CRBI/CIRC Seminar
2025-02-04 10:30 - 12:00 (America/Toronto)
CRBI/CIRC Seminar – Dr. Christo El Morr, Professor School of Health Policy & Management, York University
Dr. Rachel da Silveira Gorman, Associate Professor School of Health Policy & Management, York University
AI and Disability Justice: “Decolonizing AI through community engagement and co-design

CRBI/CIRC Seminar
2025-03-04 10:30 - 12:00
CRBI/CIRC Seminar – Dr. Brian Kim, Assistant Professor Chemistry, York University
New Frontiers in CRISPR Technologies and Applications

CRBI/CIRC Seminar
2025-03-28 12:30 - 13:30
CRBI Seminar – Dr. Qili Feng Professor in School of Life Sciences, South China Normal University, Guangzhou, China
Gene transcription regulation by DNA advanced structures
DNA advanced structures such as G4 and i-motif, have been found to play important roles in multiple biological processes. A large-scale genomic analysis of distribution and evolution of the DNA secondary structures in 37 representative species revealed that the number, density and ratios of advanced structures in the genomes gradually increased with evolution and enriched in the upstream regulatory regions of many genes, particularly transcription factor genes, suggesting that these DNA structures may have developed into an epigenetic regulation mechanism for gene transcription in genomes. Methylation modification and advanced structures in DNA molecules are two epigenetic regulation mechanisms for gene transcription. We found that the 5mC modification in G4 forming sequences inhibited the folding of the sequences into G4s. Suppression of whole-genome methylation led to a genome-wide increase in the abundance of G4s. Whole-genome bisulfite sequencing (WGBS) and G4 CUT&Tag data from HeLa and K562 cells revealed that the hypomethylated sequences around transcriptional start sites (TSSs) had a much higher abundance of G4s than the hypermethylated sequences, suggesting a negative relationship between these two epigenetic mechanisms. G4 and i-motif structures were identified in the promoter of the transcription factor gene BmPOUM2, which regulates the expression of the wing disc cuticle protein gene (BmWCP4) during metamorphosis in Bombyx mori. Disruption or deletion of the G4 and i-motif structures by base mutation, anti-sense oligonucleotides (ASOs) , inhibitory ligands or knockout resulted in significant decrease in the activity of the BmPOUM2 promoter. Two transcription factors (BmLARK and BmILF) were was identified by pull-down experiment and proved to specifically bind to the G4 and i-motif structures, respectively, and activated the transcription of BmPOUM2. All the data indicate that DNA advanced structures function as an epigenetic regulation mechanism for gene transcription and participate in regulation of insect development.

CRBI/CIRC Seminar
2025-04-01 10:45 - 12:00
CRBI/CIRC Seminar – Dr. Marios Fokaefs Assistant Professor, Electrical Engineering & Computer Science, York University
“Supporting software engineering tasks in epidemiological research – An AI approach”

CRBI/CIRC Seminar
2025-04-15 10:45 - 12:00
CRBI/CIRC Seminar – Dr. Leo Chou, Assistant Professor, Molecular Engineering, University of Toronto “DNA-Scaffolded Materials for Biomedical Research and Applications”

Dr .Nima Tabatabaei, Associate Professor, Mechanical Engineering. York University
“Molecular-Specific and Label-Free Sensing and Imaging of Biological Samples”

CRBI/CIRC Seminar
2025-05-06 10:45 - 12:00
CRBI/CIRC Seminar – Dr. Teshager Dagne Associate Professor, School of Public Policy and Administration, York University
Dr. Soren D. Frederiksen Assistant Professor, School of Public Policy and Administration, York University

CRBI/TEPD Seminar
2025-09-08 12:15 - 13:15
Mike Che, PhD., York University: “Development of a Novel Lateral Flow Immunoassay (LFIA) Architecture for machine learning Applications and Incorporating Electrophoresis-Enhanced into fusion antibody-based COVID-19 LFIA for Signal Amplification”.
Quan Le, PhD., York University: “Determination of Absolute Injection Volume in Capillary Electrophoresis by the Capillary-Volume-Plateau Calibration (CVPC)”.

CRBI/TEPD Seminar
2025-09-22 12:15 - 13:15
Taranjot Kaur, MSc., York University: “Assessment of Cytochrome P450 Function in Individual Cancer Cells Using Cytometry of Reaction Rate Constant (CRRC)”.
Zhiyuan Mao, MSc., York University: “Enhancing ACTIS: Automation and Integration of Mass Spectrometry and Fluorescence Detection”.

CRBI/TEPD Seminar
2025-10-06 12:15 - 13:15
Ayesha Maqsood, PhD., York University: “Development of a Mass Spectrometry-based Proteomics Method for Clinical Diagnostics”.
Venita Sitahal, PhD., York University: “Identifying Small Molecule Binding Sites in Proteins using Conventional and Site-Specific HDX-MS”.

CRBI/TEPD Seminar
2025-10-20 12:15 - 13:15
Asghar Arshi, PhD., York University: “Investigating the oncogenic role of circSKA3 in ovarian cancer development as a potential biomarker and therapeutic target”.
Claire Gillespie, PhD., McMaster University: “The Pharmacokinetics of Oral Tetrahydrocannabinol and Cannabidiol across the spectrum of Glomerular Filtration Rate”.

CRBI/TEPD Seminar
2025-11-03 12:15 - 13:15
Dr. Sergey Krylov, Distinguished Research Professor, York University: “Bottlenecks in DNA-Encoded Library (DEL) Technology”.

CRBI/TEPD Seminar
2025-11-17 12:15 - 13:15
Huicong Wang, MSc., York University: “Developing a photochemical approach to sequencing m1G in RNA”.
Luca Di Fabio, PhD., York University: “Performance via Proximity: Studying proximity-induced enhancement of human neutrophil elastase in degradation of extracellular protein targets via DNA aptamer recruitment”.

CRBI/TEPD Seminar
2025-12-01 12:15 - 13:15
David Guo, PhD., University of Toronto: “Engineering DNA Origami with Tunable Immunogenicity via Scaffold Sequence Design”.
Shana Alexander, PhD., University of Toronto: “Tuning immunogenicity of DNA-nanoscaffolded immune complexes”.

CRBI/TEPD Seminar
2026-01-12 12:15 - 13:15
Connor Loupelle, PhD., York University: “Deciphering the hLa-Associated Epitranscriptome: The Human La Protein Modulates Methylation Levels in Transfer RNAs”.
Minh Thu Vu, PhD., York University: “Development of sensitive aptamer-based lateral flow assay for C-reactive protein detection”.

CRBI/TEPD Seminar
2026-02-09 12:15 - 13:15
Maryam Jabbarpoor, PhD., York University: “Diastereoselective Synthesis of a-Fluoro-g-Lactams via Difluorocarbene-Triggered Cyclization and Rearrangement”.

CRBI/TEPD Seminar
2026-02-23 12:15 - 13:15
Erica Iantorno, MSc., York University: “Elucidating the Role of Penicillin-Binding Protein 4 in beta-Lactam Resistance Using Hydrogen-Deuterium Exchange Mass Spectrometry”.
Luca Rustico, MSc., York University: “Developing a Ligase-mediated Platform for the Transcription and Reverse-Transcription of XNA Aptamers”.

CRBI/TEPD Seminar
2026-03-09 12:15 - 13:15
Toby Chan, MSc., York University: “Effect of Non-additivity on High Throughput Screening”.
Liam Surry, MSc., McMaster University: “A Software Platform for Rapid Drug Adherence and Metabolomic Screening in High-Risk Psychiatric Patients using Multisegment Injection-Capillary Electrophoresis-Mass Spectrometry (MSI-CE-MS)”.

Visit from Vilnius University
2026-05-28
Prof. Daumantas Matulis and Dr. Vytautas Petrauskas as a part of ongoing collaborative discussions that began with the visit of the Lithuanian delegation to York.
Prof. Daumantas Matulis and Dr. Vytautas Petrauskas are from the Department of Biothermodynamics and Drug Design, Life Sciences Center, Vilnius University. Their research interests are closely related to biomolecular interactions, biophysical analysis, and drug discovery, so I expect the presentation and discussion to be scientifically engaging.
—
Drug Design and Protein–Ligand Binding Database for AI-ML
Prof. Daumantas Matulis
Head of Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius
University, Saulėtekio 7, Vilnius LT-10257, Lithuania Email: daumantas.matulis@bti.vu.lt,
matulis@ibt.lt
Abstract
Drug molecules exert their effects on disease-associated proteins by binding to them with high
affinity and selectivity. However, most small molecules interact only weakly with the majority of
sites on protein surfaces, and only a limited number of chemical compounds can selectively and
strongly bind to desired sites. In addition, even minor modifications to a compound’s chemical
structure may lead to substantial changes in binding affinity. We designed and investigated the
binding of over 1,000 small-molecule compounds to Carbonic Anhydrase IX, a transmembrane
protein overexpressed in hypoxic solid tumors that promotes metastasis and invasiveness, and
supports cancer cell survival under hypoxic conditions by acidifying the tumor microenvironment.
We characterized the thermodynamics of binding of these compounds across the carbonic
anhydrase enzyme family and identified the determinants of selectivity for CA IX inhibition (1) .
Fluorescent CA IX-selective compounds enabled visualization of CA IX expression in cancer cells
and tumors and demonstrated efficacy against Neuroblastoma in mouse xenograft models.
The data were assembled into the Protein-Ligand Binding Database (PLBD) to apply artificial
intelligence – machine learning approaches to drug design and are available at https://plbd.org
(2) . The database contains 8233 binding datasets of 792 compounds interacting with human CA
isozymes, Hsp90, and COVID proteases, as determined by inhibition of enzymatic activity, TSA, ITC,
and SPR techniques. The PLBD emphasizes intrinsic parameters and enthalpy, enhancing the
understanding of reaction mechanisms. The binding data are linked to 138 crystal structures of CA
complexes with ligands. The database has been built using the FAIR data principles to contain the
raw data with revision and versioning systems. The PLBD led to a deeper understanding of the
protein-ligand recognition principles and enabled the achievement of femtomolar affinities in
small-molecule drug design (3) .
References
1. Matulis, D. 2019. Carbonic anhydrase as drug target: thermodynamics and structure of inhibitor
binding. SPRINGER NATURE.
2. Lingė, D., M. Gedgaudas, A. Merkys, V. Petrauskas, A. Vaitkus, A. Grybauskas, V. Paketurytė, A.
Zubrienė, A. Zakšauskas, A. Mickevičiūtė, J. Smirnovienė, L. Baranauskienė, E. Čapkauskaitė, V.
Dudutienė, E. Urniežius, A. Konovalovas, E. Kazlauskas, K. Shubin, H.B. Schiöth, W.-Y. Chen, J.E.
Ladbury, S. Gražulis, and D. Matulis. 2023. PLBD: protein–ligand binding database of thermodynamic
and kinetic intrinsic parameters. Database 2023:baad040, doi: 10.1093/database/baad040.
3. Zubrienė, A., M. Kurtenoka, V. Paketurytė-Latvė, J. Leitans, E. Manakova, M. Žvirblis, A. Kazaks, V.
Eimonta, K. Tars, S. Gražulis, V. Petrauskas, J. Matulienė, V. Dudutienė, K. Shubin, and D. Matulis. 2026.
Achieving femtomolar affinities in structure-based drug design. Eur. Biophys. J., doi: 10.1007/s00249-
025-01812-5.
