Amir Hossein Amanzadi


I am just a human being. The following descriptions are simply social statuses that I have gained through my life, which you may or may not be interested in.

Research: I am excited about complex interdisciplinary problems in Biomedicine that can be tackled with learning-based systems. I am especially interested in the application of Graph Neural Networks (GNN) in biomedical research. Currently, my research focuses on identifying safe drug combinations for complex diseases with no standard treatments by integrating Systems Medicine and Deep Learning.

Bio: My MSc in Pharmaceutical Science was obtained from Uppsala University and my BSc in Chemistry & Mechanical Engineering (Minor) from the Sharif University of Technology allowed me to enhance my knowledge in a variety of fields, including pharmaceutical modeling, chemical synthesis, computational chemistry, structural biology, molecular dynamics (MD), systems medicine, machine learning (including deep learning) to analyze genomic data, and AI-enhanced drug discovery and development. Among my many exciting projects, I have worked on the DECISION for Liver EU project, in which I identified optimal combinatorial treatments for decompensated cirrhosis. Also, I have developed a geometric deep learning pipeline for targeted protein degradation drug design (in collaboration with Merck KGaA and Boehringer Ingelheim).

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Publications

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Protein–protein interaction prediction for targeted protein degradation
Oliver Orasch, Noah Weber, Michael Müller, Amir Amanzadi, Chiara Gasbarri, Christopher Trummer
International Journal of Molecular Sciences, 2022
Project Page / Paper / Supplemental / Video / Poster / Code /
@InProceedings{IJMS2022, 
	author = {Oliver Orasch and Noah Weber and Michael Müller and Amir Amanzadi and Chiara Gasbarri and Christopher Trummer}, 
	title = {Protein–protein interaction prediction for targeted protein degradation}, 
	booktitle = {International Journal of Molecular Sciences}, 
	year = {2022}, 
}
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Predicting safe drug combinations with Graph Neural Networks (GNN)
Amir Amanzadi
Uppsala University, 2021
Project Page / Paper / Code /
@InProceedings{UU2021, 
	author = {Amir Amanzadi}, 
	title = {Predicting safe drug combinations with Graph Neural Networks (GNN)}, 
	booktitle = {Uppsala University}, 
	year = {2021}, 
}
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Explainable polypharmacy side effect prediction with Siamese graph convolutional neural networks (Lightning Presentation)
Amir Amanzadi, Narsis Kiani
4th RSC-BMCS Conference, Royal Society of Chemistry, 2021
Project Page / Video / Code /
@InProceedings{RSC2021, 
	author = {Amir Amanzadi and Narsis Kiani}, 
	title = {Explainable polypharmacy side effect prediction with Siamese graph convolutional neural networks}, 
	booktitle = {4th RSC-BMCS Conference, Royal Society of Chemistry}, 
	year = {2021}, 
}
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Both Tough and Soft Double Network Hydrogel Nanocomposite Based on O-Carboxymethyl Chitosan/Poly(vinyl alcohol) and Graphene Oxide: A Promising Alternative for Tissue Engineering
Ali Pourjavadi, Zahra Tehrani, Hamid Salami, Farzad Seidi, Anahita Motamedi, Amir Amanzadi, Ehsan Zayerzadeh, Meisam Shabanian
Polymer Engineering & Science, 2020
Project Page / Paper /
@InProceedings{PES2020, 
	author = {Ali Pourjavadi and Zahra Tehrani and Hamid Salami and Farzad Seidi and Anahita Motamedi and Amir Amanzadi and Ehsan Zayerzadeh and Meisam Shabanian}, 
	title = {Both Tough and Soft Double Network Hydrogel Nanocomposite Based on O-Carboxymethyl Chitosan/Poly(vinyl alcohol) and Graphene Oxide: A Promising Alternative for Tissue Engineering}, 
	booktitle = {Polymer Engineering & Science}, 
	year = {2020}, 
}
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Designing a new multifunctional peptide for metal chelation and Aβ inhibition
Amir Shamloo, Mohsen Asadbegia, Vahid Khandan, Amir Amanzadi
Archives of Biochemistry and Biophysics, 2018
Project Page / Paper /
@InProceedings{ABb2018, 
	author = {Amir Shamloo and Mohsen Asadbegia and Vahid Khandan and Amir Amanzadi}, 
	title = {Designing a new multifunctional peptide for metal chelation and Aβ inhibition}, 
	booktitle = {Archives of Biochemistry and Biophysics}, 
	year = {2018}, 
}

Talks

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Application of Graph Neural Networks (GNN) in Drug Discovery
Uppsala University, Sweden, 2022
Slides / Recording

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