Publications by authors named "Soha Hassoun"

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Learning from All Views: A Multiview Contrastive Framework for Metabolite Annotation.
Yan Zhou Chen, Soha Hassoun

bioRxiv· November 2025

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General Intelligence-based Fragmentation (GIF): A framework for peak-labeled spectra simulation.
Margaret R Martin, Soha Hassoun

ArXiv· November 2025

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Optimized De Novo Molecular Generation (OMG) for Mass Spectra Annotation Using Transfer and Reinforcement Learning.
Margaret R Martin, Soha Hassoun

Anal Chem· September 2025

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JESTR: Joint Embedding Space Technique for Ranking candidate molecules for the annotation of untargeted metabolomics data.
Apurva Kalia, Yan Zhou Chen, Dilip Krishnan, Soha Hassoun

Bioinformatics· July 2025

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JESTR: Joint Embedding Space Technique for Ranking Candidate Molecules for the Annotation of Untargeted Metabolomics Data.
Apurva Kalia, Yan Zhou Chen, Dilip Krishnan, Soha Hassoun

ArXiv· June 2025

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Protein-ligand co-design: a case for improving binding affinity between type II NADH:quinone oxidoreductase and quinones.
Vladimir Porokhin, Anne M Brown, Soha Hassoun

J Comput Aided Mol Des· June 2025

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Identifying Key Properties That Drive Redox Mediator Activity in Lactiplantibacillus Plantarum.
Benjamin T Blackburn, Robyn A C Alba, Vladimir O Porokhin, Rong Cai, Arden Hatch, Soha Hassoun

Angew Chem Int Ed Engl· May 2025

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Computational Analysis of the Gut Microbiota-Mediated Drug Metabolism.
Sammie Chum, Alberto Naveira Montalvo, Soha Hassoun

bioRxiv· March 2025

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Computational analysis of the gut microbiota-mediated drug metabolism.
Sammie Chum, Alberto Naveira Montalvo, Soha Hassoun

Comput Struct Biotechnol J· March 2025

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Evaluation of search-enabled pretrained Large Language Models on retrieval tasks for the PubChem database.
Ash Sze, Soha Hassoun

Bioinform Adv· March 2025

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MassSpecGym: A benchmark for the discovery and identification of molecules.
Roman Bushuiev, Anton Bushuiev, Niek F de Jonge, Adamo Young, Fleming Kretschmer, Soha Hassoun

ArXiv· February 2025

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Molecular Structure Discovery for Untargeted Metabolomics Using Biotransformation Rules and Global Molecular Networking.
Margaret R Martin, Wout Bittremieux, Soha Hassoun

Anal Chem· February 2025

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An Ensemble Spectral Prediction (ESP) model for metabolite annotation.
Xinmeng Li, Yan Zhou Chen, Apurva Kalia, Hao Zhu, Li-Ping Liu, Soha Hassoun

Bioinformatics· August 2024

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Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota.
Francesco Balzerani, Telmo Blasco, Sergio Pérez-Burillo, Luis V Valcarcel, Soha Hassoun

NPJ Syst Biol Appl· May 2024

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Molecular structure discovery for untargeted metabolomics using biotransformation rules and global molecular networking.
Margaret R Martin, Wout Bittremieux, Soha Hassoun

bioRxiv· February 2024

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CSI: Contrastive data Stratification for Interaction prediction and its application to compound-protein interaction prediction.
Apurva Kalia, Dilip Krishnan, Soha Hassoun

Bioinformatics· August 2023

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Recent advances in mass spectrometry-based computational metabolomics.
Timothy M D Ebbels, Justin J J van der Hooft, Haley Chatelaine, Corey Broeckling, Nicola Zamboni, Soha Hassoun

Curr Opin Chem Biol· June 2023

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Using graph neural networks for site-of-metabolism prediction and its applications to ranking promiscuous enzymatic products.
Vladimir Porokhin, Li-Ping Liu, Soha Hassoun

Bioinformatics· March 2023

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Boost-RS: boosted embeddings for recommender systems and its application to enzyme-substrate interaction prediction.
Xinmeng Li, Li-Ping Liu, Soha Hassoun

Bioinformatics· May 2022

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Artificial Intelligence for Biology.
Soha Hassoun, Felicia Jefferson, Xinghua Shi, Brian Stucky, Jin Wang

Integr Comp Biol· February 2022

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Enzyme Promiscuity Prediction Using Hierarchy-Informed Multi-Label Classification.
Gian Marco Visani, Michael C Hughes, Soha Hassoun

Bioinformatics· August 2021

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Analysis of metabolic network disruption in engineered microbial hosts due to enzyme promiscuity.
Vladimir Porokhin, Sara A Amin, Trevor B Nicks, Venkatesh Endalur Gopinarayanan, Nikhil U Nair, Soha Hassoun

Metab Eng Commun· June 2021

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Learning graph representations of biochemical networks and its application to enzymatic link prediction.
Julie Jiang, Li-Ping Liu, Soha Hassoun

Bioinformatics· May 2021

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Pathway-Activity Likelihood Analysis and Metabolite Annotation for Untargeted Metabolomics Using Probabilistic Modeling.
Ramtin Hosseini, Neda Hassanpour, Li-Ping Liu, Soha Hassoun

Metabolites· May 2020

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ASAP-SML: An antibody sequence analysis pipeline using statistical testing and machine learning.
Xinmeng Li, James A Van Deventer, Soha Hassoun

PLoS Comput Biol· April 2020

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