Dr. Jennifer Geddes-McAlister

Canada Research Chair/ Assistant Professor / Director, Bioinformatics Graduate Program
Department of Molecular and Cellular Biology
Phone number: 
SSC 4457
SSC 4405/4406

My keen interest in scientific research and academics began during my undergraduate degree at the University of Lethbridge, where I investigated the impact of fungal pathogens on agricultural development and performed my first proteomics experiments. This amazing experience led to a PhD in the laboratory of Dr. Jim Kronstad at UBC, where I applied quantitative proteomics to comprehensively profile the cellular proteome and secretome of the fungal pathogen, Cryptococcus neoformans. My fascination with mass spectrometry-based proteomics and pathogenesis provided the foundation for a postdoctoral fellowship supported by NSERC and the Alexander von Humboldt Foundation in the laboratory of Prof. Dr. Matthias Mann at the Max Planck Institute of Biochemistry in Munich, Germany. During my postdoc, I combined my expertise in microbiology and proteomics with experimental systems immunology to profile the interplay between Salmonella and its host during infection. At the University of Guelph, my research group will blend cutting-edge proteomics technologies with a systems biology perspective to explore host-pathogen interactions.

  • BSc (co-op) – University of Lethbridge, Biological Sciences
  • MSc – University of Lethbridge, Biological Sciences
  • PhD – University of British Columbia, Microbiology and Immunology
  • Postdoctoral Fellow – Max Planck Institute of Biochemistry, Proteomics and Signal Transduction

We are interested in characterizing the mechanisms of pathogenesis, adaptation, and survival in fungal and bacterial microbes from a systems biology perspective through mass spectrometry-based quantitative proteomics. Specifically, research in the lab centres around the following areas:

  1. Differential patterns of pathogenic regulation between microbial species;
  2. Systems biology to elucidate microbial proteome dynamics and interactions;
  3. Mechanistic characterization of pathogenic proteins; and
  4. Mass spectrometry-based proteomics for drug discovery and repurposing.

Our long-term goals emphasize the utilization of mass spectrometry-based proteomics to fundamentally understand differential microbial adaptation and survival strategies and to integrate a novel systems biology platform for investigation of diverse biological systems, defining functional mechanisms of cellular regulation and pathogenesis.

Interested students and post-doctoral fellows are encouraged to contact me to learn more about new and exciting opportunities.

Google Scholar

(*denotes corresponding authorship)


  • Gutierrez-Gongora, D., Raouf-Alkadhimi, F., Prosser, R.S., Geddes-McAlister, J.* (In Review) Differentiated protein extracts from freshwater and terrestrial mollusks inhibits virulence factor production in Cryptococcus neoformans.
  • Ball, B., Kazi, S., Sukumaran, A., Modrakova, M., Chan, N., Pladwig, S., Geddes-McAlister, J.* (In review) The cryptococcal co-chaperone, Wos2, drives proteome remodeling and fungal survival under diverse stressors and modes of infection.
  • Geddes-McAlister, J.*, Roux-Dalvai, F., Droit, A. (In Review) Proteomics, Bioinformatics, and Infectious Diseases. Genetics and Evolution of Infectious Diseases (Book chapter; invited submission)
  • Woods, M., McAlister, J.A., Geddes-McAlister, J.* (In Review) A One Health approach to overcoming antifungal resistance. WIREs: Mechanisms of Disease (invited submission)
  • Goodyear, M.C., Seidel, L., Krieger, J.R., Geddes-McAlister, J., Levesque, R.C., Khursigara, C.M. (In Revision) Quantitative proteomics reveals unique responses to antimicrobial treatments in clinical Pseudomonas aeruginosa isolates. mSystems.
  • Geddes-McAlister, J.*, Sukumaran, A., Vogt, S.L., Rowland, J.L., Woodward, S.E., Muselius, B., Gee, L., Roach, E.J., Khursigara, C.M., Raupach, B., Finlay, B.B., Meissner, F. (In Revision). Dual perspective proteomics infectome profiling discovers Salmonella type III secretion system effector functions in macrophages. PLoS Pathogens
  • Mainprize, I., Roach, E., Geddes-McAlister, J., Khursigara, C.M., Wills, M. (In RevisionThe Proteomic Response of Borrelia burgdorferi Exposed to Doxycycline. 
  • Buchanan, R., Serajazari, M., Geddes-McAlister, J.* (In PressProteomic profiling of host response in the cereal crop Triticum aestivum to the mycotoxin, 15-acetyldeoxynivalenol, produced by the fungal pathogen, Fusarium graminearum. Methods Mol Biol: Plant-Pathogen Interactions (Invited submission; Book Chapter)
  • Liu, B., Johal, D., Buchanan, R., Ball, B., Serajazari, M., Geddes-McAlister, J.* (In Press) Quantitative phosphoproteome analysis of a cereal crop fungal pathogen’s interaction with the host. Methods Mol Biol: Plant-Pathogen Interactions (Invited submission; Book Chapter).
  • Rizakos, T., Geddes-McAlister, J.* (In Press) Purification and proteomic profiling of neutrophils derived from HL60 cells. Journal of Visualized Experiments (Invited submission)
  • Petenkova, A., Lu, X., Quellier, D., Carter, D., To, O.T., Lamb, J., Kugadas, A., Geddes-McAlister, J., Sykes, D.B., Auger, S., Fichorova, R., Distefano, M., Gadjeva, M. (In Press). Pcyox1l controls neutrophil maturation and functionality. Nature Communications.
  • Ince, L.M., Barnoud, C., Lutes, L., Pick, R., Wang, C., Sinturel, F., Chen, C.S., de Juan, A., Weber, J., Holtkamp, S.J., Geddes-McAlister, J., Hergenhan, S.M., Ebner, S., Fontannaz, P., Meyer, B., Vono, M., Jemelin, S., Dibner, C., Siegrist, C.A., Meissner, F., Graw, F., Scheiermann, C. (In Press) Benefit of circadian clocks in adaptive immunity and vaccination responses. Nature Communications.
  • Santiago-Tirado, F.H., Hurtaux, T., Geddes-McAlister, J., Nguyen, D., Helms, V., Doering, T.L., Römisch, K. (In Press). The ER protein translocation channel subunit Sbh1 controls virulence of Cryptococcus neoformans. MBio.


  • Geddes-McAlister, J.* (2022). ‘Moms in Proteomics’ pushes for change. Nature. (Invited submission)
  • Geddes-McAlister, J.* & Schriemer, D.C. (2022) 13th Annual Symposium of the Canadian National Proteomics Network. Expert Reviews of Proteomics. (Invited submission)
  • Gutierrez-Gongora, D., Raouf-Alkadhimi, F., Prosser, R.S., Geddes-McAlister, J.(2022). Assessing the putative anticryptococcal properties of crude and clarified extracts from mollusks. Journal of Visualized Experiments. (Invited submission).
  • Teelucksingh, T., Thompson, L., Gilbert, S., MacNair, C., Kuehfuss, N., Goetz, J., Geddes-McAlister, J., Brown, E., Cox, G. (2022) A genetic platform to investigate bacterial drug efflux pumps. Nature Chem Biol
  • Sukumaran, A.1, Ball, B.1, Krieger, J.R., Geddes-McAlister, J.* (2022). Cross-kingdom infection of macrophages reveals pathogen- and immune-specific global reprogramming and adaptation. MBio. 1Authors contributed equally.
  • Geddes-McAlister, J.* (2022) ‘Moms in Proteomics’ aims to bring together a community for supporting moms in STEM. The Conversation. (Invited submission)
  • Geddes-McAlister, J.* (2022) Moms in Proteomics: Building a Supportive and Unified Community. Trends in Biochemical Sciences (Invited Submission)
  • Geddes-McAlister, J.* (2022) Systems biology in fungal research. J of Fungi. (Invited submission)
  • Geddes-McAlister, J.*, McLean, M.D., Cossar, D., Prudhomme, N., Gutierrez-Gongora, D. (2022) Emerging role of mass spectrometry-based proteomics in molecular pharming. Curr Opin Chem Biol. (Invited Submission)
  • Gutierrez-Gongora, D., Geddes-McAlister, J.* (2022). Peptidases: promising antifungal targets of the human fungal pathogen, Cryptococcus neoformansFACETS. (Invited submission)
  • Meissner, F., Geddes-McAlister, J., Mann, M., Bantscheff, M. (2022) The emerging role of mass spectrometry-based proteomics in drug discovery. Nature Reviews Drug Discovery. (Invited submission)
  • Geddes-McAlister, J.* (2022) Proteomics in Systems Biology. Methods in Molecular Biology (Book; Invited Editor)
  • Ball, B., Krieger, J., Geddes-McAlister, J.* (2022) Phosphoproteomic sample preparation for global phosphorylation profiling of a fungal pathogen. Methods Mol Biol: Proteomics in Systems Biology (Invited submission; Book Chapter)
  • Liu, B., Johal, D., Ball, B., Serajazari, M., Geddes-McAlister, J.* (2022) Label-free quantitative proteomic profiling of Fusarium head blight in wheat. Methods Mol Biol: Proteomics in Systems Biology (Invited submission; Book Chapter)
  • Prudhomme, N., Krieger, J.R., McLean, M., Cossar, D., Geddes-McAlister, J.* (2022) Proteomic profiling of interplay between Agrobacterium tumefaciens and Nicotiana benthamiana for improved molecular pharming outcomesMethods Mol Biol: Proteomics in Systems Biology (Invited submission; Book Chapter)
  • Sukumaran, A., Geddes-McAlister, J.* (2022) Proteomic profiling of the interplay between a bacterial pathogen and host uncovers novel anti-virulence strategies. Methods Mol Biol: Proteomics in Systems Biology (Invited submission; Book Chapter)


  • Liu, B., Stevens-Green, R., Johal, D., Buchanan, R., Geddes-McAlister, J.* (2021). Fungal pathogens of cereal crops: Proteomic insights into fungal pathogenesis, host defense, and resistance. J Plant Physiology. (Invited submission)
  • Ball, B., Woroszchuk, E., Sukumaran, A., West, H., Afaq, A., Carruthers-Lay, D., Muselius, B., Gee, L., Langille, M., Pladwig, S., Kazi, S., Hendriks, A., Geddes-McAlister, J.* (2021) Proteomic profiling of zinc limitation in Cryptococcus neoformans reveals regulation of vesicle-associated factors. BMC Microbiology.
  • Gutierrez-Gongora, D., Geddes-McAlister, J.* (2021). From naturally-sourced protease inhibitors to new treatments for fungal infections. J of Fungi. (Invited submission)
  • Muselius, B., Durand, S.L., Geddes-McAlister, J.* (2021) Proteomics of Cryptococcus neoformans: From the lab to the clinic. Int J Molecular Sciences. (Invited submission)
  • Goodyear, M.C., Garnier, N., Krieger, J.R., Geddes-McAlister, J.*, Khursigara, C.M.* (2021) Label-free quantitative proteomics identifies unique proteomes of clinical isolates of the Liverpool Epidemic Strain of Pseudomonas aeruginosa and laboratory strain PAO1. Proteomics Clinical Applications.
  • Grafinger, O.R., Stirling, T., Geddes-McAlister, J., Coppolino, M.G. (2021) Inhibition of b1 integrin induces its association with MT1-MMP and decreases MT1-MMP internalization and cellular invasiveness. Cellular Signalling.
  • Sukumaran, A., Pladwig, S., Geddes-McAlister, J.* (2021) Zinc limitation in Klebsiella pneumoniae profiled by quantitative proteomics influences transcriptional regulation and cation transporter-associated capsule production. BMC Microbiol.
  • Retanal, C., Ball, B. & Geddes-McAlister, J.* (2021) Post-translational modifications drive success and failure of fungal-host interactions. J of Fungi (Invited submission)
  • Rosiana, S., Zhang, L., Kim, GH., Retovich, AV., Sukumaran, A., Geddes-McAlister, J., Kirienko, NV., Shapiro, RS. (2021) Systematic characterization and genetic interaction analysis of adhesins in Candida albicans virulence. Genetics.
  • Prudhomme, N., Gianetto-Hill, C., Pastora, R., Cheung, W.-F., Allen-Vercoe, E., McLean, M.D., Cossar, D., Geddes-McAlister, J.* (2021) Quantitative proteomic profiling of shake flask versus bioreactor growth reveals distinct responses of Agrobacterium tumefaciens for preparation in molecular pharming. Can. J. Microbiol.
  • Prudhomme, N., Pastora, R., Muselius, B., McLean, M.D., Cossar, D., Geddes-McAlister, J.* (2021) Exposure of Agrobacterium tumefaciens to agroinfiltration medium demonstrates cellular remodeling and may promote enhanced adaptability for molecular pharming. Can. J. Microbiol.


  • Tremblay, O., Thow, Z., Geddes-McAlister, J., A. Rod Merrill. (2020) Several New Putative Bacterial ADP-Ribosyltransferase Toxins Are Revealed from In Silico Data Mining, Including the Novel Toxin Vorin, Encoded by the Fire Blight Pathogen Erwinia amylovora. Toxins.
  • Geddes-McAlister, J.*, Sukumaran, A., Patchett, A., Hager, H.A., Dale, J.C.M., Roloson, J.L., Prudhomme, N., Bolton, K., Muselius, B., Powers, J., Newman, J.A. (2020) Examining the impacts of CO2 concentration and genetic incompatibility on perennial ryegrass-Epichloee festucae var lolii interactions. J of Fungi.
  • Van Gelder, K., Virta, L., Easlick, J., Prudhomme, N., McAlister, J., Geddes-McAlister, J., Akhtar, T. (2020) A central role for polyprenol reductase in plant dolichol biosynthesis. Plant Sci.
  • Sukumaran, A., Woroszchuk, E., Ross, T., Geddes-McAlister,  J.* (2020) Proteomics of host-bacterial interactions: new insights from dual perspectives. Can. J. Microbiol. (Invited submission).
  • Ball, B., Sukumaran, A., Geddes-McAlister,  J.* (2020) Label-Free Quantitative Proteomics Workflow for Discovery-Driven Host-Pathogen Interactions. J Visual Experiments. (Invited submission).
  • Ball, B., Langille, M., Geddes-McAlister,  J.* (2020) Fun(gi)OMICS: advanced and diverse technologies to explore emerging fungal pathogens. MBio. (Invited submission)
  • Bermas, A. and Geddes-McAlister,  J.* (2020) Experimental evolution of antifungal resistance in Cryptococcus neoformans. Curr Prot Microbiol. (Invited submission)
  • Yeung, J., Lamb, J., Krieger, J., Gadjeva, M., Geddes-McAlister,  J.* (2020) Quantitative proteomic profiling of murine ocular tissue and the extracellular environment. Curr Prot Mouse Biol. (Invited submission, cover image)
  • Geddes-McAlister, J.* (2020) Pathogenesis of Fungal and Bacterial Microbes. Pathogens. (Editorial; Invited submission)
  • Horianopoulos, L., Gluck-Thaler, L., Benoit Gelber, I., Cowen, L., Geddes-McAlister, J., Landry, C., Schwartz, I., Scott, J., Sellam, A., Sheppard, D., Spribille, T., Subramaniam, R., Walker, A., Harris, S., Shapiro, R., Gerstein, A. (2020) The Canadian Fungal Research Network: current challenges and future opportunities. Can. J. Microbiol.
  • Bermas, A., Geddes-McAlister, J.* (2020) Combatting the evolution of antifungal resistance in Cryptococcus neoformans. Mol Micro. (Invited submission)
  • Muselius, B.1, Sukumaran, A.1, Yeung, J., Geddes-McAlister, J.* (2020) Iron limitation in Klebsiella pneumoniae defines new roles for Lon protease in homeostasis and degradation by quantitative proteomics. Front Microbiol. 1Authors contributed equally.
  • Anderson, E.M., Sychantha, D., Brewer, D., Clarke, A.J., Geddes-McAlister, J.*, Khursigara, C.M.* (2020) Peptidoglycomics: Examining compositional changes in peptidoglycan between biofilm- and planktonic-derived Pseudomonas aeruginosaJ Biol Chem.
  • Yeung, J., Gadjeva, M., Geddes-McAlister, J.* (2020) Label-free quantitative proteomics distinguishes general -and site-specific host responses to Pseudomonas aeruginosa infection at the ocular surface. Proteomics.


  • Geddes-McAlister, J., Kugadas, A., Gadjeva, M. (2019) Tasked with a challenging objective: why do neutrophils fail to battle Pseudomonas aeruginosa biofilms? Pathogens. (Invited submission)
  • Ball, B., Geddes-McAlister, J.* (2019) Quantitative proteomic profiling of Cryptococcus neoformans. Curr Protoc Microbiol. (Invited submission & cover image)
  • Sukumaran, A., Coish, J., Yeung, J., Muselius, B., Gadjeva, M., MacNeil, A.J., Geddes-McAlister, J.* (2019). Decoding communication patterns of the innate immune system by quantitative proteomics. J Leukocyte Biol.
  • Geddes-McAlister, J.*, Gadjeva, M. (2019). Mass spectrometry-based quantitative proteomics of murine-derived polymorphonuclear neutrophils. Current Protocols in Immunology.
  • Ball, B., Bermas, A., Carruthers-Lay, D., Geddes-McAlister, J.* (2019) Mass Spectrometry-Based Proteomics of Fungal Pathogenesis, Host–Fungal Interactions, and Antifungal Development. J Fungi.
  • Rea, K.A., Casaretoo, J.A., Al-Abdul-Wahid, M.S., Sukumaran, A., Geddes-McAlister, J., Rothstein, S.J., Akhtar, T.A. (2019). Biosynthesis of cannflavins A and B from Cannabis sativa L. Phytochemistry.
  • Kugadas A., Geddes-McAlister, J., Guy, E., DiGiandomenico, A., Sykes, D.B., Mansour, M.K., Mirchev, R., Gadjeva, M. (2019). Employing enzymatic treatment options for management of ocular biofilm-based infections. J Leukocyte Biol.

2017 & 2018

  • Geddes-McAlister, J., Shapiro, R.S. (2018) New pathogens, new tricks: emerging, drug-resistant fungal pathogens and future prospects for antifungal therapeutics. Antimicrobial Therapeutics Reviews, Annals of the New York Academy of Sciences.
  • Kugadas A., Wright Q., Geddes-McAlister, J., Gadjeva, M. (2017) Role of microbiota in strengthening ocular mucosal barrier function through secretory IgA. Investigative Ophthalmology & Visual Science.

2015 & 2016

  • Geddes, J.M.H., Caza, M., Croll, D., Stoynov, N., Foster, L.J., Kronstad, J.W. (2016) The ubiquitin-proteasome pathway in Cryptococcus neoformans influences capsule production, is regulated by protein kinase A, and is an antifungal target. MBio.
  • Geddes, J.M.H., Croll, D., Caza, M., Stoynov, N., Foster, L.J., Kronstad, J.W. (2015) Secretome profiling of Cryptococcus neoformans reveals regulation of a subset of virulence-associated proteins and potential biomarkers by Protein Kinase A. BMC Microbiol.

2012 & earlier

  • Kronstad, J.W., Saikia, S., Nielson, E.D., Kretschmer, M., Jung, W., Hu, G., Geddes, J.M.H., Griffiths, E.J., Choi, J., Cadieux, B., Caza, M., Attarian, R. (2012) Adaptation of Cryptococcus neoformans to mammalian hosts: integrated regulation of metabolism and virulence. Eukaryotic Cell.
  • Kronstad, J.W., Attarian, R., Cadieux, B., Choi, J., D’Souza, C.A., Geddes, J.M.H., Griffiths, E.J., Hu, G., Jung, W., Kretschmer, M., Saikia, S., Wang, J. (2011) Expanding fungal pathogenesis: Cryptococcus breaks out of the opportunistic box. Nature Reviews Microbiology.
  • Geddes, J.M.H., Eudes, F., Laroche, A., Selinger, L. B. (2008) Differential expression of proteins in response to the interaction between the pathogen Fusarium graminearum and its host, Hordeum vulgare. Proteomics.
  • Geddes, J.M.H., Eudes, F., Tucker, J. R., Legge, W. G., Selinger, L.B. (2008) Evaluation of inoculation methods on Fusarium graminearum infection and deoxynivalenol production in barley. Canadian Journal of Plant Pathology.

Links and Media

Canadian National Proteomics Network



Canadian National Proteomics Network – Unity Initiative



Moms in Proteomics



In the news:

University of Guelph News

CTV Kitchener

CBC Radio – Fresh Air


Canadian Proteomics and Artificial Intelligence Consortium



Ontario Early Researcher Award




Industry Partnerships






Banting Research Foundation




Research highlights









Graduate Students:

  • Arjun Sukumaran (PhD Candidate)
  • Brianna Ball (PhD Candidate; EvoFunPath fellow)
  • Nicholas Prudhomme (PhD Candidate)
  • Benjamin Muselius (PhD Candidate)
  • Boyan Liu (PhD Candidate; EvoFunPath fellow) (Co-supervised with Dr. Rebecca Shapiro, U of Guelph)
  • Jacqueline Thomson (PhD Candidate) (Co-supervised with Dr. Jonathan Newman, Laurier University)
  • Kerry Woolnough (PBINF) (Co-supervised with Dr. Andrew Hamilton-Wright)
  • Jarod Morgenroth-Rebin (MSc)
  • Reid Buchanan (MSc; MITACS intern)
  • Michael Woods (PhD; MITACS intern)
  • Tia Rizakos (MSc)
  • Davier Gutierrez-Gongora (PhD)
  • Wilson Li (MSc) (Co-supervised with Dr. Francois Tardiff, U of Guelph)

Undergraduate Students:

  • Samiha Kazi (4th-year research project)
  • Jiaxi Liu (4th-year research project)
  • Kiyan Kheradvar (4th-year research project)
  • Effie Honeywell (4th-year research project)
  • Harjot Atwal (work study)
  • Madeleine O'Connor (work study)
  • Ryan Rosniak (work study)

Research Technician:

  • Samanta Pladwig, MSc
  • Norris Chan, MSc

Research Associate:

  • Jason McAlister, PhD

Previous Members:

  • Fouad Raouf-Alkadhimi (MBIOT)
  • Natalie Kim (MSc Bioinformatics) (Co-supervised with Dr. Jeremy Dettman, AAFC-Ottawa)
  • Oscar Gonzalez (MITACS Globalink)
  • Nicole Hendriks (4th-year literature project)
  • Breanne Murray (4th-year literature project)
  • Anchitaa Ghag, BSc, MBINF
  • Lilianne Gee (MSc) (Co-supervised with Dr. Jonathan Newman, Laurier University)
  • Oriana Robinson (4th-year research project)
  • Siobhan O'Connor (4th-year research project)
  • Christina Zanetti (4th-year research project)
  • Thuy Duyen Lisa Tran (4th-year research project)
  • Manuela Modrakova (4th-year research project)
  • Mercy Akinsola (4th-year research project)
  • Divya Vurrabindi (4th-year research project)
  • Effie Honeywell (Co-op student, work study)
  • Payton Curtis (Work study)
  • Elisa Haley (Work study)
  • Alicome Ochere (Work study)
  • Marsha Lane (Work study)
  • Maggie Cummings (Work study)
  • Anthony Hendricks (Project student)
  • Kushal Gandhi (4th year research)
  • Sarah Renaud (4th year research)
  • Arianne Bermas (MSc)
  • Syed Ali (MBINF) (Co-supervised with Dr. Lewis Lukens, U of Guelph)
  • Kerry Woolnough (MBINF) (Co-supervised with Dr. Jasmin Lalonde, U of Guelph)
  • Michael Prudencio-Brunello (4th-year research)
  • Hannah West (Co-op)
  • Duncan Carruthers-Lay (4th-year research)
  • Ammar Afaq (4th-year research)
  • Rebecca Stevens-Green (4th-year research)
  • Nadolina Brajuka (Work study)
  • Elizabeth Woroszchuk (4th-year research)
  • Jason Yeung (4th-year research)
  • Nakshdeep Grewal (4th-year literature)
  • Sagal Dirie (4th-year literature)
  • Morgan Langille (4th-year research)
  • Edison Zheng (4th-year research)
  • Leah Horlings (4th-year research)
  • Marie Pinto (4th-year literature)
  • Charmaine Retanal (4th-year literature)
  • Natalie Pagdiwala (4th-year literature)
  • Taylor Ross (4th-year research)
  • Jacob Hamilton-Rowe (4th-year research)
  • Danisha Johal (4th-year research)
  • Jake Brill (4th-year research)
  • Kristen Haydock (4th-year literature)
  • Shay-Lynn Durand (4th-year literature)
  • Effie Honeywell (Work study)
  • Daniela Samuel (Work study)

MICR*3230 Immunology

MICR*2420 Introduction to Microbiology

MCB*6500/*7500 MSc/PhD Research Topics in MCB

BINF*6890 Topics in Bioinformatics