Joseph Zaia, PhD

Professor, Biochemistry

Joseph Zaia
670 Albany St Biosquare III


The manner in which a cell responds to many growth factor stimuli depends on interactions between glycosaminoglycans (GAGs), growth factors, and growth factor receptors. Extracellular matrix GAGs binds growth factors, creating morphogens gradients essential to tissue patterning. Because these events depend on the fine structure of the GAG chains present, regulation of GAG biosynthesis is a key factor for understanding normal and disease related cellular growth
The key to exploiting an understanding of GAG structure-function relationships for human disease therapy is to winnow oligosaccharide-protein binding patterns from heterogeneous biological preparations. Toward this end, we have developed mass spectral methods for GAGs that enable comparison of structures as a function of biological variables.

The long term research aims are (1) to develop a fundamental understanding of the manner in which glycosaminoglycan expression is varied according to the cellular growth environment related to human disease and (2) to identify HS chain structures useful as therapeutic targets.

New bioinformatics methods are essential to realizing these goals. The data produced using our methods are information rich and not amenable to manual interpretation. Further, the methods needed are distinct from those used in genomics and proteomics. We are developing bioinformatics methods appropriate for interpretation of structural data on glycosaminoglycans and other carbohydrates to identify targets for disease therapy.

Other Positions

  • Member, Bioinformatics Graduate Program, Boston University
  • Member, BU-BMC Cancer Center, Boston University
  • Member, Genome Science Institute, Boston University
  • Center Faculty Member, Mass Spectrometry, Boston University School of Medicine
  • Graduate Faculty (Primary Mentor of Grad Students), Boston University School of Medicine, Graduate Medical Sciences


  • Massachusetts Institute of Technology, PhD
  • Bates College, BS

Classes Taught

  • GMSFC701
  • GMSOH751


  • Published on 10/12/2021

    Chang D, Klein JA, Nalehua MR, Hackett WE, Zaia J. Data-independent acquisition mass spectrometry for site-specific glycoproteomics characterization of SARS-CoV-2 spike protein. Anal Bioanal Chem. 2021 Oct 12. PMID: 34635934.

    Read at: PubMed
  • Published on 10/1/2021

    Zaia J. Analytical characterization of viruses. Anal Bioanal Chem. 2021 Oct 01. PMID: 34595557.

    Read at: PubMed
  • Published on 8/6/2021

    Hackett WE, Zaia J. The Need for Community Standards to Enable Accurate Comparison of Glycoproteomics Algorithm Performance. Molecules. 2021 Aug 06; 26(16). PMID: 34443345.

    Read at: PubMed
  • Published on 6/29/2021

    Maciej-Hulme ML, Dubaissi E, Shao C, Zaia J, Amaya E, Flitsch SL, Merry CLR. Selective Inhibition of Heparan Sulphate and Not Chondroitin Sulphate Biosynthesis by a Small, Soluble Competitive Inhibitor. Int J Mol Sci. 2021 Jun 29; 22(13). PMID: 34209670.

    Read at: PubMed
  • Published on 5/14/2021

    Hogan JD, Wu J, Klein JA, Lin C, Carvalho L, Zaia J. GAGrank: Software for Glycosaminoglycan Sequence Ranking Using a Bipartite Graph Model. Mol Cell Proteomics. 2021 May 14; 20:100093. PMID: 33992776.

    Read at: PubMed
  • Published on 4/1/2021

    Wu J, Chopra P, Boons GJ, Zaia J. Influence of saccharide modifications on heparin lyase III substrate specificities. Glycobiology. 2021 Apr 01. PMID: 33822051.

    Read at: PubMed
  • Published on 3/25/2021

    Chang D, Zaia J. Methods to improve quantitative glycoprotein coverage from bottom-up LC-MS data. Mass Spectrom Rev. 2021 Mar 25. PMID: 33764573.

    Read at: PubMed
  • Published on 3/1/2021

    Wang M, Shajahan A, Pepi LE, Azadi P, Zaia J. Glycoproteomic Sample Processing, LC-MS, and Data Analysis Using GlycReSoft. Curr Protoc. 2021 Mar; 1(3):e84. PMID: 33761173.

    Read at: PubMed
  • Published on 1/19/2021

    Chopra P, Joshi A, Wu J, Lu W, Yadavalli T, Wolfert MA, Shukla D, Zaia J, Boons GJ. The 3-O-sulfation of heparan sulfate modulates protein binding and lyase degradation. Proc Natl Acad Sci U S A. 2021 01 19; 118(3). PMID: 33441484.

    Read at: PubMed
  • Published on 1/8/2021

    Yang Y, Ahn J, Raghunathan R, Kallakury BV, Davidson B, Kennedy ZB, Zaia J, Goldman R. Expression of the Extracellular Sulfatase SULF2 Affects Survival of Head and Neck Squamous Cell Carcinoma Patients. Front Oncol. 2020; 10:582827. PMID: 33585200.

    Read at: PubMed

View 194 more publications: View full profile at BUMC

View all profiles