Take a look at the most recent publications by our team members.


Cardiomyocyte and endothelial cells play distinct roles in the tumour necrosis factor (TNF)-dependent atrial responses and increased atrial fibrillation vulnerability induced by endurance exercise training in mice

Cardiovascular Research, 15 Sept 2023
Lakin R,  Polidovitch N,  Yang S,  Parikh M, Liu X,  Debi R, Gao X,  Chen W,  Guzman C,  Yakobov S,  Izaddoustdar F, Wauchop M,  Lei Q,  Xu W,  Nedospasov SA,  Christoffels VM, Backx PH

Population dynamics of immunological synapse formation induced by bispecific T cell engagers predict clinical pharmacodynamics and treatment resistance

eLife, 25 Jul 2023
Liu, Zhou, Kudlacek, Qi, Dunlap, Cao

Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel SARS-CoV-2 virus

Heliyon, 04 Apr 2023
Hernandez NE, Jankowski W, Frick R, Kelow SP, Lubin JH, Simhadri V, Adolf-Bryfogle J, Khare SD, Dunbrack RL Jr.,  Gray JJ, Sauna ZE


"Computational Design of Peptide-Based Binders to Therapeutic Targets", Approaching the Next Inflection in Peptide Therapeutics: Attaining Cell Permeability and Oral Bioavailability

American Chemical Society, 2022, pp. 55-102
Mulligan VK, Hosseinzadeh P

"How to Design Peptides", Chemokine-Glycosaminoglycan Interactions: Methods and Protocols

Springer US, 15 Nov 2022
Dodd-o J, Acevedo-Jake AM, Azizogli A, Mulligan VK, Kumar VA

Multibody molecular docking on a quantum annealer

arXiv:2210.11401., 20 Oct 2022
Mohit Pandey, Tristan Zaborniak, Hans Melo, Alexey Galda, Vikram K. Mulligan

Targeting Tumor Necrosis Factor (TNF) in Atrial Stretch Dependent Adverse Atrial Remodelling and Vulval Atrial Fibrillation in a Mouse Model of Aortic Regurgitation

Canadian Journal of Cardiology, Oct 2022
Lakin R, Liu H, Chen W, Debi R, Yakobov S, PolidovitchN. BackxP

"Computational methods for peptide macrocycle drug design", Peptide therapeutics: fundamentals of design, development, and delivery

Springer International Publishing, 27 Sept 2022
Mulligan VK

Stabilizing proteins, simplified: A Rosetta‐based webtool for predicting favorable mutations

Protein Science, 21 Sept 2022
Thieker DF, Maguire JB, Kudlacek ST, Leaver-Fay A, Lyskov S, Kuhlman B

Protocol to identify host-viral protein interactions between coagulation-related proteins and their genetic variants with SARS-CoV-2 proteins

STAR Protocols Cell Press, 16 Sept 2022
Holcomb DD,  Jankowska KI, Hernandez N, Laurie K, Kames J, Hamasaki-Katagiri N, Komar AA, DiCuccio M, Kimchi-Sarfaty C

Accurate de novo design of membrane-traversing macrocycles

Cell, 15 Sept 2022
Bhardwaj G, O’Connor J, Rettie S, Huang Y,  Ramelot TA, Mulligan VK, Alpkilic GC, Palmer J, Bera AK, Bick MJ, Di Piazza M, Li X, Hosseinzadeh P, Craven TW, Tejero R, Lauko A, Choi R, Glynn C, Dong L, Griffin R, van Voorhis WC, Rodriguez J, Stewart L, Montelione GT, Craik D, Baker D

Methods and compositions for stabilized recombinant flavivirus e protein dimers

US Patent App., 15 Sept 2022
Smit Chaudhary, Patrick Huembeli, Ian MacCormack, Taylor L. Patti, Jean Kossaifi, Alexey Galda

Towards a scalable discrete quantum generative adversarial neural network

Smit Chaudhary, Patrick Huembeli, Ian MacCormack, Taylor L. Patti, Jean Kossaifi, Alexey Galda

Allele-specific activation, enzyme kinetics, and inhibitor sensitivities of EGFR exon 19 deletion mutations in lung cancer

The Proceedings of the National Academy of Sciences, 22 July 2022
Brown BP, Zhang Y, Finneran P, Yan Y, Du Z, Kim J, Hartzler AL, LeNoue-Newton ML, Smith AW, Meiler J, Lovly CM

A structural homology approach to identify potential cross-reactive antibody responses following SARS-CoV-2 infection

Scientific Reports, 06 July 2022
McGill JR, Lagassé HAD, Hernandez N, Hopkins L, Jankowski W, McCormick Q, Simhadri V, Golding B, Sauna ZE

A conserved set of mutations for stabilizing soluble envelope protein dimers from dengue and Zika viruses to advance the development of subunit vaccines

Journal of Biological Chemistry, 01 July 2022
Phan TTN, Hvasta MG, Kudlacek ST, Thiono DJ, Tripathy A, Nicely NI, de Silva AM, Kuhlman B

Adiponectin-receptor agonism mitigates chamber- specific cardiac fibrosis and mitochondrial stress in the D2.mdx mouse model of Duchenne muscular dystrophy

International Biochemistry of Exercise Conference, May 2022
Gandhi S, Delfinis LJ, Garibotti MC, Bellissimo CA, Castellani LA, Yakobov S, Edgett BA, Backx PJ, Simpson JA, Perry CGR

Ancestral Sequence Reconstruction and Alternate Amino Acid States Guide Protein Library Design for Directed Evolution

Methods in Molecular Biology, 29 Apr 2022
VanAntwerp J, Finneran P, Dolgikh B, Woldring D


Designed, highly expressing, thermostable dengue virus 2 envelope protein dimers elicit quaternary epitope antibodies

Science Advances, 15 Oct 2021
Stephan Kudlacek, Stefan Metz, Devina Thiono, Alexander M Payne, et al.

XENet: Using a new graph convolution to accelerate the timeline for protein design on quantum computers

PLOS Comp Bio, 27 Sep 2021
Maguire JB, Grattarola D, Mulligan VK, Klyshko E, Melo H

Perturbing the energy landscape for improved packing during computational protein design

Proteins: Structure, Function, and Bioinformatics, May 2021
Jack B. Maguire,Hugh K. Haddox,Devin Strickland,Samer F. Halabiya, et al.

Augmenting QAOA Ansatz with Multiparameter Problem-Independent Layer.

arXiv preprint arXiv:2205.01192
Chalupnik, M., Melo, H., Alexeev, Y., & Galda, A

Structure-Guided Stabilized DENV2 Envelope Subunit Vaccine Elicits DENV2 Neutralizing Antibody In Vivo

American Journal of Tropical Medicine and Hygiene, 01 Nov 2021
Thiono DJ, Kudlacek ST, Samaras DL, Tian S, McCracken MK, Soman SA, Gromowski GD, Jarman RG, Forsberg J, Phan TT, Kuhlman B, de Silva AM

Multibody molecular docking on a quantum annealer

arXiv:2210.11401., 20 Oct 2022
Mohit Pandey, Tristan Zaborniak, Hans Melo, Alexey Galda, Vikram K. Mulligan

Dissecting the Roles of the Autonomic Nervous System and Physical Activity on Circadian Heart Rate Fluctuations in Mice

Frontiers in Physiology, 18 Oct 2021
Barazi N, Polidovitch N, Debi R, Yakobov S, Lakin R, Backx PH

Simulating Large PEPs Tensor Networks on Small Quantum Devices

arXiv, 01 Oct 2021
Ian MacCormack, Alexey Galda, Adam L. Lyon

Current directions in combining simulation-based macromolecular modeling approaches with deep learning

Expert Opin Drug Discov., Sep 2021
Vikram Khipple Mulligan

Implementing a Ternary Decomposition of the Toffoli Gate on Fixed-Frequency Transmon Qutrits

arXiv, 01 Sep 2021
Alexey Galda, Michael Cubeddu, Naoki Kanazawa, Prineha Narang, Nathan Earnest-Noble

A conserved epitope III on hepatitis C virus E2 protein has alternate conformations facilitating cell binding or virus neutralization

PNAS, 06 July 2021
Deng L, Hernandez N, Zhong L, Holcomb DD, Yan H, Virata ML, Tarafdar S, Xu Y, He Y, Struble E, Alter HJ, Zhang P

Transferability of optimal QAOA parameters between random graphs

arXiv, 14 Jun 2021 (accepted in QCE21)
Alexey Galda, Xiaoyuan Liu, Danylo Lykov, Yuri Alexeev, Ilya Safro

Error Mitigation for Deep Quantum Optimization Circuits by Leveraging Problem Symmetries

arXiv, 09 Jun 2021 (accepted in QCE21)
Ruslan Shaydulin, Alexey Galda

Examining the role of chamber-specific mitophagy and mitochondrial bioenergetics on cardiomyopathy in Duchenne muscular dystrophy

Muscle Health Awareness Day York University Virtual Conference, May 2021
Gandhi S, Bellissimo CA, Castellani LN, Yakobov S, Simpson JA, Perry CGR

Atrial Stretch‐Dependent Tumor Necrosis Factor (TNF)‐Mediated Adverse Atrial Remodeling and Atrial Arrhythmia Inducibility in a Mouse Model of Aortic Regurgitation

The FASEB Journal, May 2021
Lakin R, Polidovitch N, Chen W, Yakobov S, Backx PH

Molecular chaperone RAP interacts with LRP1 in a dynamicbivalent mode and enhances folding of ligand-bindingregions of other LDLR family receptors

Journal of Biological Chemisty, 29 May 2021
Marakasova E, Olivares P, Karnaukhova E, Chun H, Hernandez NE, Kurasawa JH, Hassink GU, Shestopal SA, Strickland DK, Sarafanov GA

Error Rate Reduction of Single-Qubit Gates via Noise-Aware Decomposition

arXiv, 14 Apr 2021
Thomas J. Maldonado, Johannes Flick, Stefan Krastanov, Alexey Galda

Too sympathetic to exercise: abnormal autonomic and metaboreflex activation in exercising rheumatoid arthritis patients

The Journal of Physiology Apr 2021
Debi R, Yakobov S, Bhatt P, Lakin R

Experimental high-dimensional Greenberger-Horne-Zeilinger entanglement with superconducting transmon qutrits

arXiv, 12 Apr 2021
Alba Cervera-Lierta, Mario Krenn, Alán Aspuru-Guzik, Alexey Galda

The Emerging Role of Computational Design in Peptide Macrocycle Drug Discovery

Expert Opinion on Drug Discovery, 31 Mar 2020
Mulligan VK

Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1

Proc Natl Acad Sci U S A, 23 March 2021
Vikram Khipple Mulligan, Sean Workman, Tianjun Sun, Stephen Rettie, Xinting Li, Liam J Worrall, Timothy W Craven, et al.

Gene variants of coagulation related proteins that interact with SARS-CoV-2

PLOS Computational Biology, 17 March 2021
Holcomb D, Alexaki A, Hernandez N, Hunt R, Laurie K, Kames J, Hamasaki-Katagiri N, Komar AA,  DiCuccio M, Kimchi-Sarfaty C

Method for improving protein functionality using vortexing fluid shear forces

US Patent 10934324, 02 March 2021
Weiss GA, Raston CL, Yuan TZ, Ormonde C, Kudlacek ST,

Demonstration of quantum advantage by a joint detection receiver for optical communications using quantum belief propagation on a trapped-ion device

arXiv, 25 Feb 2021
Conor Delaney, Kaushik P. Seshadreesan, Ian MacCormack, Alexey Galda, Saikat Guha, Prineha Narang


Branching Quantum Convolutional Neural Networks

arXiv, 28 Dec 2020
Ian MacCormack, Conor Delaney, Alexey Galda, Nidhi Aggarwal, Prineha Narang

Computational design of mixed chirality peptide macrocycles with internal symmetry

Protein Sci. 2020 Dec;29(12):2433-2445
Vikram Khipple Mulligan, Christine S Kang, Michael R Sawaya, Stephen Rettie, Xinting L, et al.

Tensor Network Quantum Simulator With Step-Dependent Parallelization

arXiv, 04 Dec 2020
Danylo Lykov, Roman Schutski, Alexey Galda, Valerii Vinokur, Yurii Alexeev

Exercise Dose Dependent Atrial Remodelling and Atrial Fibrillation

York University, 13 Nov 2020
Yakobov S

In silico features of ADAMTS13 contributing to plasmatic ADAMTS13 levels in neonates with congenital heart disease

Thrombosis Research, Sept 2020
Katneni , Holcomb , Hernandez , Hamasaki-Katagiri , Hunt , Bar , Ibla , Kimchi-Sarfaty

Dimerization of Dengue Virus E Subunits Impacts Antibody Function and Domain Focus

Journal of Virology, 31 Aug 2020
Thomas A, Thiono DJ, Kudlacek ST, Forsberg J, Premkumar L, Tian S, Kuhlman B, de Silva AM, Metz AW

Computational Stabilization of T Cell Receptors Allows Pairing with Antibodies to Form Bispecifics

Nature Communications, 11 May 2020
Froning K, Maguire J, Sereno A, Huang F, Chang S, Weichert K, Frommelt AJ, Dong J, Wu X, Austin H, Conner EM, Fitchett JR, Heng, AR, Balasubramaniam, Hilgers MT, Kuhlman B, Demarest SJ

The Emerging Role of Computational Design in Peptide Macrocycle Drug Discovery

Expert Opinion on Drug Discovery, 31 Mar 2020
Mulligan VK

Computer-Based Design and Stabilization of the Dengue Virus Envelope Protein for Use as a Subunit Vaccine

The University of North Carolina at Chapel Hill ,  2020
Kudlacek S

Mathematical Models of Protease-Based Enzymatic Biosensors

ACS Synthetic Biology ,  04 Feb 2020
Agrawal DK, Dolan EM, Hernandez NE, Blacklock KM, Khare SD, Sontag ED

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