Publications

Kyle R Jackson, Dinler A Antunes, Amjad H Talukder, Ariana R Maleki, Kano Amagai, Avery Salmon, Arjun S Katailiha, Yulun Chiu, Romanos Fasoulis, Maurício Menegatti Rigo, Jayvee R. Abella, Brenda D Melendez, Fenge Li, Yimo Sun, Heather M Sonnemann, Vladislav Belousov, Felix Frenkel, Sune Justesen, Aman Makaju, Yang Liu, David Horn, Daniel Lopez-Ferrer, Andreas F Huhmer, Patrick Hwu, Jason Roszik, David Hawke, Lydia E Kavraki, Gregory Lizée (2022). Charge-based interactions through peptide position 4 drive diversity of antigen presentation by human leukocyte antigens class I molecules. PNAS Nexus.

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Alexander Alali, Erika O’Neil, Marc Anders, Jayvee R. Abella, Lara Shekerdemian, Tiphanie Vogel, Kristen Sexson Tejtel, Sebastian Tume (2022). Vasoplegic Shock Represents a Dominant Hemodynamic Profile of Multisystem Inflammatory Syndrome Following COVID-19 in Children and Adolescents. Pediatric Critical Care Medicine.

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Erika O’Neil, Huiming Lin, Meng Li, Lara Shekerdemian, Joseph Tonna, Ryan Barbaro, Jayvee R. Abella, Peter Rycus, Graeme MacLaren, Marc Anders, Peta Alexander (2021). ECMO Support for Influenza A: Retrospective Review of the ELSO Registry Comparing H1N1 to Other Subtypes. Critical Care Explorations.

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Ryan Melvin, Jayvee R. Abella, Raajen Patel, Joshua Hagood, Domagoj Mladinov, Dan Berkowitz (2021). Intraoperative utilization of high-resolution data for cerebral autoregulation: a feasibility study. British Journal of Anaesthesia.

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Jayvee R. Abella, Dinler Antunes, Kyle Jackson, Gregory Lizee, Cecilia Clementi, Lydia Kavraki (2020). Markov State Modeling Reveals Alternative Unbinding Pathways for Peptide-MHC Complexes. Proceedings of the National Academy of Sciences.

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Thais Arns, Dinler Antunes, Jayvee R. Abella, Mauricio Rigo, Lydia Kavraki, Silvana Giuliatti, Eduardo Donadi (2020). Structural modelling and molecular dynamics of the immune checkpoint molecule HLA-G. Frontiers in Immunology, 2882(11).

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Jayvee R. Abella, Dinler Antunes, Cecilia Clementi, Lydia Kavraki (2020). Large-Scale Structure-Based Prediction of Stable Peptide Binding to Class I HLAs Using Random Forests. Frontiers in Immunology, 1583(11).

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Dinler Antunes, Jayvee R. Abella, Sarah Hall-Swan, Didier Devaurs, Anja Conev, Mark Moll, Gregory Lizee, Lydia Kavraki (2020). HLA-Arena: A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy. JCO Clinical Cancer Informatics, 623-636(4).

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Dinler Antunes, Jayvee R. Abella, Didier Devaurs, Mauricio Rigo, Lydia Kavraki (2019). Structure-based Methods for Binding Mode and Binding Affinity Prediction for Peptide-MHC Complexes. Current Topics in Medicinal Chemistry 19(5).

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Jayvee R. Abella, Dinler Antunes, Cecilia Clementi, Lydia Kavraki (2019). APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations. Molecules, 24(5).

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Eugen Hruska, Jayvee R. Abella, Feliks Nuske, Lydia Kavraki, Cecilia Clementi (2018). Quantitative Comparison of Adaptive Sampling Methods for Protein Dynamics. The Journal of Chemical Physics 149(24).

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Didier Devaurs, Malvina Papanastasiou, Dinler Antunes, Jayvee R. Abella, Mark Moll, Daniel Ricklin, John Lambris, Lydia Kavraki (2018). Native state of complement protein C3d analysed via hydrogen exchange and conformational sampling. International Journal of Computational Biology and Drug Design 11(1,2).

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Jayvee R. Abella, Mark Moll, Lydia Kavraki (2018). Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods. Journal of Computational Biology, 25(1).

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Jayvee R. Abella, Sara Cheng, Qiantao Wang, Wei Yang, Pengyu Ren (2014). Hydration free energy from orthogonal space random walk and polarizable force field. Journal of Chemical Theory and Computation, 10(7).

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Daniel Hensley, Andrew Mark, Jayvee R. Abella, George Netscher, Eugene Wissler, Kenneth Diller (2013). 50 Years of Computer Simulation of the Human Thermoregulatory System. Journal of Biomechanical Engineering, 135(2).

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