Stacy Malaker

Member of Yale faculty since 2021

Research Interests


The overarching goal of my laboratory is to develop methods that allow for mass spectrometry (MS) analysis of mucin-domain glycoproteins, a class of densely O-glycosylated extracellular proteins. We will also study mucins in a biological context, since these proteins are integral in numerous diseases including: cancer, cystic fibrosis, and inflammatory bowel disease (IBD).  My expertise in MS instrumentation and data analysis, combined with my experience in chemical biology and glycobiology, gives my laboratory a unique ability to tackle long-standing challenges associated with glycoproteomics. These studies will ultimately allow us to unravel the complex relationship between mucins and human disease.


B.S. University of Michigan, 2009
Ph.D. University of Virginia, 2014
Postdoctoral Scholar, Stanford University, 2016-2020


Society for Glycobiology Annual Conference Travel Award, 2019
Gordon Research Conference in Glycobiology; Poster Award, 2019
Helena Anna Heenzl-Gabor Young Women in Science Travel Grant, 2018
SUMS Research Symposium Poster; First Place, 2018
France-Stanford Center for Interdisciplinary Studies Visiting Junior Scholar Fellowship, 2018
NIH F32 Ruth L. Kirschstein National Research Service Award (NRSA), 2017-2019
NIH T32 Stanford School of Medicine Immunology Training Grant (Declined), 2017-2018
Helena Anna Henzl-Gabor Young Women in Science Travel Grant, 2017
Stanford University Mass Spectrometry Seed Grant, 2016
National Research Council (NRC) Research Associateship Award (Declined), 2016
University of Virginia CGS/ProQuest Distinguished Dissertation Nominee, 2015
University of Virginia Post Doc Symposium Oral Presentation; Third Place, 2015
Achievement Rewards for College Scientists (ARCS), Danaher Scholar, 2013-2014
University of Virginia 3 Minute Thesis; First Place, 2014
Huskey Research Symposium Oral Presentation; First Place, 2014
Washington-Baltimore Mass Spectrometry Discussion Group Travel Award, 2014
Robert J. Huskey Travel Fellowship Recipient, 2014
Huskey Research Symposium Poster; First Place, 2013
Pratt Fellowship, 2013
University of Virginia Chemistry Department Fellowship, 2010-2013
Alpha Chi Sigma Presidential Award, 2010
University of Michigan Angell Scholar, 2009
University of Michigan Honors, 2007-2009

Recent Publications

Google Scholar

Sarah A. Penny and Stacy 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

Stacy 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

Stacy A. Malaker, Kayvon Pedram, Michael J. Ferracane, Barbara A. Bensing, Venkatesh Krishnan, Christian Pett, Jin Yu, Elliot C. Woods, Jessica R. Kramer, Ulrika Westerlind, Oliver Dorigo, and Carolyn R. Bertozzi. The mucin-selective protease StcE enables molecular and functional analysis of human cancer-associated mucins. PNAS. 2019, 116(15): 7278-7287.

Stacy A. Malaker, Michael J. Ferracane, Florence R. Depontieu, Angela L. Zarling, Jeffrey Shabanowitz, Dina L. Bai, Suzanne Topalian, Victor H. Engelhard, and Donald 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.

Stacy A. Malaker, Sarah A. Penny, Lora Steadman, Paisley T. Myers, Justin C. Loke, Manoj Raghavan, Dina L. Bai, Jeffrey Shabanowitz, Donald F. Hunt, Mark Cobbold. Identification of glycopeptides as post-translationally modified neoantigens in leukemia. Cancer Immunology Research. 2017, 5(5): 376-384.