Faculty

Elena Kuzmin, PhD

Assistant Professor, Biology
Canada Research Chair Tier 2 in Synthetic and Functional Genomics



Education

BSc (University of Toronto, Human Biology and Zoology)
MSc (University of Toronto, Laboratory Medicine and Pathobiology)
PhD (University of Toronto, Molecular Genetics, Profs. Charles Boone, Brenda Andrews)
PDF (McGill University, Biochemistry, Prof. Morag Park)


Teaching activities

BIOL498: Cancer Evolution


Research interests

We are a dynamic research group at the Centre for Applied Synthetic Biology (CASB). We investigate how phenotypes and disease states emerge from the interplay of genetic determinants in yeast and human cells. Using a combination of systematic genetic screening (trigenic interaction screens, high-content screens, overexpression screens and CRISPR screens), genome sequencing (bulk and single cell DNA and RNA sequencing), genome engineering and synthetic biology approaches, we aim to enhance our understanding of the genotype-to-phenotype relationship and genome evolution. We pursue several research themes focusing on mapping complex genetic interaction networks, from genetic network rewiring between distantly related yeast species, conditional functional redundancy and divergence of duplicated genes and complex genetic interaction network of large copy number variants in cancer and rare genetic disease.


Selected Publications

Retention of Duplicated Genes in Evolution
Kuzmin, E., Taylor, J.S., Boone, C.
Trends in Genetics (2022)

Inferring Copy Number from Triple Negative Breast Cancer Patient Derived Xenograft scRNAseq data using scCNA
Kuzmin, E., Monlong, J., Martinez, C., Kuasne, H., Kleinman, C., Ragoussis, J., Bourque, G., Park, M.
Methods in Molecular Biology (2021)

τ-SGA: synthetic genetic array analysis for systematically screening and quantifying trigenic interactions in yeast
Kuzmin, E., Rahman, M., VanderSluis, B., Costanzo, M., Myers, C.L., Andrews, B.J., Boone, C.
Nature Protocols (2021)

Trigenic Synthetic Genetic Array (τ-SGA) Technique For Complex Interaction Analysis
Kuzmin, E., Andrews, B.J., Boone, C.
Methods in Molecular Biology (2021)

Exploring whole-genome duplicate gene retention with complex genetic interaction analysis
Kuzmin, E., VanderSluis, B., Nguyen Ba, A.N., Wang, W., Koch, N.E., Usaj, M., Khmelinskii, A., Mattiazzi Usaj, M., van Leeuwen, J., Kraus, O., Tresenrider, A., Pryszlak, M., Hu, M.C., Varriano, B., Costanzo, M., Knop, M., Moses, A., Myers, C.L., Andrews, B.J., Boone, C.
Science (2020)

Global Genetic Networks and the Genotype to Phenotype Relationship
Costanzo, M., Kuzmin, E., van Leeuwen, J., Mair, B., Moffat, J., Boone, C., Andrews, B.
Cell (2019)

Dispersible hydrogel force sensors reveal patterns of solid mechanical stress in multicellular spheroid cultures
Lee, W., Kalashnikov, N., Mock, S., Halaoui, R., Kuzmin, E., Putnam A.J., Takayama, S., Park, M., McCaffrey, L., Zhao, R., Leask, R. L., Moraes, C.
Nature Communications (2019)

Systematic Analysis of Complex Genetic Interactions
Kuzmin, E., VanderSluis, B., Wang, W., Tan, G., Deshpande, R., Chen, Y., Usaj, M., Balint, A., Mattiazzi Usaj, M., van Leeuwen, J., Koch, E.N., Pons, C., Dagilis, A.J., Pryszlak, M., Wang, J.Z.Y., Hanchard, J., Riggi, M., Xu, K., Heydari, H., San Luis, B. Shuteriqi, E., Zhu, H., Van Dyk, N., Sharifpoor, S., Costanzo, M., Loewith, R., Caudy, A.A., Bolnick, D., Brown, G.W., Andrews, B.J., Boone, C., Myers, C.L.
Science (2018)

Kibra (WWC1) is a metastatic suppressor gene affected by chromosome 5q loss in human breast cancers
Knight, J.F., Sung, V.Y.C., Kuzmin, E., Couzens, A.L., de Verteuil, D.A., Johnson, R.M., Gruosso, T., Lee, W., Saleh, S.M., Zuo, D., Guiot, M.C., Davis, R.R., Zhao, H., Gregg, J.P., Moraes, C., Gingras, A.C., Park, M.
Cell Reports (2018)

Exploring genetic suppression interactions on a global scale
van Leeuwen, J., Pons, C., Mellor, J.C., Yamaguchi, T.N., Friesen, H., Koschwanez, J., Mattiazzi Ušaj, M., Pechlaner, M., Takar, M., Ušaj, M., VanderSluis, B., Andrusiak, K., Bansal, P., Baryshnikova, A., Boone, C.E., Cao, J., Cote, A., Gebbia, M., Horecka, G., Horecka, I., Kuzmin, E., Legro, N., Liang, W., van Lieshout, N., McNee, M., San Luis, B.J., Shaeri, F., Shuteriqi, E., Sun, S., Yang, L., Youn, J.Y., Yuen, M., Costanzo, M., Gingras, A.C., Aloy, P., Oostenbrink, C., Murray, A., Graham, T.R., Myers, C.L., Andrews, B.J., Roth, F.P., Boone, C.
Science (2016)

A global genetic interaction network maps a wiring diagram of cellular function
Costanzo, M., VanderSluis, B., Koch, E.N., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, S.D., Pelechano, V., Styles, E.B., Billmann, M., van Leeuwen, J., van Dyk, N., Lin, Z., Kuzmin, E., Nelson, J., Piotrowski, J.S., Srikumar, T., Bahr, S., Chen, Y., Deshpande, R., Kurat, C.F., Li, S.C., Li, Z., Mattiazzi Usaj, M., Okada, H., Pascoe, N., San Luis, B.J., Sharifpoor, S., Shuteriqi, E., Simpkins, S.W., Snider, J., Garadi Suresh, H., Tan, Y., Zhu, H., Malod-Dognin, M., Janjic, V., Przulj, N., Troyanskaya, O.G., Stagljar, I., Xia, T., Ohya, Y., Gingras, A.C., Raught, B., Boutros, M., Steinmetz, L.M., Moore, C.L., Rosebrock, A.P., Caudy, A.A., Myers, C.L., Andrews, B., Boone, C.
Science (2016)

Synthetic Genetic Arrays: Automation of Yeast Genetics
Kuzmin, E., Costanzo, M., Andrews, B.J., Boone, C.
Cold Spring Harbor Protocols (2016)

Synthetic Genetic Array Analysis
Kuzmin, E., Costanzo, M., Andrews, B.J., Boone, C.
Cold Spring Harbor Protocols (2016)

Chemical genomics-based antifungal drug discovery: targeting glycosylphosphatidylinositol (GPI) precursor biosynthesis
Mann, P.A., McLellan, C.A., Koseoglu, S., Si, Q., Kuzmin, E., Flattery, A., Harris, G., Sher, X., Murgolo, N., Wang, H., Devito, K., de Pedro, N., Genilloud, O., Nielsen Kahn, J., Jian, B., Costanzo, M., Boone, C., Garlisi, C.G., Lindquist, S., Roemer, T.
ACS Infectious Disease (2015)

Synthetic Genetic Array Analysis for Global Mapping of Genetic Networks in Yeast
Kuzmin, E., Sharifpoor, S., Baryshnikova, A., Costanzo, M., Myers, C.L., Andrews, B., Boone, C.
Methods in Molecular Biology (2014)

A comparative genomic approach for identifying synthetic lethal interactions in human cancer
Deshpande, R., Asiedu, M., Klebig, M., Sutor, S., Kuzmin, E., Nelson, J., Piotrowski, J., Shin, S.H., Yoshida, M., Costanzo, M., Boone, C., Wigle, D.A., Myers, C.L.
Cancer Research (2013)

SGAtools: one-stop analysis and visualization of array-based genetic interaction screens
Wagih, O., Usaj, M., Baryshnikova, A., Vandersluis, B., Kuzmin, E., Costanzo, M., Myers, C.L., Andrews, B.J., Boone, C.M., Parts, L.
Nucleic Acids Research (2013)

Dosage suppression genetic interaction networks enhance functional wiring diagrams of the cell
Magtanong, L., Ho, C.H., Barker, S.L.*, Jiao, W., Baryshnikova, A., Bahr, S., Smith, A.M., Heisler, L.E., Choy, J.S., Kuzmin, E., Andrusiak, K., Kobylianski, A., Li, Z., Costanzo, M., Basrai, M.A., Giaever, G., Nislow, C., Andrews, B., Boone, C.
Nature Biotechnology (2011)

Transient limb ischemia remotely preconditions through a humoral mechanism acting directly on the myocardium: evidence suggesting cross-species protection
Shimizu, M., Tropak, M., Diaz, R.J., Suto, F., Surendra, H., Kuzmin, E., Li, J., Gross, G., Wilson, G.J., Callahan, J.W., Redington, A.N.
Clinical Science (2009)

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