PUBLISHED WORK
Full list of publications here
** Indicates corresponding author ǂ Denotes equal contribution
REVEALING THE HUMAN MUCINOME
2021
Stacy A. Malaker**ǂ, Nicholas M. Rileyǂ, D. Judy Shon, Kayvon Pedram, Venkatesh Krishnan, Oliver Dorigo, and Carolyn R. Bertozzi**. Revealing the human mucinome. bioRXiv
CLASSIFICATION, STRUCTURAL BIOLOGY, AND APPLICATIONS OF MUCIN-DEGRADING PROTEASES: A SYSTEMIC REVIEW
2021
Invited review article: D. Judy Shon, Angel Kuo, Michael J. Ferracane, and Stacy A. Malaker**. Classification, structural biology, and applications of mucin-degrading proteases: a systemic review. Under review
VECTORMOD: METHOD FOR BOTTOM-UP PROTEOMICS CHARACTERIZATION OF RAAV CAPSID PTMS AND VECTOR IMPURITIES
2021
Invited article: Neil G. Rumachik, Stacy A. Malaker**, and Nicole K. Paulk**. VectorMOD: method for bottom-up proteomics characterization of rAAV capsid PTMs and vector impurities. Under review.
GENOME-WIDE CRISPR SCREENS REVEAL A SPECIFIC LIGAND FOR GLYCAN-BINDING IMMUNE CHECKPOINT RECEPTOR SIGLEC-7
2021
Simon P. Wisnovsky, Leonhard Mockl, Stacy A. Malaker, Kayvon Pedram, Gaelen Hess, Nicholas M. Riley, Melissa A. Gray, Benhamin A.H. Smith, Michael C. Bassik, W.E. Moerner, and Carolyn 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
GENERATING ORTHOGONAL GLYCOSYLTRANSFERASE-NUCLEOTIDE SUGAR PAIRS AS NEXT GENERATION GLYCOBIOLOGY TOOLS
2021
Anna Coice, Stacy A. Malaker**, and Benjamin Schumann**. Generating Orthogonal Glycosyltransferase-Nucleotide Sugar Pairs as Next Generation Glycobiology Tools. Current Opinion in Chemical Biology. 2021, 60: 66-78. link
ON-TISSUE SPATIALLY-RESOLVED GLYCOPROTEOMICS GUIDED BY N-GLYCAN IMAGING REVEAL GLOBAL DYSREGULATION OF CANINE GLIOMA GLYCOPROTEOMIC LANDSCAPE
2020
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. bioRXiv
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
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
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
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
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
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
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
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
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
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
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
MAMMALIAN Y-RNAS ARE GLYCOSYLATED AT DISCRETE GUANOSINE RESIDUES WITH N-TYPE GLYCANS
2019
R.A. Flynn, B.A.H. Smith, A. Johnson, K. Pedram, B.M. George, S.A. Malaker, K. Majzoub, J.E. Carette, and C.R. Bertozzi. Mammalian Y-RNAs are glycosylated at discrete guanosine residues with N-type glycans. bioRXiv
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
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
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
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
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
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