topalian, V.H. Engelhard, and D.F. Hunt. Identification and Characterization of Complex Glycosylated Peptides Presented by the MHC Class II Processing Pathway in Melanoma. Journal of Proteome Research. 2017, 16(1): 228-237. link
(1) MHC CLASS I–ASSOCIATED PHOSPHOPEPTIDES ARE THE TARGETS OF MEMORY-LIKE IMMUNITY IN LEUKEMIA
2013
M. Cobbold, H. De La Pena, A. Norris, J. Polefrone, J.E. Turner, J. Qian, A.M. English, Je.G. Abelin, S.A. Malaker, A.L. Zarling, H-W. Huang, S.A. Penny, S. Freeman, J. Shabanowitz, G. Pratt, C. Craddock, M.E. Williams, D.F. Hunt, and V.H. Engelhard. MHC Class I–Associated Phosphopeptides Are the Targets of Memory-like Immunity in Leukemia. Science Translational Medicine. 5(203) 203ra125 (2013). link